CELLULASES, NUCLEIC ACIDS ENCODING THEM AND METHODS FOR MAKING AND USING THEM

Abstract

This invention relates to molecular and cellular biology and biochemistry. In one aspect, the invention provides polypeptides having cellulase activity, e.g., endoglucanase, cellobiohydrolase, mannanase and/or β-glucosidase activity, polynucleotides encoding these polypeptides, and methods of making and using these polynucleotides and polypeptides. In one aspect, the invention is directed to polypeptides cellulase activity, e.g., endoglucanase, cellobiohydrolase, mannanase and/or β-glucosidase activity, including thermostable and thermotolerant activity, and polynucleotides encoding these enzymes, and making and using these polynucleotides and polypeptides. The polypeptides of the invention can be used in a variety of pharmaceutical, agricultural, food and feed processing and industrial contexts.

Description

FIELD OF THE INVENTION

[0002] This invention relates to molecular and cellular biology and biochemistry. In one aspect, the invention provides polypeptides having cellulase activity, e.g., endoglucanase, cellobiohydrolase, mannanase and/or β-glucosidase activity, polynucleotides encoding these polypeptides, and methods of making and using these polynucleotides and polypeptides. In one aspect, the invention is directed to polypeptides having cellulase activity, e.g., endoglucanase, cellobiohydrolase, mannanase and/or β-glucosidase activity, including thermostable and thermotolerant activity, and polynucleotides encoding these enzymes, and making and using these polynucleotides and polypeptides. The polypeptides of the invention can be used in a variety of pharmaceutical, agricultural and industrial contexts.

BACKGROUND

[0003] Cellulose is the most abundant renewable resource on earth. It is composed of a linear chain of β 1-4 glucose units with the repeating unit being cellobiose, which is a glucose dimer having a structure as shown in FIG. 5. The polymer is degraded by a suite of enzymes which include endoglucanases (EG) which randomly hydrolyze the cellulose polymer, and cellobiohydrolases (CBH) which remove terminal cellobiose residues from cellulose. Cellobiose and cello-oligosaccharides are hydrolyzed to glucose by β-glucosidases (BG). All three of these enzymes are necessary for the complete breakdown of cellulose to glucose. For each of these three enzymes different structural variants exist that perform the same function. In addition, fungi and bacteria are known to produce multiple forms of the same structural variants in addition to different structural variants.

[0004] Further complicating this system is the fact that some anaerobic bacteria and fungi are known to produce these enzymes in multi-enzyme complexes which contain multiple enzymes all attached to an enzyme scaffold with molecular weights above 2 million daltons. Why is such a complex system of enzymes necessary for such a simple molecule? Some researchers believe that this complexity is due to the recalcitrant nature of the substrate. The cellulose chains form microfibrils that pack into a crystalline matrix via hydrogen bonding of adjacent chains. This structure is highly resistant to chemical or enzymatic degradation.

[0005] CBHs are thought to be the key enzyme in the degradation of this crystalline cellulose because of the nature of their enzymatic attack on cellulose. EGs unlike CBHs have an open cleft that attacks the cellulose chain at a perpendicular angle. CBHs attack the chain directly via a tunnel containing the active site. The current thought is that the cellulose chains enter the tunnel and at the same time, adjacent hydrogen bonding is disrupted. Once the cellobiohydrolases have established this "foothold" on the substrate, the EGs can then come in and more readily attack the substrate.

[0006] A major deficiency of known CBHs is their low catalytic activity. Some groups argue that the low activity stems from the fact that energy from hydrolysis is transferred to kinetic energy to disrupt hydrogen bonds and enable the enzyme to move along the substrate. CBHs are exo-acting enzymes and are found in 6 of the 90 families of glycosyl hydrolases. They include families 5, 6, 7, 9, 10 and 48. Family 5 contains many different types of glycosyl hydrolases including cellulases, mannanases and xylanases. Although most cellulases in this family are endoglucanases, there are examples of cellobiohydrolases, most notably CelO from Clostridium thermocellum. Family 6 contains only endoglucanases or cellobiohydrolases with more cellobiohydrolase members than endoglucanases. The enzymes have an inverting mechanism and crystallographic studies suggest that the enzyme has a distorted α/β barrel structure containing seven, not eight parallel β-strands. Family 7 enzymes are also composed of both endoglucanases and cellobiohydrolases with more cellobiohydrolases and only known members are from fungi. The enzyme has a retaining mechanism and the crystal structure suggests a β-jellyroll structure. Family 9 contains endoglucanases, cellobiohydrolases and β-glucosidases with a preponderance of endoglucanases. However, Thermobifida fusca produces an endo/exo-1,4-glucanase, the crystal structure of which suggests a (α/α)₆ barrel fold. The enzyme has characteristics of both endo and exo-glucanases CBHs. Family 10 contains only 2 members described as cellobiohydrolases with mainly the rest described as xylanases. Cellobiohydrolases and xylanases from family 10 have activity on methyl-umbelliferyl cellobioside. Family 48 contains mainly bacterial and anaerobic fungal cellobiohydrolases and endoglucanases. The structure is a (α/α)₆ barrel fold similar to family 9.

[0007] There is a need for less expensive and renewable sources of fuel for road vehicles. New fuel sources will be more attractive if they produce nonharmful endproducts after combustion. Ethanol offers an attractive alternative to petroleum based fuels and can be obtained through the fermentation of monomeric sugars derived from starch or lignocellulose. However, current economics do not support the widespread use of ethanol due to the high cost of generating it. One area of research aimed at decreasing costs is enhancement of the technical efficacy of the enzymes that can be used to generate fermentable sugars from lignocellulose. The development of enzymes that more efficiently digest feedstock will translate to decreased ethanol production costs. More efficient processes will decrease the United State's reliance on foreign oil and the price fluctuations that may be related to that reliance. Using cleaner fuels for transportation like bioethanol also may decrease net CO₂ emissions that are believed to be partially responsible for global warming.

SUMMARY

[0008] The invention provides cellulases, e.g., endoglucanases, cellobiohydrolases and/or β-glucosidase (beta-glucosidases), and methods for making and using them. In one aspect, the enzymes of the invention have an increased catalytic rate to improve the process of substrate hydrolysis. This increased efficiency in catalytic rate leads to an increased efficiency in producing sugars, which can be useful in industrial applications, e.g., the sugars so produced can be used by microorganisms for ethanol production. In one aspect, the invention provides highly active (e.g., having an increased catalytic rate) cellobiohydrolases, endoglucanases and beta-glucosidase. The invention provides industrial applications (e.g., biomass to ethanol) using enzymes of the invention having decreased enzyme costs, e.g., decreased costs in biomass to ethanol processes. Thus, the invention provides efficient processes for producing bioethanol and bioethanol-comprising compositions, including fuels comprising bioethanol, from any biomass.

[0009] In one aspect, the enzymes of the invention have a glucanase, e.g., an endoglucanase, activity, e.g., catalyzing hydrolysis of internal endo-β-1,4- and/or β-1,3-glucanase linkages. In one aspect, the endoglucanase activity (e.g., endo-1,4-beta-D-glucan 4-glucano hydrolase activity) comprises hydrolysis of 1,4- and/or β-1,3-beta-D-glycosidic linkages in cellulose, cellulose derivatives (e.g., carboxy methyl cellulose and hydroxy ethyl cellulose) lichenin, beta-1,4 bonds in mixed beta-1,3 glucans, such as cereal beta-D-glucans or xyloglucans and other plant material containing cellulosic parts.

[0010] In one aspect, the enzymes of the invention have endoglucanase (e.g., endo-beta-1,4-glucanases, EC 3.2.1.4; endo-beta-1,3(1)-glucanases, EC 3.2.1.6; endo-beta-1,3-glucanases, EC 3.2.1.39) activity and can hydrolyze internal β-1,4- and/or β-1,3-glucosidic linkages in cellulose and glucan to produce smaller molecular weight glucose and glucose oligomers. The invention provides methods for producing smaller molecular weight glucose and glucose oligomers using these enzymes of the invention.

[0011] In one aspect, the enzymes of the invention are used to generate glucans, e.g., polysaccharides formed from 1,4-β- and/or 1,3-glycoside-linked D-glucopyranose. In one aspect, the endoglucanases of the invention are used in the food industry, e.g., for baking and fruit and vegetable processing, breakdown of agricultural waste, in the manufacture of animal feed, in pulp and paper production, textile manufacture and household and industrial cleaning agents. In one aspect, the enzymes, e.g., endoglucanases, of the invention are produced by a microorganism, e.g., by a fungi and/or a bacteria.

[0012] In one aspect, the enzymes, e.g., endoglucanases, of the invention are used to hydrolyze beta-glucans (β-glucans) which are major non-starch polysaccharides of cereals. The glucan content of a polysaccharide can vary significantly depending on variety and growth conditions. The physicochemical properties of this polysaccharide are such that it gives rise to viscous solutions or even gels under oxidative conditions. In addition glucans have high water-binding capacity. All of these characteristics present problems for several industries including brewing, baking, animal nutrition. In brewing applications, the presence of glucan results in wort filterability and haze formation issues. In baking applications (especially for cookies and crackers), glucans can create sticky doughs that are difficult to machine and reduce biscuit size. Thus, the enzymes, e.g., endoglucanases, of the invention are used to decrease the amount of β-glucan in a β-glucan-comprising composition, e.g., enzymes of the invention are used in processes to decrease the viscosity of solutions or gels; to decrease the water-binding capacity of a composition, e.g., a β-glucan-comprising composition; in brewing processes (e.g., to increase wort filterability and decrease haze formation), to decrease the stickiness of doughs, e.g., those for making cookies, breads, biscuits and the like.

[0013] In addition, carbohydrates (e.g., β-glucan) are implicated in rapid rehydration of baked products resulting in loss of crispiness and reduced shelf-life. Thus, the enzymes, e.g., endoglucanases, of the invention are used to retain crispiness, increase crispiness, or reduce the rate of loss of crispiness, and to increase the shelf-life of any carbohydrate-comprising food, feed or drink, e.g., a β-glucan-comprising food, feed or drink.

[0014] Enzymes, e.g., endoglucanases, of the invention are used to decrease the viscosity of gut contents (e.g., in animals, such as ruminant animals, or humans), e.g., those with cereal diets. Thus, in alternative aspects, enzymes, e.g., endoglucanases, of the invention are used to positively affect the digestibility of a food or feed and animal (e.g., human or domestic animal) growth rate, and in one aspect, are used to higher generate feed conversion efficiencies. For monogastric animal feed applications with cereal diets, beta-glucan is a contributing factor to viscosity of gut contents and thereby adversely affects the digestibility of the feed and animal growth rate. For ruminant animals, these beta-glucans represent substantial components of fiber intake and more complete digestion of glucans would facilitate higher feed conversion efficiencies. Accordingly, the invention provides animal feeds and foods comprising endoglucanases of the invention, and in one aspect, these enzymes are active in an animal digestive tract, e.g., in a stomach and/or intestine.

[0015] Enzymes, e.g., endoglucanases, of the invention are used to digest cellulose or any beta-1,4-linked glucan-comprising synthetic or natural material, including those found in any plant material. Enzymes, e.g., endoglucanases, of the invention are used as commercial enzymes to digest cellulose, e.g., in the wood processing, pulp and/or paper industry, in textile manufacture and in household and industrial cleaning agents, and/or in biomass waste processing.

[0016] In one aspect the invention provides compositions (e.g., pharmaceutical compositions, foods, feeds, drugs, dietary supplements) comprising the enzymes, polypeptides or polynucleotides of the invention. These compositions can be formulated in a variety of forms, e.g., as tablets, gels, pills, implants, liquids, sprays, powders, food, feed pellets or as any type of encapsulated form.

[0017] The invention provides isolated or recombinant nucleic acids comprising a nucleic acid sequence having at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more, or complete (100%) sequence identity to an exemplary nucleic acid of the invention, including 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 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 ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:71, SEQ ID NO:73, SEQ ID NO:75, SEQ ID NO:77, SEQ ID NO:79, SEQ ID NO:81, SEQ ID NO:83, SEQ ID NO:85, SEQ ID NO:87, SEQ ID NO:89, SEQ ID NO:91, SEQ ID NO:93, SEQ ID NO:95, SEQ ID NO:97, SEQ ID NO:99, SEQ ID NO:101, SEQ ID NO:103, SEQ ID NO:105, SEQ ID NO:107, SEQ ID NO:109, SEQ ID NO:111, SEQ ID NO:113, SEQ ID NO:115, SEQ ID NO:117, SEQ ID NO:119, SEQ ID NO:121, SEQ ID NO:123, SEQ ID NO:125, SEQ ID NO:127, SEQ ID NO:129, SEQ ID NO:131, SEQ ID NO:133, SEQ ID NO:135, SEQ ID NO:137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:143, SEQ ID NO:145, SEQ ID NO:147, SEQ ID NO:149, SEQ ID NO:151, SEQ ID NO:153, SEQ ID NO:155, SEQ ID NO:157, SEQ ID NO:159, SEQ ID NO:161, SEQ ID NO:163 and SEQ ID NO:165; see also Tables 1, 2, and 3, Examples 1 and 4, below, and Sequence Listing, over a region of at least about 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850, 1900, 1950, 2000, 2050, 2100, 2200, 2250, 2300, 2350, 2400, 2450, 2500, or more residues; and in alternative aspects, these nucleic acids encode at least one polypeptide having a cellulase activity, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity, or encode a polypeptide capable of generating an antibody that can specifically bind to a polypeptide of the invention, or, these nucleic acids can be used as probes for identifying or isolating cellulase-encoding nucleic acids, or to inhibit the expression of cellulase-expressing nucleic acids (all these aspects referred to as the "nucleic acids of the invention"). In one aspect, the sequence identities are determined by analysis with a sequence comparison algorithm or by a visual inspection.

[0018] Nucleic acids of the invention also include isolated or recombinant nucleic acids encoding an exemplary enzyme of the invention, including a polypeptide having a sequence as set forth 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 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:143, 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 and SEQ ID NO:166, see also Tables 1, 2, and 3, Examples 1 and 4, below, and the Sequence Listing, and subsequences thereof and variants thereof. In one aspect, the polypeptide has a cellulase activity, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity.

[0019] In one aspect, the invention provides cellulase-encoding, e.g., endoglucanase-, cellobiohydrolase- and/or beta-glucosidase-encoding nucleic acids having a common novelty in that they are derived from mixed cultures. The invention provides cellulose-degrading enzyme-encoding nucleic acids isolated from mixed cultures comprising a polynucleotide of the invention, e.g., a sequence having at least about 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more, or complete (100%) sequence identity to an exemplary nucleic acid of the invention, e.g., 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 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 ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:71, SEQ ID NO:73, SEQ ID NO:75, SEQ ID NO:77, SEQ ID NO:79, SEQ ID NO:81, SEQ ID NO:83, SEQ ID NO:85, SEQ ID NO:87, SEQ ID NO:89, SEQ ID NO:91, SEQ ID NO:93, SEQ ID NO:95, SEQ ID NO:97, SEQ ID NO:99, SEQ ID NO:101, SEQ ID NO:103, SEQ ID NO:105, SEQ ID NO:107, SEQ ID NO:109, SEQ ID NO:111, SEQ ID NO:113, SEQ ID NO:115, SEQ ID NO:117, SEQ ID NO:119, SEQ ID NO:121, SEQ ID NO:123, SEQ ID NO:125, SEQ ID NO:127, SEQ ID NO:129, SEQ ID NO:131, SEQ ID NO:133, SEQ ID NO:135, SEQ ID NO:137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:143, SEQ ID NO:145, SEQ ID NO:147, SEQ ID NO:149, SEQ ID NO:151, SEQ ID NO:153, SEQ ID NO:155, SEQ ID NO:157, SEQ ID NO:159, SEQ ID NO:161, SEQ ID NO:163 and SEQ ID NO:165, and see Tables 1, 2, and 3, Examples 1 and 4, below, and Sequence Listing, over a region of at least about 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, or more.

[0020] In one aspect, the invention provides cellulase enzyme-, e.g., endoglucanase enzyme-, cellobiohydrolase enzyme- and/or beta-glucosidase enzyme-encoding nucleic acids, including exemplary polynucleotide sequences of the invention, see also Tables 1, 2, and 3, Examples 1 and 4, below, and Sequence Listing, and the polypeptides encoded by them, including enzymes of the invention, e.g., exemplary polypeptides of the invention, e.g., 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 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:143, 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 or SEQ ID NO:166, see also Table 1 and Sequence Listing, having a common novelty in that they are derived from a common source, e.g., an environmental source. In one aspect, the invention also provides cellulase enzyme-, e.g., endoglucanase enzyme-, cellobiohydrolase enzyme- and/or beta-glucosidase enzyme-encoding nucleic acids with a common novelty in that they are derived from environmental sources, e.g., mixed environmental sources.

[0021] In one aspect, the sequence comparison algorithm is a BLAST version 2.2.2 algorithm where a filtering setting is set to blastall-p blastp-d "nr pataa"-F F, and all other options are set to default.

[0022] Another aspect of the invention is an isolated or recombinant nucleic acid including at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850, 1900, 1950, 2000, 2050, 2100, 2200, 2250, 2300, 2350, 2400, 2450, 2500, or more consecutive bases of a nucleic acid sequence of the invention, sequences substantially identical thereto, and the sequences complementary thereto.

[0023] In one aspect, the isolated or recombinant nucleic acid encodes a polypeptide having a cellulase activity, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity, which is thermostable. The polypeptide can retain a cellulase activity under conditions comprising a temperature range of between about 37° C. to about 95° C.; between about 55° C. to about 85° C., between about 70° C. to about 95° C., or, between about 90° C. to about 95° C. The polypeptide can retain a cellulase activity in temperatures in the range between about 1° C. to about 5° C., between about 5° C. to about 15° C., between about 15° C. to about 25° C., between about 25° C. to about 37° C., between about 37° C. to about 95° C., 96° C., 97° C., 98° C. or 99° C., between about 55° C. to about 85° C., between about 70° C. to about 75° C., or between about 90° C. to about 99° C., or 95° C., 96° C., 97° C., 98° C. or 99° C., or more.

[0024] In another aspect, the isolated or recombinant nucleic acid encodes a polypeptide having a cellulase activity, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity, which is thermotolerant. The polypeptide can retain a cellulase activity after exposure to a temperature in the range from greater than 37° C. to about 95° C. or anywhere in the range from greater than 55° C. to about 85° C. The polypeptide can retain a cellulase activity after exposure to a temperature in the range between about 1° C. to about 5° C., between about 5° C. to about 15° C., between about 15° C. to about 25° C., between about 25° C. to about 37° C., between about 37° C. to about 95° C., 96° C., 97° C., 98° C. or 99° C., between about 55° C. to about 85° C., between about 70° C. to about 75° C., or between about 90° C. to about 95° C., or more. In one aspect, the polypeptide retains a cellulase activity after exposure to a temperature in the range from greater than 90° C. to about 99° C., or 95° C., 96° C., 97° C., 98° C. or 99° C., at about pH 4.5, or more.

[0025] The invention provides isolated or recombinant nucleic acids comprising a sequence that hybridizes under stringent conditions to a nucleic acid of the invention, including an exemplary sequence of the invention, e.g., a sequence as set forth in 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 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 ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:71, SEQ ID NO:73, SEQ ID NO:75, SEQ ID NO:77, SEQ ID NO:79, SEQ ID NO:81, SEQ ID NO:83, SEQ ID NO:85, SEQ ID NO:87, SEQ ID NO:89, SEQ ID NO:91, SEQ ID NO:93, SEQ ID NO:95, SEQ ID NO:97, SEQ ID NO:99, SEQ ID NO:101, SEQ ID NO:103, SEQ ID NO:105, SEQ ID NO:107, SEQ ID NO:109, SEQ ID NO:111, SEQ ID NO:113, SEQ ID NO:115, SEQ ID NO:117, SEQ ID NO:119, SEQ ID NO:121, SEQ ID NO:123, SEQ ID NO:125, SEQ ID NO:127, SEQ ID NO:129, SEQ ID NO:131, SEQ ID NO:133, SEQ ID NO:135, SEQ ID NO:137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:143, SEQ ID NO:145, SEQ ID NO:147, SEQ ID NO:149, SEQ ID NO:151, SEQ ID NO:153, SEQ ID NO:155, SEQ ID NO:157, SEQ ID NO:159, SEQ ID NO:161, SEQ ID NO:163 or SEQ ID NO:165 (see also Tables 1, 2, and 3, Examples 1 and 4, below,), or fragments or subsequences thereof. In one aspect, the nucleic acid encodes a polypeptide having a cellulase activity, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity. The nucleic acid can be at least about 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200 or more residues in length or the full length of the gene or transcript. In one aspect, the stringent conditions comprise a wash step comprising a wash in 0.2×SSC at a temperature of about 65° C. for about 15 minutes.

[0026] The invention provides a nucleic acid probe for identifying or isolating a nucleic acid encoding a polypeptide having a cellulase activity, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity, wherein the probe comprises at least about 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000 or more, consecutive bases of a sequence comprising a sequence of the invention, or fragments or subsequences thereof, wherein the probe identifies the nucleic acid by binding or hybridization. The probe can comprise an oligonucleotide comprising at least about 10 to 50, about 20 to 60, about 30 to 70, about 40 to 80, or about 60 to 100 consecutive bases of a sequence comprising a sequence of the invention, or fragments or subsequences thereof.

[0027] The invention provides a nucleic acid probe for identifying or isolating a nucleic acid encoding a polypeptide having a cellulase activity, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity, wherein the probe comprises a nucleic acid comprising a sequence at least about 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000 or more residues of a nucleic acid of the invention, e.g., a polynucleotide having at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more, or complete (100%) sequence identity to an exemplary nucleic acid of the invention. In one aspect, the sequence identities are determined by analysis with a sequence comparison algorithm or by visual inspection. In alternative aspects, the probe can comprise an oligonucleotide comprising at least about 10 to 50, about 20 to 60, about 30 to 70, about 40 to 80, or about 60 to 100 consecutive bases of a nucleic acid sequence of the invention, or a subsequence thereof.

[0028] The invention provides an amplification primer pair for amplifying (e.g., by PCR) a nucleic acid encoding a polypeptide having a cellulase activity, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity, wherein the primer pair is capable of amplifying a nucleic acid comprising a sequence of the invention, or fragments or subsequences thereof. One or each member of the amplification primer sequence pair can comprise an oligonucleotide comprising at least about 10 to 50, or more, consecutive bases of the sequence, or about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36 or more consecutive bases of the sequence. The invention provides amplification primer pairs, wherein the primer pair comprises a first member having a sequence as set forth by about the first (the 5') 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36 or more residues of a nucleic acid of the invention, and a second member having a sequence as set forth by about the first (the 5') 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36 or more residues of the complementary strand of the first member.

[0029] The invention provides cellulase-encoding, e.g., endoglucanase-, cellobiohydrolase- and/or beta-glucosidase-encoding nucleic acids generated by amplification, e.g., polymerase chain reaction (PCR), using an amplification primer pair of the invention. The invention provides cellulase-encoding, e.g., endoglucanase-, cellobiohydrolase- and/or beta-glucosidase-encoding nucleic acids generated by amplification, e.g., polymerase chain reaction (PCR), using an amplification primer pair of the invention. The invention provides methods of making a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme by amplification, e.g., polymerase chain reaction (PCR), using an amplification primer pair of the invention. In one aspect, the amplification primer pair amplifies a nucleic acid from a library, e.g., a gene library, such as an environmental library.

[0030] The invention provides methods of amplifying a nucleic acid encoding a polypeptide having a cellulase activity, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity comprising amplification of a template nucleic acid with an amplification primer sequence pair capable of amplifying a nucleic acid sequence of the invention, or fragments or subsequences thereof.

[0031] The invention provides expression cassettes comprising a nucleic acid of the invention or a subsequence thereof. In one aspect, the expression cassette can comprise the nucleic acid that is operably linked to a promoter. The promoter can be a viral, bacterial, mammalian or plant promoter. In one aspect, the plant promoter can be a potato, rice, corn, wheat, tobacco or barley promoter. The promoter can be a constitutive promoter. The constitutive promoter can comprise CaMV35S. In another aspect, the promoter can be an inducible promoter. In one aspect, the promoter can be a tissue-specific promoter or an environmentally regulated or a developmentally regulated promoter. Thus, the promoter can be, e.g., a seed-specific, a leaf-specific, a root-specific, a stem-specific or an abscission-induced promoter. In one aspect, the expression cassette can further comprise a plant or plant virus expression vector.

[0032] The invention provides cloning vehicles comprising an expression cassette (e.g., a vector) of the invention or a nucleic acid of the invention. The cloning vehicle can be a viral vector, a plasmid, a phage, a phagemid, a cosmid, a fosmid, a bacteriophage or an artificial chromosome. The viral vector can comprise an adenovirus vector, a retroviral vector or an adeno-associated viral vector. The cloning vehicle can comprise a bacterial artificial chromosome (BAC), a plasmid, a bacteriophage P1-derived vector (PAC), a yeast artificial chromosome (YAC), or a mammalian artificial chromosome (MAC).

[0033] The invention provides transformed cell comprising a nucleic acid of the invention or an expression cassette (e.g., a vector) of the invention, or a cloning vehicle of the invention. In one aspect, the transformed cell can be a bacterial cell, a mammalian cell, a fungal cell, a yeast cell, an insect cell or a plant cell. In one aspect, the plant cell can be soybeans, rapeseed, oilseed, tomato, cane sugar, a cereal, a potato, wheat, rice, corn, tobacco or barley cell.

[0034] The invention provides transgenic non-human animals comprising a nucleic acid of the invention or an expression cassette (e.g., a vector) of the invention. In one aspect, the animal is a mouse, a rat, a pig, a goat or a sheep.

[0035] The invention provides transgenic plants comprising a nucleic acid of the invention or an expression cassette (e.g., a vector) of the invention. The transgenic plant can be a cereal plant, a corn plant, a potato plant, a tomato plant, a wheat plant, an oilseed plant, a rapeseed plant, a soybean plant, a rice plant, a barley plant or a tobacco plant.

[0036] The invention provides transgenic seeds comprising a nucleic acid of the invention or an expression cassette (e.g., a vector) of the invention. The transgenic seed can be a cereal plant, a corn seed, a wheat kernel, an oilseed, a rapeseed, a soybean seed, a palm kernel, a sunflower seed, a sesame seed, a peanut or a tobacco plant seed.

[0037] The invention provides an antisense oligonucleotide comprising a nucleic acid sequence complementary to or capable of hybridizing under stringent conditions to a nucleic acid of the invention. The invention provides methods of inhibiting the translation of a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme message in a cell comprising administering to the cell or expressing in the cell an antisense oligonucleotide comprising a nucleic acid sequence complementary to or capable of hybridizing under stringent conditions to a nucleic acid of the invention. In one aspect, the antisense oligonucleotide is between about 10 to 50, about 20 to 60, about 30 to 70, about 40 to 80, or about 60 to 100 bases in length, e.g., 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or more bases in length. The invention provides methods of inhibiting the translation of a cellulase enzyme, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme message in a cell comprising administering to the cell or expressing in the cell an antisense oligonucleotide comprising a nucleic acid sequence complementary to or capable of hybridizing under stringent conditions to a nucleic acid of the invention.

[0038] The invention provides double-stranded inhibitory RNA (RNAi, or RNA interference) molecules (including small interfering RNA, or siRNAs, for inhibiting transcription, and microRNAs, or miRNAs, for inhibiting translation) comprising a subsequence of a sequence of the invention. In one aspect, the siRNA is between about 21 to 24 residues, or, about at least 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or more duplex nucleotides in length. The invention provides methods of inhibiting the expression of a cellulase enzyme, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme in a cell comprising administering to the cell or expressing in the cell a double-stranded inhibitory RNA (siRNA or miRNA), wherein the RNA comprises a subsequence of a sequence of the invention.

[0039] The invention provides isolated or recombinant polypeptides comprising an amino acid sequence having at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more, or complete (100%) sequence identity to an exemplary polypeptide or peptide of the invention over a region of at least about 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350 or more residues, or over the full length of the polypeptide. In one aspect, the sequence identities are determined by analysis with a sequence comparison algorithm or by a visual inspection. Exemplary polypeptide or peptide sequences of the invention include 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 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:143, 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 and SEQ ID NO:166 (see also Tables 1, 2, and 3, Examples 1 and 4, below, and Sequence Listing), and subsequences thereof and variants thereof. Exemplary polypeptides also include fragments of at least about 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600 or more residues in length, or over the full length of an enzyme. Polypeptide or peptide sequences of the invention include sequence encoded by a nucleic acid of the invention. Polypeptide or peptide sequences of the invention include polypeptides or peptides specifically bound by an antibody of the invention (e.g., epitopes), or polypeptides or peptides that can generate an antibody of the invention (e.g., an immunogen).

[0040] In one aspect, a polypeptide of the invention has at least one cellulase enzyme, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity. In alternative aspects, a polynucleotide of the invention encodes a polypeptide that has at least one cellulase enzyme, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity.

[0041] In one aspect, the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity is thermostable. The polypeptide can retain a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity under conditions comprising a temperature range of between about 1° C. to about 5° C., between about 5° C. to about 15° C., between about 15° C. to about 25° C., between about 25° C. to about 37° C., between about 37° C. to about 95° C., between about 55° C. to about 85° C., between about 70° C. to about 75° C., or between about 90° C. to about 95° C., or more. In another aspect, the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity can be thermotolerant. The polypeptide can retain a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity after exposure to a temperature in the range from greater than 37° C. to about 95° C., or in the range from greater than 55° C. to about 85° C. In one aspect, the polypeptide can retain a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity after exposure to a temperature in the range from greater than 90° C. to about 95° C. at pH 4.5.

[0042] Another aspect of the invention provides an isolated or recombinant polypeptide or peptide comprising at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150 or more consecutive bases of a polypeptide or peptide sequence of the invention, sequences substantially identical thereto, and the sequences complementary thereto. The peptide can be, e.g., an immunogenic fragment, a motif (e.g., a binding site), a signal sequence, a prepro sequence or an active site.

[0043] The invention provides isolated or recombinant nucleic acids comprising a sequence encoding a polypeptide having a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity and a signal sequence, wherein the nucleic acid comprises a sequence of the invention. The signal sequence can be derived from another cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme or a non-cellulase, e.g., non-endoglucanase, non-cellobiohydrolase and/or non-beta-glucosidase enzyme (a heterologous) enzyme. The invention provides isolated or recombinant nucleic acids comprising a sequence encoding a polypeptide having a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity, wherein the sequence does not contain a signal sequence and the nucleic acid comprises a sequence of the invention. In one aspect, the invention provides an isolated or recombinant polypeptide comprising a polypeptide of the invention lacking all or part of a signal sequence. In one aspect, the isolated or recombinant polypeptide can comprise the polypeptide of the invention comprising a heterologous signal sequence, such as a heterologous cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme signal sequence or non-cellulase, e.g., non-endoglucanase, non-cellobiohydrolase and/or non-beta-glucosidase enzyme signal sequence.

[0044] In one aspect, the invention provides chimeric proteins comprising a first domain comprising a signal sequence of the invention and at least a second domain. The protein can be a fusion protein. The second domain can comprise an enzyme. The enzyme can be a non-enzyme.

[0045] The invention provides chimeric polypeptides comprising at least a first domain comprising signal peptide (SP), a prepro sequence and/or a catalytic domain (CD) of the invention and at least a second domain comprising a heterologous polypeptide or peptide, wherein the heterologous polypeptide or peptide is not naturally associated with the signal peptide (SP), prepro sequence and/or catalytic domain (CD). In one aspect, the heterologous polypeptide or peptide is not a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme. The heterologous polypeptide or peptide can be amino terminal to, carboxy terminal to or on both ends of the signal peptide (SP), prepro sequence and/or catalytic domain (CD).

[0046] The invention provides isolated or recombinant nucleic acids encoding a chimeric polypeptide, wherein the chimeric polypeptide comprises at least a first domain comprising signal peptide (SP), a prepro domain and/or a catalytic domain (CD) of the invention and at least a second domain comprising a heterologous polypeptide or peptide, wherein the heterologous polypeptide or peptide is not naturally associated with the signal peptide (SP), prepro domain and/or catalytic domain (CD).

[0047] The invention provides isolated or recombinant signal sequences (e.g., signal peptides) consisting of or comprising a sequence as set forth in residues 1 to 14, 1 to 15, 1 to 16, 1 to 17, 1 to 18, 1 to 19, 1 to 20, 1 to 21, 1 to 22, 1 to 23, 1 to 24, 1 to 25, 1 to 26, 1 to 27, 1 to 28, 1 to 28, 1 to 30, 1 to 31, 1 to 32, 1 to 33, 1 to 34, 1 to 35, 1 to 36, 1 to 37, 1 to 38, 1 to 40, 1 to 41, 1 to 42, 1 to 43, 1 to 44, 1 to 45, 1 to 46 or 1 to 47, of a polypeptide of the invention, e.g., the exemplary 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 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:143, 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 or SEQ ID NO:166 (see Tables 1, 2, and 3, Examples 1 and 4, below, and Sequence Listing). In one aspect, the invention provides signal sequences comprising the first 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70 or more amino terminal residues of a polypeptide of the invention.

[0048] In one aspect, the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity comprises a specific activity at about 37° C. in the range from about 1 to about 1200 units per milligram of protein, or, about 100 to about 1000 units per milligram of protein. In another aspect, the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity comprises a specific activity from about 100 to about 1000 units per milligram of protein, or, from about 500 to about 750 units per milligram of protein. Alternatively, the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity comprises a specific activity at 37° C. in the range from about 1 to about 750 units per milligram of protein, or, from about 500 to about 1200 units per milligram of protein. In one aspect, the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity comprises a specific activity at 37° C. in the range from about 1 to about 500 units per milligram of protein, or, from about 750 to about 1000 units per milligram of protein. In another aspect, the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity comprises a specific activity at 37° C. in the range from about 1 to about 250 units per milligram of protein. Alternatively, the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity comprises a specific activity at 37° C. in the range from about 1 to about 100 units per milligram of protein.

[0049] In another aspect, the thermotolerance comprises retention of at least half of the specific activity of the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme at 37° C. after being heated to the elevated temperature. Alternatively, the thermotolerance can comprise retention of specific activity at 37° C. in the range from about 1 to about 1200 units per milligram of protein, or, from about 500 to about 1000 units per milligram of protein, after being heated to the elevated temperature. In another aspect, the thermotolerance can comprise retention of specific activity at 37° C. in the range from about 1 to about 500 units per milligram of protein after being heated to the elevated temperature.

[0050] The invention provides the isolated or recombinant polypeptide of the invention, wherein the polypeptide comprises at least one glycosylation site. In one aspect, glycosylation can be an N-linked glycosylation. In one aspect, the polypeptide can be glycosylated after being expressed in a P. pastoris or a S. pombe.

[0051] In one aspect, the polypeptide can retain cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity under conditions comprising about pH 6.5, pH 6, pH 5.5, pH 5, pH 4.5 or pH 4 or more acidic. In another aspect, the polypeptide can retain a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity under conditions comprising about pH 7, pH 7.5 pH 8.0, pH 8.5, pH 9, pH 9.5, pH 10, pH 10.5 or pH 11 or more basic pH. In one aspect, the polypeptide can retain a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity after exposure to conditions comprising about pH 6.5, pH 6, pH 5.5, pH 5, pH 4.5 or pH 4 or more acidic pH. In another aspect, the polypeptide can retain a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity after exposure to conditions comprising about pH 7, pH 7.5 pH 8.0, pH 8.5, pH 9, pH 9.5, pH 10, pH 10.5 or pH 11 or more basic pH.

[0052] In one aspect, the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme of the invention has activity at under alkaline conditions, e.g., the alkaline conditions of the gut, e.g., the small intestine. In one aspect, the polypeptide can retains activity after exposure to the acidic pH of the stomach.

[0053] The invention provides protein preparations comprising a polypeptide (including peptides) of the invention, wherein the protein preparation comprises a liquid, a solid or a gel. The invention provides heterodimers comprising a polypeptide of the invention and a second protein or domain. The second member of the heterodimer can be a different cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme, a different enzyme or another protein. In one aspect, the second domain can be a polypeptide and the heterodimer can be a fusion protein. In one aspect, the second domain can be an epitope or a tag. In one aspect, the invention provides homodimers comprising a polypeptide of the invention.

[0054] The invention provides immobilized polypeptides (including peptides) having cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity, wherein the immobilized polypeptide comprises a polypeptide of the invention, a polypeptide encoded by a nucleic acid of the invention, or a polypeptide comprising a polypeptide of the invention and a second domain. In one aspect, the polypeptide can be immobilized on a cell, a metal, a resin, a polymer, a ceramic, a glass, a microelectrode, a graphitic particle, a bead, a gel, a plate, an array or a capillary tube.

[0055] The invention also provides arrays comprising an immobilized nucleic acid of the invention, including, e.g., probes of the invention. The invention also provides arrays comprising an antibody of the invention.

[0056] The invention provides isolated or recombinant antibodies that specifically bind to a polypeptide of the invention or to a polypeptide encoded by a nucleic acid of the invention. These antibodies of the invention can be a monoclonal or a polyclonal antibody. The invention provides hybridomas comprising an antibody of the invention, e.g., an antibody that specifically binds to a polypeptide of the invention or to a polypeptide encoded by a nucleic acid of the invention. The invention provides nucleic acids encoding these antibodies.

[0057] The invention provides method of isolating or identifying a polypeptide having cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity comprising the steps of: (a) providing an antibody of the invention; (b) providing a sample comprising polypeptides; and (c) contacting the sample of step (b) with the antibody of step (a) under conditions wherein the antibody can specifically bind to the polypeptide, thereby isolating or identifying a polypeptide having a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity.

[0058] The invention provides methods of making an anti-cellulase, e.g., anti-endoglucanase, anti-cellobiohydrolase and/or anti-beta-glucosidase enzyme antibody comprising administering to a non-human animal a nucleic acid of the invention or a polypeptide of the invention or subsequences thereof in an amount sufficient to generate a humoral immune response, thereby making an anti-cellulase, e.g., anti-endoglucanase, anti-cellobiohydrolase and/or anti-beta-glucosidase enzyme antibody. The invention provides methods of making an anti-cellulase, e.g., anti-endoglucanase, anti-cellobiohydrolase and/or anti-beta-glucosidase immune response (cellular or humoral) comprising administering to a non-human animal a nucleic acid of the invention or a polypeptide of the invention or subsequences thereof in an amount sufficient to generate an immune response (cellular or humoral).

[0059] The invention provides methods of producing a recombinant polypeptide comprising the steps of: (a) providing a nucleic acid of the invention operably linked to a promoter; and (b) expressing the nucleic acid of step (a) under conditions that allow expression of the polypeptide, thereby producing a recombinant polypeptide. In one aspect, the method can further comprise transforming a host cell with the nucleic acid of step (a) followed by expressing the nucleic acid of step (a), thereby producing a recombinant polypeptide in a transformed cell.

[0060] The invention provides methods for identifying a polypeptide having cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity comprising the following steps: (a) providing a polypeptide of the invention; or a polypeptide encoded by a nucleic acid of the invention; (b) providing cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme substrate; and (c) contacting the polypeptide or a fragment or variant thereof of step (a) with the substrate of step (b) and detecting a decrease in the amount of substrate or an increase in the amount of a reaction product, wherein a decrease in the amount of the substrate or an increase in the amount of the reaction product detects a polypeptide having a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity. In one aspect, the substrate is a cellulose-comprising compound.

[0061] The invention provides methods for identifying cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme substrate comprising the following steps: (a) providing a polypeptide of the invention; or a polypeptide encoded by a nucleic acid of the invention; (b) providing a test substrate; and (c) contacting the polypeptide of step (a) with the test substrate of step (b) and detecting a decrease in the amount of substrate or an increase in the amount of reaction product, wherein a decrease in the amount of the substrate or an increase in the amount of a reaction product identifies the test substrate as a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme substrate.

[0062] The invention provides methods of determining whether a test compound specifically binds to a polypeptide comprising the following steps: (a) expressing a nucleic acid or a vector comprising the nucleic acid under conditions permissive for translation of the nucleic acid to a polypeptide, wherein the nucleic acid comprises a nucleic acid of the invention, or, providing a polypeptide of the invention; (b) providing a test compound; (c) contacting the polypeptide with the test compound; and (d) determining whether the test compound of step (b) specifically binds to the polypeptide.

[0063] The invention provides methods for identifying a modulator of a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity comprising the following steps: (a) providing a polypeptide of the invention or a polypeptide encoded by a nucleic acid of the invention; (b) providing a test compound; (c) contacting the polypeptide of step (a) with the test compound of step (b) and measuring an activity of the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme, wherein a change in the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity measured in the presence of the test compound compared to the activity in the absence of the test compound provides a determination that the test compound modulates the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity. In one aspect, the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity can be measured by providing a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme substrate and detecting a decrease in the amount of the substrate or an increase in the amount of a reaction product, or, an increase in the amount of the substrate or a decrease in the amount of a reaction product. A decrease in the amount of the substrate or an increase in the amount of the reaction product with the test compound as compared to the amount of substrate or reaction product without the test compound identifies the test compound as an activator of cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity. An increase in the amount of the substrate or a decrease in the amount of the reaction product with the test compound as compared to the amount of substrate or reaction product without the test compound identifies the test compound as an inhibitor of cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity.

[0064] The invention provides computer systems comprising a processor and a data storage device wherein said data storage device has stored thereon a polypeptide sequence or a nucleic acid sequence of the invention (e.g., a polypeptide or peptide encoded by a nucleic acid of the invention). In one aspect, the computer system can further comprise a sequence comparison algorithm and a data storage device having at least one reference sequence stored thereon. In another aspect, the sequence comparison algorithm comprises a computer program that indicates polymorphisms. In one aspect, the computer system can further comprise an identifier that identifies one or more features in said sequence. The invention provides computer readable media having stored thereon a polypeptide sequence or a nucleic acid sequence of the invention. The invention provides methods for identifying a feature in a sequence comprising the steps of: (a) reading the sequence using a computer program which identifies one or more features in a sequence, wherein the sequence comprises a polypeptide sequence or a nucleic acid sequence of the invention; and (b) identifying one or more features in the sequence with the computer program. The invention provides methods for comparing a first sequence to a second sequence comprising the steps of: (a) reading the first sequence and the second sequence through use of a computer program which compares sequences, wherein the first sequence comprises a polypeptide sequence or a nucleic acid sequence of the invention; and (b) determining differences between the first sequence and the second sequence with the computer program. The step of determining differences between the first sequence and the second sequence can further comprise the step of identifying polymorphisms. In one aspect, the method can further comprise an identifier that identifies one or more features in a sequence. In another aspect, the method can comprise reading the first sequence using a computer program and identifying one or more features in the sequence.

[0065] The invention provides methods for isolating or recovering a nucleic acid encoding a polypeptide having a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity from an environmental sample comprising the steps of: (a) providing an amplification primer sequence pair for amplifying a nucleic acid encoding a polypeptide having a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity, wherein the primer pair is capable of amplifying a nucleic acid of the invention; (b) isolating a nucleic acid from the environmental sample or treating the environmental sample such that nucleic acid in the sample is accessible for hybridization to the amplification primer pair; and, (c) combining the nucleic acid of step (b) with the amplification primer pair of step (a) and amplifying nucleic acid from the environmental sample, thereby isolating or recovering a nucleic acid encoding a polypeptide having a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity from an environmental sample. One or each member of the amplification primer sequence pair can comprise an oligonucleotide comprising an amplification primer sequence pair of the invention, e.g., having at least about 10 to 50 consecutive bases of a sequence of the invention.

[0066] The invention provides methods for isolating or recovering a nucleic acid encoding a polypeptide having a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity from an environmental sample comprising the steps of: (a) providing a polynucleotide probe comprising a nucleic acid of the invention or a subsequence thereof; (b) isolating a nucleic acid from the environmental sample or treating the environmental sample such that nucleic acid in the sample is accessible for hybridization to a polynucleotide probe of step (a); (c) combining the isolated nucleic acid or the treated environmental sample of step (b) with the polynucleotide probe of step (a); and (d) isolating a nucleic acid that specifically hybridizes with the polynucleotide probe of step (a), thereby isolating or recovering a nucleic acid encoding a polypeptide having a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity from an environmental sample. The environmental sample can comprise a water sample, a liquid sample, a soil sample, an air sample or a biological sample. In one aspect, the biological sample can be derived from a bacterial cell, a protozoan cell, an insect cell, a yeast cell, a plant cell, a fungal cell or a mammalian cell.

[0067] The invention provides methods of generating a variant of a nucleic acid encoding a polypeptide having a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity comprising the steps of: (a) providing a template nucleic acid comprising a nucleic acid of the invention; and (b) modifying, deleting or adding one or more nucleotides in the template sequence, or a combination thereof, to generate a variant of the template nucleic acid. In one aspect, the method can further comprise expressing the variant nucleic acid to generate a variant cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme polypeptide. The modifications, additions or deletions can be introduced by a method comprising error-prone PCR, shuffling, oligonucleotide-directed mutagenesis, assembly PCR, sexual PCR mutagenesis, in vivo mutagenesis, cassette mutagenesis, recursive ensemble mutagenesis, exponential ensemble mutagenesis, site-specific mutagenesis, gene reassembly, Gene Site Saturation Mutagenesis (GSSM), synthetic ligation reassembly (SLR), Chromosomal Saturation Mutagenesis (CSM) or a combination thereof. In another aspect, the modifications, additions or deletions are introduced by a method comprising recombination, recursive sequence recombination, phosphothioate-modified DNA mutagenesis, uracil-containing template mutagenesis, gapped duplex mutagenesis, point mismatch repair mutagenesis, repair-deficient host strain mutagenesis, chemical mutagenesis, radiogenic mutagenesis, deletion mutagenesis, restriction-selection mutagenesis, restriction-purification mutagenesis, artificial gene synthesis, ensemble mutagenesis, chimeric nucleic acid multimer creation and a combination thereof.

[0068] In one aspect, the method can be iteratively repeated until a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme having an altered or different activity or an altered or different stability from that of a polypeptide encoded by the template nucleic acid is produced. In one aspect, the variant cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme polypeptide is thermotolerant, and retains some activity after being exposed to an elevated temperature. In another aspect, the variant cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme polypeptide has increased glycosylation as compared to the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme encoded by a template nucleic acid. Alternatively, the variant cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase polypeptide has a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity under a high temperature, wherein the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme encoded by the template nucleic acid is not active under the high temperature. In one aspect, the method can be iteratively repeated until a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme coding sequence having an altered codon usage from that of the template nucleic acid is produced. In another aspect, the method can be iteratively repeated until a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme gene having higher or lower level of message expression or stability from that of the template nucleic acid is produced.

[0069] The invention provides methods for modifying codons in a nucleic acid encoding a polypeptide having a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity to increase its expression in a host cell, the method comprising the following steps: (a) providing a nucleic acid of the invention encoding a polypeptide having a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity; and, (b) identifying a non-preferred or a less preferred codon in the nucleic acid of step (a) and replacing it with a preferred or neutrally used codon encoding the same amino acid as the replaced codon, wherein a preferred codon is a codon over-represented in coding sequences in genes in the host cell and a non-preferred or less preferred codon is a codon under-represented in coding sequences in genes in the host cell, thereby modifying the nucleic acid to increase its expression in a host cell.

[0070] The invention provides methods for modifying codons in a nucleic acid encoding a polypeptide having a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity; the method comprising the following steps: (a) providing a nucleic acid of the invention; and, (b) identifying a codon in the nucleic acid of step (a) and replacing it with a different codon encoding the same amino acid as the replaced codon, thereby modifying codons in a nucleic acid encoding a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme.

[0071] The invention provides methods for modifying codons in a nucleic acid encoding a polypeptide having a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity to increase its expression in a host cell, the method comprising the following steps: (a) providing a nucleic acid of the invention encoding a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme polypeptide; and, (b) identifying a non-preferred or a less preferred codon in the nucleic acid of step (a) and replacing it with a preferred or neutrally used codon encoding the same amino acid as the replaced codon, wherein a preferred codon is a codon over-represented in coding sequences in genes in the host cell and a non-preferred or less preferred codon is a codon under-represented in coding sequences in genes in the host cell, thereby modifying the nucleic acid to increase its expression in a host cell.

[0072] The invention provides methods for modifying a codon in a nucleic acid encoding a polypeptide having a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity to decrease its expression in a host cell, the method comprising the following steps: (a) providing a nucleic acid of the invention; and (b) identifying at least one preferred codon in the nucleic acid of step (a) and replacing it with a non-preferred or less preferred codon encoding the same amino acid as the replaced codon, wherein a preferred codon is a codon over-represented in coding sequences in genes in a host cell and a non-preferred or less preferred codon is a codon under-represented in coding sequences in genes in the host cell, thereby modifying the nucleic acid to decrease its expression in a host cell. In one aspect, the host cell can be a bacterial cell, a fungal cell, an insect cell, a yeast cell, a plant cell or a mammalian cell.

[0073] The invention provides methods for producing a library of nucleic acids encoding a plurality of modified cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme active sites or substrate binding sites, wherein the modified active sites or substrate binding sites are derived from a first nucleic acid comprising a sequence encoding a first active site or a first substrate binding site the method comprising the following steps: (a) providing a first nucleic acid encoding a first active site or first substrate binding site, wherein the first nucleic acid sequence comprises a sequence that hybridizes under stringent conditions to a nucleic acid of the invention, and the nucleic acid encodes a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme active site or a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme substrate binding site; (b) providing a set of mutagenic oligonucleotides that encode naturally-occurring amino acid variants at a plurality of targeted codons in the first nucleic acid; and, (c) using the set of mutagenic oligonucleotides to generate a set of active site-encoding or substrate binding site-encoding variant nucleic acids encoding a range of amino acid variations at each amino acid codon that was mutagenized, thereby producing a library of nucleic acids encoding a plurality of modified cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme active sites or substrate binding sites. In one aspect, the method comprises mutagenizing the first nucleic acid of step (a) by a method comprising an optimized directed evolution system, Gene Site Saturation Mutagenesis (GSSM), synthetic ligation reassembly (SLR), error-prone PCR, shuffling, oligonucleotide-directed mutagenesis, assembly PCR, sexual PCR mutagenesis, in vivo mutagenesis, cassette mutagenesis, recursive ensemble mutagenesis, exponential ensemble mutagenesis, site-specific mutagenesis, gene reassembly, and a combination thereof. In another aspect, the method comprises mutagenizing the first nucleic acid of step (a) or variants by a method comprising recombination, recursive sequence recombination, phosphothioate-modified DNA mutagenesis, uracil-containing template mutagenesis, gapped duplex mutagenesis, point mismatch repair mutagenesis, repair-deficient host strain mutagenesis, chemical mutagenesis, radiogenic mutagenesis, deletion mutagenesis, restriction-selection mutagenesis, restriction-purification mutagenesis, artificial gene synthesis, ensemble mutagenesis, chimeric nucleic acid multimer creation and a combination thereof.

[0074] The invention provides methods for making a small molecule comprising the following steps: (a) providing a plurality of biosynthetic enzymes capable of synthesizing or modifying a small molecule, wherein one of the enzymes comprises a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme encoded by a nucleic acid of the invention; (b) providing a substrate for at least one of the enzymes of step (a); and (c) reacting the substrate of step (b) with the enzymes under conditions that facilitate a plurality of biocatalytic reactions to generate a small molecule by a series of biocatalytic reactions. The invention provides methods for modifying a small molecule comprising the following steps: (a) providing a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme, wherein the enzyme comprises a polypeptide of the invention, or, a polypeptide encoded by a nucleic acid of the invention, or a subsequence thereof; (b) providing a small molecule; and (c) reacting the enzyme of step (a) with the small molecule of step (b) under conditions that facilitate an enzymatic reaction catalyzed by the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme, thereby modifying a small molecule by a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymatic reaction. In one aspect, the method can comprise a plurality of small molecule substrates for the enzyme of step (a), thereby generating a library of modified small molecules produced by at least one enzymatic reaction catalyzed by the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme. In one aspect, the method can comprise a plurality of additional enzymes under conditions that facilitate a plurality of biocatalytic reactions by the enzymes to form a library of modified small molecules produced by the plurality of enzymatic reactions. In another aspect, the method can further comprise the step of testing the library to determine if a particular modified small molecule that exhibits a desired activity is present within the library. The step of testing the library can further comprise the steps of systematically eliminating all but one of the biocatalytic reactions used to produce a portion of the plurality of the modified small molecules within the library by testing the portion of the modified small molecule for the presence or absence of the particular modified small molecule with a desired activity, and identifying at least one specific biocatalytic reaction that produces the particular modified small molecule of desired activity.

[0075] The invention provides methods for determining a functional fragment of a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme comprising the steps of: (a) providing a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme, wherein the enzyme comprises a polypeptide of the invention, or a polypeptide encoded by a nucleic acid of the invention, or a subsequence thereof; and (b) deleting a plurality of amino acid residues from the sequence of step (a) and testing the remaining subsequence for a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity, thereby determining a functional fragment of a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme. In one aspect, the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity is measured by providing a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme substrate and detecting a decrease in the amount of the substrate or an increase in the amount of a reaction product.

[0076] The invention provides methods for whole cell engineering of new or modified phenotypes by using real-time metabolic flux analysis, the method comprising the following steps: (a) making a modified cell by modifying the genetic composition of a cell, wherein the genetic composition is modified by addition to the cell of a nucleic acid of the invention; (b) culturing the modified cell to generate a plurality of modified cells; (c) measuring at least one metabolic parameter of the cell by monitoring the cell culture of step (b) in real time; and, (d) analyzing the data of step (c) to determine if the measured parameter differs from a comparable measurement in an unmodified cell under similar conditions, thereby identifying an engineered phenotype in the cell using real-time metabolic flux analysis. In one aspect, the genetic composition of the cell can be modified by a method comprising deletion of a sequence or modification of a sequence in the cell, or, knocking out the expression of a gene. In one aspect, the method can further comprise selecting a cell comprising a newly engineered phenotype. In another aspect, the method can comprise culturing the selected cell, thereby generating a new cell strain comprising a newly engineered phenotype.

[0077] The invention provides methods of increasing thermotolerance or thermostability of a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme polypeptide, the method comprising glycosylating a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme polypeptide, wherein the polypeptide comprises at least thirty contiguous amino acids of a polypeptide of the invention; or a polypeptide encoded by a nucleic acid sequence of the invention, thereby increasing the thermotolerance or thermostability of the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase polypeptide. In one aspect, the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme specific activity can be thermostable or thermotolerant at a temperature in the range from greater than about 37° C. to about 95° C.

[0078] The invention provides methods for overexpressing a recombinant cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase polypeptide in a cell comprising expressing a vector comprising a nucleic acid comprising a nucleic acid of the invention or a nucleic acid sequence of the invention, wherein the sequence identities are determined by analysis with a sequence comparison algorithm or by visual inspection, wherein overexpression is effected by use of a high activity promoter, a dicistronic vector or by gene amplification of the vector.

[0079] The invention provides methods of making a transgenic plant comprising the following steps: (a) introducing a heterologous nucleic acid sequence into the cell, wherein the heterologous nucleic sequence comprises a nucleic acid sequence of the invention, thereby producing a transformed plant cell; and (b) producing a transgenic plant from the transformed cell. In one aspect, the step (a) can further comprise introducing the heterologous nucleic acid sequence by electroporation or microinjection of plant cell protoplasts. In another aspect, the step (a) can further comprise introducing the heterologous nucleic acid sequence directly to plant tissue by DNA particle bombardment. Alternatively, the step (a) can further comprise introducing the heterologous nucleic acid sequence into the plant cell DNA using an Agrobacterium tumefaciens host. In one aspect, the plant cell can be a cane sugar, beet, soybean, tomato, potato, corn, rice, wheat, tobacco or barley cell.

[0080] The invention provides methods of expressing a heterologous nucleic acid sequence in a plant cell comprising the following steps: (a) transforming the plant cell with a heterologous nucleic acid sequence operably linked to a promoter, wherein the heterologous nucleic sequence comprises a nucleic acid of the invention; (b) growing the plant under conditions wherein the heterologous nucleic acids sequence is expressed in the plant cell. The invention provides methods of expressing a heterologous nucleic acid sequence in a plant cell comprising the following steps: (a) transforming the plant cell with a heterologous nucleic acid sequence operably linked to a promoter, wherein the heterologous nucleic sequence comprises a sequence of the invention; (b) growing the plant under conditions wherein the heterologous nucleic acids sequence is expressed in the plant cell.

[0081] The invention provides feeds or foods comprising a polypeptide of the invention, or a polypeptide encoded by a nucleic acid of the invention. In one aspect, the invention provides a food, feed, a liquid, e.g., a beverage (such as a fruit juice or a beer), a bread or a dough or a bread product, or a beverage precursor (e.g., a wort), comprising a polypeptide of the invention. The invention provides food or nutritional supplements for an animal comprising a polypeptide of the invention, e.g., a polypeptide encoded by the nucleic acid of the invention.

[0082] In one aspect, the polypeptide in the food or nutritional supplement can be glycosylated. The invention provides edible enzyme delivery matrices comprising a polypeptide of the invention, e.g., a polypeptide encoded by the nucleic acid of the invention. In one aspect, the delivery matrix comprises a pellet. In one aspect, the polypeptide can be glycosylated. In one aspect, the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity is thermotolerant.

[0083] In another aspect, the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity is thermostable.

[0084] The invention provides a food, a feed or a nutritional supplement comprising a polypeptide of the invention. The invention provides methods for utilizing a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme as a nutritional supplement in an animal diet, the method comprising: preparing a nutritional supplement containing a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme comprising at least thirty contiguous amino acids of a polypeptide of the invention; and administering the nutritional supplement to an animal. The animal can be a human, a ruminant or a monogastric animal. The cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme can be prepared by expression of a polynucleotide encoding the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme in an organism selected from the group consisting of a bacterium, a yeast, a plant, an insect, a fungus and an animal. The organism can be selected from the group consisting of an S. pombe, S. cerevisiae, Pichia pastoris, E. coli, Streptomyces sp., Bacillus sp. and Lactobacillus sp.

[0085] The invention provides edible enzyme delivery matrix comprising a thermostable recombinant cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme, e.g., a polypeptide of the invention. The invention provides methods for delivering a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme supplement to an animal, the method comprising: preparing an edible enzyme delivery matrix in the form of pellets comprising a granulate edible carrier and a thermostable recombinant cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme, wherein the pellets readily disperse the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme contained therein into aqueous media, and administering the edible enzyme delivery matrix to the animal. The recombinant cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme can comprise a polypeptide of the invention. The cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme can be glycosylated to provide thermostability at pelletizing conditions. The delivery matrix can be formed by pelletizing a mixture comprising a grain germ and a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme. The pelletizing conditions can include application of steam. The pelletizing conditions can comprise application of a temperature in excess of about 80° C. for about 5 minutes and the enzyme retains a specific activity of at least 350 to about 900 units per milligram of enzyme.

[0086] In one aspect, invention provides a pharmaceutical composition comprising a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme of the invention, or a polypeptide encoded by a nucleic acid of the invention. In one aspect, the pharmaceutical composition acts as a digestive aid.

[0087] In certain aspects, a cellulose-containing compound is contacted a polypeptide of the invention having a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity at a pH in the range of between about pH 3.0 to 9.0, 10.0, 11.0 or more. In other aspects, a cellulose-containing compound is contacted with the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme at a temperature of about 55° C., 60° C., 65° C., 70° C., 75° C., 80° C., 85° C., 90° C., or more.

[0088] The details of one or more aspects of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and drawings, and from the claims.

[0089] All publications, patents, patent applications, GenBank sequences and ATCC deposits, cited herein are hereby expressly incorporated by reference for all purposes.

BRIEF DESCRIPTION OF DRAWINGS

[0090] The following drawings are illustrative of aspects of the invention and are not meant to limit the scope of the invention as encompassed by the claims.

[0091] FIG. 1 is a block diagram of a computer system.

[0092] FIG. 2 is a flow diagram illustrating one aspect of a process for comparing a new nucleotide or protein sequence with a database of sequences in order to determine the homology levels between the new sequence and the sequences in the database.

[0093] FIG. 3 is a flow diagram illustrating one aspect of a process in a computer for determining whether two sequences are homologous.

[0094] FIG. 4 is a flow diagram illustrating one aspect of an identifier process 300 for detecting the presence of a feature in a sequence.

[0095] FIG. 5 is an illustration of the structure of cellobiose.

[0096] FIGS. 6 and 7 illustrate the results of a TLC analysis of reaction products from cellohexaose, as discussed in detail in Example 1, below.

[0097] FIG. 8 illustrates in graph form data showing the release of cellobiose from PASC by the exemplary enzyme 22/22a (a CBH) of the invention, as discussed in detail in Example 2, below.

[0098] FIG. 9 illustrates in graph form data showing the release of cellobiose from AVICEL® MCC by the exemplary enzyme 22/22a (a CBH) of the invention, as discussed in detail in Example 2, below.

[0099] FIG. 10 illustrates in graphic form data showing a typical GIGAMATRIX® breakout, where active clones expressing enzyme able to hydrolyze methylumbelliferyl cellobioside are identified, as discussed in detail in Example 4, below.

[0100] FIG. 11 illustrates in graph form data showing the activity of selected enzymes against phosphoric acid-swollen cellulose (PASC) by capillary electrophoresis (CE) analysis, as discussed in detail in Example 4, below.

[0101] FIG. 12 illustrates in graph form data from assays of an exemplary enzyme of the invention and subclone variants in AVICEL® Microcrystalline Cellulose (MCC), where the reaction products were analyzed by the BCA reducing sugar assay, as discussed in detail in Example 4, below.

[0102] FIG. 13 illustrates in graph form data from primary GSSM screening assays, as discussed in detail in Example 4, below.

[0103] FIG. 14 illustrates in graph form data from secondary GSSM screening assays, as discussed in detail in Example 4, below.

[0104] FIG. 15 illustrates in graph form data from mixed, or "blended", GSSM screening assays, as discussed in detail in Example 4, below.

[0105] Like reference symbols in the various drawings indicate like elements.

DETAILED DESCRIPTION

[0106] The invention provides polypeptides with cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity, polynucleotides encoding them, and methods of making and using these polynucleotides and polypeptides. The invention also provides cellulase enzymes, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes, polynucleotides encoding these enzymes, the use of such polynucleotides and polypeptides.

[0107] In one aspect, the invention provides a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase, with an increased catalytic rate, improving the process of substrate hydrolysis. This increased efficiency in catalytic rate leads to an increased efficiency in producing sugars that will subsequently be used by microorganisms for ethanol production. In one aspect, microorganisms generating enzyme of the invention are used with ethanol-producing microorganisms. Thus, the invention provides methods for ethanol production and making "clean fuels" based on ethanol, e.g., for transportation using bioethanol.

[0108] In one aspect the invention provides compositions (e.g., enzyme preparations, feeds, drugs, dietary supplements) comprising the enzymes, polypeptides or polynucleotides of the invention. These compositions can be formulated in a variety of forms, e.g., as liquids, gels, pills, tablets, sprays, powders, food, feed pellets or encapsulated forms, including nanoencapsulated forms.

[0109] Assays for measuring cellulase activity, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity, e.g., for determining if a polypeptide has cellulase activity, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity, are well known in the art and are within the scope of the invention; see, e.g., Baker W L, Panow A, Estimation of cellulase activity using a glucose-oxidase-Cu(II) reducing assay for glucose, J Biochem Biophys Methods. 1991 December, 23(4):265-73; Sharrock K R, Cellulase assay methods: a review, J Biochem Biophys Methods. 1988 October, 17(2):81-105; Carder J H, Detection and quantitation of cellulase by Congo red staining of substrates in a cup-plate diffusion assay, Anal Biochem. 1986 Feb. 15, 153(1):75-9; Canevascini G., A cellulase assay coupled to cellobiose dehydrogenase, Anal Biochem. 1985 June, 147(2):419-27; Huang J S, Tang J, Sensitive assay for cellulase and dextranase. Anal Biochem. 1976 June, 73(2):369-77.

[0110] The pH of reaction conditions utilized by the invention is another variable parameter for which the invention provides. In certain aspects, the pH of the reaction is conducted in the range of about 3.0 to about 9.0. In other aspects, the pH is about 4.5 or the pH is about 7.5 or the pH is about 9. Reaction conditions conducted under alkaline conditions also can be advantageous, e.g., in some industrial or pharmaceutical applications of enzymes of the invention.

[0111] The invention provides cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase polypeptides of the invention in a variety of forms and formulations. In the methods of the invention, cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase polypeptides of the invention are used in a variety of forms and formulations. For example, purified cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase polypeptides can be used in enzyme preparations deployed in bioethanol production or in pharmaceutical or dietary aid applications. Alternatively, the enzymes of the invention can be used directly in processes to produce bioethanol, make clean fuels, process biowastes, process foods, liquids or feeds, and the like.

[0112] Alternatively, the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase polypeptides of the invention can be expressed in a microorganism using procedures known in the art. In other aspects, the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase polypeptides of the invention can be immobilized on a solid support prior to use in the methods of the invention. Methods for immobilizing enzymes on solid supports are commonly known in the art, for example J. Mol. Cat. B: Enzymatic 6 (1999) 29-39; Chivata et al. Biocatalysis: Immobilized cells and enzymes, J. Mol. Cat. 37 (1986) 1-24: Sharma et al., Immobilized Biomaterials Techniques and Applications, Angew. Chem. Int. Ed. Engl. 21 (1982) 837-54: Laskin (Ed.), Enzymes and Immobilized Cells in Biotechnology.

Nucleic Acids, Probes and Inhibitory Molecules

[0113] The invention provides isolated and recombinant nucleic acids, e.g., see Tables 1, 2, and 3, Examples 1 and 4, below, and Sequence Listing; nucleic acids encoding polypeptides, including the exemplary polynucleotide sequences of the invention, e.g., see Table 1 and Sequence Listing; including expression cassettes such as expression vectors and various cloning vehicles comprising nucleic acids of the invention. The invention also includes methods for discovering, identifying or isolated new cellulases, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase polypeptide sequences using the nucleic acids of the invention. The invention also includes methods for inhibiting the expression of cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase encoding genes and transcripts using the nucleic acids of the invention.

[0114] Also provided are methods for modifying the nucleic acids of the invention, including making variants of nucleic acids of the invention, by, e.g., synthetic ligation reassembly, optimized directed evolution system and/or saturation mutagenesis such as gene site saturation mutagenesis (GSSM). The term "saturation mutagenesis", Gene Site Saturation Mutagenesis, or "GSSM" includes a method that uses degenerate oligonucleotide primers to introduce point mutations into a polynucleotide, as described in detail, below. The term "optimized directed evolution system" or "optimized directed evolution" includes a method for reassembling fragments of related nucleic acid sequences, e.g., related genes, and explained in detail, below. The term "synthetic ligation reassembly" or "SLR" includes a method of ligating oligonucleotide fragments in a non-stochastic fashion, and explained in detail, below. The term "variant" refers to polynucleotides or polypeptides of the invention modified at one or more base pairs, codons, introns, exons, or amino acid residues (respectively) yet still retain the biological activity of a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase of the invention. Variants can be produced by any number of means included methods such as, for example, error-prone PCR, shuffling, oligonucleotide-directed mutagenesis, assembly PCR, sexual PCR mutagenesis, in vivo mutagenesis, cassette mutagenesis, recursive ensemble mutagenesis, exponential ensemble mutagenesis, site-specific mutagenesis, gene reassembly, GSSM and any combination thereof.

[0115] The nucleic acids of the invention can be made, isolated and/or manipulated by, e.g., cloning and expression of cDNA libraries, amplification of message or genomic DNA by PCR, and the like. For example, exemplary sequences of the invention were initially derived from environmental sources. Thus, in one aspect, the invention provides cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme-encoding nucleic acids, and the polypeptides encoded by them, having a common novelty in that they are derived from a common source, e.g., an environmental, mixed culture, or a bacterial source.

[0116] In practicing the methods of the invention, homologous genes can be modified by manipulating a template nucleic acid, as described herein. The invention can be practiced in conjunction with any method or protocol or device known in the art, which are well described in the scientific and patent literature.

[0117] The phrases "nucleic acid" or "nucleic acid sequence" as used herein refer to an oligonucleotide, nucleotide, polynucleotide, or to a fragment of any of these, to DNA or RNA of genomic or synthetic origin which may be single-stranded or double-stranded and may represent a sense or antisense (complementary) strand, to peptide nucleic acid (PNA), or to any DNA-like or RNA-like material, natural or synthetic in origin. The phrases "nucleic acid" or "nucleic acid sequence" includes oligonucleotide, nucleotide, polynucleotide, or to a fragment of any of these, to DNA or RNA (e.g., mRNA, rRNA, tRNA, iRNA) of genomic or synthetic origin which may be single-stranded or double-stranded and may represent a sense or antisense strand, to peptide nucleic acid (PNA), or to any DNA-like or RNA-like material, natural or synthetic in origin, including, e.g., iRNA, ribonucleoproteins (e.g., e.g., double stranded iRNAs, e.g., iRNPs). The term encompasses nucleic acids, i.e., oligonucleotides, containing known analogues of natural nucleotides. The term also encompasses nucleic-acid-like structures with synthetic backbones, see e.g., Mata (1997) Toxicol. Appl. Pharmacol. 144:189-197; Strauss-Soukup (1997) Biochemistry 36:8692-8698; Samstag (1996) Antisense Nucleic Acid Drug Dev 6:153-156. "Oligonucleotide" includes either a single stranded polydeoxynucleotide or two complementary polydeoxynucleotide strands which may be chemically synthesized. Such synthetic oligonucleotides have no 5' phosphate and thus will not ligate to another oligonucleotide without adding a phosphate with an ATP in the presence of a kinase. A synthetic oligonucleotide can ligate to a fragment that has not been dephosphorylated.

[0118] A "coding sequence of" or a "nucleotide sequence encoding" a particular polypeptide or protein, is a nucleic acid sequence which is transcribed and translated into a polypeptide or protein when placed under the control of appropriate regulatory sequences. The term "gene" means the segment of DNA involved in producing a polypeptide chain; it includes regions preceding and following the coding region (leader and trailer) as well as, where applicable, intervening sequences (introns) between individual coding segments (exons). A promoter sequence is "operably linked to" a coding sequence when RNA polymerase which initiates transcription at the promoter will transcribe the coding sequence into mRNA. "Operably linked" as used herein refers to a functional relationship between two or more nucleic acid (e.g., DNA) segments. It can refer to the functional relationship of transcriptional regulatory sequence to a transcribed sequence. For example, a promoter is operably linked to a coding sequence, such as a nucleic acid of the invention, if it stimulates or modulates the transcription of the coding sequence in an appropriate host cell or other expression system. Generally, promoter transcriptional regulatory sequences that are operably linked to a transcribed sequence are physically contiguous to the transcribed sequence, i.e., they are cis-acting. However, some transcriptional regulatory sequences, such as enhancers, need not be physically contiguous or located in close proximity to the coding sequences whose transcription they enhance.

[0119] The term "expression cassette" as used herein refers to a nucleotide sequence which is capable of affecting expression of a structural gene (i.e., a protein coding sequence, such as a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme of the invention) in a host compatible with such sequences. Expression cassettes include at least a promoter operably linked with the polypeptide coding sequence; and, optionally, with other sequences, e.g., transcription termination signals. Additional factors necessary or helpful in effecting expression may also be used, e.g., enhancers, alpha-factors. Thus, expression cassettes also include plasmids, expression vectors, recombinant viruses, any form of recombinant "naked DNA" vector, and the like. A "vector" comprises a nucleic acid which can infect, transfect, transiently or permanently transduce a cell. It will be recognized that a vector can be a naked nucleic acid, or a nucleic acid complexed with protein or lipid. The vector optionally comprises viral or bacterial nucleic acids and/or proteins, and/or membranes (e.g., a cell membrane, a viral lipid envelope, etc.). Vectors include, but are not limited to replicons (e.g., RNA replicons, bacteriophages) to which fragments of DNA may be attached and become replicated. Vectors thus include, but are not limited to RNA, autonomous self-replicating circular or linear DNA or RNA (e.g., plasmids, viruses, and the like, see, e.g., U.S. Pat. No. 5,217,879), and include both the expression and non-expression plasmids. Where a recombinant microorganism or cell culture is described as hosting an "expression vector" this includes both extra-chromosomal circular and linear DNA and DNA that has been incorporated into the host chromosome(s). Where a vector is being maintained by a host cell, the vector may either be stably replicated by the cells during mitosis as an autonomous structure, or is incorporated within the host's genome.

[0120] As used herein, the term "recombinant" encompasses nucleic acids adjacent to a "backbone" nucleic acid to which it is not adjacent in its natural environment. In one aspect, to be "enriched" the nucleic acids will represent about 5% or more of the number of nucleic acid inserts in a population of nucleic acid backbone molecules. Backbone molecules according to the invention include nucleic acids such as expression vectors, self-replicating nucleic acids, viruses, integrating nucleic acids and other vectors or nucleic acids used to maintain or manipulate a nucleic acid insert of interest. In one aspect, the enriched nucleic acids represent about 15% or more of the number of nucleic acid inserts in the population of recombinant backbone molecules. In one aspect, the enriched nucleic acids represent about 50% or more of the number of nucleic acid inserts in the population of recombinant backbone molecules. In a one aspect, the enriched nucleic acids represent about 90% or more of the number of nucleic acid inserts in the population of recombinant backbone molecules.

[0121] One aspect of the invention is an isolated or recombinant nucleic acid comprising one of the sequences of the invention, or a fragment comprising at least 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, 150, 200, 300, 400, or 500 or more consecutive bases of a nucleic acid of the invention. The isolated or recombinant nucleic acids may comprise DNA, including cDNA, genomic DNA and synthetic DNA. The DNA may be double-stranded or single-stranded and if single stranded may be the coding strand or non-coding (anti-sense) strand. Alternatively, the isolated or recombinant nucleic acids comprise RNA.

[0122] The isolated or recombinant nucleic acids of the invention may be used to prepare one of the polypeptides of the invention, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 or more consecutive amino acids of one of the polypeptides of the invention. Accordingly, another aspect of the invention is an isolated or recombinant nucleic acid which encodes one of the polypeptides of the invention, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 or more consecutive amino acids of one of the polypeptides of the invention. The coding sequences of these nucleic acids may be identical to one of the coding sequences of one of the nucleic acids of the invention or may be different coding sequences which encode one of the of the invention having at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 or more consecutive amino acids of one of the polypeptides of the invention, as a result of the redundancy or degeneracy of the genetic code. The genetic code is well known to those of skill in the art and can be obtained, e.g., on page 214 of B. Lewin, Genes VI, Oxford University Press, 1997.

[0123] The nucleic acids encoding polypeptides of the invention include but are not limited to: the coding sequence of a nucleic acid of the invention and additional coding sequences, such as leader sequences or proprotein sequences and non-coding sequences, such as introns or non-coding sequences 5' and/or 3' of the coding sequence. Thus, as used herein, the term "polynucleotide encoding a polypeptide" encompasses a polynucleotide which includes the coding sequence for the polypeptide as well as a polynucleotide which includes additional coding and/or non-coding sequence.

[0124] In one aspect, the nucleic acid sequences of the invention are mutagenized using conventional techniques, such as site directed mutagenesis, or other techniques familiar to those skilled in the art, to introduce silent changes into the polynucleotides o of the invention. As used herein, "silent changes" include, for example, changes which do not alter the amino acid sequence encoded by the polynucleotide. Such changes may be desirable in order to increase the level of the polypeptide produced by host cells containing a vector encoding the polypeptide by introducing codons or codon pairs which occur frequently in the host organism.

[0125] The invention also relates to polynucleotides which have nucleotide changes which result in amino acid substitutions, additions, deletions, fusions and truncations in the polypeptides of the invention. Such nucleotide changes may be introduced using techniques such as site directed mutagenesis, random chemical mutagenesis, exonuclease III deletion and other recombinant DNA techniques. Alternatively, such nucleotide changes may be naturally occurring allelic variants which are isolated by identifying nucleic acids which specifically hybridize to probes comprising at least 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, 150, 200, 300, 400, or 500 consecutive bases of one of the sequences of the invention (or the sequences complementary thereto) under conditions of high, moderate, or low stringency as provided herein.

[0126] General Techniques

[0127] The nucleic acids used to practice this invention, whether RNA, siRNA, miRNA, antisense nucleic acid, cDNA, genomic DNA, vectors, viruses or hybrids thereof, may be isolated from a variety of sources, genetically engineered, amplified, and/or expressed/generated recombinantly. Recombinant polypeptides (e.g., cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes) generated from these nucleic acids can be individually isolated or cloned and tested for a desired activity. Any recombinant expression system can be used, including bacterial, mammalian, yeast, insect or plant cell expression systems.

[0128] Alternatively, these nucleic acids can be synthesized in vitro by well-known chemical synthesis techniques, as described in, e.g., Adams (1983) J. Am. Chem. Soc. 105:661; Belousov (1997) Nucleic Acids Res. 25:3440-3444; Frenkel (1995) Free Radic. Biol. Med. 19:373-380; Blommers (1994) Biochemistry 33:7886-7896; Narang (1979) Meth. Enzymol. 68:90; Brown (1979) Meth. Enzymol. 68:109; Beaucage (1981) Tetra. Lett. 22:1859; U.S. Pat. No. 4,458,066.

[0129] Techniques for the manipulation of nucleic acids, such as, e.g., subcloning, labeling probes (e.g., random-primer labeling using Klenow polymerase, nick translation, amplification), sequencing, hybridization and the like are well described in the scientific and patent literature, see, e.g., Sambrook, ed., MOLECULAR CLONING: A LABORATORY MANUAL (2ND ED.), Vols. 1-3, Cold Spring Harbor Laboratory, (1989); CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, Ausubel, ed. John Wiley & Sons, Inc., New York (1997); LABORATORY TECHNIQUES IN BIOCHEMISTRY AND MOLECULAR BIOLOGY: HYBRIDIZATION WITH NUCLEIC ACID PROBES, Part I. Theory and Nucleic Acid Preparation, Tijssen, ed. Elsevier, N.Y. (1993).

[0130] Another useful means of obtaining and manipulating nucleic acids used to practice the methods of the invention is to clone from genomic samples, and, if desired, screen and re-clone inserts isolated or amplified from, e.g., genomic clones or cDNA clones. Sources of nucleic acid used in the methods of the invention include genomic or cDNA libraries contained in, e.g., mammalian artificial chromosomes (MACs), see, e.g., U.S. Pat. Nos. 5,721,118; 6,025,155; human artificial chromosomes, see, e.g., Rosenfeld (1997) Nat. Genet. 15:333-335; yeast artificial chromosomes (YAC); bacterial artificial chromosomes (BAC); P1 artificial chromosomes, see, e.g., Woon (1998) Genomics 50:306-316; P1-derived vectors (PACs), see, e.g., Kern (1997) Biotechniques 23:120-124; cosmids, recombinant viruses, phages or plasmids.

[0131] In one aspect, a nucleic acid encoding a polypeptide of the invention is assembled in appropriate phase with a leader sequence capable of directing secretion of the translated polypeptide or fragment thereof.

[0132] The invention provides fusion proteins and nucleic acids encoding them. A polypeptide of the invention can be fused to a heterologous peptide or polypeptide, such as N-terminal identification peptides which impart desired characteristics, such as increased stability or simplified purification. Peptides and polypeptides of the invention can also be synthesized and expressed as fusion proteins with one or more additional domains linked thereto for, e.g., producing a more immunogenic peptide, to more readily isolate a recombinantly synthesized peptide, to identify and isolate antibodies and antibody-expressing B cells, and the like. Detection and purification facilitating domains include, e.g., metal chelating peptides such as polyhistidine tracts and histidine-tryptophan modules that allow purification on immobilized metals, protein A domains that allow purification on immobilized immunoglobulin, and the domain utilized in the FLAGS extension/affinity purification system (Immunex Corp, Seattle Wash.). The inclusion of a cleavable linker sequences such as Factor Xa or enterokinase (Invitrogen, San Diego Calif.) between a purification domain and the motif-comprising peptide or polypeptide to facilitate purification. For example, an expression vector can include an epitope-encoding nucleic acid sequence linked to six histidine residues followed by a thioredoxin and an enterokinase cleavage site (see e.g., Williams (1995) Biochemistry 34:1787-1797; Dobeli (1998) Protein Expr. Purif. 12:404-414). The histidine residues facilitate detection and purification while the enterokinase cleavage site provides a means for purifying the epitope from the remainder of the fusion protein. Technology pertaining to vectors encoding fusion proteins and application of fusion proteins are well described in the scientific and patent literature, see e.g., Kroll (1993) DNA Cell. Biol., 12:441-53.

[0133] Transcriptional and Translational Control Sequences

[0134] The invention provides nucleic acid (e.g., DNA) sequences of the invention operatively linked to expression (e.g., transcriptional or translational) control sequence(s), e.g., promoters or enhancers, to direct or modulate RNA synthesis/expression. The expression control sequence can be in an expression vector. Exemplary bacterial promoters include lacI, lacZ, T3, T7, gpt, lambda PR, PL and trp. Exemplary eukaryotic promoters include CMV immediate early, HSV thymidine kinase, early and late SV40, LTRs from retrovirus, and mouse metallothionein I.

[0135] As used herein, the term "promoter" includes all sequences capable of driving transcription of a coding sequence in a cell, e.g., a plant or animal cell. Thus, promoters used in the constructs of the invention include cis-acting transcriptional control elements and regulatory sequences that are involved in regulating or modulating the timing and/or rate of transcription of a gene. For example, a promoter can be a cis-acting transcriptional control element, including an enhancer, a promoter, a transcription terminator, an origin of replication, a chromosomal integration sequence, 5' and 3' untranslated regions, or an intronic sequence, which are involved in transcriptional regulation. These cis-acting sequences can interact with proteins or other biomolecules to carry out (turn on/off, regulate, modulate, etc.) transcription. "Constitutive" promoters are those that drive expression continuously under most environmental conditions and states of development or cell differentiation. "Inducible" or "regulatable" promoters direct expression of the nucleic acid of the invention under the influence of environmental conditions or developmental conditions. Examples of environmental conditions that may affect transcription by inducible promoters include anaerobic conditions, elevated temperature, drought, or the presence of light.

[0136] "Tissue-specific" promoters are transcriptional control elements that are only active in particular cells or tissues or organs, e.g., in plants or animals. Tissue-specific regulation may be achieved by certain intrinsic factors which ensure that genes encoding proteins specific to a given tissue are expressed. Such factors are known to exist in mammals and plants so as to allow for specific tissues to develop.

[0137] Promoters suitable for expressing a polypeptide in bacteria include the E. coli lac or trp promoters, the lad promoter, the lacZ promoter, the T3 promoter, the T7 promoter, the gpt promoter, the lambda PR promoter, the lambda PL promoter, promoters from operons encoding glycolytic enzymes such as 3-phosphoglycerate kinase (PGK), and the acid phosphatase promoter. Eukaryotic promoters include the CMV immediate early promoter, the HSV thymidine kinase promoter, heat shock promoters, the early and late SV40 promoter, LTRs from retroviruses, and the mouse metallothionein-I promoter. Other promoters known to control expression of genes in prokaryotic or eukaryotic cells or their viruses may also be used. Promoters suitable for expressing the polypeptide or fragment thereof in bacteria include the E. coli lac or trp promoters, the lac/promoter, the lacZ promoter, the T3 promoter, the T7 promoter, the gpt promoter, the lambda P_R promoter, the lambda P_L promoter, promoters from operons encoding glycolytic enzymes such as 3-phosphoglycerate kinase (PGK) and the acid phosphatase promoter. Fungal promoters include the α-factor promoter. Eukaryotic promoters include the CMV immediate early promoter, the HSV thymidine kinase promoter, heat shock promoters, the early and late SV40 promoter, LTRs from retroviruses and the mouse metallothionein-I promoter. Other promoters known to control expression of genes in prokaryotic or eukaryotic cells or their viruses may also be used.

[0138] Tissue-Specific Plant Promoters

[0139] The invention provides expression cassettes that can be expressed in a tissue-specific manner, e.g., that can express a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme of the invention in a tissue-specific manner. The invention also provides plants or seeds that express a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme of the invention in a tissue-specific manner. The tissue-specificity can be seed specific, stem specific, leaf specific, root specific, fruit specific and the like.

[0140] The term "plant" includes whole plants, plant parts (e.g., leaves, stems, flowers, roots, etc.), plant protoplasts, seeds and plant cells and progeny of same. The class of plants which can be used in the method of the invention is generally as broad as the class of higher plants amenable to transformation techniques, including angiosperms (monocotyledonous and dicotyledonous plants), as well as gymnosperms. It includes plants of a variety of ploidy levels, including polyploid, diploid, haploid and hemizygous states. As used herein, the term "transgenic plant" includes plants or plant cells into which a heterologous nucleic acid sequence has been inserted, e.g., the nucleic acids and various recombinant constructs (e.g., expression cassettes) of the invention.

[0141] In one aspect, a constitutive promoter such as the CaMV 35S promoter can be used for expression in specific parts of the plant or seed or throughout the plant. For example, for overexpression, a plant promoter fragment can be employed which will direct expression of a nucleic acid in some or all tissues of a plant, e.g., a regenerated plant. Such promoters are referred to herein as "constitutive" promoters and are active under most environmental conditions and states of development or cell differentiation. Examples of constitutive promoters include the cauliflower mosaic virus (CaMV) 35S transcription initiation region, the 1'- or 2'-promoter derived from T-DNA of Agrobacterium tumefaciens, and other transcription initiation regions from various plant genes known to those of skill. Such genes include, e.g., ACT11 from Arabidopsis (Huang (1996) Plant Mol. Biol. 33:125-139); Cat3 from Arabidopsis (GenBank No. U43147, Zhong (1996) Mol. Gen. Genet. 251:196-203); the gene encoding stearoyl-acyl carrier protein desaturase from Brassica napus (Genbank No. X74782, Solocombe (1994) Plant Physiol. 104:1167-1176); GPc1 from maize (GenBank No. X15596; Martinez (1989) J. Mol. Biol. 208:551-565); the Gpc2 from maize (GenBank No. U45855, Manjunath (1997) Plant Mol. Biol. 33:97-112); plant promoters described in U.S. Pat. Nos. 4,962,028; 5,633,440.

[0142] The invention uses tissue-specific or constitutive promoters derived from viruses which can include, e.g., the tobamovirus subgenomic promoter (Kumagai (1995) Proc. Natl. Acad. Sci. USA 92:1679-1683; the rice tungro bacilliform virus (RTBV), which replicates only in phloem cells in infected rice plants, with its promoter which drives strong phloem-specific reporter gene expression; the cassava vein mosaic virus (CVMV) promoter, with highest activity in vascular elements, in leaf mesophyll cells, and in root tips (Verdaguer (1996) Plant Mol. Biol. 31:1129-1139).

[0143] In one aspect, the plant promoter directs expression of cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme-expressing nucleic acid in a specific tissue, organ or cell type (i.e. tissue-specific promoters) or may be otherwise under more precise environmental or developmental control or under the control of an inducible promoter. Examples of environmental conditions that may affect transcription include anaerobic conditions, elevated temperature, the presence of light, or sprayed with chemicals/hormones. For example, the invention incorporates the drought-inducible promoter of maize (Busk (1997) supra); the cold, drought, and high salt inducible promoter from potato (Kirch (1997) Plant Mol. Biol. 33:897 909).

[0144] In one aspect, tissue-specific promoters promote transcription only within a certain time frame of developmental stage within that tissue. See, e.g., Blazquez (1998) Plant Cell 10:791-800, characterizing the Arabidopsis LEAFY gene promoter. See also Cardon (1997) Plant J 12:367-77, describing the transcription factor SPL3, which recognizes a conserved sequence motif in the promoter region of the A. thaliana floral meristem identity gene AP1; and Mandel (1995) Plant Molecular Biology, Vol. 29, pp 995-1004, describing the meristem promoter eIF4. Tissue specific promoters which are active throughout the life cycle of a particular tissue can be used. In one aspect, the nucleic acids of the invention are operably linked to a promoter active primarily only in cotton fiber cells. In one aspect, the nucleic acids of the invention are operably linked to a promoter active primarily during the stages of cotton fiber cell elongation, e.g., as described by Rinehart (1996) supra. The nucleic acids can be operably linked to the Fbl2A gene promoter to be preferentially expressed in cotton fiber cells (Ibid). See also, John (1997) Proc. Natl. Acad. Sci. USA 89:5769-5773; John, et al., U.S. Pat. Nos. 5,608,148 and 5,602,321, describing cotton fiber-specific promoters and methods for the construction of transgenic cotton plants. Root-specific promoters may also be used to express the nucleic acids of the invention. Examples of root-specific promoters include the promoter from the alcohol dehydrogenase gene (DeLisle (1990) Int. Rev. Cytol. 123:39-60). Other promoters that can be used to express the nucleic acids of the invention include, e.g., ovule-specific, embryo-specific, endosperm-specific, integument-specific, seed coat-specific promoters, or some combination thereof; a leaf-specific promoter (see, e.g., Busk (1997) Plant J. 11:1285 1295, describing a leaf-specific promoter in maize); the ORF13 promoter from Agrobacterium rhizogenes (which exhibits high activity in roots, see, e.g., Hansen (1997) supra); a maize pollen specific promoter (see, e.g., Guerrero (1990) Mol. Gen. Genet. 224:161 168); a tomato promoter active during fruit ripening, senescence and abscission of leaves and, to a lesser extent, of flowers can be used (see, e.g., Blume (1997) Plant J. 12:731 746); a pistil-specific promoter from the potato SK2 gene (see, e.g., Ficker (1997) Plant Mol. Biol. 35:425 431); the Blec4 gene from pea, which is active in epidermal tissue of vegetative and floral shoot apices of transgenic alfalfa making it a useful tool to target the expression of foreign genes to the epidermal layer of actively growing shoots or fibers; the ovule-specific BEL1 gene (see, e.g., Reiser (1995) Cell 83:735-742, GenBank No. U39944); and/or, the promoter in Klee, U.S. Pat. No. 5,589,583, describing a plant promoter region is capable of conferring high levels of transcription in meristematic tissue and/or rapidly dividing cells.

[0145] In one aspect, plant promoters which are inducible upon exposure to plant hormones, such as auxins, are used to express the nucleic acids of the invention. For example, the invention can use the auxin-response elements E1 promoter fragment (AuxREs) in the soybean (Glycine max L.) (Liu (1997) Plant Physiol. 115:397-407); the auxin-responsive Arabidopsis GST6 promoter (also responsive to salicylic acid and hydrogen peroxide) (Chen (1996) Plant J. 10: 955-966); the auxin-inducible parC promoter from tobacco (Sakai (1996) 37:906-913); a plant biotin response element (Streit (1997) Mol. Plant. Microbe Interact. 10:933-937); and, the promoter responsive to the stress hormone abscisic acid (Sheen (1996) Science 274:1900-1902).

[0146] The nucleic acids of the invention can also be operably linked to plant promoters which are inducible upon exposure to chemicals reagents which can be applied to the plant, such as herbicides or antibiotics. For example, the maize In2-2 promoter, activated by benzenesulfonamide herbicide safeners, can be used (De Veylder (1997) Plant Cell Physiol. 38:568-577); application of different herbicide safeners induces distinct gene expression patterns, including expression in the root, hydathodes, and the shoot apical meristem. Coding sequence can be under the control of, e.g., a tetracycline-inducible promoter, e.g., as described with transgenic tobacco plants containing the Avena sativa L. (oat) arginine decarboxylase gene (Masgrau (1997) Plant J. 11:465-473); or, a salicylic acid-responsive element (Stange (1997) Plant J. 11:1315-1324). Using chemically- (e.g., hormone- or pesticide-) induced promoters, i.e., promoter responsive to a chemical which can be applied to the transgenic plant in the field, expression of a polypeptide of the invention can be induced at a particular stage of development of the plant. Thus, the invention also provides for transgenic plants containing an inducible gene encoding for polypeptides of the invention whose host range is limited to target plant species, such as corn, rice, barley, soybean, tomato, wheat, potato or other crops, inducible at any stage of development of the crop.

[0147] One of skill will recognize that a tissue-specific plant promoter may drive expression of operably linked sequences in tissues other than the target tissue. Thus, in one aspect, a tissue-specific promoter is one that drives expression preferentially in the target tissue or cell type, but may also lead to some expression in other tissues as well.

[0148] The nucleic acids of the invention can also be operably linked to plant promoters which are inducible upon exposure to chemicals reagents. These reagents include, e.g., herbicides, synthetic auxins, or antibiotics which can be applied, e.g., sprayed, onto transgenic plants. Inducible expression of the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme-producing nucleic acids of the invention will allow the grower to select plants with the optimal cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme expression and/or activity. The development of plant parts can thus controlled. In this way the invention provides the means to facilitate the harvesting of plants and plant parts. For example, in various embodiments, the maize In2-2 promoter, activated by benzenesulfonamide herbicide safeners, is used (De Veylder (1997) Plant Cell Physiol. 38:568-577); application of different herbicide safeners induces distinct gene expression patterns, including expression in the root, hydathodes, and the shoot apical meristem. Coding sequences of the invention are also under the control of a tetracycline-inducible promoter, e.g., as described with transgenic tobacco plants containing the Avena sativa L. (oat) arginine decarboxylase gene (Masgrau (1997) Plant J. 11:465-473); or, a salicylic acid-responsive element (Stange (1997) Plant J. 11:1315-1324).

[0149] In some aspects, proper polypeptide expression may require polyadenylation region at the 3'-end of the coding region. The polyadenylation region can be derived from the natural gene, from a variety of other plant (or animal or other) genes, or from genes in the Agrobacterial T-DNA.

[0150] Expression Vectors and Cloning Vehicles

[0151] The invention provides expression vectors and cloning vehicles comprising nucleic acids of the invention, e.g., sequences encoding the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes of the invention. Expression vectors and cloning vehicles of the invention can comprise viral particles, baculovirus, phage, plasmids, phagemids, cosmids, fosmids, bacterial artificial chromosomes, viral DNA (e.g., vaccinia, adenovirus, foul pox virus, pseudorabies and derivatives of SV40), P1-based artificial chromosomes, yeast plasmids, yeast artificial chromosomes, and any other vectors specific for specific hosts of interest (such as bacillus, Aspergillus and yeast). Vectors of the invention can include chromosomal, non-chromosomal and synthetic DNA sequences. Large numbers of suitable vectors are known to those of skill in the art, and are commercially available. Exemplary vectors are include: bacterial: pQE® vectors (Qiagen), pBLUESCRIPT® plasmids, pNH vectors, (lambda-ZAP vectors (Stratagene); ptrc99a, pKK223-3, pDR540, pRIT2T (Pharmacia); Eukaryotic: pXT1, pSG5 (Stratagene), pSVK3, pBPV, pMSG, pSVLSV40 (Pharmacia). However, any other plasmid or other vector may be used so long as they are replicable and viable in the host. Low copy number or high copy number vectors may be employed with the present invention. "Plasmids" can be commercially available, publicly available on an unrestricted basis, or can be constructed from available plasmids in accord with published procedures. Equivalent plasmids to those described herein are known in the art and will be apparent to the ordinarily skilled artisan.

[0152] The expression vector can comprise a promoter, a ribosome binding site for translation initiation and a transcription terminator. The vector may also include appropriate sequences for amplifying expression. Mammalian expression vectors can comprise an origin of replication, any necessary ribosome binding sites, a polyadenylation site, splice donor and acceptor sites, transcriptional termination sequences, and 5' flanking non-transcribed sequences. In some aspects, DNA sequences derived from the SV40 splice and polyadenylation sites may be used to provide the required non-transcribed genetic elements.

[0153] In one aspect, the expression vectors contain one or more selectable marker genes to permit selection of host cells containing the vector. Such selectable markers include genes encoding dihydrofolate reductase or genes conferring neomycin resistance for eukaryotic cell culture, genes conferring tetracycline or ampicillin resistance in E. coli, and the S. cerevisiae TRP 1 gene. Promoter regions can be selected from any desired gene using chloramphenicol transferase (CAT) vectors or other vectors with selectable markers.

[0154] In one aspect, vectors for expressing the polypeptide or fragment thereof in eukaryotic cells contain enhancers to increase expression levels. Enhancers are cis-acting elements of DNA that can be from about 10 to about 300 bp in length. They can act on a promoter to increase its transcription. Exemplary enhancers include the SV40 enhancer on the late side of the replication origin by 100 to 270, the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and the adenovirus enhancers.

[0155] A nucleic acid sequence can be inserted into a vector by a variety of procedures. In general, the sequence is ligated to the desired position in the vector following digestion of the insert and the vector with appropriate restriction endonucleases. Alternatively, blunt ends in both the insert and the vector may be ligated. A variety of cloning techniques are known in the art, e.g., as described in Ausubel and Sambrook. Such procedures and others are deemed to be within the scope of those skilled in the art.

[0156] The vector can be in the form of a plasmid, a viral particle, or a phage. Other vectors include chromosomal, non-chromosomal and synthetic DNA sequences, derivatives of SV40; bacterial plasmids, phage DNA, baculovirus, yeast plasmids, vectors derived from combinations of plasmids and phage DNA, viral DNA such as vaccinia, adenovirus, fowl pox virus, and pseudorabies. A variety of cloning and expression vectors for use with prokaryotic and eukaryotic hosts are described by, e.g., Sambrook.

[0157] Particular bacterial vectors which can be used include the commercially available plasmids comprising genetic elements of the well known cloning vector pBR322 (ATCC 37017), pKK223-3 (Pharmacia Fine Chemicals, Uppsala, Sweden), GEM1 (Promega Biotec, Madison, Wis., USA) pQE70, pQE60, pQE-9 (Qiagen), pD10, psiX174 pBLUESCRIPT II KS, pNH8A, pNH16a, pNH18A, pNH46A (Stratagene), ptrc99a, pKK223-3, pKK233-3, DR540, pRIT5 (Pharmacia), pKK232-8 and pCM7. Particular eukaryotic vectors include pSV2CAT, pOG44, pXT1, pSG (Stratagene) pSVK3, pBPV, pMSG, and pSVL (Pharmacia). However, any other vector may be used as long as it is replicable and viable in the host cell.

[0158] The nucleic acids of the invention can be expressed in expression cassettes, vectors or viruses and transiently or stably expressed in plant cells and seeds. One exemplary transient expression system uses episomal expression systems, e.g., cauliflower mosaic virus (CaMV) viral RNA generated in the nucleus by transcription of an episomal mini-chromosome containing supercoiled DNA, see, e.g., Covey (1990) Proc. Natl. Acad. Sci. USA 87:1633-1637. Alternatively, coding sequences, i.e., all or sub-fragments of sequences of the invention can be inserted into a plant host cell genome becoming an integral part of the host chromosomal DNA. Sense or antisense transcripts can be expressed in this manner. A vector comprising the sequences (e.g., promoters or coding regions) from nucleic acids of the invention can comprise a marker gene that confers a selectable phenotype on a plant cell or a seed. For example, the marker may encode biocide resistance, e.g., antibiotic resistance, such as resistance to kanamycin, G418, bleomycin, hygromycin, or herbicide resistance, such as resistance to chlorosulfuron or Basta.

[0159] Expression vectors capable of expressing nucleic acids and proteins in plants are well known in the art, and can include, e.g., vectors from Agrobacterium spp., potato virus X (see, e.g., Angell (1997) EMBO J. 16:3675-3684), tobacco mosaic virus (see, e.g., Casper (1996) Gene 173:69-73), tomato bushy stunt virus (see, e.g., Hillman (1989) Virology 169:42-50), tobacco etch virus (see, e.g., Dolja (1997) Virology 234:243-252), bean golden mosaic virus (see, e.g., Morinaga (1993) Microbiol Immunol. 37:471-476), cauliflower mosaic virus (see, e.g., Cecchini (1997) Mol. Plant Microbe Interact. 10:1094-1101), maize Ac/Ds transposable element (see, e.g., Rubin (1997) Mol. Cell. Biol. 17:6294-6302; Kunze (1996) Curr. Top. Microbiol. Immunol. 204:161-194), and the maize suppressor-mutator (Spm) transposable element (see, e.g., Schlappi (1996) Plant Mol. Biol. 32:717-725); and derivatives thereof.

[0160] In one aspect, the expression vector can have two replication systems to allow it to be maintained in two organisms, for example in mammalian or insect cells for expression and in a prokaryotic host for cloning and amplification. Furthermore, for integrating expression vectors, the expression vector can contain at least one sequence homologous to the host cell genome. It can contain two homologous sequences which flank the expression construct. The integrating vector can be directed to a specific locus in the host cell by selecting the appropriate homologous sequence for inclusion in the vector. Constructs for integrating vectors are well known in the art.

[0161] Expression vectors of the invention may also include a selectable marker gene to allow for the selection of bacterial strains that have been transformed, e.g., genes which render the bacteria resistant to drugs such as ampicillin, chloramphenicol, erythromycin, kanamycin, neomycin and tetracycline. Selectable markers can also include biosynthetic genes, such as those in the histidine, tryptophan and leucine biosynthetic pathways.

[0162] The DNA sequence in the expression vector is operatively linked to an appropriate expression control sequence(s) (promoter) to direct RNA synthesis. Particular named bacterial promoters include lacI, lacZ, T3, T7, gpt, lambda P_R, P_L, and trp. Eukaryotic promoters include CMV immediate early, HSV thymidine kinase, early and late SV40, LTRs from retrovirus and mouse metallothionein-I. Selection of the appropriate vector and promoter is well within the level of ordinary skill in the art. The expression vector also contains a ribosome binding site for translation initiation and a transcription terminator. The vector may also include appropriate sequences for amplifying expression. Promoter regions can be selected from any desired gene using chloramphenicol transferase (CAT) vectors or other vectors with selectable markers. In addition, the expression vectors in one aspect contain one or more selectable marker genes to provide a phenotypic trait for selection of transformed host cells such as dihydrofolate reductase or neomycin resistance for eukaryotic cell culture, or such as tetracycline or ampicillin resistance in E. coli.

[0163] Mammalian expression vectors may also comprise an origin of replication, any necessary ribosome binding sites, a polyadenylation site, splice donor and acceptor sites, transcriptional termination sequences and 5' flanking nontranscribed sequences. In some aspects, DNA sequences derived from the SV40 splice and polyadenylation sites may be used to provide the required nontranscribed genetic elements.

[0164] Vectors for expressing the polypeptide or fragment thereof in eukaryotic cells may also contain enhancers to increase expression levels. Enhancers are cis-acting elements of DNA, usually from about 10 to about 300 bp in length that act on a promoter to increase its transcription. Examples include the SV40 enhancer on the late side of the replication origin by 100 to 270, the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin and the adenovirus enhancers.

[0165] In addition, the expression vectors can contain one or more selectable marker genes to permit selection of host cells containing the vector. Such selectable markers include genes encoding dihydrofolate reductase or genes conferring neomycin resistance for eukaryotic cell culture, genes conferring tetracycline or ampicillin resistance in E. coli and the S. cerevisiae TRP1 gene.

[0166] In some aspects, the nucleic acid encoding one of the polypeptides of the invention, or fragments comprising at least about 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 or more consecutive amino acids thereof is assembled in appropriate phase with a leader sequence capable of directing secretion of the translated polypeptide or fragment thereof. In one aspect, the nucleic acid can encode a fusion polypeptide in which one of the polypeptides of the invention, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 or more consecutive amino acids thereof is fused to heterologous peptides or polypeptides, such as N-terminal identification peptides which impart desired characteristics, such as increased stability or simplified purification.

[0167] The appropriate DNA sequence may be inserted into the vector by a variety of procedures. In general, the DNA sequence is ligated to the desired position in the vector following digestion of the insert and the vector with appropriate restriction endonucleases. Alternatively, blunt ends in both the insert and the vector may be ligated. A variety of cloning techniques are disclosed in Ausubel et al. Current Protocols in Molecular Biology, John Wiley 503 Sons, Inc. 1997 and Sambrook et al., Molecular Cloning: A Laboratory Manual 2nd Ed., Cold Spring Harbor Laboratory Press (1989. Such procedures and others are deemed to be within the scope of those skilled in the art.

[0168] The vector may be, for example, in the form of a plasmid, a viral particle, or a phage. Other vectors include chromosomal, nonchromosomal and synthetic DNA sequences, derivatives of SV40; bacterial plasmids, phage DNA, baculovirus, yeast plasmids, vectors derived from combinations of plasmids and phage DNA, viral DNA such as vaccinia, adenovirus, fowl pox virus and pseudorabies. A variety of cloning and expression vectors for use with prokaryotic and eukaryotic hosts are described by Sambrook, et al., Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor, N.Y., (1989).

[0169] Host Cells and Transformed Cells

[0170] The invention also provides a transformed cell comprising a nucleic acid sequence of the invention, e.g., a sequence encoding a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme of the invention, or a vector of the invention. The host cell may be any of the host cells familiar to those skilled in the art, including prokaryotic cells, eukaryotic cells, such as bacterial cells, fungal cells, yeast cells, mammalian cells, insect cells, or plant cells. Exemplary bacterial cells include any species of Streptomyces, Staphylococcus or Bacillus, or the exemplary species E. coli, Bacillus subtilis, Bacillus cereus, Salmonella typhimurium. Exemplary insect cells include any species of Spodoptera or Drosophila, including Drosophila S2 and Spodoptera Sf9. Exemplary animal cells include CHO, COS or Bowes melanoma or any mouse or human cell line. The selection of an appropriate host is within the abilities of those skilled in the art. Techniques for transforming a wide variety of higher plant species are well known and described in the technical and scientific literature. See, e.g., Weising (1988) Ann. Rev. Genet. 22:421-477; U.S. Pat. No. 5,750,870.

[0171] The vector can be introduced into the host cells using any of a variety of techniques, including transformation, transfection, transduction, viral infection, gene guns, or Ti-mediated gene transfer. Particular methods include calcium phosphate transfection, DEAE-Dextran mediated transfection, lipofection, or electroporation (Davis, L., Dibner, M., Battey, I., Basic Methods in Molecular Biology, (1986)).

[0172] In one aspect, the nucleic acids or vectors of the invention are introduced into the cells for screening, thus, the nucleic acids enter the cells in a manner suitable for subsequent expression of the nucleic acid. The method of introduction is largely dictated by the targeted cell type. Exemplary methods include CaPO₄ precipitation, liposome fusion, lipofection (e.g., LIPOFECTIN®), electroporation, viral infection, etc. The candidate nucleic acids may stably integrate into the genome of the host cell (for example, with retroviral introduction) or may exist either transiently or stably in the cytoplasm (i.e. through the use of traditional plasmids, utilizing standard regulatory sequences, selection markers, etc.). As many pharmaceutically important screens require human or model mammalian cell targets, retroviral vectors capable of transfecting such targets can be used.

[0173] Where appropriate, the engineered host cells can be cultured in conventional nutrient media modified as appropriate for activating promoters, selecting transformants or amplifying the genes of the invention. Following transformation of a suitable host strain and growth of the host strain to an appropriate cell density, the selected promoter may be induced by appropriate means (e.g., temperature shift or chemical induction) and the cells may be cultured for an additional period to allow them to produce the desired polypeptide or fragment thereof.

[0174] Cells can be harvested by centrifugation, disrupted by physical or chemical means, and the resulting crude extract is retained for further purification. Microbial cells employed for expression of proteins can be disrupted by any convenient method, including freeze-thaw cycling, sonication, mechanical disruption, or use of cell lysing agents. Such methods are well known to those skilled in the art. The expressed polypeptide or fragment thereof can be recovered and purified from recombinant cell cultures by methods including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography and lectin chromatography. Protein refolding steps can be used, as necessary, in completing configuration of the polypeptide. If desired, high performance liquid chromatography (HPLC) can be employed for final purification steps.

[0175] The constructs in host cells can be used in a conventional manner to produce the gene product encoded by the recombinant sequence. Depending upon the host employed in a recombinant production procedure, the polypeptides produced by host cells containing the vector may be glycosylated or may be non-glycosylated. Polypeptides of the invention may or may not also include an initial methionine amino acid residue.

[0176] Cell-free translation systems can also be employed to produce a polypeptide of the invention. Cell-free translation systems can use mRNAs transcribed from a DNA construct comprising a promoter operably linked to a nucleic acid encoding the polypeptide or fragment thereof. In some aspects, the DNA construct may be linearized prior to conducting an in vitro transcription reaction. The transcribed mRNA is then incubated with an appropriate cell-free translation extract, such as a rabbit reticulocyte extract, to produce the desired polypeptide or fragment thereof.

[0177] The expression vectors can contain one or more selectable marker genes to provide a phenotypic trait for selection of transformed host cells such as dihydrofolate reductase or neomycin resistance for eukaryotic cell culture, or such as tetracycline or ampicillin resistance in E. coli.

[0178] Host cells containing the polynucleotides of interest, e.g., nucleic acids of the invention, can be cultured in conventional nutrient media modified as appropriate for activating promoters, selecting transformants or amplifying genes. The culture conditions, such as temperature, pH and the like, are those previously used with the host cell selected for expression and will be apparent to the ordinarily skilled artisan. The clones which are identified as having the specified enzyme activity may then be sequenced to identify the polynucleotide sequence encoding an enzyme having the enhanced activity.

[0179] The invention provides a method for overexpressing a recombinant cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme in a cell comprising expressing a vector comprising a nucleic acid of the invention, e.g., a nucleic acid comprising a nucleic acid sequence with at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more sequence identity to an exemplary sequence of the invention over a region of at least about 100 residues, wherein the sequence identities are determined by analysis with a sequence comparison algorithm or by visual inspection, or, a nucleic acid that hybridizes under stringent conditions to a nucleic acid sequence of the invention. The overexpression can be effected by any means, e.g., use of a high activity promoter, a dicistronic vector or by gene amplification of the vector.

[0180] The nucleic acids of the invention can be expressed, or overexpressed, in any in vitro or in vivo expression system. Any cell culture systems can be employed to express, or over-express, recombinant protein, including bacterial, insect, yeast, fungal or mammalian cultures. Over-expression can be effected by appropriate choice of promoters, enhancers, vectors (e.g., use of replicon vectors, dicistronic vectors (see, e.g., Gurtu (1996) Biochem. Biophys. Res. Commun. 229:295-8), media, culture systems and the like. In one aspect, gene amplification using selection markers, e.g., glutamine synthetase (see, e.g., Sanders (1987) Dev. Biol. Stand. 66:55-63), in cell systems are used to overexpress the polypeptides of the invention. The host cell may be any of the host cells familiar to those skilled in the art, including prokaryotic cells, eukaryotic cells, mammalian cells, insect cells, or plant cells. The selection of an appropriate host is within the abilities of those skilled in the art.

[0181] The vector may be introduced into the host cells using any of a variety of techniques, including transformation, transfection, transduction, viral infection, gene guns, or Ti-mediated gene transfer. Particular methods include calcium phosphate transfection, DEAE-Dextran mediated transfection, lipofection, or electroporation (Davis, L., Dibner, M., Battey, I., Basic Methods in Molecular Biology, (1986)).

[0182] Where appropriate, the engineered host cells can be cultured in conventional nutrient media modified as appropriate for activating promoters, selecting transformants or amplifying the genes of the invention. Following transformation of a suitable host strain and growth of the host strain to an appropriate cell density, the selected promoter may be induced by appropriate means (e.g., temperature shift or chemical induction) and the cells may be cultured for an additional period to allow them to produce the desired polypeptide or fragment thereof.

[0183] Cells can be harvested by centrifugation, disrupted by physical or chemical means and the resulting crude extract is retained for further purification. Microbial cells employed for expression of proteins can be disrupted by any convenient method, including freeze-thaw cycling, sonication, mechanical disruption, or use of cell lysing agents. Such methods are well known to those skilled in the art. The expressed polypeptide or fragment thereof can be recovered and purified from recombinant cell cultures by methods including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography and lectin chromatography. Protein refolding steps can be used, as necessary, in completing configuration of the polypeptide. If desired, high performance liquid chromatography (HPLC) can be employed for final purification steps.

[0184] Various mammalian cell culture systems can also be employed to express recombinant protein. Examples of mammalian expression systems include the COS-7 lines of monkey kidney fibroblasts (described by Gluzman, Cell, 23:175, 1981) and other cell lines capable of expressing proteins from a compatible vector, such as the C127, 3T3, CHO, HeLa and BHK cell lines.

[0185] The constructs in host cells can be used in a conventional manner to produce the gene product encoded by the recombinant sequence. Depending upon the host employed in a recombinant production procedure, the polypeptides produced by host cells containing the vector may be glycosylated or may be non-glycosylated. Polypeptides of the invention may or may not also include an initial methionine amino acid residue.

[0186] Alternatively, the polypeptides of the invention, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 or more consecutive amino acids thereof can be synthetically produced by conventional peptide synthesizers, e.g., as discussed below. In other aspects, fragments or portions of the polypeptides may be employed for producing the corresponding full-length polypeptide by peptide synthesis; therefore, the fragments may be employed as intermediates for producing the full-length polypeptides.

[0187] Cell-free translation systems can also be employed to produce one of the polypeptides of the invention, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 or more consecutive amino acids thereof using mRNAs transcribed from a DNA construct comprising a promoter operably linked to a nucleic acid encoding the polypeptide or fragment thereof. In some aspects, the DNA construct may be linearized prior to conducting an in vitro transcription reaction. The transcribed mRNA is then incubated with an appropriate cell-free translation extract, such as a rabbit reticulocyte extract, to produce the desired polypeptide or fragment thereof.

[0188] Amplification of Nucleic Acids

[0189] In practicing the invention, nucleic acids of the invention and nucleic acids encoding the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes of the invention, or modified nucleic acids of the invention, can be reproduced by amplification, e.g., PCR. Amplification can also be used to clone or modify the nucleic acids of the invention. Thus, the invention provides amplification primer sequence pairs for amplifying nucleic acids of the invention. One of skill in the art can design amplification primer sequence pairs for any part of or the full length of these sequences.

[0190] In one aspect, the invention provides a nucleic acid amplified by an amplification primer pair of the invention, e.g., a primer pair as set forth by about the first (the 5') 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 or more residues of a nucleic acid of the invention, and about the first (the 5') 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 or more residues of the complementary strand. The invention provides amplification primer sequence pairs for amplifying a nucleic acid encoding a polypeptide having a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity, wherein the primer pair is capable of amplifying a nucleic acid comprising a sequence of the invention, or fragments or subsequences thereof. One or each member of the amplification primer sequence pair can comprise an oligonucleotide comprising at least about 10 to 50 or more consecutive bases of the sequence, or about 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 or more consecutive bases of the sequence. The invention provides amplification primer pairs, wherein the primer pair comprises a first member having a sequence as set forth by about the first (the 5') 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 or more residues of a nucleic acid of the invention, and a second member having a sequence as set forth by about the first (the 5') 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 or more residues of the complementary strand of the first member.

[0191] The invention provides cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes generated by amplification, e.g., polymerase chain reaction (PCR), using an amplification primer pair of the invention. The invention provides methods of making a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme by amplification, e.g., PCR, using an amplification primer pair of the invention. In one aspect, the amplification primer pair amplifies a nucleic acid from a library, e.g., a gene library, such as an environmental library.

[0192] Amplification reactions can also be used to quantify the amount of nucleic acid in a sample (such as the amount of message in a cell sample), label the nucleic acid (e.g., to apply it to an array or a blot), detect the nucleic acid, or quantify the amount of a specific nucleic acid in a sample. In one aspect of the invention, message isolated from a cell or a cDNA library are amplified.

[0193] The skilled artisan can select and design suitable oligonucleotide amplification primers. Amplification methods are also well known in the art, and include, e.g., polymerase chain reaction, PCR (see, e.g., PCR PROTOCOLS, A GUIDE TO METHODS AND APPLICATIONS, ed. Innis, Academic Press, N.Y. (1990) and PCR STRATEGIES (1995), ed. Innis, Academic Press, Inc., N.Y., ligase chain reaction (LCR) (see, e.g., Wu (1989) Genomics 4:560; Landegren (1988) Science 241:1077; Barringer (1990) Gene 89:117); transcription amplification (see, e.g., Kwoh (1989) Proc. Natl. Acad. Sci. USA 86:1173); and, self-sustained sequence replication (see, e.g., Guatelli (1990) Proc. Natl. Acad. Sci. USA 87:1874); Q Beta replicase amplification (see, e.g., Smith (1997) J. Clin. Microbiol. 35:1477-1491), automated Q-beta replicase amplification assay (see, e.g., Burg (1996) Mol. Cell. Probes 10:257-271) and other RNA polymerase mediated techniques (e.g., NASBA, Cangene, Mississauga, Ontario); see also Berger (1987) Methods Enzymol. 152:307-316; Sambrook; Ausubel; U.S. Pat. Nos. 4,683,195 and 4,683,202; Sooknanan (1995) Biotechnology 13:563-564.

Determining Sequence Identity in Nucleic Acids and Polypeptides

[0194] The invention provides nucleic acids comprising sequences having at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more, or complete (100%) sequence identity (homology) to an exemplary nucleic acid of the invention (see also Tables 1, 2, and 3, Examples 1 and 4, below, and Sequence Listing) over a region of at least about 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550 or more, residues. The invention provides polypeptides comprising sequences having at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more, or complete (100%) sequence identity to an exemplary polypeptide of the invention (see Tables 1, 2, and 3, Examples 1 and 4, below, and Sequence Listing). The extent of sequence identity (homology) may be determined using any computer program and associated parameters, including those described herein, such as BLAST 2.2.2. or FASTA version 3.0t78, with the default parameters.

[0195] Nucleic acid sequences of the invention can comprise at least 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, 150, 200, 300, 400, or 500 or more consecutive nucleotides of an exemplary sequence of the invention and sequences substantially identical thereto. Homologous sequences and fragments of nucleic acid sequences of the invention can refer to a sequence having at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more sequence identity (homology) to these sequences. Homology (sequence identity) may be determined using any of the computer programs and parameters described herein, including FASTA version 3.0t78 with the default parameters. Homologous sequences also include RNA sequences in which uridines replace the thymines in the nucleic acid sequences of the invention. The homologous sequences may be obtained using any of the procedures described herein or may result from the correction of a sequencing error. It will be appreciated that the nucleic acid sequences of the invention can be represented in the traditional single character format (See the inside back cover of Stryer, Lubert. Biochemistry, 3rd Ed., W. H Freeman & Co., New York.) or in any other format which records the identity of the nucleotides in a sequence.

[0196] In various aspects, sequence comparison programs identified herein are used in this aspect of the invention, i.e., to determine if a nucleic acid or polypeptide sequence is within the scope of the invention. However, protein and/or nucleic acid sequence identities (homologies) may be evaluated using any sequence comparison algorithm or program known in the art. Such algorithms and programs include, but are by no means limited to, TBLASTN, BLASTP, FASTA, TFASTA and CLUSTALW (see, e.g., Pearson and Lipman, Proc. Natl. Acad. Sci. USA 85(8):2444-2448, 1988; Altschul et al., J. Mol. Biol. 215(3):403-410, 1990; Thompson Nucleic Acids Res. 22(2):4673-4680, 1994; Higgins et al., Methods Enzymol. 266:383-402, 1996; Altschul et al., J. Mol. Biol. 215(3):403-410, 1990; Altschul et al., Nature Genetics 3:266-272, 1993).

[0197] In one aspect, homology or identity is measured using sequence analysis software (e.g., Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, 1710 University Avenue, Madison, Wis. 53705). Such software matches similar sequences by assigning degrees of homology to various deletions, substitutions and other modifications. In one aspect, the terms "homology" and "identity" in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same when compared and aligned for maximum correspondence over a comparison window or designated region as measured using any number of sequence comparison algorithms or by manual alignment and visual inspection. In one aspect, for sequence comparison, one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters.

[0198] A "comparison window", as used herein, includes reference to a segment of any one of the number of contiguous positions selected from the group consisting of from 20 to 600, usually about 50 to about 200, more usually about 100 to about 150 in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. Methods of alignment of sequence for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482, 1981, by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443, 1970, by the search for similarity method of person & Lipman, Proc. Nat'l. Acad. Sci. USA 85:2444, 1988, by computerized implementations of these algorithms (GAP, BESTFIT, FASTA and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by manual alignment and visual inspection. Other algorithms for determining homology or identity include, for example, in addition to a BLAST program (Basic Local Alignment Search Tool at the National Center for Biological Information), ALIGN, AMAS (Analysis of Multiply Aligned Sequences), AMPS (Protein Multiple Sequence Alignment), ASSET (Aligned Segment Statistical Evaluation Tool), BANDS, BESTSCOR, BIOSCAN (Biological Sequence Comparative Analysis Node), BLIMPS (BLocks IMProved Searcher), FASTA, Intervals & Points, BMB, CLUSTAL V, CLUSTAL W, CONSENSUS, LCONSENSUS, WCONSENSUS, Smith-Waterman algorithm, DARWIN, Las Vegas algorithm, FNAT (Forced Nucleotide Alignment Tool), Framealign, Framesearch, DYNAMIC, FILTER, FSAP (Fristensky Sequence Analysis Package), GAP (Global Alignment Program), GENAL, GIBBS, GenQuest, ISSC (Sensitive Sequence Comparison), LALIGN (Local Sequence Alignment), LCP (Local Content Program), MACAW (Multiple Alignment Construction & Analysis Workbench), MAP (Multiple Alignment Program), MBLKP, MBLKN, PIMA (Pattern-Induced Multi-sequence Alignment), SAGA (Sequence Alignment by Genetic Algorithm) and WHAT-IF. Such alignment programs can also be used to screen genome databases to identify polynucleotide sequences having substantially identical sequences. A number of genome databases are available, for example, a substantial portion of the human genome is available as part of the Human Genome Sequencing Project (Gibbs, 1995). At least twenty-one other genomes have already been sequenced, including, for example, M. genitalium (Fraser et al., 1995), M. jannaschii (Bult et al., 1996), H. influenzae (Fleischmann et al., 1995), E. coli (Blattner et al., 1997) and yeast (S. cerevisiae) (Mewes et al., 1997) and D. melanogaster (Adams et al., 2000). Significant progress has also been made in sequencing the genomes of model organism, such as mouse, C. elegans and Arabadopsis sp. Several databases containing genomic information annotated with some functional information are maintained by different organizations and may be accessible via the internet.

[0199] In one aspect, BLAST and BLAST 2.0 algorithms are used, which are described in Altschul et al., Nuc. Acids Res. 25:3389-3402, 1977 and Altschul et al., J. Mol. Biol. 215:403-410, 1990, respectively. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, M=5, N=-4 and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength of 3 and expectations (E) of 10 and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915, 1989) alignments (B) of 50, expectation (E) of 10, M=5, N=-4 and a comparison of both strands.

[0200] The BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Natl. Acad. Sci. USA 90:5873, 1993). One measure of similarity provided by BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a references sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.2, more in one aspect less than about 0.01 and most in one aspect less than about 0.001.

[0201] In one aspect, protein and nucleic acid sequence homologies are evaluated using the Basic Local Alignment Search Tool ("BLAST") In particular, five specific BLAST programs are used to perform the following task:

[0202] (1) BLASTP and BLAST3 compare an amino acid query sequence against a protein sequence database;

[0203] (2) BLASTN compares a nucleotide query sequence against a nucleotide sequence database;

[0204] (3) BLASTX compares the six-frame conceptual translation products of a query nucleotide sequence (both strands) against a protein sequence database;

[0205] (4) TBLASTN compares a query protein sequence against a nucleotide sequence database translated in all six reading frames (both strands); and

[0206] (5) TBLASTX compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.

[0207] The BLAST programs identify homologous sequences by identifying similar segments, which are referred to herein as "high-scoring segment pairs," between a query amino or nucleic acid sequence and a test sequence which is in one aspect obtained from a protein or nucleic acid sequence database. High-scoring segment pairs are in one aspect identified (i.e., aligned) by means of a scoring matrix, many of which are known in the art. In one aspect, the scoring matrix used is the BLOSUM62 matrix (Gonnet (1992) Science 256:1443-1445; Henikoff and Henikoff (1993) Proteins 17:49-61). Less in one aspect, the PAM or PAM250 matrices may also be used (see, e.g., Schwartz and Dayhoff, eds., 1978, Matrices for Detecting Distance Relationships: Atlas of Protein Sequence and Structure, Washington: National Biomedical Research Foundation). BLAST programs are accessible through the U.S. National Library of Medicine.

[0208] The parameters used with the above algorithms may be adapted depending on the sequence length and degree of homology studied. In some aspects, the parameters may be the default parameters used by the algorithms in the absence of instructions from the user.

Computer Systems and Computer Program Products

[0209] The invention provides computers, computer systems, computer readable mediums, computer programs products and the like recorded or stored thereon the nucleic acid and polypeptide sequences of the invention. Additionally, in practicing the methods of the invention, e.g., to determine and identify sequence identities (to determine whether a nucleic acid is within the scope of the invention), structural homologies, motifs and the like in silico, a nucleic acid or polypeptide sequence of the invention can be stored, recorded, and manipulated on any medium which can be read and accessed by a computer.

[0210] As used herein, the words "recorded" and "stored" refer to a process for storing information on a computer medium. A skilled artisan can readily adopt any known methods for recording information on a computer readable medium to generate manufactures comprising one or more of the nucleic acid and/or polypeptide sequences of the invention. As used herein, the terms "computer," "computer program" and "processor" are used in their broadest general contexts and incorporate all such devices, as described in detail, below. A "coding sequence of" or a "sequence encodes" a particular polypeptide or protein, is a nucleic acid sequence which is transcribed and translated into a polypeptide or protein when placed under the control of appropriate regulatory sequences.

[0211] The polypeptides of the invention include exemplary sequences of the invention and sequences substantially identical thereto, and subsequences (fragments) of any of the preceding sequences. In one aspect, substantially identical, or homologous, polypeptide sequences refer to a polypeptide sequence having at least 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more, or complete (100%) sequence identity (homology) to an exemplary sequence of the invention.

[0212] Homology (sequence identity) may be determined using any of the computer programs and parameters described herein. A nucleic acid or polypeptide sequence of the invention can be stored, recorded and manipulated on any medium which can be read and accessed by a computer. As used herein, the words "recorded" and "stored" refer to a process for storing information on a computer medium. A skilled artisan can readily adopt any of the presently known methods for recording information on a computer readable medium to generate manufactures comprising one or more of the nucleic acid sequences of the invention, one or more of the polypeptide sequences of the invention. Another aspect of the invention is a computer readable medium having recorded thereon at least 2, 5, 10, 15, or 20 or more nucleic acid or polypeptide sequences of the invention.

[0213] Another aspect of the invention is a computer readable medium having recorded thereon one or more of the nucleic acid sequences of the invention. Another aspect of the invention is a computer readable medium having recorded thereon one or more of the polypeptide sequences of the invention. Another aspect of the invention is a computer readable medium having recorded thereon at least 2, 5, 10, 15, or 20 or more of the nucleic acid or polypeptide sequences as set forth above.

[0214] Computer readable media include magnetically readable media, optically readable media, electronically readable media and magnetic/optical media. For example, the computer readable media may be a hard disk, a floppy disk, a magnetic tape, CD-ROM, Digital Versatile Disk (DVD), Random Access Memory (RAM), or Read Only Memory (ROM) as well as other types of other media known to those skilled in the art.

[0215] Aspects of the invention include systems (e.g., internet based systems), e.g., computer systems which store and manipulate the sequence information described herein. One example of a computer system 100 is illustrated in block diagram form in FIG. 1. As used herein, "a computer system" refers to the hardware components, software components and data storage components used to analyze a nucleotide sequence of a nucleic acid sequence of the invention, or a polypeptide sequence of the invention. In one aspect, the computer system 100 includes a processor for processing, accessing and manipulating the sequence data. The processor 105 can be any well-known type of central processing unit, such as, for example, the Pentium III from Intel Corporation, or similar processor from Sun, Motorola, Compaq, AMD or International Business Machines.

[0216] In one aspect, the computer system 100 is a general purpose system that comprises the processor 105 and one or more internal data storage components 110 for storing data and one or more data retrieving devices for retrieving the data stored on the data storage components. A skilled artisan can readily appreciate that any one of the currently available computer systems are suitable.

[0217] In one particular aspect, the computer system 100 includes a processor 105 connected to a bus which is connected to a main memory 115 (in one aspect implemented as RAM) and one or more internal data storage devices 110, such as a hard drive and/or other computer readable media having data recorded thereon. In some aspects, the computer system 100 further includes one or more data retrieving device 118 for reading the data stored on the internal data storage devices 110.

[0218] The data retrieving device 118 may represent, for example, a floppy disk drive, a compact disk drive, a magnetic tape drive, or a modem capable of connection to a remote data storage system (e.g., via the internet) etc. In some aspects, the internal data storage device 110 is a removable computer readable medium such as a floppy disk, a compact disk, a magnetic tape, etc. containing control logic and/or data recorded thereon. The computer system 100 may advantageously include or be programmed by appropriate software for reading the control logic and/or the data from the data storage component once inserted in the data retrieving device.

[0219] The computer system 100 includes a display 120 which is used to display output to a computer user. It should also be noted that the computer system 100 can be linked to other computer systems 125a-c in a network or wide area network to provide centralized access to the computer system 100.

[0220] Software for accessing and processing the nucleotide sequences of a nucleic acid sequence of the invention, or a polypeptide sequence of the invention, (such as search tools, compare tools and modeling tools etc.) may reside in main memory 115 during execution.

[0221] In some aspects, the computer system 100 may further comprise a sequence comparison algorithm for comparing a nucleic acid sequence of the invention, or a polypeptide sequence of the invention, stored on a computer readable medium to a reference nucleotide or polypeptide sequence(s) stored on a computer readable medium. A "sequence comparison algorithm" refers to one or more programs which are implemented (locally or remotely) on the computer system 100 to compare a nucleotide sequence with other nucleotide sequences and/or compounds stored within a data storage means. For example, the sequence comparison algorithm may compare the nucleotide sequences of a nucleic acid sequence of the invention, or a polypeptide sequence of the invention, stored on a computer readable medium to reference sequences stored on a computer readable medium to identify homologies or structural motifs.

[0222] FIG. 2 is a flow diagram illustrating one aspect of a process 200 for comparing a new nucleotide or protein sequence with a database of sequences in order to determine the homology levels between the new sequence and the sequences in the database. The database of sequences can be a private database stored within the computer system 100, or a public database such as GENBANK that is available through the Internet.

[0223] The process 200 begins at a start state 201 and then moves to a state 202 wherein the new sequence to be compared is stored to a memory in a computer system 100. As discussed above, the memory could be any type of memory, including RAM or an internal storage device.

[0224] The process 200 then moves to a state 204 wherein a database of sequences is opened for analysis and comparison. The process 200 then moves to a state 206 wherein the first sequence stored in the database is read into a memory on the computer. A comparison is then performed at a state 210 to determine if the first sequence is the same as the second sequence. It is important to note that this step is not limited to performing an exact comparison between the new sequence and the first sequence in the database. Well-known methods are known to those of skill in the art for comparing two nucleotide or protein sequences, even if they are not identical. For example, gaps can be introduced into one sequence in order to raise the homology level between the two tested sequences. The parameters that control whether gaps or other features are introduced into a sequence during comparison are normally entered by the user of the computer system.

[0225] Once a comparison of the two sequences has been performed at the state 210, a determination is made at a decision state 210 whether the two sequences are the same. Of course, the term "same" is not limited to sequences that are absolutely identical. Sequences that are within the homology parameters entered by the user will be marked as "same" in the process 200.

[0226] If a determination is made that the two sequences are the same, the process 200 moves to a state 214 wherein the name of the sequence from the database is displayed to the user. This state notifies the user that the sequence with the displayed name fulfills the homology constraints that were entered. Once the name of the stored sequence is displayed to the user, the process 200 moves to a decision state 218 wherein a determination is made whether more sequences exist in the database. If no more sequences exist in the database, then the process 200 terminates at an end state 220. However, if more sequences do exist in the database, then the process 200 moves to a state 224 wherein a pointer is moved to the next sequence in the database so that it can be compared to the new sequence. In this manner, the new sequence is aligned and compared with every sequence in the database.

[0227] It should be noted that if a determination had been made at the decision state 212 that the sequences were not homologous, then the process 200 would move immediately to the decision state 218 in order to determine if any other sequences were available in the database for comparison.

[0228] Accordingly, one aspect of the invention is a computer system comprising a processor, a data storage device having stored thereon a nucleic acid sequence of the invention, or a polypeptide sequence of the invention, a data storage device having retrievably stored thereon reference nucleotide sequences or polypeptide sequences to be compared to a nucleic acid sequence of the invention, or a polypeptide sequence of the invention and a sequence comparer for conducting the comparison. The sequence comparer may indicate a homology level between the sequences compared or identify structural motifs in the above described nucleic acid code a nucleic acid sequence of the invention, or a polypeptide sequence of the invention, or it may identify structural motifs in sequences which are compared to these nucleic acid codes and polypeptide codes. In some aspects, the data storage device may have stored thereon the sequences of at least 2, 5, 10, 15, 20, 25, 30 or 40 or more of the nucleic acid sequences of the invention, or the polypeptide sequences of the invention.

[0229] Another aspect of the invention is a method for determining the level of homology between a nucleic acid sequence of the invention, or a polypeptide sequence of the invention and a reference nucleotide sequence. The method including reading the nucleic acid code or the polypeptide code and the reference nucleotide or polypeptide sequence through the use of a computer program which determines homology levels and determining homology between the nucleic acid code or polypeptide code and the reference nucleotide or polypeptide sequence with the computer program. The computer program may be any of a number of computer programs for determining homology levels, including those specifically enumerated herein, (e.g., BLAST2N with the default parameters or with any modified parameters). The method may be implemented using the computer systems described above. The method may also be performed by reading at least 2, 5, 10, 15, 20, 25, 30 or 40 or more of the above described nucleic acid sequences of the invention, or the polypeptide sequences of the invention through use of the computer program and determining homology between the nucleic acid codes or polypeptide codes and reference nucleotide sequences or polypeptide sequences.

[0230] FIG. 3 is a flow diagram illustrating one aspect of a process 250 in a computer for determining whether two sequences are homologous. The process 250 begins at a start state 252 and then moves to a state 254 wherein a first sequence to be compared is stored to a memory. The second sequence to be compared is then stored to a memory at a state 256. The process 250 then moves to a state 260 wherein the first character in the first sequence is read and then to a state 262 wherein the first character of the second sequence is read. It should be understood that if the sequence is a nucleotide sequence, then the character would normally be either A, T, C, G or U. If the sequence is a protein sequence, then it is in one aspect in the single letter amino acid code so that the first and sequence sequences can be easily compared.

[0231] A determination is then made at a decision state 264 whether the two characters are the same. If they are the same, then the process 250 moves to a state 268 wherein the next characters in the first and second sequences are read. A determination is then made whether the next characters are the same. If they are, then the process 250 continues this loop until two characters are not the same. If a determination is made that the next two characters are not the same, the process 250 moves to a decision state 274 to determine whether there are any more characters either sequence to read.

[0232] If there are not any more characters to read, then the process 250 moves to a state 276 wherein the level of homology between the first and second sequences is displayed to the user. The level of homology is determined by calculating the proportion of characters between the sequences that were the same out of the total number of sequences in the first sequence. Thus, if every character in a first 100 nucleotide sequence aligned with a every character in a second sequence, the homology level would be 100%.

[0233] Alternatively, the computer program may be a computer program which compares the nucleotide sequences of a nucleic acid sequence as set forth in the invention, to one or more reference nucleotide sequences in order to determine whether the nucleic acid code of the invention, differs from a reference nucleic acid sequence at one or more positions. Optionally such a program records the length and identity of inserted, deleted or substituted nucleotides with respect to the sequence of either the reference polynucleotide or a nucleic acid sequence of the invention. In one aspect, the computer program may be a program which determines whether a nucleic acid sequence of the invention, contains a single nucleotide polymorphism (SNP) with respect to a reference nucleotide sequence.

[0234] Accordingly, another aspect of the invention is a method for determining whether a nucleic acid sequence of the invention, differs at one or more nucleotides from a reference nucleotide sequence comprising the steps of reading the nucleic acid code and the reference nucleotide sequence through use of a computer program which identifies differences between nucleic acid sequences and identifying differences between the nucleic acid code and the reference nucleotide sequence with the computer program. In some aspects, the computer program is a program which identifies single nucleotide polymorphisms. The method may be implemented by the computer systems described above and the method illustrated in FIG. 3. The method may also be performed by reading at least 2, 5, 10, 15, 20, 25, 30, or 40 or more of the nucleic acid sequences of the invention and the reference nucleotide sequences through the use of the computer program and identifying differences between the nucleic acid codes and the reference nucleotide sequences with the computer program.

[0235] In other aspects the computer based system may further comprise an identifier for identifying features within a nucleic acid sequence of the invention or a polypeptide sequence of the invention. An "identifier" refers to one or more programs which identifies certain features within a nucleic acid sequence of the invention, or a polypeptide sequence of the invention. In one aspect, the identifier may comprise a program which identifies an open reading frame in a nucleic acid sequence of the invention.

[0236] FIG. 4 is a flow diagram illustrating one aspect of an identifier process 300 for detecting the presence of a feature in a sequence. The process 300 begins at a start state 302 and then moves to a state 304 wherein a first sequence that is to be checked for features is stored to a memory 115 in the computer system 100. The process 300 then moves to a state 306 wherein a database of sequence features is opened. Such a database would include a list of each feature's attributes along with the name of the feature. For example, a feature name could be "Initiation Codon" and the attribute would be "ATG". Another example would be the feature name "TAATAA Box" and the feature attribute would be "TAATAA". An example of such a database is produced by the University of Wisconsin Genetics Computer Group. Alternatively, the features may be structural polypeptide motifs such as alpha helices, beta sheets, or functional polypeptide motifs such as enzymatic active sites, helix-turn-helix motifs or other motifs known to those skilled in the art.

[0237] Once the database of features is opened at the state 306, the process 300 moves to a state 308 wherein the first feature is read from the database. A comparison of the attribute of the first feature with the first sequence is then made at a state 310. A determination is then made at a decision state 316 whether the attribute of the feature was found in the first sequence. If the attribute was found, then the process 300 moves to a state 318 wherein the name of the found feature is displayed to the user.

[0238] The process 300 then moves to a decision state 320 wherein a determination is made whether move features exist in the database. If no more features do exist, then the process 300 terminates at an end state 324. However, if more features do exist in the database, then the process 300 reads the next sequence feature at a state 326 and loops back to the state 310 wherein the attribute of the next feature is compared against the first sequence. It should be noted, that if the feature attribute is not found in the first sequence at the decision state 316, the process 300 moves directly to the decision state 320 in order to determine if any more features exist in the database.

[0239] Accordingly, another aspect of the invention is a method of identifying a feature within a nucleic acid sequence of the invention, or a polypeptide sequence of the invention, comprising reading the nucleic acid code(s) or polypeptide code(s) through the use of a computer program which identifies features therein and identifying features within the nucleic acid code(s) with the computer program. In one aspect, computer program comprises a computer program which identifies open reading frames. The method may be performed by reading a single sequence or at least 2, 5, 10, 15, 20, 25, 30, or 40 or more of the nucleic acid sequences of the invention, or the polypeptide sequences of the invention, through the use of the computer program and identifying features within the nucleic acid codes or polypeptide codes with the computer program.

[0240] A nucleic acid sequence of the invention, or a polypeptide sequence of the invention, may be stored and manipulated in a variety of data processor programs in a variety of formats. For example, a nucleic acid sequence of the invention, or a polypeptide sequence of the invention, may be stored as text in a word processing file, such as Microsoft WORD® or WORDPERFECT® or as an ASCII file in a variety of database programs familiar to those of skill in the art, such as DB2®, SYBASE®, or ORACLE®. In addition, many computer programs and databases may be used as sequence comparison algorithms, identifiers, or sources of reference nucleotide sequences or polypeptide sequences to be compared to a nucleic acid sequence of the invention, or a polypeptide sequence of the invention. The following list is intended not to limit the invention but to provide guidance to programs and databases which are useful with the nucleic acid sequences of the invention, or the polypeptide sequences of the invention.

[0241] The programs and databases which may be used include, but are not limited to: MACPATTERN® (EMBL), DISCOVERYBASE® (Molecular Applications Group), GENEMINE® (Molecular Applications Group), LOOK® (Molecular Applications Group), MACLOOK® (Molecular Applications Group), BLAST and BLAST2 (NCBI), BLASTN and BLASTX (Altschul et al, J. Mol. Biol. 215: 403, 1990), FASTA (Pearson and Lipman, Proc. Natl. Acad. Sci. USA, 85: 2444, 1988), FASTDB (Brutlag et al. Comp. App. Biosci. 6:237-245, 1990), CATALYST® (Molecular Simulations Inc.), Catalyst/SHAPE® (Molecular Simulations Inc.), Cerius².DBAccess® (Molecular Simulations Inc.), HYPOGEN® (Molecular Simulations Inc.), INSIGHT II® (Molecular Simulations Inc.), DISCOVER® (Molecular Simulations Inc.), CHARMm® (Molecular Simulations Inc.), FELIX® (Molecular Simulations Inc.), DELPHI® (Molecular Simulations Inc.), QuanteMM®, (Molecular Simulations Inc.), Homology (Molecular Simulations Inc.), MODELER® (Molecular Simulations Inc.), ISIS® (Molecular Simulations Inc.), Quanta/Protein Design (Molecular Simulations Inc.), WebLab (Molecular Simulations Inc.), WebLab Diversity Explorer (Molecular Simulations Inc.), Gene Explorer (Molecular Simulations Inc.), SeqFold (Molecular Simulations Inc.), the MDL Available Chemicals Directory database, the MDL Drug Data Report data base, the Comprehensive Medicinal Chemistry database, Derwents's World Drug Index database, the BioByteMasterFile database, the Genbank database and the Genseqn database. Many other programs and data bases would be apparent to one of skill in the art given the present disclosure.

[0242] Motifs which may be detected using the above programs include sequences encoding leucine zippers, helix-turn-helix motifs, glycosylation sites, ubiquitination sites, alpha helices and beta sheets, signal sequences encoding signal peptides which direct the secretion of the encoded proteins, sequences implicated in transcription regulation such as homeoboxes, acidic stretches, enzymatic active sites, substrate binding sites and enzymatic cleavage sites.

Hybridization of Nucleic Acids

[0243] The invention provides isolated or recombinant nucleic acids that hybridize under stringent conditions to an exemplary sequence of the invention (e.g., 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 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 ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:71, SEQ ID NO:73, SEQ ID NO:75, SEQ ID NO:77, SEQ ID NO:79, SEQ ID NO:81, SEQ ID NO:83, SEQ ID NO:85, SEQ ID NO:87, SEQ ID NO:89, SEQ ID NO:91, SEQ ID NO:93, SEQ ID NO:95, SEQ ID NO:97, SEQ ID NO:99, SEQ ID NO:101, SEQ ID NO:103, SEQ ID NO:105, SEQ ID NO:107, SEQ ID NO:109, SEQ ID NO:111, SEQ ID NO:113, SEQ ID NO:115, SEQ ID NO:117, SEQ ID NO:119, SEQ ID NO:121, SEQ ID NO:123, SEQ ID NO:125, SEQ ID NO:127, SEQ ID NO:129, SEQ ID NO:131, SEQ ID NO:133, SEQ ID NO:135, SEQ ID NO:137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:143, SEQ ID NO:145, SEQ ID NO:147, SEQ ID NO:149, SEQ ID NO:151, SEQ ID NO:153, SEQ ID NO:155, SEQ ID NO:157, SEQ ID NO:159, SEQ ID NO:161, SEQ ID NO:163 or SEQ ID NO:165 (see also Tables 1, 2, and 3, Examples 1 and 4, below, and Sequence Listing)). The stringent conditions can be highly stringent conditions, medium stringent conditions and/or low stringent conditions, including the high and reduced stringency conditions described herein. In one aspect, it is the stringency of the wash conditions that set forth the conditions which determine whether a nucleic acid is within the scope of the invention, as discussed below.

[0244] "Hybridization" refers to the process by which a nucleic acid strand joins with a complementary strand through base pairing. Hybridization reactions can be sensitive and selective so that a particular sequence of interest can be identified even in samples in which it is present at low concentrations. Suitably stringent conditions can be defined by, for example, the concentrations of salt or formamide in the prehybridization and hybridization solutions, or by the hybridization temperature and are well known in the art. In alternative aspects, stringency can be increased by reducing the concentration of salt, increasing the concentration of formamide, or raising the hybridization temperature. In alternative aspects, nucleic acids of the invention are defined by their ability to hybridize under various stringency conditions (e.g., high, medium, and low), as set forth herein.

[0245] In one aspect, hybridization under high stringency conditions comprise about 50% formamide at about 37° C. to 42° C. In one aspect, hybridization conditions comprise reduced stringency conditions in about 35% to 25% formamide at about 30° C. to 35° C. In one aspect, hybridization conditions comprise high stringency conditions, e.g., at 42° C. in 50% formamide, 5×SSPE, 0.3% SDS and 200 n/ml sheared and denatured salmon sperm DNA. In one aspect, hybridization conditions comprise these reduced stringency conditions, but in 35% formamide at a reduced temperature of 35° C. The temperature range corresponding to a particular level of stringency can be further narrowed by calculating the purine to pyrimidine ratio of the nucleic acid of interest and adjusting the temperature accordingly. Variations on the above ranges and conditions are well known in the art.

[0246] In alternative aspects, nucleic acids of the invention as defined by their ability to hybridize under stringent conditions can be between about five residues and the full length of nucleic acid of the invention; e.g., they can be at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 55, 60, 65, 70, 75, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, or more, residues in length. Nucleic acids shorter than full length are also included. These nucleic acids can be useful as, e.g., hybridization probes, labeling probes, PCR oligonucleotide probes, siRNA or miRNA (single or double stranded), antisense or sequences encoding antibody binding peptides (epitopes), motifs, active sites and the like.

[0247] In one aspect, nucleic acids of the invention are defined by their ability to hybridize under high stringency comprises conditions of about 50% formamide at about 37° C. to 42° C. In one aspect, nucleic acids of the invention are defined by their ability to hybridize under reduced stringency comprising conditions in about 35% to 25% formamide at about 30° C. to 35° C.

[0248] Alternatively, nucleic acids of the invention are defined by their ability to hybridize under high stringency comprising conditions at 42° C. in 50% formamide, 5×SSPE, 0.3% SDS, and a repetitive sequence blocking nucleic acid, such as cot-1 or salmon sperm DNA (e.g., 200 n/ml sheared and denatured salmon sperm DNA). In one aspect, nucleic acids of the invention are defined by their ability to hybridize under reduced stringency conditions comprising 35% or 40% formamide at a reduced temperature of 35° C. or 42° C.

[0249] In nucleic acid hybridization reactions, the conditions used to achieve a particular level of stringency will vary, depending on the nature of the nucleic acids being hybridized. For example, the length, degree of complementarity, nucleotide sequence composition (e.g., GC v. AT content) and nucleic acid type (e.g., RNA v. DNA) of the hybridizing regions of the nucleic acids can be considered in selecting hybridization conditions. An additional consideration is whether one of the nucleic acids is immobilized, for example, on a filter.

[0250] Hybridization may be carried out under conditions of low stringency, moderate stringency or high stringency. As an example of nucleic acid hybridization, a polymer membrane containing immobilized denatured nucleic acids is first prehybridized for 30 minutes at 45° C. in a solution consisting of 0.9 M NaCl, 50 mM NaH₂PO₄, pH 7.0, 5.0 mM Na₂EDTA, 0.5% SDS, 10×Denhardt's and 0.5 mg/ml polyriboadenylic acid. Approximately 2×10⁷ cpm (specific activity 4-9×10⁸ cpm/ug) of ³²P end-labeled oligonucleotide probe are then added to the solution. After 12-16 hours of incubation, the membrane is washed for 30 minutes at room temperature in 1×SET (150 mM NaCl, 20 mM Tris hydrochloride, pH 7.8, 1 mM Na₂EDTA) containing 0.5% SDS, followed by a 30 minute wash in fresh 1×SET at T_m-10° C. for the oligonucleotide probe. The membrane is then exposed to auto-radiographic film for detection of hybridization signals. All of the foregoing hybridizations would be considered to be under conditions of high stringency.

[0251] Following hybridization, a filter can be washed to remove any non-specifically bound detectable probe. The stringency used to wash the filters can also be varied depending on the nature of the nucleic acids being hybridized, the length of the nucleic acids being hybridized, the degree of complementarity, the nucleotide sequence composition (e.g., GC v. AT content) and the nucleic acid type (e.g., RNA v. DNA). Examples of progressively higher stringency condition washes are as follows: 2×SSC, 0.1% SDS at room temperature for 15 minutes (low stringency); 0.1×SSC, 0.5% SDS at room temperature for 30 minutes to 1 hour (moderate stringency); 0.1×SSC, 0.5% SDS for 15 to 30 minutes at between the hybridization temperature and 68° C. (high stringency); and 0.15M NaCl for 15 minutes at 72° C. (very high stringency). A final low stringency wash can be conducted in 0.1×SSC at room temperature. The examples above are merely illustrative of one set of conditions that can be used to wash filters. One of skill in the art would know that there are numerous recipes for different stringency washes. Some other examples are given below.

[0252] In one aspect, hybridization conditions comprise a wash step comprising a wash for 30 minutes at room temperature in a solution comprising 1× 150 mM NaCl, 20 mM Tris hydrochloride, pH 7.8, 1 mM Na₂EDTA, 0.5% SDS, followed by a 30 minute wash in fresh solution.

[0253] Nucleic acids which have hybridized to the probe are identified by autoradiography or other conventional techniques.

[0254] The above procedures may be modified to identify nucleic acids having decreasing levels of sequence identity (homology) to the probe sequence. For example, to obtain nucleic acids of decreasing sequence identity (homology) to the detectable probe, less stringent conditions may be used. For example, the hybridization temperature may be decreased in increments of 5° C. from 68° C. to 42° C. in a hybridization buffer having a Na+ concentration of approximately 1M. Following hybridization, the filter may be washed with 2×SSC, 0.5% SDS at the temperature of hybridization. These conditions are considered to be "moderate" conditions above 50° C. and "low" conditions below 50° C. A specific example of "moderate" hybridization conditions is when the above hybridization is conducted at 55° C. A specific example of "low stringency" hybridization conditions is when the above hybridization is conducted at 45° C.

[0255] Alternatively, the hybridization may be carried out in buffers, such as 6×SSC, containing formamide at a temperature of 42° C. In this case, the concentration of formamide in the hybridization buffer may be reduced in 5% increments from 50% to 0% to identify clones having decreasing levels of homology to the probe. Following hybridization, the filter may be washed with 6×SSC, 0.5% SDS at 50° C. These conditions are considered to be "moderate" conditions above 25% formamide and "low" conditions below 25% formamide. A specific example of "moderate" hybridization conditions is when the above hybridization is conducted at 30% formamide. A specific example of "low stringency" hybridization conditions is when the above hybridization is conducted at 10% formamide.

[0256] However, the selection of a hybridization format may not be critical--it is the stringency of the wash conditions that set forth the conditions which determine whether a nucleic acid is within the scope of the invention. Wash conditions used to identify nucleic acids within the scope of the invention include, e.g.: a salt concentration of about 0.02 molar at pH 7 and a temperature of at least about 50° C. or about 55° C. to about 60° C.; or, a salt concentration of about 0.15 M NaCl at 72° C. for about 15 minutes; or, a salt concentration of about 0.2×SSC at a temperature of at least about 50° C. or about 55° C. to about 60° C. for about 15 to about 20 minutes; or, the hybridization complex is washed twice with a solution with a salt concentration of about 2×SSC containing 0.1% SDS at room temperature for 15 minutes and then washed twice by 0.1×SSC containing 0.1% SDS at 68° C. for 15 minutes; or, equivalent conditions. See Sambrook, Tijssen and Ausubel for a description of SSC buffer and equivalent conditions.

[0257] These methods may be used to isolate or identify nucleic acids of the invention. For example, the preceding methods may be used to isolate or identify nucleic acids having a sequence with at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more sequence identity (homology) to a nucleic acid sequence selected from the group consisting of one of the sequences of the invention, or fragments comprising at least about 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, 150, 200, 300, 400, or 500 consecutive bases thereof and the sequences complementary thereto. Sequence identity (homology) may be measured using the alignment algorithm. For example, the homologous polynucleotides may have a coding sequence which is a naturally occurring allelic variant of one of the coding sequences described herein. Such allelic variants may have a substitution, deletion or addition of one or more nucleotides when compared to the nucleic acids of the invention. Additionally, the above procedures may be used to isolate nucleic acids which encode polypeptides having at least about 99%, 95%, at least 90%, at least 85%, at least 80%, at least 75%, at least 70%, at least 65%, at least 60%, at least 55%, or at least 50% sequence identity (homology) to a polypeptide of the invention, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof as determined using a sequence alignment algorithm (e.g., such as the FASTA version 3.0t78 algorithm with the default parameters).

Oligonucleotides Probes and Methods for Using them

[0258] The invention also provides nucleic acid probes that can be used, e.g., for identifying, amplifying, or isolating nucleic acids encoding a polypeptide having a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity or fragments thereof or for identifying cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme genes. In one aspect, the probe comprises at least about 10 consecutive bases of a nucleic acid of the invention. Alternatively, a probe of the invention can be at least about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 130, 150 or about 10 to 50, about 20 to 60 about 30 to 70, consecutive bases of a sequence as set forth in a nucleic acid of the invention. The probes identify a nucleic acid by binding and/or hybridization. The probes can be used in arrays of the invention, see discussion below, including, e.g., capillary arrays. The probes of the invention can also be used to isolate other nucleic acids or polypeptides.

[0259] The isolated or recombinant nucleic acids of the invention, the sequences complementary thereto, or a fragment comprising at least about 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, 150, 200, 300, 400, or 500 consecutive bases of one of the sequences of the invention, or the sequences complementary thereto may also be used as probes to determine whether a biological sample, such as a soil sample, contains an organism having a nucleic acid sequence of the invention or an organism from which the nucleic acid was obtained. In such procedures, a biological sample potentially harboring the organism from which the nucleic acid was isolated is obtained and nucleic acids are obtained from the sample. The nucleic acids are contacted with the probe under conditions which permit the probe to specifically hybridize to any complementary sequences from which are present therein.

[0260] Where necessary, conditions which permit the probe to specifically hybridize to complementary sequences may be determined by placing the probe in contact with complementary sequences from samples known to contain the complementary sequence as well as control sequences which do not contain the complementary sequence. Hybridization conditions, such as the salt concentration of the hybridization buffer, the formamide concentration of the hybridization buffer, or the hybridization temperature, may be varied to identify conditions which allow the probe to hybridize specifically to complementary nucleic acids.

[0261] If the sample contains the organism from which the nucleic acid was isolated, specific hybridization of the probe is then detected. Hybridization may be detected by labeling the probe with a detectable agent such as a radioactive isotope, a fluorescent dye or an enzyme capable of catalyzing the formation of a detectable product.

[0262] Many methods for using the labeled probes to detect the presence of complementary nucleic acids in a sample are familiar to those skilled in the art. These include Southern Blots, Northern Blots, colony hybridization procedures and dot blots. Protocols for each of these procedures are provided in Ausubel et al. Current Protocols in Molecular Biology, John Wiley 503 Sons, Inc. (1997) and Sambrook et al., Molecular Cloning: A Laboratory Manual 2nd Ed., Cold Spring Harbor Laboratory Press (1989.

[0263] Alternatively, more than one probe (at least one of which is capable of specifically hybridizing to any complementary sequences which are present in the nucleic acid sample), may be used in an amplification reaction to determine whether the sample contains an organism containing a nucleic acid sequence of the invention (e.g., an organism from which the nucleic acid was isolated). In one aspect, the probes comprise oligonucleotides. In one aspect, the amplification reaction may comprise a PCR reaction. PCR protocols are described in Ausubel and Sambrook, supra. Alternatively, the amplification may comprise a ligase chain reaction, 3SR, or strand displacement reaction. (See Barany, F., "The Ligase Chain Reaction in a PCR World", PCR Methods and Applications 1:5-16, 1991; E. Fahy et al., "Self-sustained Sequence Replication (3SR): An Isothermal Transcription-based Amplification System Alternative to PCR", PCR Methods and Applications 1:25-33, 1991; and Walker G. T. et al., "Strand Displacement Amplification--an Isothermal in vitro DNA Amplification Technique", Nucleic Acid Research 20:1691-1696, 1992). In such procedures, the nucleic acids in the sample are contacted with the probes, the amplification reaction is performed and any resulting amplification product is detected. The amplification product may be detected by performing gel electrophoresis on the reaction products and staining the gel with an intercalator such as ethidium bromide. Alternatively, one or more of the probes may be labeled with a radioactive isotope and the presence of a radioactive amplification product may be detected by autoradiography after gel electrophoresis.

[0264] Probes derived from sequences near the ends of the sequences of the invention, may also be used in chromosome walking procedures to identify clones containing genomic sequences located adjacent to the sequences of the invention. Such methods allow the isolation of genes which encode additional proteins from the host organism.

[0265] In one aspect, the isolated or recombinant nucleic acids of the invention, the sequences complementary thereto, or a fragment comprising at least 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, 150, 200, 300, 400, or 500 or more consecutive bases of one of the sequences of the invention, or the sequences complementary thereto are used as probes to identify and isolate related nucleic acids. In some aspects, the related nucleic acids may be cDNAs or genomic DNAs from organisms other than the one from which the nucleic acid was isolated. For example, the other organisms may be related organisms. In such procedures, a nucleic acid sample is contacted with the probe under conditions which permit the probe to specifically hybridize to related sequences. Hybridization of the probe to nucleic acids from the related organism is then detected using any of the methods described above.

[0266] By varying the stringency of the hybridization conditions used to identify nucleic acids, such as cDNAs or genomic DNAs, which hybridize to the detectable probe, nucleic acids having different levels of homology to the probe can be identified and isolated. Stringency may be varied by conducting the hybridization at varying temperatures below the melting temperatures of the probes. The melting temperature, T_m, is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly complementary probe. Very stringent conditions are selected to be equal to or about 5° C. lower than the T_m for a particular probe. The melting temperature of the probe may be calculated using the following formulas:

[0267] For probes between 14 and 70 nucleotides in length the melting temperature (T_m) is calculated using the formula: T_m=81.5+16.6(log [Na+])+0.41(fraction G+C)-(600/N) where N is the length of the probe.

[0268] If the hybridization is carried out in a solution containing formamide, the melting temperature may be calculated using the equation: T_m=81.5+16.6(log [Na+])+0.41(fraction G+C)-(0.63% formamide)-(600/N) where N is the length of the probe.

[0269] Prehybridization may be carried out in 6×SSC, 5×Denhardt's reagent, 0.5% SDS, 100 μg denatured fragmented salmon sperm DNA or 6×SSC, 5×Denhardt's reagent, 0.5% SDS, 100 μg denatured fragmented salmon sperm DNA, 50% formamide. The formulas for SSC and Denhardt's solutions are listed in Sambrook et al., supra.

[0270] In one aspect, hybridization is conducted by adding the detectable probe to the prehybridization solutions listed above. Where the probe comprises double stranded DNA, it is denatured before addition to the hybridization solution. In one aspect, the filter is contacted with the hybridization solution for a sufficient period of time to allow the probe to hybridize to cDNAs or genomic DNAs containing sequences complementary thereto or homologous thereto. For probes over 200 nucleotides in length, the hybridization may be carried out at 15-25° C. below the T_m For shorter probes, such as oligonucleotide probes, the hybridization may be conducted at 5-10° C. below the T_m. In one aspect, for hybridizations in 6×SSC, the hybridization is conducted at approximately 68° C. Usually, for hybridizations in 50% formamide containing solutions, the hybridization is conducted at approximately 42° C.

Inhibiting Expression of Cellulase Enzymes

[0271] The invention provides nucleic acids complementary to (e.g., antisense sequences to) the nucleic acids of the invention, e.g., cellulase enzyme-encoding nucleic acids, e.g., nucleic acids comprising antisense, siRNA, miRNA, ribozymes. Nucleic acids of the invention comprising antisense sequences can be capable of inhibiting the transport, splicing or transcription of cellulase enzyme-encoding genes. The inhibition can be effected through the targeting of genomic DNA or messenger RNA. The transcription or function of targeted nucleic acid can be inhibited, for example, by hybridization and/or cleavage. One exemplary set of inhibitors provided by the present invention includes oligonucleotides which are able to either bind cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme gene or message, in either case preventing or inhibiting the production or function of a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme. The association can be through sequence specific hybridization. Another useful class of inhibitors includes oligonucleotides which cause inactivation or cleavage of cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme message. The oligonucleotide can have enzyme activity which causes such cleavage, such as ribozymes. The oligonucleotide can be chemically modified or conjugated to an enzyme or composition capable of cleaving the complementary nucleic acid. A pool of many different such oligonucleotides can be screened for those with the desired activity. Thus, the invention provides various compositions for the inhibition of cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme expression on a nucleic acid and/or protein level, e.g., antisense, siRNA, miRNA and ribozymes comprising cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme sequences of the invention and the anti-cellulase, e.g., anti-endoglucanase, anti-cellobiohydrolase and/or anti-beta-glucosidase antibodies of the invention.

[0272] Inhibition of cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme expression can have a variety of industrial applications. For example, inhibition of cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme expression can slow or prevent spoilage. In one aspect, use of compositions of the invention that inhibit the expression and/or activity of cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes, e.g., antibodies, antisense oligonucleotides, ribozymes, siRNA and miRNA are used to slow or prevent spoilage. Thus, in one aspect, the invention provides methods and compositions comprising application onto a plant or plant product (e.g., a cereal, a grain, a fruit, seed, root, leaf, etc.) antibodies, antisense oligonucleotides, ribozymes, siRNA and miRNA of the invention to slow or prevent spoilage. These compositions also can be expressed by the plant (e.g., a transgenic plant) or another organism (e.g., a bacterium or other microorganism transformed with a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme gene of the invention).

[0273] The compositions of the invention for the inhibition of cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme expression (e.g., antisense, iRNA, ribozymes, antibodies) can be used as pharmaceutical compositions, e.g., as anti-pathogen agents or in other therapies, e.g., as anti-microbials for, e.g., Salmonella.

[0274] Antisense Oligonucleotides

[0275] The invention provides antisense oligonucleotides capable of binding cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme message which, in one aspect, can inhibit cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity by targeting mRNA. Strategies for designing antisense oligonucleotides are well described in the scientific and patent literature, and the skilled artisan can design such cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme oligonucleotides using the novel reagents of the invention. For example, gene walking/RNA mapping protocols to screen for effective antisense oligonucleotides are well known in the art, see, e.g., Ho (2000) Methods Enzymol. 314:168-183, describing an RNA mapping assay, which is based on standard molecular techniques to provide an easy and reliable method for potent antisense sequence selection. See also Smith (2000) Eur. J. Pharm. Sci. 11:191-198.

[0276] Naturally occurring nucleic acids are used as antisense oligonucleotides. The antisense oligonucleotides can be of any length; for example, in alternative aspects, the antisense oligonucleotides are between about 5 to 100, about 10 to 80, about 15 to 60, about 18 to 40. The optimal length can be determined by routine screening. The antisense oligonucleotides can be present at any concentration. The optimal concentration can be determined by routine screening. A wide variety of synthetic, non-naturally occurring nucleotide and nucleic acid analogues are known which can address this potential problem. For example, peptide nucleic acids (PNAs) containing non-ionic backbones, such as N-(2-aminoethyl) glycine units can be used. Antisense oligonucleotides having phosphorothioate linkages can also be used, as described in WO 97/03211; WO 96/39154; Mata (1997) Toxicol Appl Pharmacol 144:189-197; Antisense Therapeutics, ed. Agrawal (Humana Press, Totowa, N.J., 1996). Antisense oligonucleotides having synthetic DNA backbone analogues provided by the invention can also include phosphoro-dithioate, methylphosphonate, phosphoramidate, alkyl phosphotriester, sulfamate, 3'-thioacetal, methylene(methylimino), 3'-N-carbamate, and morpholino carbamate nucleic acids, as described above.

[0277] Combinatorial chemistry methodology can be used to create vast numbers of oligonucleotides that can be rapidly screened for specific oligonucleotides that have appropriate binding affinities and specificities toward any target, such as the sense and antisense cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme sequences of the invention (see, e.g., Gold (1995) J. of Biol. Chem. 270:13581-13584).

[0278] Inhibitory Ribozymes

[0279] The invention provides ribozymes capable of binding cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme message. These ribozymes can inhibit cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity by, e.g., targeting mRNA. Strategies for designing ribozymes and selecting the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme-specific antisense sequence for targeting are well described in the scientific and patent literature, and the skilled artisan can design such ribozymes using the novel reagents of the invention. Ribozymes act by binding to a target RNA through the target RNA binding portion of a ribozyme which is held in close proximity to an enzymatic portion of the RNA that cleaves the target RNA. Thus, the ribozyme recognizes and binds a target RNA through complementary base-pairing, and once bound to the correct site, acts enzymatically to cleave and inactivate the target RNA. Cleavage of a target RNA in such a manner will destroy its ability to direct synthesis of an encoded protein if the cleavage occurs in the coding sequence. After a ribozyme has bound and cleaved its RNA target, it can be released from that RNA to bind and cleave new targets repeatedly.

[0280] In some circumstances, the enzymatic nature of a ribozyme can be advantageous over other technologies, such as antisense technology (where a nucleic acid molecule simply binds to a nucleic acid target to block its transcription, translation or association with another molecule) as the effective concentration of ribozyme necessary to effect a therapeutic treatment can be lower than that of an antisense oligonucleotide. This potential advantage reflects the ability of the ribozyme to act enzymatically. Thus, a single ribozyme molecule is able to cleave many molecules of target RNA. In one aspect, a ribozyme is a highly specific inhibitor, with the specificity of inhibition depending not only on the base pairing mechanism of binding, but also on the mechanism by which the molecule inhibits the expression of the RNA to which it binds. That is, the inhibition is caused by cleavage of the RNA target and so specificity is defined as the ratio of the rate of cleavage of the targeted RNA over the rate of cleavage of non-targeted RNA. This cleavage mechanism is dependent upon factors additional to those involved in base pairing. Thus, the specificity of action of a ribozyme can be greater than that of antisense oligonucleotide binding the same RNA site.

[0281] The ribozyme of the invention, e.g., an enzymatic ribozyme RNA molecule, can be formed in a hammerhead motif, a hairpin motif, as a hepatitis delta virus motif, a group I intron motif and/or an RNaseP-like RNA in association with an RNA guide sequence. Examples of hammerhead motifs are described by, e.g., Rossi (1992) Aids Research and Human Retroviruses 8:183; hairpin motifs by Hampel (1989) Biochemistry 28:4929, and Hampel (1990) Nuc. Acids Res. 18:299; the hepatitis delta virus motif by Perrotta (1992) Biochemistry 31:16; the RNaseP motif by Guerrier-Takada (1983) Cell 35:849; and the group I intron by Cech U.S. Pat. No. 4,987,071. The recitation of these specific motifs is not intended to be limiting. Those skilled in the art will recognize that a ribozyme of the invention, e.g., an enzymatic RNA molecule of this invention, can have a specific substrate binding site complementary to one or more of the target gene RNA regions. A ribozyme of the invention can have a nucleotide sequence within or surrounding that substrate binding site which imparts an RNA cleaving activity to the molecule.

[0282] RNA Interference (RNAi)

[0283] In one aspect, the invention provides an RNA inhibitory molecule, a so-called "RNAi" molecule, comprising a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme sequence of the invention. The RNAi molecule can comprise a double-stranded RNA (dsRNA) molecule, e.g., siRNA and/or miRNA. The RNAi molecule, e.g., siRNA and/or miRNA, can inhibit expression of a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme gene. In one aspect, the RNAi molecule, e.g., siRNA and/or miRNA, is about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more duplex nucleotides in length. While the invention is not limited by any particular mechanism of action, the RNAi can enter a cell and cause the degradation of a single-stranded RNA (ssRNA) of similar or identical sequences, including endogenous mRNAs. When a cell is exposed to double-stranded RNA (dsRNA), mRNA from the homologous gene is selectively degraded by a process called RNA interference (RNAi). A possible basic mechanism behind RNAi is the breaking of a double-stranded RNA (dsRNA) matching a specific gene sequence into short pieces called short interfering RNA, which trigger the degradation of mRNA that matches its sequence. In one aspect, the RNAi's of the invention are used in gene-silencing therapeutics, see, e.g., Shuey (2002) Drug Discov. Today 7:1040-1046. In one aspect, the invention provides methods to selectively degrade RNA using the RNAi's molecules, e.g., siRNA and/or miRNA, of the invention. The process may be practiced in vitro, ex vivo or in vivo. In one aspect, the RNAi molecules of the invention can be used to generate a loss-of-function mutation in a cell, an organ or an animal. Methods for making and using RNAi molecules, e.g., siRNA and/or miRNA, for selectively degrade RNA are well known in the art, see, e.g., U.S. Pat. Nos. 6,506,559; 6,511,824; 6,515,109; 6,489,127.

Modification of Nucleic Acids--Making Variant Enzymes of the Invention

[0284] The invention provides methods of generating variants of the nucleic acids of the invention, e.g., those encoding a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme. These methods can be repeated or used in various combinations to generate cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes having an altered or different activity or an altered or different stability from that of a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme encoded by the template nucleic acid. These methods also can be repeated or used in various combinations, e.g., to generate variations in gene/message expression, message translation or message stability. In another aspect, the genetic composition of a cell is altered by, e.g., modification of a homologous gene ex vivo, followed by its reinsertion into the cell.

[0285] For example, in one aspect, the invention provides isolated or recombinant nucleic acids having a sequence comprising at least one nucleotide base residue modification of SEQ ID NO:163, wherein the modification comprises one or more of the following changes: a nucleotide at any one of positions 265 to 267 is modified to CGT, CGC, CGA, CGG, AGA or AGG; a nucleotide at any one of positions 307 to 309 is modified to GGT, GGC, GGA or GGG; a nucleotide at any one of positions 328 to 330 is modified to GGT, GGC, GGA or GGG; a nucleotide at any one of positions 340 to 342 is modified to TTA, TTG, CTT, CTC, CTA or CTG; a nucleotide at any one of positions 469 to 471 is modified to TCT, TCC, TCA, TCG, AGT or AGC; a nucleotide at any one of positions 1441 to 1443 is modified to TTT or TTC; a nucleotide at any one of positions 1648 to 1650 is modified to AAT or AAC; or, a nucleotide at any one of positions 1768 to 1770 is modified to CGT, CGC, CGA, CGG, AGA or AGG. In another aspect, the invention provides isolated or recombinant polypeptides having a sequence comprising at least one amino acid residue modification of SEQ ID NO:164, wherein the modification comprises one or more of the following changes: a methionine at amino acid position 89 is modified to arginine; a phenylalanine at amino acid position 103 is modified to glycine; a proline at amino acid position 110 is modified to glycine; a tyrosine at amino acid position 114 is modified to leucine; an alanine at amino acid position 157 is modified to serine; a tryptophan at amino acid position 481 is modified to phenylalanine; a proline at amino acid position 550 is modified to asparagine; or a glycine at amino acid position 590 is modified to arginine.

[0286] In another aspect, the invention provides isolated or recombinant nucleic acids having a sequence comprising a nucleotide residue sequence modification of an exemplary sequence of the invention (e.g., SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, etc.) wherein the modification comprises one or more of the following changes: a nucleotide at the equivalent of any one of positions 265 to 267 of SEQ ID NO:163 are changed to CGT, CGC, CGA, CGG, AGA or AGG; a nucleotide at the equivalent of any one of positions 307 to 309 of SEQ ID NO:163 are changed to GGT, GGC, GGA or GGG; a nucleotide at the equivalent of any one of positions 328 to 330 of SEQ ID NO:163 are changed to GGT, GGC, GGA or GGG; a nucleotide at the equivalent of any one of positions 340 to 342 of SEQ ID NO:163 are changed to TTA, TTG, CTT, CTC, CTA or CTG; a nucleotide at the equivalent of any one of positions 469 to 471 of SEQ ID NO:163 are changed to TCT, TCC, TCA, TCG, AGT or AGC; a nucleotide at the equivalent of positions 1441 to 1443 of SEQ ID NO:163 are changed to TTT or TTC; a nucleotide at the equivalent of any one of positions 1648 to 1650 of SEQ ID NO:163 are changed to AAT or AAC; or a nucleotide at the equivalent of any one of positions 1768 to 1770 of SEQ ID NO:163 are changed to CGT, CGC, CGA, CGG, AGA or AGG. In another aspect, the invention provides isolated or recombinant nucleic acids having a sequence comprising a nucleotide residue sequence modification of any nucleic acid of the invention, wherein the modification comprises one or more of the following changes: a nucleotide at the equivalent of any one of positions 265 to 267 of SEQ ID NO:163 are changed to CGT, CGC, CGA, CGG, AGA or AGG; a nucleotide at the equivalent of any one of positions 307 to 309 of SEQ ID NO:163 are changed to GGT, GGC, GGA or GGG; a nucleotide at the equivalent of any one of positions 328 to 330 of SEQ ID NO:163 are changed to GGT, GGC, GGA or GGG; a nucleotide at the equivalent of any one of positions 340 to 342 of SEQ ID NO:163 are changed to TTA, TTG, CTT, CTC, CTA or CTG; a nucleotide at the equivalent of any one of positions 469 to 471 of SEQ ID NO:163 are changed to TCT, TCC, TCA, TCG, AGT or AGC; a nucleotide at the equivalent of positions 1441 to 1443 of SEQ ID NO:163 are changed to TTT or TTC; a nucleotide at the equivalent of any one of positions 1648 to 1650 of SEQ ID NO:163 are changed to AAT or AAC; or, a nucleotide at the equivalent of any one of positions 1768 to 1770 of SEQ ID NO:163 are changed to CGT, CGC, CGA, CGG, AGA or AGG.

[0287] In another aspect, the invention provides isolated or recombinant polypeptides having a sequence comprising an amino acid residue modification of an exemplary sequence of the invention (e.g., SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, etc.) wherein the modification comprises one or more of the following changes: an amino acid at the equivalent of the methionine at amino acid position 89 of SEQ ID NO:164 is changed to an arginine; an amino acid at the equivalent of the phenylalanine at amino acid position 103 of SEQ ID NO:164 is changed to a glycine; an amino acid at the equivalent of the proline at amino acid position 110 of SEQ ID NO:164 is changed to a glycine; an amino acid at the equivalent of the tyrosine at amino acid position 114 of SEQ ID NO:164 is changed to a leucine; an amino acid at the equivalent of the alanine at amino acid position 157 of SEQ ID NO:164 is changed to a serine; an amino acid at the equivalent of the tryptophan at amino acid position 481 of SEQ ID NO:164 is changed to a phenylalanine; an amino acid at the equivalent of the proline at amino acid position 550 of SEQ ID NO:164 is changed to an asparagine; or an amino acid at the equivalent of the glycine at amino acid position 590 of SEQ ID NO:164 is changed to an arginine.

[0288] In another aspect, the invention provides isolated or recombinant polypeptides having a sequence comprising an amino acid residue modification of any polypeptide of the invention, wherein the modification comprises one or more of the following changes: an amino acid at the equivalent of the methionine at amino acid position 89 of SEQ ID NO:164 is changed to an arginine; an amino acid at the equivalent of the phenylalanine at amino acid position 103 of SEQ ID NO:164 is changed to a glycine; an amino acid at the equivalent of the proline at amino acid position 110 of SEQ ID NO:164 is changed to a glycine; an amino acid at the equivalent of the tyrosine at amino acid position 114 of SEQ ID NO:164 is changed to a leucine; an amino acid at the equivalent of the alanine at amino acid position 157 of SEQ ID NO:164 is changed to a serine; an amino acid at the equivalent of the tryptophan at amino acid position 481 of SEQ ID NO:164 is changed to a phenylalanine; an amino acid at the equivalent of the proline at amino acid position 550 of SEQ ID NO:164 is changed to an asparagine; or an amino acid at the equivalent of the glycine at amino acid position 590 of SEQ ID NO:164 is changed to an arginine.

[0289] A nucleic acid of the invention can be altered by any means. For example, random or stochastic methods, or, non-stochastic, or "directed evolution," methods, see, e.g., U.S. Pat. No. 6,361,974. Methods for random mutation of genes are well known in the art, see, e.g., U.S. Pat. No. 5,830,696. For example, mutagens can be used to randomly mutate a gene. Mutagens include, e.g., ultraviolet light or gamma irradiation, or a chemical mutagen, e.g., mitomycin, nitrous acid, photoactivated psoralens, alone or in combination, to induce DNA breaks amenable to repair by recombination. Other chemical mutagens include, for example, sodium bisulfite, nitrous acid, hydroxylamine, hydrazine or formic acid. Other mutagens are analogues of nucleotide precursors, e.g., nitrosoguanidine, 5-bromouracil, 2-aminopurine, or acridine. These agents can be added to a PCR reaction in place of the nucleotide precursor thereby mutating the sequence. Intercalating agents such as proflavine, acriflavine, quinacrine and the like can also be used.

[0290] Any technique in molecular biology can be used, e.g., random PCR mutagenesis, see, e.g., Rice (1992) Proc. Natl. Acad. Sci. USA 89:5467-5471; or, combinatorial multiple cassette mutagenesis, see, e.g., Crameri (1995) Biotechniques 18:194-196. Alternatively, nucleic acids, e.g., genes, can be reassembled after random, or "stochastic," fragmentation, see, e.g., U.S. Pat. Nos. 6,291,242; 6,287,862; 6,287,861; 5,955,358; 5,830,721; 5,824,514; 5,811,238; 5,605,793. In alternative aspects, modifications, additions or deletions are introduced by error-prone PCR, shuffling, oligonucleotide-directed mutagenesis, assembly PCR, sexual PCR mutagenesis, in vivo mutagenesis, cassette mutagenesis, recursive ensemble mutagenesis, exponential ensemble mutagenesis, site-specific mutagenesis, gene reassembly, Gene Site Saturation Mutagenesis (GSSM), synthetic ligation reassembly (SLR), recombination, recursive sequence recombination, phosphothioate-modified DNA mutagenesis, uracil-containing template mutagenesis, gapped duplex mutagenesis, point mismatch repair mutagenesis, repair-deficient host strain mutagenesis, chemical mutagenesis, radiogenic mutagenesis, deletion mutagenesis, restriction-selection mutagenesis, restriction-purification mutagenesis, artificial gene synthesis, ensemble mutagenesis, chimeric nucleic acid multimer creation, Chromosomal Saturation Mutagenesis (CSM) and/or a combination of these and other methods.

[0291] The following publications describe a variety of recursive recombination procedures and/or methods which can be incorporated into the methods of the invention: Stemmer (1999) "Molecular breeding of viruses for targeting and other clinical properties" Tumor Targeting 4:1-4; Ness (1999) Nature Biotechnology 17:893-896; Chang (1999) "Evolution of a cytokine using DNA family shuffling" Nature Biotechnology 17:793-797; Minshull (1999) "Protein evolution by molecular breeding" Current Opinion in Chemical Biology 3:284-290; Christians (1999) "Directed evolution of thymidine kinase for AZT phosphorylation using DNA family shuffling" Nature Biotechnology 17:259-264; Crameri (1998) "DNA shuffling of a family of genes from diverse species accelerates directed evolution" Nature 391:288-291; Crameri (1997) "Molecular evolution of an arsenate detoxification pathway by DNA shuffling," Nature Biotechnology 15:436-438; Zhang (1997) "Directed evolution of an effective fucosidase from a galactosidase by DNA shuffling and screening" Proc. Natl. Acad. Sci. USA 94:4504-4509; Patten et al. (1997) "Applications of DNA Shuffling to Pharmaceuticals and Vaccines" Current Opinion in Biotechnology 8:724-733; Crameri et al. (1996) "Construction and evolution of antibody-phage libraries by DNA shuffling" Nature Medicine 2:100-103; Gates et al. (1996) "Affinity selective isolation of ligands from peptide libraries through display on a lac repressor `headpiece dimer`" Journal of Molecular Biology 255:373-386; Stemmer (1996) "Sexual PCR and Assembly PCR" In: The Encyclopedia of Molecular Biology. VCH Publishers, New York. pp. 447-457; Crameri and Stemmer (1995) "Combinatorial multiple cassette mutagenesis creates all the permutations of mutant and wildtype cassettes" BioTechniques 18:194-195; Stemmer et al. (1995) "Single-step assembly of a gene and entire plasmid form large numbers of oligodeoxyribonucleotides" Gene, 164:49-53; Stemmer (1995) "The Evolution of Molecular Computation" Science 270: 1510; Stemmer (1995) "Searching Sequence Space" Bio/Technology 13:549-553; Stemmer (1994) "Rapid evolution of a protein in vitro by DNA shuffling" Nature 370:389-391; and Stemmer (1994) "DNA shuffling by random fragmentation and reassembly: In vitro recombination for molecular evolution." Proc. Natl. Acad. Sci. USA 91:10747-10751.

[0292] Mutational methods of generating diversity include, for example, site-directed mutagenesis (Ling et al. (1997) "Approaches to DNA mutagenesis: an overview" Anal Biochem. 254(2): 157-178; Dale et al. (1996) "Oligonucleotide-directed random mutagenesis using the phosphorothioate method" Methods Mol. Biol. 57:369-374; Smith (1985) "In vitro mutagenesis" Aim. Rev. Genet. 19:423-462; Botstein & Shortle (1985) "Strategies and applications of in vitro mutagenesis" Science 229:1193-1201; Carter (1986) "Site-directed mutagenesis" Biochem. J. 237:1-7; and Kunkel (1987) "The efficiency of oligonucleotide directed mutagenesis" in Nucleic Acids & Molecular Biology (Eckstein, F. and Lilley, D. M. J. eds., Springer Verlag, Berlin)); mutagenesis using uracil containing templates (Kunkel (1985) "Rapid and efficient site-specific mutagenesis without phenotypic selection" Proc. Natl. Acad. Sci. USA 82:488-492; Kunkel et al. (1987) "Rapid and efficient site-specific mutagenesis without phenotypic selection" Methods in Enzymol. 154, 367-382; and Bass et al. (1988) "Mutant Trp repressors with new DNA-binding specificities" Science 242:240-245); oligonucleotide-directed mutagenesis (Methods in Enzymol. 100: 468-500 (1983); Methods in Enzymol. 154: 329-350 (1987); Zoller (1982) "Oligonucleotide-directed mutagenesis using M13-derived vectors: an efficient and general procedure for the production of point mutations in any DNA fragment" Nucleic Acids Res. 10:6487-6500; Zoller & Smith (1983) "Oligonucleotide-directed mutagenesis of DNA fragments cloned into M13 vectors" Methods in Enzymol. 100:468-500; and Zoller (1987) Oligonucleotide-directed mutagenesis: a simple method using two oligonucleotide primers and a single-stranded DNA template" Methods in Enzymol. 154:329-350); phosphorothioate-modified DNA mutagenesis (Taylor (1985) "The use of phosphorothioate-modified DNA in restriction enzyme reactions to prepare nicked DNA" Nucl. Acids Res. 13: 8749-8764; Taylor (1985) "The rapid generation of oligonucleotide-directed mutations at high frequency using phosphorothioate-modified DNA" Nucl. Acids Res. 13: 8765-8787 (1985); Nakamaye (1986) "Inhibition of restriction endonuclease Nci I cleavage by phosphorothioate groups and its application to oligonucleotide-directed mutagenesis" Nucl. Acids Res. 14: 9679-9698; Sayers (1988) "Y-T Exonucleases in phosphorothioate-based oligonucleotide-directed mutagenesis" Nucl. Acids Res. 16:791-802; and Sayers et al. (1988) "Strand specific cleavage of phosphorothioate-containing DNA by reaction with restriction endonucleases in the presence of ethidium bromide" Nucl. Acids Res. 16: 803-814); mutagenesis using gapped duplex DNA (Kramer et al. (1984) "The gapped duplex DNA approach to oligonucleotide-directed mutation construction" Nucl. Acids Res. 12: 9441-9456; Kramer & Fritz (1987) Methods in Enzymol. "Oligonucleotide-directed construction of mutations via gapped duplex DNA" 154:350-367; Kramer (1988) "Improved enzymatic in vitro reactions in the gapped duplex DNA approach to oligonucleotide-directed construction of mutations" Nucl. Acids Res. 16: 7207; and Fritz (1988) "Oligonucleotide-directed construction of mutations: a gapped duplex DNA procedure without enzymatic reactions in vitro" Nucl. Acids Res. 16: 6987-6999).

[0293] Additional protocols that can be used to practice the invention include point mismatch repair (Kramer (1984) "Point Mismatch Repair" Cell 38:879-887), mutagenesis using repair-deficient host strains (Carter et al. (1985) "Improved oligonucleotide site-directed mutagenesis using M13 vectors" Nucl. Acids Res. 13: 4431-4443; and Carter (1987) "Improved oligonucleotide-directed mutagenesis using M13 vectors" Methods in Enzymol. 154: 382-403), deletion mutagenesis (Eghtedarzadeh (1986) "Use of oligonucleotides to generate large deletions" Nucl. Acids Res. 14: 5115), restriction-selection and restriction-selection and restriction-purification (Wells et al. (1986) "Importance of hydrogen-bond formation in stabilizing the transition state of subtilisin" Phil. Trans. R. Soc. Lond. A 317: 415-423), mutagenesis by total gene synthesis (Nambiar et al. (1984) "Total synthesis and cloning of a gene coding for the ribonuclease S protein" Science 223: 1299-1301; Sakamar and Khorana (1988) "Total synthesis and expression of a gene for the a-subunit of bovine rod outer segment guanine nucleotide-binding protein (transducin)" Nucl. Acids Res. 14: 6361-6372; Wells et al. (1985) "Cassette mutagenesis: an efficient method for generation of multiple mutations at defined sites" Gene 34:315-323; and Grundstrom et al. (1985) "Oligonucleotide-directed mutagenesis by microscale `shot-gun` gene synthesis" Nucl. Acids Res. 13: 3305-3316), double-strand break repair (Mandecki (1986); Arnold (1993) "Protein engineering for unusual environments" Current Opinion in Biotechnology 4:450-455. "Oligonucleotide-directed double-strand break repair in plasmids of Escherichia coli: a method for site-specific mutagenesis" Proc. Natl. Acad. Sci. USA, 83:7177-7181). Additional details on many of the above methods can be found in Methods in Enzymology Volume 154, which also describes useful controls for trouble-shooting problems with various mutagenesis methods.

[0294] Protocols that can be used to practice the invention are described, e.g., in U.S. Pat. No. 5,605,793 to Stemmer (Feb. 25, 1997), "Methods for In Vitro Recombination;" U.S. Pat. No. 5,811,238 to Stemmer et al. (Sep. 22, 1998) "Methods for Generating Polynucleotides having Desired Characteristics by Iterative Selection and Recombination;" U.S. Pat. No. 5,830,721 to Stemmer et al. (Nov. 3, 1998), "DNA Mutagenesis by Random Fragmentation and Reassembly;" U.S. Pat. No. 5,834,252 to Stemmer, et al. (Nov. 10, 1998) "End-Complementary Polymerase Reaction;" U.S. Pat. No. 5,837,458 to Minshull, et al. (Nov. 17, 1998), "Methods and Compositions for Cellular and Metabolic Engineering;" WO 95/22625, Stemmer and Crameri, "Mutagenesis by Random Fragmentation and Reassembly;" WO 96/33207 by Stemmer and Lipschutz "End Complementary Polymerase Chain Reaction;" WO 97/20078 by Stemmer and Crameri "Methods for Generating Polynucleotides having Desired Characteristics by Iterative Selection and Recombination;" WO 97/35966 by Minshull and Stemmer, "Methods and Compositions for Cellular and Metabolic Engineering;" WO 99/41402 by Punnonen et al. "Targeting of Genetic Vaccine Vectors;" WO 99/41383 by Punnonen et al. "Antigen Library Immunization;" WO 99/41369 by Punnonen et al. "Genetic Vaccine Vector Engineering;" WO 99/41368 by Punnonen et al. "Optimization of Immunomodulatory Properties of Genetic Vaccines;" EP 752008 by Stemmer and Crameri, "DNA Mutagenesis by Random Fragmentation and Reassembly;" EP 0932670 by Stemmer "Evolving Cellular DNA Uptake by Recursive Sequence Recombination;" WO 99/23107 by Stemmer et al., "Modification of Virus Tropism and Host Range by Viral Genome Shuffling;" WO 99/21979 by Apt et al., "Human Papillomavirus Vectors;" WO 98/31837 by del Cardayre et al. "Evolution of Whole Cells and Organisms by Recursive Sequence Recombination;" WO 98/27230 by Patten and Stemmer, "Methods and Compositions for Polypeptide Engineering;" WO 98/27230 by Stemmer et al., "Methods for Optimization of Gene Therapy by Recursive Sequence Shuffling and Selection," WO 00/00632, "Methods for Generating Highly Diverse Libraries," WO 00/09679, "Methods for Obtaining in Vitro Recombined Polynucleotide Sequence Banks and Resulting Sequences," WO 98/42832 by Arnold et al., "Recombination of Polynucleotide Sequences Using Random or Defined Primers," WO 99/29902 by Arnold et al., "Method for Creating Polynucleotide and Polypeptide Sequences," WO 98/41653 by Vind, "An in Vitro Method for Construction of a DNA Library," WO 98/41622 by Borchert et al., "Method for Constructing a Library Using DNA Shuffling," and WO 98/42727 by Pati and Zarling, "Sequence Alterations using Homologous Recombination."

[0295] Protocols that can be used to practice the invention (providing details regarding various diversity generating methods) are described, e.g., in U.S. patent application serial no. (USSN) 09/407,800, "SHUFFLING OF CODON ALTERED GENES" by Patten et al. filed Sep. 28, 1999; "EVOLUTION OF WHOLE CELLS AND ORGANISMS BY RECURSIVE SEQUENCE RECOMBINATION" by del Cardayre et al., U.S. Pat. No. 6,379,964; "OLIGONUCLEOTIDE MEDIATED NUCLEIC ACID RECOMBINATION" by Crameri et al., U.S. Pat. Nos. 6,319,714; 6,368,861; 6,376,246; 6,423,542; 6,426,224 and PCT/US00/01203; "USE OF CODON-VARIED OLIGONUCLEOTIDE SYNTHESIS FOR SYNTHETIC SHUFFLING" by Welch et al., U.S. Pat. No. 6,436,675; "METHODS FOR MAKING CHARACTER STRINGS, POLYNUCLEOTIDES & POLYPEPTIDES HAVING DESIRED CHARACTERISTICS" by Selifonov et al., filed Jan. 18, 2000, (PCT/US00/01202) and, e.g. "METHODS FOR MAKING CHARACTER STRINGS, POLYNUCLEOTIDES & POLYPEPTIDES HAVING DESIRED CHARACTERISTICS" by Selifonov et al., filed Jul. 18, 2000 (U.S. Ser. No. 09/618,579); "METHODS OF POPULATING DATA STRUCTURES FOR USE IN EVOLUTIONARY SIMULATIONS" by Selifonov and Stemmer, filed Jan. 18, 2000 (PCT/US00/01138); and "SINGLE-STRANDED NUCLEIC ACID TEMPLATE-MEDIATED RECOMBINATION AND NUCLEIC ACID FRAGMENT ISOLATION" by Affholter, filed Sep. 6, 2000 (U.S. Ser. No. 09/656,549); and U.S. Pat. Nos. 6,177,263; 6,153,410.

[0296] Non-stochastic, or "directed evolution," methods include, e.g., saturation mutagenesis, such as Gene Site Saturation Mutagenesis (GSSM), synthetic ligation reassembly (SLR), or a combination thereof are used to modify the nucleic acids of the invention to generate cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes with new or altered properties (e.g., activity under highly acidic or alkaline conditions, high or low temperatures, and the like). Polypeptides encoded by the modified nucleic acids can be screened for an activity before testing for glucan hydrolysis or other activity. Any testing modality or protocol can be used, e.g., using a capillary array platform. See, e.g., U.S. Pat. Nos. 6,361,974; 6,280,926; 5,939,250.

[0297] Gene Site Saturation Mutagenesis, or, GSSM

[0298] The invention also provides methods for making enzyme using Gene Site Saturation mutagenesis, or, GSSM, as described herein, and also in U.S. Pat. Nos. 6,171,820 and 6,579,258. In one aspect, codon primers containing a degenerate N,N,G/T sequence are used to introduce point mutations into a polynucleotide, e.g., a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme or an antibody of the invention, so as to generate a set of progeny polypeptides in which a full range of single amino acid substitutions is represented at each amino acid position, e.g., an amino acid residue in an enzyme active site or ligand binding site targeted to be modified. These oligonucleotides can comprise a contiguous first homologous sequence, a degenerate N,N,G/T sequence, and, optionally, a second homologous sequence. The downstream progeny translational products from the use of such oligonucleotides include all possible amino acid changes at each amino acid site along the polypeptide, because the degeneracy of the N,N,G/T sequence includes codons for all 20 amino acids. In one aspect, one such degenerate oligonucleotide (comprised of, e.g., one degenerate N,N,G/T cassette) is used for subjecting each original codon in a parental polynucleotide template to a full range of codon substitutions. In another aspect, at least two degenerate cassettes are used--either in the same oligonucleotide or not, for subjecting at least two original codons in a parental polynucleotide template to a full range of codon substitutions. For example, more than one N,N,G/T sequence can be contained in one oligonucleotide to introduce amino acid mutations at more than one site. This plurality of N,N,G/T sequences can be directly contiguous, or separated by one or more additional nucleotide sequence(s). In another aspect, oligonucleotides serviceable for introducing additions and deletions can be used either alone or in combination with the codons containing an N,N,G/T sequence, to introduce any combination or permutation of amino acid additions, deletions, and/or substitutions.

[0299] In one aspect, simultaneous mutagenesis of two or more contiguous amino acid positions is done using an oligonucleotide that contains contiguous N,N,G/T triplets, i.e. a degenerate (N,N,G/T)n sequence. In another aspect, degenerate cassettes having less degeneracy than the N,N,G/T sequence are used. For example, it may be desirable in some instances to use (e.g. in an oligonucleotide) a degenerate triplet sequence comprised of only one N, where said N can be in the first second or third position of the triplet. Any other bases including any combinations and permutations thereof can be used in the remaining two positions of the triplet. Alternatively, it may be desirable in some instances to use (e.g. in an oligo) a degenerate N,N,N triplet sequence.

[0300] In one aspect, use of degenerate triplets (e.g., N,N,G/T triplets) allows for systematic and easy generation of a full range of possible natural amino acids (for a total of 20 amino acids) into each and every amino acid position in a polypeptide (in alternative aspects, the methods also include generation of less than all possible substitutions per amino acid residue, or codon, position). For example, for a 100 amino acid polypeptide, 2000 distinct species (i.e. 20 possible amino acids per position X 100 amino acid positions) can be generated. Through the use of an oligonucleotide or set of oligonucleotides containing a degenerate N,N,G/T triplet, 32 individual sequences can code for all 20 possible natural amino acids. Thus, in a reaction vessel in which a parental polynucleotide sequence is subjected to saturation mutagenesis using at least one such oligonucleotide, there are generated 32 distinct progeny polynucleotides encoding 20 distinct polypeptides. In contrast, the use of a non-degenerate oligonucleotide in site-directed mutagenesis leads to only one progeny polypeptide product per reaction vessel. Nondegenerate oligonucleotides can optionally be used in combination with degenerate primers disclosed; for example, nondegenerate oligonucleotides can be used to generate specific point mutations in a working polynucleotide. This provides one means to generate specific silent point mutations, point mutations leading to corresponding amino acid changes, and point mutations that cause the generation of stop codons and the corresponding expression of polypeptide fragments.

[0301] In one aspect, each saturation mutagenesis reaction vessel contains polynucleotides encoding at least 20 progeny polypeptide (e.g., cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes) molecules such that all 20 natural amino acids are represented at the one specific amino acid position corresponding to the codon position mutagenized in the parental polynucleotide (other aspects use less than all 20 natural combinations). The 32-fold degenerate progeny polypeptides generated from each saturation mutagenesis reaction vessel can be subjected to clonal amplification (e.g. cloned into a suitable host, e.g., E. coli host, using, e.g., an expression vector) and subjected to expression screening. When an individual progeny polypeptide is identified by screening to display a favorable change in property (when compared to the parental polypeptide, such as increased glucan hydrolysis activity under alkaline or acidic conditions), it can be sequenced to identify the correspondingly favorable amino acid substitution contained therein.

[0302] In one aspect, upon mutagenizing each and every amino acid position in a parental polypeptide using saturation mutagenesis as disclosed herein, favorable amino acid changes may be identified at more than one amino acid position. One or more new progeny molecules can be generated that contain a combination of all or part of these favorable amino acid substitutions. For example, if 2 specific favorable amino acid changes are identified in each of 3 amino acid positions in a polypeptide, the permutations include 3 possibilities at each position (no change from the original amino acid, and each of two favorable changes) and 3 positions. Thus, there are 3×3×3 or 27 total possibilities, including 7 that were previously examined--6 single point mutations (i.e. 2 at each of three positions) and no change at any position.

[0303] In yet another aspect, site-saturation mutagenesis can be used together with shuffling, chimerization, recombination and other mutagenizing processes, along with screening. This invention provides for the use of any mutagenizing process(es), including saturation mutagenesis, in an iterative manner. In one exemplification, the iterative use of any mutagenizing process(es) is used in combination with screening.

[0304] The invention also provides for the use of proprietary codon primers (containing a degenerate N,N,N sequence) to introduce point mutations into a polynucleotide, so as to generate a set of progeny polypeptides in which a full range of single amino acid substitutions is represented at each amino acid position (Gene Site Saturation Mutagenesis (GSSM)). The oligos used are comprised contiguously of a first homologous sequence, a degenerate N,N,N sequence and in one aspect but not necessarily a second homologous sequence. The downstream progeny translational products from the use of such oligos include all possible amino acid changes at each amino acid site along the polypeptide, because the degeneracy of the N,N,N sequence includes codons for all 20 amino acids.

[0305] In one aspect, one such degenerate oligo (comprised of one degenerate N,N,N cassette) is used for subjecting each original codon in a parental polynucleotide template to a full range of codon substitutions. In another aspect, at least two degenerate N,N,N cassettes are used--either in the same oligo or not, for subjecting at least two original codons in a parental polynucleotide template to a full range of codon substitutions. Thus, more than one N,N,N sequence can be contained in one oligo to introduce amino acid mutations at more than one site. This plurality of N,N,N sequences can be directly contiguous, or separated by one or more additional nucleotide sequence(s). In another aspect, oligos serviceable for introducing additions and deletions can be used either alone or in combination with the codons containing an N,N,N sequence, to introduce any combination or permutation of amino acid additions, deletions and/or substitutions.

[0306] In one aspect, it is possible to simultaneously mutagenize two or more contiguous amino acid positions using an oligo that contains contiguous N,N,N triplets, i.e. a degenerate (N,N,N)_n sequence. In another aspect, the present invention provides for the use of degenerate cassettes having less degeneracy than the N,N,N sequence. For example, it may be desirable in some instances to use (e.g. in an oligo) a degenerate triplet sequence comprised of only one N, where the N can be in the first second or third position of the triplet. Any other bases including any combinations and permutations thereof can be used in the remaining two positions of the triplet. Alternatively, it may be desirable in some instances to use (e.g., in an oligo) a degenerate N,N,N triplet sequence, N,N,G/T, or an N,N, G/C triplet sequence.

[0307] In one aspect, use of a degenerate triplet (such as N,N,G/T or an N,N, G/C triplet sequence) is advantageous for several reasons. In one aspect, this invention provides a means to systematically and fairly easily generate the substitution of the full range of possible amino acids (for a total of 20 amino acids) into each and every amino acid position in a polypeptide. Thus, for a 100 amino acid polypeptide, the invention provides a way to systematically and fairly easily generate 2000 distinct species (i.e., 20 possible amino acids per position times 100 amino acid positions). It is appreciated that there is provided, through the use of an oligo containing a degenerate N,N,G/T or an N,N, G/C triplet sequence, 32 individual sequences that code for 20 possible amino acids. Thus, in a reaction vessel in which a parental polynucleotide sequence is subjected to saturation mutagenesis using one such oligo, there are generated 32 distinct progeny polynucleotides encoding 20 distinct polypeptides. In contrast, the use of a non-degenerate oligo in site-directed mutagenesis leads to only one progeny polypeptide product per reaction vessel.

[0308] This invention also provides for the use of nondegenerate oligos, which can optionally be used in combination with degenerate primers disclosed. It is appreciated that in some situations, it is advantageous to use nondegenerate oligos to generate specific point mutations in a working polynucleotide. This provides a means to generate specific silent point mutations, point mutations leading to corresponding amino acid changes and point mutations that cause the generation of stop codons and the corresponding expression of polypeptide fragments.

[0309] Thus, in one aspect of this invention, each saturation mutagenesis reaction vessel contains polynucleotides encoding at least 20 progeny polypeptide molecules such that all 20 amino acids are represented at the one specific amino acid position corresponding to the codon position mutagenized in the parental polynucleotide. The 32-fold degenerate progeny polypeptides generated from each saturation mutagenesis reaction vessel can be subjected to clonal amplification (e.g., cloned into a suitable E. coli host using an expression vector) and subjected to expression screening. When an individual progeny polypeptide is identified by screening to display a favorable change in property (when compared to the parental polypeptide), it can be sequenced to identify the correspondingly favorable amino acid substitution contained therein.

[0310] In one aspect, upon mutagenizing each and every amino acid position in a parental polypeptide using saturation mutagenesis as disclosed herein, a favorable amino acid changes is identified at more than one amino acid position. One or more new progeny molecules can be generated that contain a combination of all or part of these favorable amino acid substitutions. For example, if 2 specific favorable amino acid changes are identified in each of 3 amino acid positions in a polypeptide, the permutations include 3 possibilities at each position (no change from the original amino acid and each of two favorable changes) and 3 positions. Thus, there are 3×3×3 or 27 total possibilities, including 7 that were previously examined--6 single point mutations (i.e., 2 at each of three positions) and no change at any position.

[0311] The invention provides for the use of saturation mutagenesis in combination with additional mutagenization processes, such as process where two or more related polynucleotides are introduced into a suitable host cell such that a hybrid polynucleotide is generated by recombination and reductive reassortment.

[0312] In addition to performing mutagenesis along the entire sequence of a gene, the instant invention provides that mutagenesis can be use to replace each of any number of bases in a polynucleotide sequence, wherein the number of bases to be mutagenized is in one aspect every integer from 15 to 100,000. Thus, instead of mutagenizing every position along a molecule, one can subject every or a discrete number of bases (in one aspect a subset totaling from 15 to 100,000) to mutagenesis. In one aspect, a separate nucleotide is used for mutagenizing each position or group of positions along a polynucleotide sequence. A group of 3 positions to be mutagenized may be a codon. The mutations can be introduced using a mutagenic primer, containing a heterologous cassette, also referred to as a mutagenic cassette. Exemplary cassettes can have from 1 to 500 bases. Each nucleotide position in such heterologous cassettes be N, A, C, G, T, A/C, A/G, A/T, C/G, C/T, G/T, C/G/T, A/G/T, A/C/T, A/C/G, or E, where E is any base that is not A, C, G, or T (E can be referred to as a designer oligo).

[0313] In one aspect, saturation mutagenesis is comprised of mutagenizing a complete set of mutagenic cassettes (wherein each cassette is in one aspect about 1-500 bases in length) in defined polynucleotide sequence to be mutagenized (wherein the sequence to be mutagenized is in one aspect from about 15 to 100,000 bases in length). Thus, a group of mutations (ranging from 1 to 100 mutations) is introduced into each cassette to be mutagenized. A grouping of mutations to be introduced into one cassette can be different or the same from a second grouping of mutations to be introduced into a second cassette during the application of one round of saturation mutagenesis. Such groupings are exemplified by deletions, additions, groupings of particular codons and groupings of particular nucleotide cassettes.

[0314] In one aspect, defined sequences to be mutagenized include a whole gene, pathway, cDNA, an entire open reading frame (ORF) and entire promoter, enhancer, repressor/transactivator, origin of replication, intron, operator, or any polynucleotide functional group. Generally, a "defined sequences" for this purpose may be any polynucleotide that a 15 base-polynucleotide sequence and polynucleotide sequences of lengths between 15 bases and 15,000 bases (this invention specifically names every integer in between). Considerations in choosing groupings of codons include types of amino acids encoded by a degenerate mutagenic cassette.

[0315] In one aspect, a grouping of mutations that can be introduced into a mutagenic cassette, this invention specifically provides for degenerate codon substitutions (using degenerate oligos) that code for 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 and 20 amino acids at each position and a library of polypeptides encoded thereby.

[0316] Synthetic Ligation Reassembly (SLR)

[0317] The invention provides a non-stochastic gene modification system termed "synthetic ligation reassembly," or simply "SLR," a "directed evolution process," to generate polypeptides, e.g., cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes or antibodies of the invention, with new or altered properties.

[0318] SLR is a method of ligating oligonucleotide fragments together non-stochastically. This method differs from stochastic oligonucleotide shuffling in that the nucleic acid building blocks are not shuffled, concatenated or chimerized randomly, but rather are assembled non-stochastically. See, e.g., U.S. Pat. Nos. 6,773,900; 6,740,506; 6,713,282; 6,635,449; 6,605,449; 6,537,776. In one aspect, SLR comprises the following steps: (a) providing a template polynucleotide, wherein the template polynucleotide comprises sequence encoding a homologous gene; (b) providing a plurality of building block polynucleotides, wherein the building block polynucleotides are designed to cross-over reassemble with the template polynucleotide at a predetermined sequence, and a building block polynucleotide comprises a sequence that is a variant of the homologous gene and a sequence homologous to the template polynucleotide flanking the variant sequence; (c) combining a building block polynucleotide with a template polynucleotide such that the building block polynucleotide cross-over reassembles with the template polynucleotide to generate polynucleotides comprising homologous gene sequence variations.

[0319] SLR does not depend on the presence of high levels of homology between polynucleotides to be rearranged. Thus, this method can be used to non-stochastically generate libraries (or sets) of progeny molecules comprised of over 10¹⁰⁰ different chimeras. SLR can be used to generate libraries comprised of over 10¹⁰⁰⁰ different progeny chimeras. Thus, aspects of the present invention include non-stochastic methods of producing a set of finalized chimeric nucleic acid molecule shaving an overall assembly order that is chosen by design. This method includes the steps of generating by design a plurality of specific nucleic acid building blocks having serviceable mutually compatible ligatable ends, and assembling these nucleic acid building blocks, such that a designed overall assembly order is achieved.

[0320] The mutually compatible ligatable ends of the nucleic acid building blocks to be assembled are considered to be "serviceable" for this type of ordered assembly if they enable the building blocks to be coupled in predetermined orders. Thus, the overall assembly order in which the nucleic acid building blocks can be coupled is specified by the design of the ligatable ends. If more than one assembly step is to be used, then the overall assembly order in which the nucleic acid building blocks can be coupled is also specified by the sequential order of the assembly step(s). In one aspect, the annealed building pieces are treated with an enzyme, such as a ligase (e.g. T4 DNA ligase), to achieve covalent bonding of the building pieces.

[0321] In one aspect, the design of the oligonucleotide building blocks is obtained by analyzing a set of progenitor nucleic acid sequence templates that serve as a basis for producing a progeny set of finalized chimeric polynucleotides. These parental oligonucleotide templates thus serve as a source of sequence information that aids in the design of the nucleic acid building blocks that are to be mutagenized, e.g., chimerized or shuffled. In one aspect of this method, the sequences of a plurality of parental nucleic acid templates are aligned in order to select one or more demarcation points. The demarcation points can be located at an area of homology, and are comprised of one or more nucleotides. These demarcation points are in one aspect shared by at least two of the progenitor templates. The demarcation points can thereby be used to delineate the boundaries of oligonucleotide building blocks to be generated in order to rearrange the parental polynucleotides. The demarcation points identified and selected in the progenitor molecules serve as potential chimerization points in the assembly of the final chimeric progeny molecules. A demarcation point can be an area of homology (comprised of at least one homologous nucleotide base) shared by at least two parental polynucleotide sequences. Alternatively, a demarcation point can be an area of homology that is shared by at least half of the parental polynucleotide sequences, or, it can be an area of homology that is shared by at least two thirds of the parental polynucleotide sequences. Even more in one aspect a serviceable demarcation points is an area of homology that is shared by at least three fourths of the parental polynucleotide sequences, or, it can be shared by at almost all of the parental polynucleotide sequences. In one aspect, a demarcation point is an area of homology that is shared by all of the parental polynucleotide sequences.

[0322] In one aspect, a ligation reassembly process is performed exhaustively in order to generate an exhaustive library of progeny chimeric polynucleotides. In other words, all possible ordered combinations of the nucleic acid building blocks are represented in the set of finalized chimeric nucleic acid molecules. At the same time, in another aspect, the assembly order (i.e. the order of assembly of each building block in the 5' to 3 sequence of each finalized chimeric nucleic acid) in each combination is by design (or non-stochastic) as described above. Because of the non-stochastic nature of this invention, the possibility of unwanted side products is greatly reduced.

[0323] In another aspect, the ligation reassembly method is performed systematically. For example, the method is performed in order to generate a systematically compartmentalized library of progeny molecules, with compartments that can be screened systematically, e.g. one by one. In other words this invention provides that, through the selective and judicious use of specific nucleic acid building blocks, coupled with the selective and judicious use of sequentially stepped assembly reactions, a design can be achieved where specific sets of progeny products are made in each of several reaction vessels. This allows a systematic examination and screening procedure to be performed. Thus, these methods allow a potentially very large number of progeny molecules to be examined systematically in smaller groups. Because of its ability to perform chimerizations in a manner that is highly flexible yet exhaustive and systematic as well, particularly when there is a low level of homology among the progenitor molecules, these methods provide for the generation of a library (or set) comprised of a large number of progeny molecules. Because of the non-stochastic nature of the instant ligation reassembly invention, the progeny molecules generated in one aspect comprise a library of finalized chimeric nucleic acid molecules having an overall assembly order that is chosen by design. The saturation mutagenesis and optimized directed evolution methods also can be used to generate different progeny molecular species. It is appreciated that the invention provides freedom of choice and control regarding the selection of demarcation points, the size and number of the nucleic acid building blocks, and the size and design of the couplings. It is appreciated, furthermore, that the requirement for intermolecular homology is highly relaxed for the operability of this invention. In fact, demarcation points can even be chosen in areas of little or no intermolecular homology. For example, because of codon wobble, i.e. the degeneracy of codons, nucleotide substitutions can be introduced into nucleic acid building blocks without altering the amino acid originally encoded in the corresponding progenitor template. Alternatively, a codon can be altered such that the coding for an originally amino acid is altered. This invention provides that such substitutions can be introduced into the nucleic acid building block in order to increase the incidence of intermolecular homologous demarcation points and thus to allow an increased number of couplings to be achieved among the building blocks, which in turn allows a greater number of progeny chimeric molecules to be generated.

[0324] Synthetic Gene Reassembly

[0325] In one aspect, the present invention provides a non-stochastic method termed synthetic gene reassembly, that is somewhat related to stochastic shuffling, save that the nucleic acid building blocks are not shuffled or concatenated or chimerized randomly, but rather are assembled non-stochastically. See, e.g., U.S. Pat. No. 6,537,776.

[0326] The synthetic gene reassembly method does not depend on the presence of a high level of homology between polynucleotides to be shuffled. The invention can be used to non-stochastically generate libraries (or sets) of progeny molecules comprised of over 10¹⁰⁰ different chimeras. Conceivably, synthetic gene reassembly can even be used to generate libraries comprised of over 10¹⁰⁰⁰ different progeny chimeras.

[0327] Thus, in one aspect, the invention provides a non-stochastic method of producing a set of finalized chimeric nucleic acid molecules having an overall assembly order that is chosen by design, which method is comprised of the steps of generating by design a plurality of specific nucleic acid building blocks having serviceable mutually compatible ligatable ends and assembling these nucleic acid building blocks, such that a designed overall assembly order is achieved.

[0328] The mutually compatible ligatable ends of the nucleic acid building blocks to be assembled are considered to be "serviceable" for this type of ordered assembly if they enable the building blocks to be coupled in predetermined orders. Thus, in one aspect, the overall assembly order in which the nucleic acid building blocks can be coupled is specified by the design of the ligatable ends and, if more than one assembly step is to be used, then the overall assembly order in which the nucleic acid building blocks can be coupled is also specified by the sequential order of the assembly step(s). In a one aspect of the invention, the annealed building pieces are treated with an enzyme, such as a ligase (e.g., T4 DNA ligase) to achieve covalent bonding of the building pieces.

[0329] In a another aspect, the design of nucleic acid building blocks is obtained upon analysis of the sequences of a set of progenitor nucleic acid templates that serve as a basis for producing a progeny set of finalized chimeric nucleic acid molecules. These progenitor nucleic acid templates thus serve as a source of sequence information that aids in the design of the nucleic acid building blocks that are to be mutagenized, i.e. chimerized or shuffled.

[0330] In one exemplification, the invention provides for the chimerization of a family of related genes and their encoded family of related products. In a particular exemplification, the encoded products are enzymes. The cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes of the present invention can be mutagenized in accordance with the methods described herein.

[0331] Thus according to one aspect of the invention, the sequences of a plurality of progenitor nucleic acid templates (e.g., polynucleotides of the invention) are aligned in order to select one or more demarcation points, which demarcation points can be located at an area of homology. The demarcation points can be used to delineate the boundaries of nucleic acid building blocks to be generated. Thus, the demarcation points identified and selected in the progenitor molecules serve as potential chimerization points in the assembly of the progeny molecules.

[0332] In one aspect, a serviceable demarcation point is an area of homology (comprised of at least one homologous nucleotide base) shared by at least two progenitor templates, but the demarcation point can be an area of homology that is shared by at least half of the progenitor templates, at least two thirds of the progenitor templates, at least three fourths of the progenitor templates and in one aspect at almost all of the progenitor templates. Even more in one aspect still a serviceable demarcation point is an area of homology that is shared by all of the progenitor templates.

[0333] In a one aspect, the gene reassembly process is performed exhaustively in order to generate an exhaustive library. In other words, all possible ordered combinations of the nucleic acid building blocks are represented in the set of finalized chimeric nucleic acid molecules. At the same time, the assembly order (i.e. the order of assembly of each building block in the 5' to 3 sequence of each finalized chimeric nucleic acid) in each combination is by design (or non-stochastic). Because of the non-stochastic nature of the method, the possibility of unwanted side products is greatly reduced.

[0334] In another aspect, the method provides that the gene reassembly process is performed systematically, for example to generate a systematically compartmentalized library, with compartments that can be screened systematically, e.g., one by one. In other words the invention provides that, through the selective and judicious use of specific nucleic acid building blocks, coupled with the selective and judicious use of sequentially stepped assembly reactions, an experimental design can be achieved where specific sets of progeny products are made in each of several reaction vessels. This allows a systematic examination and screening procedure to be performed. Thus, it allows a potentially very large number of progeny molecules to be examined systematically in smaller groups.

[0335] Because of its ability to perform chimerizations in a manner that is highly flexible yet exhaustive and systematic as well, particularly when there is a low level of homology among the progenitor molecules, the instant invention provides for the generation of a library (or set) comprised of a large number of progeny molecules. Because of the non-stochastic nature of the instant gene reassembly invention, the progeny molecules generated in one aspect comprise a library of finalized chimeric nucleic acid molecules having an overall assembly order that is chosen by design. In a particularly aspect, such a generated library is comprised of greater than 10³ to greater than 10¹⁰⁰⁰ different progeny molecular species.

[0336] In one aspect, a set of finalized chimeric nucleic acid molecules, produced as described is comprised of a polynucleotide encoding a polypeptide. According to one aspect, this polynucleotide is a gene, which may be a man-made gene. According to another aspect, this polynucleotide is a gene pathway, which may be a man-made gene pathway. The invention provides that one or more man-made genes generated by the invention may be incorporated into a man-made gene pathway, such as pathway operable in a eukaryotic organism (including a plant).

[0337] In another exemplification, the synthetic nature of the step in which the building blocks are generated allows the design and introduction of nucleotides (e.g., one or more nucleotides, which may be, for example, codons or introns or regulatory sequences) that can later be optionally removed in an in vitro process (e.g., by mutagenesis) or in an in vivo process (e.g., by utilizing the gene splicing ability of a host organism). It is appreciated that in many instances the introduction of these nucleotides may also be desirable for many other reasons in addition to the potential benefit of creating a serviceable demarcation point.

[0338] Thus, according to another aspect, the invention provides that a nucleic acid building block can be used to introduce an intron. Thus, the invention provides that functional introns may be introduced into a man-made gene of the invention. The invention also provides that functional introns may be introduced into a man-made gene pathway of the invention. Accordingly, the invention provides for the generation of a chimeric polynucleotide that is a man-made gene containing one (or more) artificially introduced intron(s).

[0339] The invention also provides for the generation of a chimeric polynucleotide that is a man-made gene pathway containing one (or more) artificially introduced intron(s). In one aspect, the artificially introduced intron(s) are functional in one or more host cells for gene splicing much in the way that naturally-occurring introns serve functionally in gene splicing. The invention provides a process of producing man-made intron-containing polynucleotides to be introduced into host organisms for recombination and/or splicing.

[0340] A man-made gene produced using the invention can also serve as a substrate for recombination with another nucleic acid. Likewise, a man-made gene pathway produced using the invention can also serve as a substrate for recombination with another nucleic acid. In one aspect, the recombination is facilitated by, or occurs at, areas of homology between the man-made, intron-containing gene and a nucleic acid, which serves as a recombination partner. In one aspect, the recombination partner may also be a nucleic acid generated by the invention, including a man-made gene or a man-made gene pathway. Recombination may be facilitated by or may occur at areas of homology that exist at the one (or more) artificially introduced intron(s) in the man-made gene.

[0341] In one aspect, the synthetic gene reassembly method of the invention utilizes a plurality of nucleic acid building blocks, each of which in one aspect has two ligatable ends. The two ligatable ends on each nucleic acid building block may be two blunt ends (i.e. each having an overhang of zero nucleotides), or in one aspect one blunt end and one overhang, or more in one aspect still two overhangs. In one aspect, a useful overhang for this purpose may be a 3' overhang or a 5' overhang. Thus, a nucleic acid building block may have a 3' overhang or alternatively a 5' overhang or alternatively two 3' overhangs or alternatively two 5' overhangs. The overall order in which the nucleic acid building blocks are assembled to form a finalized chimeric nucleic acid molecule is determined by purposeful experimental design and is not random.

[0342] In one aspect, a nucleic acid building block is generated by chemical synthesis of two single-stranded nucleic acids (also referred to as single-stranded oligos) and contacting them so as to allow them to anneal to form a double-stranded nucleic acid building block. A double-stranded nucleic acid building block can be of variable size. The sizes of these building blocks can be small or large. Exemplary sizes for building block range from 1 base pair (not including any overhangs) to 100,000 base pairs (not including any overhangs). Other exemplary size ranges are also provided, which have lower limits of from 1 bp to 10,000 bp (including every integer value in between) and upper limits of from 2 bp to 100,000 bp (including every integer value in between).

[0343] Many methods exist by which a double-stranded nucleic acid building block can be generated that is serviceable for the invention; and these are known in the art and can be readily performed by the skilled artisan. According to one aspect, a double-stranded nucleic acid building block is generated by first generating two single stranded nucleic acids and allowing them to anneal to form a double-stranded nucleic acid building block. The two strands of a double-stranded nucleic acid building block may be complementary at every nucleotide apart from any that form an overhang; thus containing no mismatches, apart from any overhang(s). According to another aspect, the two strands of a double-stranded nucleic acid building block are complementary at fewer than every nucleotide apart from any that form an overhang. Thus, according to this aspect, a double-stranded nucleic acid building block can be used to introduce codon degeneracy. In one aspect the codon degeneracy is introduced using the site-saturation mutagenesis described herein, using one or more N,N,G/T cassettes or alternatively using one or more N,N,N cassettes.

[0344] The in vivo recombination method of the invention can be performed blindly on a pool of unknown hybrids or alleles of a specific polynucleotide or sequence. However, it is not necessary to know the actual DNA or RNA sequence of the specific polynucleotide. The approach of using recombination within a mixed population of genes can be useful for the generation of any useful proteins, for example, a cellulase of the invention or a variant thereof. This approach may be used to generate proteins having altered specificity or activity. The approach may also be useful for the generation of hybrid nucleic acid sequences, for example, promoter regions, introns, exons, enhancer sequences, 31 untranslated regions or 51 untranslated regions of genes. Thus this approach may be used to generate genes having increased rates of expression. This approach may also be useful in the study of repetitive DNA sequences. Finally, this approach may be useful to make ribozymes or aptamers of the invention.

[0345] In one aspect the invention described herein is directed to the use of repeated cycles of reductive reassortment, recombination and selection which allow for the directed molecular evolution of highly complex linear sequences, such as DNA, RNA or proteins thorough recombination.

[0346] Optimized Directed Evolution System

[0347] The invention provides a non-stochastic gene modification system termed "optimized directed evolution system" to generate polypeptides, e.g., cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes or antibodies of the invention, with new or altered properties. In one aspect, optimized directed evolution is directed to the use of repeated cycles of reductive reassortment, recombination and selection that allow for the directed molecular evolution of nucleic acids through recombination.

[0348] Optimized directed evolution allows generation of a large population of evolved chimeric sequences, wherein the generated population is significantly enriched for sequences that have a predetermined number of crossover events. A crossover event is a point in a chimeric sequence where a shift in sequence occurs from one parental variant to another parental variant. Such a point is normally at the juncture of where oligonucleotides from two parents are ligated together to form a single sequence. This method allows calculation of the correct concentrations of oligonucleotide sequences so that the final chimeric population of sequences is enriched for the chosen number of crossover events. This provides more control over choosing chimeric variants having a predetermined number of crossover events.

[0349] In addition, this method provides a convenient means for exploring a tremendous amount of the possible protein variant space in comparison to other systems. Previously, if one generated, for example, 10¹³ chimeric molecules during a reaction, it would be extremely difficult to test such a high number of chimeric variants for a particular activity. Moreover, a significant portion of the progeny population would have a very high number of crossover events which resulted in proteins that were less likely to have increased levels of a particular activity. By using these methods, the population of chimerics molecules can be enriched for those variants that have a particular number of crossover events. Thus, although one can still generate 10¹³ chimeric molecules during a reaction, each of the molecules chosen for further analysis most likely has, for example, only three crossover events. Because the resulting progeny population can be skewed to have a predetermined number of crossover events, the boundaries on the functional variety between the chimeric molecules is reduced. This provides a more manageable number of variables when calculating which oligonucleotide from the original parental polynucleotides might be responsible for affecting a particular trait.

[0350] One method for creating a chimeric progeny polynucleotide sequence is to create oligonucleotides corresponding to fragments or portions of each parental sequence. Each oligonucleotide in one aspect includes a unique region of overlap so that mixing the oligonucleotides together results in a new variant that has each oligonucleotide fragment assembled in the correct order. Alternatively protocols for practicing these methods of the invention can be found in U.S. Pat. Nos. 6,773,900; 6,740,506; 6,713,282; 6,635,449; 6,605,449; 6,537,776; 6,361,974.

[0351] The number of oligonucleotides generated for each parental variant bears a relationship to the total number of resulting crossovers in the chimeric molecule that is ultimately created. For example, three parental nucleotide sequence variants might be provided to undergo a ligation reaction in order to find a chimeric variant having, for example, greater activity at high temperature. As one example, a set of 50 oligonucleotide sequences can be generated corresponding to each portions of each parental variant. Accordingly, during the ligation reassembly process there could be up to 50 crossover events within each of the chimeric sequences. The probability that each of the generated chimeric polynucleotides will contain oligonucleotides from each parental variant in alternating order is very low. If each oligonucleotide fragment is present in the ligation reaction in the same molar quantity it is likely that in some positions oligonucleotides from the same parental polynucleotide will ligate next to one another and thus not result in a crossover event. If the concentration of each oligonucleotide from each parent is kept constant during any ligation step in this example, there is a 1/3 chance (assuming 3 parents) that an oligonucleotide from the same parental variant will ligate within the chimeric sequence and produce no crossover.

[0352] Accordingly, a probability density function (PDF) can be determined to predict the population of crossover events that are likely to occur during each step in a ligation reaction given a set number of parental variants, a number of oligonucleotides corresponding to each variant, and the concentrations of each variant during each step in the ligation reaction. The statistics and mathematics behind determining the PDF is described below. By utilizing these methods, one can calculate such a probability density function, and thus enrich the chimeric progeny population for a predetermined number of crossover events resulting from a particular ligation reaction. Moreover, a target number of crossover events can be predetermined, and the system then programmed to calculate the starting quantities of each parental oligonucleotide during each step in the ligation reaction to result in a probability density function that centers on the predetermined number of crossover events. These methods are directed to the use of repeated cycles of reductive reassortment, recombination and selection that allow for the directed molecular evolution of a nucleic acid encoding a polypeptide through recombination. This system allows generation of a large population of evolved chimeric sequences, wherein the generated population is significantly enriched for sequences that have a predetermined number of crossover events. A crossover event is a point in a chimeric sequence where a shift in sequence occurs from one parental variant to another parental variant. Such a point is normally at the juncture of where oligonucleotides from two parents are ligated together to form a single sequence. The method allows calculation of the correct concentrations of oligonucleotide sequences so that the final chimeric population of sequences is enriched for the chosen number of crossover events. This provides more control over choosing chimeric variants having a predetermined number of crossover events.

[0353] In addition, these methods provide a convenient means for exploring a tremendous amount of the possible protein variant space in comparison to other systems. By using the methods described herein, the population of chimerics molecules can be enriched for those variants that have a particular number of crossover events. Thus, although one can still generate 10¹³ chimeric molecules during a reaction, each of the molecules chosen for further analysis most likely has, for example, only three crossover events. Because the resulting progeny population can be skewed to have a predetermined number of crossover events, the boundaries on the functional variety between the chimeric molecules is reduced. This provides a more manageable number of variables when calculating which oligonucleotide from the original parental polynucleotides might be responsible for affecting a particular trait.

[0354] In one aspect, the method creates a chimeric progeny polynucleotide sequence by creating oligonucleotides corresponding to fragments or portions of each parental sequence. Each oligonucleotide in one aspect includes a unique region of overlap so that mixing the oligonucleotides together results in a new variant that has each oligonucleotide fragment assembled in the correct order. See also U.S. Pat. Nos. 6,773,900; 6,740,506; 6,713,282; 6,635,449; 6,605,449; 6,537,776; 6,361,974.

[0355] Determining Crossover Events

[0356] Aspects of the invention include a system and software that receive a desired crossover probability density function (PDF), the number of parent genes to be reassembled, and the number of fragments in the reassembly as inputs. The output of this program is a "fragment PDF" that can be used to determine a recipe for producing reassembled genes, and the estimated crossover PDF of those genes. The processing described herein is in one aspect performed in MATLAB® (The Mathworks, Natick, Mass.) a programming language and development environment for technical computing.

[0357] Iterative Processes

[0358] Any process of the invention can be iteratively repeated, e.g., a nucleic acid encoding an altered or new cellulase phenotype, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme of the invention, can be identified, re-isolated, again modified, re-tested for activity. This process can be iteratively repeated until a desired phenotype is engineered. For example, an entire biochemical anabolic or catabolic pathway can be engineered into a cell, including, e.g., cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity.

[0359] Similarly, if it is determined that a particular oligonucleotide has no affect at all on the desired trait (e.g., a new cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme phenotype), it can be removed as a variable by synthesizing larger parental oligonucleotides that include the sequence to be removed. Since incorporating the sequence within a larger sequence prevents any crossover events, there will no longer be any variation of this sequence in the progeny polynucleotides. This iterative practice of determining which oligonucleotides are most related to the desired trait, and which are unrelated, allows more efficient exploration all of the possible protein variants that might be provide a particular trait or activity.

[0360] In Vivo Shuffling

[0361] In various aspects, in vivo shuffling of molecules is used in methods of the invention to provide variants of polypeptides of the invention, e.g., antibodies of the invention or cellulases of the invention, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes, and the like. In vivo shuffling can be performed utilizing the natural property of cells to recombine multimers. While recombination in vivo has provided the major natural route to molecular diversity, genetic recombination remains a relatively complex process that involves 1) the recognition of homologies; 2) strand cleavage, strand invasion, and metabolic steps leading to the production of recombinant chiasma; and finally 3) the resolution of chiasma into discrete recombined molecules. The formation of the chiasma requires the recognition of homologous sequences.

[0362] In another aspect, the invention includes a method for producing a hybrid polynucleotide from at least a first polynucleotide and a second polynucleotide. The invention can be used to produce a hybrid polynucleotide by introducing at least a first polynucleotide and a second polynucleotide (e.g., one, or both, being an exemplary cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme-encoding sequence of the invention) which share at least one region of partial sequence homology into a suitable host cell. The regions of partial sequence homology promote processes which result in sequence reorganization producing a hybrid polynucleotide. The term "hybrid polynucleotide", as used herein, is any nucleotide sequence which results from the method of the present invention and contains sequence from at least two original polynucleotide sequences. Such hybrid polynucleotides can result from intermolecular recombination events which promote sequence integration between DNA molecules. In addition, such hybrid polynucleotides can result from intramolecular reductive reassortment processes which utilize repeated sequences to alter a nucleotide sequence within a DNA molecule.

[0363] In one aspect, vivo reassortment focuses on "inter-molecular" processes collectively referred to as "recombination"; which in bacteria, is generally viewed as a "RecA-dependent" phenomenon. The invention can rely on recombination processes of a host cell to recombine and re-assort sequences, or the cells' ability to mediate reductive processes to decrease the complexity of quasi-repeated sequences in the cell by deletion. This process of "reductive reassortment" occurs by an "intra-molecular", RecA-independent process.

[0364] In another aspect of the invention, novel polynucleotides can be generated by the process of reductive reassortment. The method involves the generation of constructs containing consecutive sequences (original encoding sequences), their insertion into an appropriate vector and their subsequent introduction into an appropriate host cell. The reassortment of the individual molecular identities occurs by combinatorial processes between the consecutive sequences in the construct possessing regions of homology, or between quasi-repeated units. The reassortment process recombines and/or reduces the complexity and extent of the repeated sequences and results in the production of novel molecular species. Various treatments may be applied to enhance the rate of reassortment. These could include treatment with ultra-violet light, or DNA damaging chemicals and/or the use of host cell lines displaying enhanced levels of "genetic instability". Thus the reassortment process may involve homologous recombination or the natural property of quasi-repeated sequences to direct their own evolution.

[0365] Repeated or "quasi-repeated" sequences play a role in genetic instability. In one aspect, "quasi-repeats" are repeats that are not restricted to their original unit structure. Quasi-repeated units can be presented as an array of sequences in a construct; consecutive units of similar sequences. Once ligated, the junctions between the consecutive sequences become essentially invisible and the quasi-repetitive nature of the resulting construct is now continuous at the molecular level. The deletion process the cell performs to reduce the complexity of the resulting construct operates between the quasi-repeated sequences. The quasi-repeated units provide a practically limitless repertoire of templates upon which slippage events can occur. In one aspect, the constructs containing the quasi-repeats thus effectively provide sufficient molecular elasticity that deletion (and potentially insertion) events can occur virtually anywhere within the quasi-repetitive units.

[0366] When the quasi-repeated sequences are all ligated in the same orientation, for instance head to tail or vice versa, the cell cannot distinguish individual units. Consequently, the reductive process can occur throughout the sequences. In contrast, when for example, the units are presented head to head, rather than head to tail, the inversion delineates the endpoints of the adjacent unit so that deletion formation will favor the loss of discrete units. Thus, it is preferable with the present method that the sequences are in the same orientation. Random orientation of quasi-repeated sequences will result in the loss of reassortment efficiency, while consistent orientation of the sequences will offer the highest efficiency. However, while having fewer of the contiguous sequences in the same orientation decreases the efficiency, it may still provide sufficient elasticity for the effective recovery of novel molecules. Constructs can be made with the quasi-repeated sequences in the same orientation to allow higher efficiency.

[0367] Sequences can be assembled in a head to tail orientation using any of a variety of methods, including the following:

[0368] a) Primers that include a poly-A head and poly-T tail which when made single-stranded would provide orientation can be utilized. This is accomplished by having the first few bases of the primers made from RNA and hence easily removed RNaseH.

[0369] b) Primers that include unique restriction cleavage sites can be utilized. Multiple sites, a battery of unique sequences and repeated synthesis and ligation steps would be required.

[0370] c) The inner few bases of the primer could be thiolated and an exonuclease used to produce properly tailed molecules.

[0371] In one aspect, the recovery of the re-assorted sequences relies on the identification of cloning vectors with a reduced repetitive index (RI). The re-assorted encoding sequences can then be recovered by amplification. The products are re-cloned and expressed. The recovery of cloning vectors with reduced RI can be affected by:

[0372] 1) The use of vectors only stably maintained when the construct is reduced in complexity.

[0373] 2) The physical recovery of shortened vectors by physical procedures. In this case, the cloning vector would be recovered using standard plasmid isolation procedures and size fractionated on either an agarose gel, or column with a low molecular weight cut off utilizing standard procedures.

[0374] 3) The recovery of vectors containing interrupted genes which can be selected when insert size decreases.

[0375] 4) The use of direct selection techniques with an expression vector and the appropriate selection.

[0376] Encoding sequences (for example, genes) from related organisms may demonstrate a high degree of homology and encode quite diverse protein products. These types of sequences are particularly useful in the present invention as quasi-repeats. However, while the examples illustrated below demonstrate the reassortment of nearly identical original encoding sequences (quasi-repeats), this process is not limited to such nearly identical repeats.

[0377] The following example demonstrates an exemplary method of the invention. Encoding nucleic acid sequences (quasi-repeats) derived from three (3) unique species are described. Each sequence encodes a protein with a distinct set of properties. Each of the sequences differs by a single or a few base pairs at a unique position in the sequence. The quasi-repeated sequences are separately or collectively amplified and ligated into random assemblies such that all possible permutations and combinations are available in the population of ligated molecules. The number of quasi-repeat units can be controlled by the assembly conditions. The average number of quasi-repeated units in a construct is defined as the repetitive index (RI).

[0378] Once formed, the constructs may, or may not be size fractionated on an agarose gel according to published protocols, inserted into a cloning vector and transfected into an appropriate host cell. The cells are then propagated and "reductive reassortment" is effected. The rate of the reductive reassortment process may be stimulated by the introduction of DNA damage if desired. Whether the reduction in RI is mediated by deletion formation between repeated sequences by an "intra-molecular" mechanism, or mediated by recombination-like events through "inter-molecular" mechanisms is immaterial. The end result is a reassortment of the molecules into all possible combinations.

[0379] Optionally, the method comprises the additional step of screening the library members of the shuffled pool to identify individual shuffled library members having the ability to bind or otherwise interact, or catalyze a particular reaction (e.g., such as catalytic domain of an enzyme) with a predetermined macromolecule, such as for example a proteinaceous receptor, an oligosaccharide, virion, or other predetermined compound or structure.

[0380] The polypeptides that are identified from such libraries can be used for therapeutic, diagnostic, research and related purposes (e.g., catalysts, solutes for increasing osmolarity of an aqueous solution and the like) and/or can be subjected to one or more additional cycles of shuffling and/or selection.

[0381] In another aspect, it is envisioned that prior to or during recombination or reassortment, polynucleotides generated by the method of the invention can be subjected to agents or processes which promote the introduction of mutations into the original polynucleotides. The introduction of such mutations would increase the diversity of resulting hybrid polynucleotides and polypeptides encoded therefrom. The agents or processes which promote mutagenesis can include, but are not limited to: (+)--CC-1065, or a synthetic analog such as (+)--CC-1065-(N3-Adenine (See Sun and Hurley, (1992); an N-acetylated or deacetylated 4'-fluoro-4-aminobiphenyl adduct capable of inhibiting DNA synthesis (See, for example, van de Poll et al. (1992)); or a N-acetylated or deacetylated 4-aminobiphenyl adduct capable of inhibiting DNA synthesis (See also, van de Poll et al. (1992), pp. 751-758); trivalent chromium, a trivalent chromium salt, a polycyclic aromatic hydrocarbon (PAH) DNA adduct capable of inhibiting DNA replication, such as 7-bromomethyl-benz[a]anthracene ("BMA"), tris(2,3-dibromopropyl)phosphate ("Tris-BP"), 1,2-dibromo-3-chloropropane ("DBCP"), 2-bromoacrolein (2BA), benzo[a]pyrene-7,8-dihydrodiol-9-10-epoxide ("BPDE"), a platinum(II) halogen salt, N-hydroxy-2-amino-3-methylimidazo[4,5-f]-quinoline ("N-hydroxy-IQ") and N-hydroxy-2-amino-1-methyl-6-phenylimidazo[4,5-j]-pyridine ("N-hydroxy-PhIP"). Exemplary means for slowing or halting PCR amplification consist of UV light (+)--CC-1065 and (+)--CC-1065-(N3-Adenine). Particularly encompassed means are DNA adducts or polynucleotides comprising the DNA adducts from the polynucleotides or polynucleotides pool, which can be released or removed by a process including heating the solution comprising the polynucleotides prior to further processing.

[0382] In another aspect the invention is directed to a method of producing recombinant proteins having biological activity by treating a sample comprising double-stranded template polynucleotides encoding a wild-type protein under conditions according to the invention which provide for the production of hybrid or re-assorted polynucleotides.

[0383] Producing Sequence Variants

[0384] The invention also provides additional methods for making sequence variants of the nucleic acid (e.g., cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme) sequences of the invention. The invention also provides additional methods for isolating cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes using the nucleic acids and polypeptides of the invention. In one aspect, the invention provides for variants of a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme coding sequence (e.g., a gene, cDNA or message) of the invention, which can be altered by any means, including, e.g., random or stochastic methods, or, non-stochastic, or "directed evolution," methods, as described above.

[0385] The isolated variants may be naturally occurring. Variant can also be created in vitro. Variants may be created using genetic engineering techniques such as site directed mutagenesis, random chemical mutagenesis, Exonuclease III deletion procedures, and standard cloning techniques. Alternatively, such variants, fragments, analogs, or derivatives may be created using chemical synthesis or modification procedures. Other methods of making variants are also familiar to those skilled in the art. These include procedures in which nucleic acid sequences obtained from natural isolates are modified to generate nucleic acids which encode polypeptides having characteristics which enhance their value in industrial or laboratory applications. In such procedures, a large number of variant sequences having one or more nucleotide differences with respect to the sequence obtained from the natural isolate are generated and characterized. These nucleotide differences can result in amino acid changes with respect to the polypeptides encoded by the nucleic acids from the natural isolates.

[0386] For example, variants may be created using error prone PCR. In one aspect of error prone PCR, the PCR is performed under conditions where the copying fidelity of the DNA polymerase is low, such that a high rate of point mutations is obtained along the entire length of the PCR product. Error prone PCR is described, e.g., in Leung (1989) Technique 1:11-15) and Caldwell (1992) PCR Methods Applic. 2:28-33. Briefly, in such procedures, nucleic acids to be mutagenized are mixed with PCR primers, reaction buffer, MgCl₂, MnCl₂, Taq polymerase and an appropriate concentration of dNTPs for achieving a high rate of point mutation along the entire length of the PCR product. For example, the reaction may be performed using 20 (moles of nucleic acid to be mutagenized, 30 pmole of each PCR primer, a reaction buffer comprising 50 mM KCl, 10 mM Tris HCl (pH 8.3) and 0.01% gelatin, 7 mM MgCl₂, 0.5 mM MnCl₂, 5 units of Taq polymerase, 0.2 mM dGTP, 0.2 mM dATP, 1 mM dCTP, and 1 mM dTTP. PCR may be performed for 30 cycles of 94° C. for 1 min, 45° C. for 1 min, and 72° C. for 1 min. However, it will be appreciated that these parameters may be varied as appropriate. The mutagenized nucleic acids are cloned into an appropriate vector and the activities of the polypeptides encoded by the mutagenized nucleic acids are evaluated.

[0387] In one aspect, variants are created using oligonucleotide directed mutagenesis to generate site-specific mutations in any cloned DNA of interest. Oligonucleotide mutagenesis is described, e.g., in Reidhaar-Olson (1988) Science 241:53-57. Briefly, in such procedures a plurality of double stranded oligonucleotides bearing one or more mutations to be introduced into the cloned DNA are synthesized and inserted into the cloned DNA to be mutagenized. In one aspect, clones containing the mutagenized DNA are recovered, expressed, and the activities of the polypeptide encoded therein assessed.

[0388] Another method for generating variants is assembly PCR. Assembly PCR involves the assembly of a PCR product from a mixture of small DNA fragments. A large number of different PCR reactions occur in parallel in the same vial, with the products of one reaction priming the products of another reaction. Assembly PCR is described in, e.g., U.S. Pat. No. 5,965,408.

[0389] In one aspect, sexual PCR mutagenesis is an exemplary method of generating variants of the invention. In one aspect of sexual PCR mutagenesis forced homologous recombination occurs between DNA molecules of different but highly related DNA sequence in vitro, as a result of random fragmentation of the DNA molecule based on sequence homology, followed by fixation of the crossover by primer extension in a PCR reaction. Sexual PCR mutagenesis is described, e.g., in Stemmer (1994) Proc. Natl. Acad. Sci. USA 91:10747-10751. Briefly, in such procedures a plurality of nucleic acids to be recombined are digested with DNase to generate fragments having an average size of 50-200 nucleotides. Fragments of the desired average size are purified and resuspended in a PCR mixture. PCR is conducted under conditions which facilitate recombination between the nucleic acid fragments. For example, PCR may be performed by resuspending the purified fragments at a concentration of 10-30 ng/μl in a solution of 0.2 mM of each dNTP, 2.2 mM MgCl₂, 50 mM KCL, 10 mM Tris HCl, pH 9.0, and 0.1% Triton X-100. 2.5 units of Taq polymerase per 100:1 of reaction mixture is added and PCR is performed using the following regime: 94° C. for 60 seconds, 94° C. for 30 seconds, 50-55° C. for 30 seconds, 72° C. for 30 seconds (30-45 times) and 72° C. for 5 minutes. However, it will be appreciated that these parameters may be varied as appropriate. In some aspects, oligonucleotides may be included in the PCR reactions. In other aspects, the Klenow fragment of DNA polymerase I may be used in a first set of PCR reactions and Taq polymerase may be used in a subsequent set of PCR reactions. Recombinant sequences are isolated and the activities of the polypeptides they encode are assessed.

[0390] In one aspect, variants are created by in vivo mutagenesis. In some aspects, random mutations in a sequence of interest are generated by propagating the sequence of interest in a bacterial strain, such as an E. coli strain, which carries mutations in one or more of the DNA repair pathways. Such "mutator" strains have a higher random mutation rate than that of a wild-type parent. Propagating the DNA in one of these strains will eventually generate random mutations within the DNA. Mutator strains suitable for use for in vivo mutagenesis are described in PCT Publication No. WO 91/16427, published Oct. 31, 1991, entitled "Methods for Phenotype Creation from Multiple Gene Populations".

[0391] Variants may also be generated using cassette mutagenesis. In cassette mutagenesis a small region of a double stranded DNA molecule is replaced with a synthetic oligonucleotide "cassette" that differs from the native sequence. The oligonucleotide often contains completely and/or partially randomized native sequence.

[0392] Recursive ensemble mutagenesis may also be used to generate variants. Recursive ensemble mutagenesis is an algorithm for protein engineering (protein mutagenesis) developed to produce diverse populations of phenotypically related mutants whose members differ in amino acid sequence. This method uses a feedback mechanism to control successive rounds of combinatorial cassette mutagenesis. Recursive ensemble mutagenesis is described, e.g., in Arkin (1992) Proc. Natl. Acad. Sci. USA 89:7811-7815.

[0393] In some aspects, variants are created using exponential ensemble mutagenesis. Exponential ensemble mutagenesis is a process for generating combinatorial libraries with a high percentage of unique and functional mutants, wherein small groups of residues are randomized in parallel to identify, at each altered position, amino acids which lead to functional proteins. Exponential ensemble mutagenesis is described, e.g., in Delegrave (1993) Biotechnology Res. 11:1548-1552. Random and site-directed mutagenesis are described, e.g., in Arnold (1993) Current Opinion in Biotechnology 4:450-455.

[0394] In some aspects, the variants are created using shuffling procedures wherein portions of a plurality of nucleic acids which encode distinct polypeptides are fused together to create chimeric nucleic acid sequences which encode chimeric polypeptides as described in U.S. Pat. No. 5,965,408, filed Jul. 9, 1996, entitled, "Method of DNA Reassembly by Interrupting Synthesis" and U.S. Pat. No. 5,939,250, filed May 22, 1996, entitled, "Production of Enzymes Having Desired Activities by Mutagenesis.

[0395] The variants of the polypeptides of the invention may be variants in which one or more of the amino acid residues of the polypeptides of the sequences of the invention are substituted with a conserved or non-conserved amino acid residue (in one aspect a conserved amino acid residue) and such substituted amino acid residue may or may not be one encoded by the genetic code.

[0396] In one aspect, conservative substitutions are those that substitute a given amino acid in a polypeptide by another amino acid of like characteristics. In one aspect, conservative substitutions of the invention comprise the following replacements: replacements of an aliphatic amino acid such as Alanine, Valine, Leucine and Isoleucine with another aliphatic amino acid; replacement of a Serine with a Threonine or vice versa; replacement of an acidic residue such as Aspartic acid and Glutamic acid with another acidic residue; replacement of a residue bearing an amide group, such as Asparagine and Glutamine, with another residue bearing an amide group; exchange of a basic residue such as Lysine and Arginine with another basic residue; and replacement of an aromatic residue such as Phenylalanine, Tyrosine with another aromatic residue.

[0397] Other variants are those in which one or more of the amino acid residues of a polypeptide of the invention includes a substituent group. In one aspect, other variants are those in which the polypeptide is associated with another compound, such as a compound to increase the half-life of the polypeptide (for example, polyethylene glycol). Additional variants are those in which additional amino acids are fused to the polypeptide, such as a leader sequence, a secretory sequence, a proprotein sequence or a sequence which facilitates purification, enrichment, or stabilization of the polypeptide.

[0398] In some aspects, the fragments, derivatives and analogs retain the same biological function or activity as the polypeptides of the invention. In other aspects, the fragment, derivative, or analog includes a proprotein, such that the fragment, derivative, or analog can be activated by cleavage of the proprotein portion to produce an active polypeptide.

[0399] Optimizing Codons to Achieve High Levels of Protein Expression in Host Cells

[0400] The invention provides methods for modifying cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase, enzyme-encoding nucleic acids to modify (e.g., optimize) codon usage. In one aspect, the invention provides methods for modifying codons in a nucleic acid encoding a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme to increase or decrease its expression in a host cell. The invention also provides nucleic acids encoding a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme modified to increase its expression in a host cell, cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme so modified, and methods of making the modified cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes. The method comprises identifying a "non-preferred" or a "less preferred" codon in cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase, enzyme-encoding nucleic acid and replacing one or more of these non-preferred or less preferred codons with a "preferred codon" encoding the same amino acid as the replaced codon and at least one non-preferred or less preferred codon in the nucleic acid has been replaced by a preferred codon encoding the same amino acid. A preferred codon is a codon over-represented in coding sequences in genes in the host cell and a non-preferred or less preferred codon is a codon under-represented in coding sequences in genes in the host cell.

[0401] Host cells for expressing the nucleic acids, expression cassettes and vectors of the invention include bacteria, yeast, fungi, plant cells, insect cells and mammalian cells (see discussion, above). Thus, the invention provides methods for optimizing codon usage in all of these cells, codon-altered nucleic acids and polypeptides made by the codon-altered nucleic acids. Exemplary host cells include gram negative bacteria, such as Escherichia coli; gram positive bacteria, such as Streptomyces sp., Lactobacillus gasseri, Lactococcus lactis, Lactococcus cremoris, Bacillus subtilis, Bacillus cereus. Exemplary host cells also include eukaryotic organisms, e.g., various yeast, such as Saccharomyces sp., including Saccharomyces cerevisiae, Schizosaccharomyces pombe, Pichia pastoris, and Kluyveromyces lactis, Hansenula polymorpha, Aspergillus niger, and mammalian cells and cell lines and insect cells and cell lines. Thus, the invention also includes nucleic acids and polypeptides optimized for expression in these organisms and species.

[0402] For example, the codons of a nucleic acid encoding a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme isolated from a bacterial cell are modified such that the nucleic acid is optimally expressed in a bacterial cell different from the bacteria from which the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme was derived, a yeast, a fungi, a plant cell, an insect cell or a mammalian cell. Methods for optimizing codons are well known in the art, see, e.g., U.S. Pat. No. 5,795,737; Baca (2000) Int. J. Parasitol. 30:113-118; Hale (1998) Protein Expr. Purif. 12:185-188; Narum (2001) Infect. Immun. 69:7250-7253. See also Narum (2001) Infect. Immun. 69:7250-7253, describing optimizing codons in mouse systems; Outchkourov (2002) Protein Expr. Purif. 24:18-24, describing optimizing codons in yeast; Feng (2000) Biochemistry 39:15399-15409, describing optimizing codons in E. coli; Humphreys (2000) Protein Expr. Purif. 20:252-264, describing optimizing codon usage that affects secretion in E. coli.

Transgenic Non-Human Animals

[0403] The invention provides transgenic non-human animals comprising a nucleic acid, a polypeptide (e.g., a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme), an expression cassette or vector or a transfected or transformed cell of the invention. The invention also provides methods of making and using these transgenic non-human animals.

[0404] The transgenic non-human animals can be, e.g., dogs, goats, rabbits, sheep, pigs (including all swine, hogs and related animals), cows, rats and mice, comprising the nucleic acids of the invention. These animals can be used, e.g., as in vivo models to study cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity, or, as models to screen for agents that change the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity in vivo. The coding sequences for the polypeptides to be expressed in the transgenic non-human animals can be designed to be constitutive, or, under the control of tissue-specific, developmental-specific or inducible transcriptional regulatory factors.

[0405] Transgenic non-human animals can be designed and generated using any method known in the art; see, e.g., U.S. Pat. Nos. 6,211,428; 6,187,992; 6,156,952; 6,118,044; 6,111,166; 6,107,541; 5,959,171; 5,922,854; 5,892,070; 5,880,327; 5,891,698; 5,639,940; 5,573,933; 5,387,742; 5,087,571, describing making and using transformed cells and eggs and transgenic mice, rats, rabbits, sheep, pigs and cows. See also, e.g., Pollock (1999) J. Immunol. Methods 231:147-157, describing the production of recombinant proteins in the milk of transgenic dairy animals; Baguisi (1999) Nat. Biotechnol. 17:456-461, demonstrating the production of transgenic goats. U.S. Pat. No. 6,211,428, describes making and using transgenic non-human mammals which express in their brains a nucleic acid construct comprising a DNA sequence. U.S. Pat. No. 5,387,742, describes injecting cloned recombinant or synthetic DNA sequences into fertilized mouse eggs, implanting the injected eggs in pseudo-pregnant females, and growing to term transgenic mice. U.S. Pat. No. 6,187,992, describes making and using a transgenic mouse.

[0406] "Knockout animals" can also be used to practice the methods of the invention. For example, in one aspect, the transgenic or modified animals of the invention comprise a "knockout animal," e.g., a "knockout mouse," engineered not to express an endogenous gene, which is replaced with a gene expressing a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme of the invention, or, a fusion protein comprising a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme of the invention.

Transgenic Plants and Seeds

[0407] The invention provides transgenic plants and seeds comprising a nucleic acid, a polypeptide (e.g., a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme), an expression cassette or vector or a transfected or transformed cell of the invention. The invention also provides plant products, e.g., oils, seeds, leaves, extracts and the like, comprising a nucleic acid and/or a polypeptide (e.g., a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme) of the invention. The transgenic plant can be dicotyledonous (a dicot) or monocotyledonous (a monocot). The invention also provides methods of making and using these transgenic plants and seeds. The transgenic plant or plant cell expressing a polypeptide of the present invention may be constructed in accordance with any method known in the art. See, for example, U.S. Pat. No. 6,309,872.

[0408] Nucleic acids and expression constructs of the invention can be introduced into a plant cell by any means. For example, nucleic acids or expression constructs can be introduced into the genome of a desired plant host, or, the nucleic acids or expression constructs can be episomes. Introduction into the genome of a desired plant can be such that the host's cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme production is regulated by endogenous transcriptional or translational control elements. The invention also provides "knockout plants" where insertion of gene sequence by, e.g., homologous recombination, has disrupted the expression of the endogenous gene. Means to generate "knockout" plants are well-known in the art, see, e.g., Strepp (1998) Proc Natl. Acad. Sci. USA 95:4368-4373; Miao (1995) Plant J 7:359-365. See discussion on transgenic plants, below.

[0409] The nucleic acids of the invention can be used to confer desired traits on essentially any plant, e.g., on starch-producing plants, such as potato, tomato, soybean, beets, corn, wheat, rice, barley, and the like. Nucleic acids of the invention can be used to manipulate metabolic pathways of a plant in order to optimize or alter host's expression of cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme. The can change cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity in a plant. Alternatively, a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme of the invention can be used in production of a transgenic plant to produce a compound not naturally produced by that plant. This can lower production costs or create a novel product.

[0410] In one aspect, the first step in production of a transgenic plant involves making an expression construct for expression in a plant cell. These techniques are well known in the art. They can include selecting and cloning a promoter, a coding sequence for facilitating efficient binding of ribosomes to mRNA and selecting the appropriate gene terminator sequences. One exemplary constitutive promoter is CaMV35S, from the cauliflower mosaic virus, which generally results in a high degree of expression in plants. Other promoters are more specific and respond to cues in the plant's internal or external environment. An exemplary light-inducible promoter is the promoter from the cab gene, encoding the major chlorophyll a/b binding protein.

[0411] In one aspect, the nucleic acid is modified to achieve greater expression in a plant cell. For example, a sequence of the invention is likely to have a higher percentage of A-T nucleotide pairs compared to that seen in a plant, some of which prefer G-C nucleotide pairs. Therefore, A-T nucleotides in the coding sequence can be substituted with G-C nucleotides without significantly changing the amino acid sequence to enhance production of the gene product in plant cells.

[0412] Selectable marker gene can be added to the gene construct in order to identify plant cells or tissues that have successfully integrated the transgene. This may be necessary because achieving incorporation and expression of genes in plant cells is a rare event, occurring in just a few percent of the targeted tissues or cells. Selectable marker genes encode proteins that provide resistance to agents that are normally toxic to plants, such as antibiotics or herbicides. Only plant cells that have integrated the selectable marker gene will survive when grown on a medium containing the appropriate antibiotic or herbicide. As for other inserted genes, marker genes also require promoter and termination sequences for proper function.

[0413] In one aspect, making transgenic plants or seeds comprises incorporating sequences of the invention and, optionally, marker genes into a target expression construct (e.g., a plasmid), along with positioning of the promoter and the terminator sequences. This can involve transferring the modified gene into the plant through a suitable method. For example, a construct may be introduced directly into the genomic DNA of the plant cell using techniques such as electroporation and microinjection of plant cell protoplasts, or the constructs can be introduced directly to plant tissue using ballistic methods, such as DNA particle bombardment. For example, see, e.g., Christou (1997) Plant Mol. Biol. 35:197-203; Pawlowski (1996) Mol. Biotechnol. 6:17-30; Klein (1987) Nature 327:70-73; Takumi (1997) Genes Genet. Syst. 72:63-69, discussing use of particle bombardment to introduce transgenes into wheat; and Adam (1997) supra, for use of particle bombardment to introduce YACs into plant cells. For example, Rinehart (1997) supra, used particle bombardment to generate transgenic cotton plants. Apparatus for accelerating particles is described U.S. Pat. No. 5,015,580; and, the commercially available BioRad (Biolistics) PDS-2000 particle acceleration instrument; see also, John, U.S. Pat. No. 5,608,148; and Ellis, U.S. Pat. No. 5,681,730, describing particle-mediated transformation of gymnosperms.

[0414] In one aspect, protoplasts can be immobilized and injected with a nucleic acids, e.g., an expression construct. Although plant regeneration from protoplasts is not easy with cereals, plant regeneration is possible in legumes using somatic embryogenesis from protoplast derived callus. Organized tissues can be transformed with naked DNA using gene gun technique, where DNA is coated on tungsten microprojectiles, shot 1/100th the size of cells, which carry the DNA deep into cells and organelles. Transformed tissue is then induced to regenerate, usually by somatic embryogenesis. This technique has been successful in several cereal species including maize and rice.

[0415] Nucleic acids, e.g., expression constructs, can also be introduced in to plant cells using recombinant viruses. Plant cells can be transformed using viral vectors, such as, e.g., tobacco mosaic virus derived vectors (Rouwendal (1997) Plant Mol. Biol. 33:989-999), see Porta (1996) "Use of viral replicons for the expression of genes in plants," Mol. Biotechnol. 5:209-221.

[0416] Alternatively, nucleic acids, e.g., an expression construct, can be combined with suitable T-DNA flanking regions and introduced into a conventional Agrobacterium tumefaciens host vector. The virulence functions of the Agrobacterium tumefaciens host will direct the insertion of the construct and adjacent marker into the plant cell DNA when the cell is infected by the bacteria. Agrobacterium tumefaciens-mediated transformation techniques, including disarming and use of binary vectors, are well described in the scientific literature. See, e.g., Horsch (1984) Science 233:496-498; Fraley (1983) Proc. Natl. Acad. Sci. USA 80:4803 (1983); Gene Transfer to Plants, Potrykus, ed. (Springer-Verlag, Berlin 1995). The DNA in an A. tumefaciens cell is contained in the bacterial chromosome as well as in another structure known as a Ti (tumor-inducing) plasmid. The Ti plasmid contains a stretch of DNA termed T-DNA (˜20 kb long) that is transferred to the plant cell in the infection process and a series of vir (virulence) genes that direct the infection process. A. tumefaciens can only infect a plant through wounds: when a plant root or stem is wounded it gives off certain chemical signals, in response to which, the vir genes of A. tumefaciens become activated and direct a series of events necessary for the transfer of the T-DNA from the Ti plasmid to the plant's chromosome. The T-DNA then enters the plant cell through the wound. One speculation is that the T-DNA waits until the plant DNA is being replicated or transcribed, then inserts itself into the exposed plant DNA. In order to use A. tumefaciens as a transgene vector, the tumor-inducing section of T-DNA have to be removed, while retaining the T-DNA border regions and the vir genes. The transgene is then inserted between the T-DNA border regions, where it is transferred to the plant cell and becomes integrated into the plant's chromosomes.

[0417] The invention provides for the transformation of monocotyledonous plants using the nucleic acids of the invention, including important cereals, see Hiei (1997) Plant Mol. Biol. 35:205-218. See also, e.g., Horsch, Science (1984) 233:496; Fraley (1983) Proc. Natl. Acad. Sci. USA 80:4803; Thykjaer (1997) supra; Park (1996) Plant Mol. Biol. 32:1135-1148, discussing T-DNA integration into genomic DNA. See also D'Halluin, U.S. Pat. No. 5,712,135, describing a process for the stable integration of a DNA comprising a gene that is functional in a cell of a cereal, or other monocotyledonous plant.

[0418] In one aspect, the third step involves selection and regeneration of whole plants capable of transmitting the incorporated target gene to the next generation. Such regeneration techniques may use manipulation of certain phytohormones in a tissue culture growth medium. In one aspect, the method uses a biocide and/or herbicide marker that has been introduced together with the desired nucleotide sequences. Plant regeneration from cultured protoplasts is described in Evans et al., Protoplasts Isolation and Culture, Handbook of Plant Cell Culture, pp. 124-176, MacMillilan Publishing Company, New York, 1983; and Binding, Regeneration of Plants, Plant Protoplasts, pp. 21-73, CRC Press, Boca Raton, 1985. Regeneration can also be obtained from plant callus, explants, organs, or parts thereof. Such regeneration techniques are described generally in Klee (1987) Ann. Rev. of Plant Phys. 38:467-486. To obtain whole plants from transgenic tissues such as immature embryos, they can be grown under controlled environmental conditions in a series of media containing nutrients and hormones, a process known as tissue culture. Once whole plants are generated and produce seed, evaluation of the progeny begins.

[0419] In one aspect, after the expression cassette is stably incorporated in transgenic plants, it can be introduced into other plants by sexual crossing. Any of a number of standard breeding techniques can be used, depending upon the species to be crossed. Since transgenic expression of the nucleic acids of the invention leads to phenotypic changes, plants comprising the recombinant nucleic acids of the invention can be sexually crossed with a second plant to obtain a final product. Thus, the seed of the invention can be derived from a cross between two transgenic plants of the invention, or a cross between a plant of the invention and another plant. The desired effects (e.g., expression of the polypeptides of the invention to produce a plant in which flowering behavior is altered) can be enhanced when both parental plants express the polypeptides (e.g., a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme) of the invention. The desired effects can be passed to future plant generations by standard propagation means.

[0420] In one aspect, the nucleic acids and polypeptides of the invention are expressed in or inserted in any plant or seed. Transgenic plants of the invention can be dicotyledonous or monocotyledonous. Examples of monocot transgenic plants of the invention are grasses, such as meadow grass (blue grass, Poa), forage grass such as festuca, lolium, temperate grass, such as Agrostis, and cereals, e.g., wheat, oats, rye, barley, rice, sorghum, and maize (corn). Examples of dicot transgenic plants of the invention are tobacco, legumes, such as lupins, potato, sugar beet, pea, bean and soybean, and cruciferous plants (family Brassicaceae), such as cauliflower, rape seed, and the closely related model organism Arabidopsis thaliana. Thus, the transgenic plants and seeds of the invention include a broad range of plants, including, but not limited to, species from the genera Anacardium, Arachis, Asparagus, Atropa, Avena, Brassica, Citrus, Citrullus, Capsicum, Carthamus, Cocos, Coffea, Cucumis, Cucurbita, Daucus, Elaeis, Fragaria, Glycine, Gossypium, Helianthus, Heterocallis, Hordeum, Hyoscyamus, Lactuca, Linum, Lolium, Lupinus, Lycopersicon, Malus, Manihot, Majorana, Medicago, Nicotiana, Olea, Oryza, Panieum, Pannisetum, Persea, Phaseolus, Pistachia, Pisum, Pyrus, Prunus, Raphanus, Ricinus, Secale, Senecio, Sinapis, Solanum, Sorghum, Theobromus, Trigonella, Triticum, Vicia, Vitis, Vigna, and Zea.

[0421] In alternative embodiments, the nucleic acids of the invention are expressed in plants which contain fiber cells, including, e.g., cotton, silk cotton tree (Kapok, Ceiba pentandra), desert willow, creosote bush, winterfat, balsa, ramie, kenaf, hemp, roselle, jute, sisal abaca and flax. In alternative embodiments, the transgenic plants of the invention can be members of the genus Gossypium, including members of any Gossypium species, such as G. arboreum; G. herbaceum, G. barbadense, and G. hirsutum.

[0422] The invention also provides for transgenic plants to be used for producing large amounts of the polypeptides (e.g., a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme or antibody) of the invention. For example, see Palmgren (1997) Trends Genet. 13:348; Chong (1997) Transgenic Res. 6:289-296 (producing human milk protein beta-casein in transgenic potato plants using an auxin-inducible, bidirectional mannopine synthase (mas1',2') promoter with Agrobacterium tumefaciens-mediated leaf disc transformation methods).

[0423] Using known procedures, one of skill can screen for plants of the invention by detecting the increase or decrease of transgene mRNA or protein in transgenic plants. Means for detecting and quantitation of mRNAs or proteins are well known in the art.

Polypeptides and Peptides

[0424] In one aspect, the invention provides isolated or recombinant polypeptides having a sequence identity (e.g., at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more, or complete (100%) sequence identity, or homology) to an exemplary sequence of the invention, e.g., proteins having a sequence as set forth 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 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:143, 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 or SEQ ID NO:166 (see also Tables 1, 2, and 3, Examples 1 and 4, below, and Sequence Listing)). The percent sequence identity can be over the full length of the polypeptide, or, the identity can be over a region of at least about 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700 or more residues.

[0425] Polypeptides of the invention can also be shorter than the full length of exemplary polypeptides. In alternative aspects, the invention provides polypeptides (peptides, fragments) ranging in size between about 5 and the full length of a polypeptide, e.g., an enzyme, such as a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme; exemplary sizes being of about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 100, 125, 150, 175, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, or more residues, e.g., contiguous residues of an exemplary cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme of the invention. Peptides of the invention (e.g., a subsequence of an exemplary polypeptide of the invention) can be useful as, e.g., labeling probes, antigens (immunogens), toleragens, motifs, cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme active sites (e.g., "catalytic domains"), signal sequences and/or prepro domains.

[0426] In alternative aspects, polypeptides of the invention having cellulase activity, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity are members of a genus of polypeptides sharing specific structural elements, e.g., amino acid residues, that correlate with cellulase activity, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity. These shared structural elements can be used for the routine generation of cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase variants. These shared structural elements of cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes of the invention can be used as guidance for the routine generation of cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes variants within the scope of the genus of polypeptides of the invention.

[0427] As used herein, the terms "cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase" encompass any polypeptide or enzymes capable of catalyzing the complete or partial breakdown and/or hydrolysis of cellulose (e.g., exemplary polypeptides of the invention, see also Tables 1, 2, and 3, Examples 1 and 4, below), or any modification of a cellulose or lignocellulotic material, e.g., a biomass material comprising lignocellulose.

[0428] In some aspects, a polypeptide of the invention can have an alternative enzymatic activity, for example, as set forth in Table 3, below. For example, the polypeptide having a sequence as set forth in SEQ ID NO:164, encoded, e.g., by SEQ ID NO:163, can have Alkaline endoglucanase/cellulase activity; the polypeptide having a sequence as set forth in SEQ ID NO:110, encoded, e.g., by SEQ ID NO:109, can have xylanase activity; the polypeptide having a sequence as set forth in SEQ ID NO:12, encoded, e.g., by SEQ ID NO:11, can have NAD binding oxidoreductase activity; the polypeptide having a sequence as set forth in SEQ ID NO:118, encoded, e.g., by SEQ ID NO:117, can have short chain dehydrogenase activity; the polypeptide having a sequence as set forth in SEQ ID NO:14, encoded, e.g., by SEQ ID NO:13, can have NADH dependent dehydrogenase activity; the polypeptide having a sequence as set forth in SEQ ID NO:138, encoded, e.g., by SEQ ID NO:137, can have peptidase activity; the polypeptide having a sequence as set forth in SEQ ID NO:162, encoded, e.g., by SEQ ID NO:161, can have Alkaline endoglucanase activity, in addition to cellulase activity; the polypeptide having a sequence as set forth in SEQ ID NO:42, encoded, e.g., by SEQ ID NO:41, can have cysteinyl tRNA synthetase activity; the polypeptide having a sequence as set forth in SEQ ID NO:32, encoded, e.g., by SEQ ID NO:31, can have cellodextrin phosphorylase activity; the polypeptide having a sequence as set forth in SEQ ID NO:50, encoded, e.g., by SEQ ID NO:49, can have fdhd/narq oxidoreductase activity; the polypeptide having a sequence as set forth in SEQ ID NO:54, encoded, e.g., by SEQ ID NO:53, can have a radical S-adenosylmethionine (SAM) activity; the polypeptide having a sequence as set forth in SEQ ID NO:58, encoded, e.g., by SEQ ID NO:57, can have a subtilisin like protease activity; etc., as set forth below:

TABLE-US-00001 TABLE 3 Signalp Cleavage EC SEQ ID NO: Enzymatic Activity Site Signal Sequence Source Number 163, 164 Alkaline endoglucanase/cellulase 1-30 MSCRTLMSRRVGWGLLLWGGLFL Unknown RTGSVTG 1, 2 ORF 001-family 1 (β-glucosidase) Unknown 3.2.1.21 101, 102 ORF 003-family 5 (cellulase) 1-29 MRNHLNVPFYFIFFFLIASIFTV Unknown 3.2.1.4 CSSSTA 103, 104 family 5 (cellulase) 1-20 MLIIGGLLVLLGFSSCGRQA Unknown 3.2.1.4 105, 106 family 5 (cellulase) Unknown 3.2.1.4 107, 108 family 5 (cellulase) 1-32 MEKQICSNVFSTMLIIGGLLVLL Unknown 3.2.1.4 GFSSCGRQA 109, 110 family 10 (xylanase) 1-28 MKTHSFNLRSRITLLTAALLFIG Unknown 3.2.1.8 ATAGA 11, 12 ORF 003-NAD binding Unknown 1.1.1.18 oxidoreductase 111, 112 family 5 (cellulase) 1-22 MRRLITIILATAVAILSTTSCS Unknown 3.2.1.4 113, 114 ORF 003-family 10 1-27 MKVTRTAVAGIVAAAVLITIGT Unknown 3.2.1.8 STASA 115, 116 ORF 004-short chain dehydrogenase Unknown 1.1.1.100 117, 118 ORF 011-short chain dehydrogenase 1-19 MPKVMLVTGGSRGIGAAVA Unknown 1 . . . 119, 120 ORF 002-oxidoreductase Unknown 1.4.3.16 121, 122 ORF 004-family 5 (cellulase) Unknown 3.2.1.4 123, 124 ORF 006-family 1 (β-glucosidase) Unknown 3.2.1.21 125, 126 ORF 009-family 1 (β-glucosidase) Unknown 3.2.1.21 127, 128 ORF 004-short chain dehydrogenase Unknown 1.1.1.100 129, 130 ORF 010-short chain dehydrogenase 1-19 MPKVMLVTGGSRGIGAAVA Unknown 1 . . . 13, 14 ORF 005-NADH dependent Unknown 1.1.1.18 dehydrogenase 131, 132 ORF 007-family 5 (cellulase) Unknown 3.2.1.4 133, 134 ORF 006-family 1 (β-glucosidase) Unknown 3.2.1.21 135, 136 ORF 001-cellulase (glycosyl Unknown 3.2.1.4 hydrolase family 5) 137, 138 ORF 001-peptidase_M37 Unknown 3.5.1. 139, 140 ORF 001-threonine dehydrogenase Unknown 1 . . . 141, 142 ORF 005-family 1 (β-glucosidase) Unknown 3.2.1.21 143, 144 ORF 003-family 1 (β-glucosidase) Unknown 3.2.1.21 145, 146 ORF 002-family 1 (β-glucosidase) Unknown 3.2.1.21 147, 148 family 10 (xylanase) 1-26 MLKVLRKPIISGLALALLLPAGA Unknown 3.2.1.8 AGA 149, 150 family 5 (cellulase) Unknown 3.2.1.4 15, 16 ORF-007-family 1 (β-glucosidase) Unknown 3.2.1.21 151, 152 family 5 (cellulase) Unknown 3.2.1.4 153, 154 family 5 (cellulase) Unknown 3.2.1.4 155, 156 family 5 (cellulase) Unknown 3.2.1.4 157, 158 family 5 (cellulase) Unknown 3.2.1.4 159, 160 family 10 (xylanase) Unknown 3.2.1.8 161, 162 Alkaline endoglucanase/cellulase 1-30 MSCRTLMSRRVGWGLLLWGGLFL Unknown RTGSVTG 165, 166 xylanase 17, 18 ORF 005-β-lactamase 1-23 MRYVLISCLALASLCAQPLPVST Unknown 3.5.2.6 19, 20 ORF 008-family 10 (xylanase) 1-20 MPVLFALFLVASSCAAQSLA Unknown 3.2.1.8 21, 22 ORF 001-family 5 (cellulase) Clostridium 3.2.1.4 thermocellum 23, 24 ORF 003-Family 16 + CBM 1-26 MYKRLLSSVLIIMLLLSAWSPIS Clostridium 3.2.1. VQA thermocellum 25, 26 ORF 001-family 1 (β-glucosidase) Clostridium 3.2.1.21 thermocellum 27, 28 ORF 002-family 1 (β-glucosidase) Unknown 3.2.1.21 29, 30 ORF 004-family 1 (β-glucosidase) Unknown 3.2.1.21 3, 4 ORF 008-family 1 (β-glucosidase) Unknown 3.2.1.21 31, 32 ORF 002-cellodextrin Unknown 2.4.1.20 phosphorylase 33, 34 ORF 006-family 1 (β-glucosidase) Unknown 3.2.1.21 35, 36 ORF 007-family 5 (cellulase) 1-23 MNKILKLFSSLLLFAGICPALQA Unknown 3.2.1.4 37, 38 ORF 011-family 1 (β-glucosidase) Unknown 3.2.1.21 39, 40 ORF 004-putative oxidoreductase Unknown 4.1.1. 41, 42 ORF 004-cysteinyl tRNA synthetase Unknown 6.1.1.16 43, 44 ORF 011- Unknown 45, 46 ORF 006-family 1 (β-glucosidase) Unknown 3.2.1.21 47, 48 ORF 002-family 1 (β-glucosidase) Unknown 3.2.1.21 49, 50 ORF 006-fdhd/narq oxidoreductase Unknown 5, 6 ORF 012-family 6 (cellulase) 1-29 MTRRSIVRSSSNKWLVLAGAALL Unknown 3.2.1.91 ACTALG 51, 52 ORF 001-family 5 (cellulase) 1-20 MSRGILILVMLSVLSGAALA Unknown 3.2.1.4 53, 54 ORF 002-Radical SAM family Unknown 1 . . . 55, 56 ORF 004-family 1 (β-glucosidase) Unknown 3.2.1.21 57, 58 ORF 001-subtilisin like protease Unknown 59, 60 family 5 (cellulase) Unknown 3.2.1.4 61, 62 family 5 (cellulase) ORF 1 1-52 MVWTPARSTLAGSSEIPLMTMNI Unknown 3.2.1.4 FPNRKDSRMSLWIKLGILCMMAG TVMVHG 63, 64 family 5 (cellulase) ORF 4 1-24 MKRREFMLGGAGVAALASTLGVS Unknown 3.2.1.4 A 65, 66 family 10 (xylanase) 1-39 MNTLLPRRRLWSSTAILRTLAAG Unknown 3.2.1.8 ALAAGMVLAPVSAANA 67, 68 family 5 (cellulase)-ORF 2 1-23 MKYIFSYIIMMILIGFIPVYGFG Unknown 3.2.1.4 69, 70 family 26 (mannanase)-ORF4 1-20 MSFKNHILLSLLIVLLFFSA Unknown 3.2.1.78 7, 8 ORF 003-Isocitrate dehydrogenase Unknown 1.1.1.42 71, 72 family 5 (cellulase) 1-21 MKLLKLLIFLLITVIFSDVSA Unknown 3.2.1.4 73, 74 family 10 (xylanase) Unknown 3.2.1.21 75, 76 family 5 (cellulase) 1-21 MLRKLIVSVFGFVMLTSAAAA Unknown 3.2.1.4 77, 78 family 5 (cellulase) 1-28 MKRKRVFIHSLIVFFLMIGSFTS Unknown 3.2.1.4 CGSVA 79, 80 family 5 (cellulase) 1-25 MKYKAIFIYLIVLILFYSINIYA Unknown 3.2.1.4 NA 81, 82 family 5 (cellulase) 1-25 MNLLAQYFSGLFLIFLISIFFVS Unknown 3.2.1.4 SA 83, 84 ORF 008-dehydrogenase Unknown 3.5.4.25 85, 86 ORF 008-family 1 (β-glucosidase) Unknown 3.2.1.21 87, 88 family 5 (cellulase) 1-23 MRKSVFTLAVFLSALFAFTSCQN Unknown 3.2.1.4 89, 90 family 5 (cellulase) 1-29 MKRSVSIFIACLLMTVLTISGVA Unknown 3.2.1.4 APEASA 9, 10 ORF 004-family 10 (xylanase) 1-26 MRSVRIVTFALAAALAVPLVTST Unknown 3.2.1.8 ATA 91, 92 ORF 001-family 3 Unknown 3.2.1.52 93, 94 ORF 002-alpha-rhamnosidase Unknown 95, 96 ORF 001-family 3 Unknown 3.2.1.21 97, 98 ORF 003-beta-glucuronidase Unknown 3.2.1.31 99, 100 ORF 012-family 1 (β-glucosidase) Unknown 3.2.1.21

[0429] "Amino acid" or "amino acid sequence" as used herein refer to an oligopeptide, peptide, polypeptide, or protein sequence, or to a fragment, portion, or subunit of any of these and to naturally occurring or synthetic molecules. "Amino acid" or "amino acid sequence" include an oligopeptide, peptide, polypeptide, or protein sequence, or to a fragment, portion, or subunit of any of these, and to naturally occurring or synthetic molecules. The term "polypeptide" as used herein, refers to amino acids joined to each other by peptide bonds or modified peptide bonds, i.e., peptide isosteres and may contain modified amino acids other than the 20 gene-encoded amino acids. The polypeptides may be modified by either natural processes, such as post-translational processing, or by chemical modification techniques which are well known in the art. Modifications can occur anywhere in the polypeptide, including the peptide backbone, the amino acid side-chains and the amino or carboxyl termini. It will be appreciated that the same type of modification may be present in the same or varying degrees at several sites in a given polypeptide. Also a given polypeptide may have many types of modifications. Modifications include acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of a phosphatidylinositol, cross-linking cyclization, disulfide bond formation, demethylation, formation of covalent cross-links, formation of cysteine, formation of pyroglutamate, formylation, gamma-carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristolyation, oxidation, pegylation, glucan hydrolase processing, phosphorylation, prenylation, racemization, selenoylation, sulfation and transfer-RNA mediated addition of amino acids to protein such as arginylation. (See Creighton, T. E., Proteins--Structure and Molecular Properties 2nd Ed., W.H. Freeman and Company, New York (1993); Posttranslational Covalent Modification of Proteins, B. C. Johnson, Ed., Academic Press, New York, pp. 1-12 (1983)). The peptides and polypeptides of the invention also include all "mimetic" and "peptidomimetic" forms, as described in further detail, below.

[0430] As used herein, the term "isolated" means that the material (e.g., a protein or nucleic acid of the invention) is removed from its original environment (e.g., the natural environment if it is naturally occurring). For example, a naturally-occurring polynucleotide or polypeptide present in a living animal is not isolated, but the same polynucleotide or polypeptide, separated from some or all of the coexisting materials in the natural system, is isolated. Such polynucleotides could be part of a vector and/or such polynucleotides or polypeptides could be part of a composition and still be isolated in that such vector or composition is not part of its natural environment. As used herein, the term "purified" does not require absolute purity; rather, it is intended as a relative definition. Individual nucleic acids obtained from a library have been conventionally purified to electrophoretic homogeneity. The sequences obtained from these clones could not be obtained directly either from the library or from total human DNA. The purified nucleic acids of the invention have been purified from the remainder of the genomic DNA in the organism by at least 10⁴-10⁶ fold. In one aspect, the term "purified" includes nucleic acids which have been purified from the remainder of the genomic DNA or from other sequences in a library or other environment by at least one order of magnitude, e.g., in one aspect, two or three orders, or, four or five orders of magnitude.

[0431] "Recombinant" polypeptides or proteins refer to polypeptides or proteins produced by recombinant DNA techniques; i.e., produced from cells transformed by an exogenous DNA construct encoding the desired polypeptide or protein. "Synthetic" polypeptides or protein are those prepared by chemical synthesis. Solid-phase chemical peptide synthesis methods can also be used to synthesize the polypeptide or fragments of the invention. Such method have been known in the art since the early 1960's (Merrifield, R. B., J. Am. Chem. Soc., 85:2149-2154, 1963) (See also Stewart, J. M. and Young, J. D., Solid Phase Peptide Synthesis, 2nd Ed., Pierce Chemical Co., Rockford, Ill., pp. 11-12)) and have recently been employed in commercially available laboratory peptide design and synthesis kits (Cambridge Research Biochemicals). Such commercially available laboratory kits have generally utilized the teachings of H. M. Geysen et al, Proc. Natl. Acad. Sci., USA, 81:3998 (1984) and provide for synthesizing peptides upon the tips of a multitude of "rods" or "pins" all of which are connected to a single plate.

[0432] The phrase "substantially identical" in the context of two nucleic acids or polypeptides, refers to two or more sequences that have, e.g., at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more nucleotide or amino acid residue (sequence) identity, when compared and aligned for maximum correspondence, as measured using one of the known sequence comparison algorithms or by visual inspection. In alternative aspects, the substantial identity exists over a region of at least about 100 or more residues and most commonly the sequences are substantially identical over at least about 150 to 200 or more residues. In some aspects, the sequences are substantially identical over the entire length of the coding regions.

[0433] Additionally a "substantially identical" amino acid sequence is a sequence that differs from a reference sequence by one or more conservative or non-conservative amino acid substitutions, deletions, or insertions. In one aspect, the substitution occurs at a site that is not the active site of the molecule, or, alternatively the substitution occurs at a site that is the active site of the molecule, provided that the polypeptide essentially retains its functional (enzymatic) properties. A conservative amino acid substitution, for example, substitutes one amino acid for another of the same class (e.g., substitution of one hydrophobic amino acid, such as isoleucine, valine, leucine, or methionine, for another, or substitution of one polar amino acid for another, such as substitution of arginine for lysine, glutamic acid for aspartic acid or glutamine for asparagine). One or more amino acids can be deleted, for example, from a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase polypeptide, resulting in modification of the structure of the polypeptide, without significantly altering its biological activity. For example, amino- or carboxyl-terminal amino acids that are not required for cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme biological activity can be removed. Modified polypeptide sequences of the invention can be assayed for cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme biological activity by any number of methods, including contacting the modified polypeptide sequence with a substrate and determining whether the modified polypeptide decreases the amount of specific substrate in the assay or increases the bioproducts of the enzymatic reaction of a functional cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase polypeptide with the substrate.

[0434] "Fragments" as used herein are a portion of a naturally occurring protein which can exist in at least two different conformations. Fragments can have the same or substantially the same amino acid sequence as the naturally occurring protein. Fragments which have different three dimensional structures as the naturally occurring protein are also included. An example of this, is a "pro-form" molecule, such as a low activity proprotein that can be modified by cleavage to produce a mature enzyme with significantly higher activity.

[0435] In one aspect, the invention provides crystal (three-dimensional) structures of proteins and peptides, e.g., cellulases, of the invention; which can be made and analyzed using the routine protocols well known in the art, e.g., as described in MacKenzie (1998) Crystal structure of the family 7 endoglucanase I (Cel7B) from Humicola insolens at 2.2 A resolution and identification of the catalytic nucleophile by trapping of the covalent glycosyl-enzyme intermediate, Biochem. J. 335:409-416; Sakon (1997) Structure and mechanism of endo/exocellulase E4 from Thermomonospora fusca, Nat. Struct. Biol 4:810-818; Varrot (1999) Crystal structure of the catalytic core domain of the family 6 cellobiohydrolase II, Cel6A, from Humicola insolens, at 1.92 A resolution, Biochem. J. 337:297-304; illustrating and identifying specific structural elements as guidance for the routine generation of cellulase variants of the invention, and as guidance for identifying enzyme species within the scope of the invention.

[0436] Polypeptides and peptides of the invention can be isolated from natural sources, be synthetic, or be recombinantly generated polypeptides. Peptides and proteins can be recombinantly expressed in vitro or in vivo. The peptides and polypeptides of the invention can be made and isolated using any method known in the art. Polypeptide and peptides of the invention can also be synthesized, whole or in part, using chemical methods well known in the art. See e.g., Caruthers (1980) Nucleic Acids Res. Symp. Ser. 215-223; Horn (1980) Nucleic Acids Res. Symp. Ser. 225-232; Banga, A. K., Therapeutic Peptides and Proteins, Formulation, Processing and Delivery Systems (1995) Technomic Publishing Co., Lancaster, Pa. For example, peptide synthesis can be performed using various solid-phase techniques (see e.g., Roberge (1995) Science 269:202; Merrifield (1997) Methods Enzymol. 289:3-13) and automated synthesis may be achieved, e.g., using the ABI 431A Peptide Synthesizer (Perkin Elmer) in accordance with the instructions provided by the manufacturer.

[0437] The peptides and polypeptides of the invention can also be glycosylated. The glycosylation can be added post-translationally either chemically or by cellular biosynthetic mechanisms, wherein the later incorporates the use of known glycosylation motifs, which can be native to the sequence or can be added as a peptide or added in the nucleic acid coding sequence. The glycosylation can be O-linked or N-linked.

[0438] The peptides and polypeptides of the invention, as defined above, include all "mimetic" and "peptidomimetic" forms. The terms "mimetic" and "peptidomimetic" refer to a synthetic chemical compound which has substantially the same structural and/or functional characteristics of the polypeptides of the invention. The mimetic can be either entirely composed of synthetic, non-natural analogues of amino acids, or, is a chimeric molecule of partly natural peptide amino acids and partly non-natural analogs of amino acids. The mimetic can also incorporate any amount of natural amino acid conservative substitutions as long as such substitutions also do not substantially alter the mimetic's structure and/or activity. As with polypeptides of the invention which are conservative variants or members of a genus of polypeptides of the invention (e.g., having about 50% or more sequence identity to an exemplary sequence of the invention), routine experimentation will determine whether a mimetic is within the scope of the invention, i.e., that its structure and/or function is not substantially altered. Thus, in one aspect, a mimetic composition is within the scope of the invention if it has a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes activity.

[0439] Polypeptide mimetic compositions of the invention can contain any combination of non-natural structural components. In alternative aspect, mimetic compositions of the invention include one or all of the following three structural groups: a) residue linkage groups other than the natural amide bond ("peptide bond") linkages; b) non-natural residues in place of naturally occurring amino acid residues; or c) residues which induce secondary structural mimicry, i.e., to induce or stabilize a secondary structure, e.g., a beta turn, gamma turn, beta sheet, alpha helix conformation, and the like. For example, a polypeptide of the invention can be characterized as a mimetic when all or some of its residues are joined by chemical means other than natural peptide bonds. Individual peptidomimetic residues can be joined by peptide bonds, other chemical bonds or coupling means, such as, e.g., glutaraldehyde, N-hydroxysuccinimide esters, bifunctional maleimides, N,N'-dicyclohexylcarbodiimide (DCC) or N,N'-diisopropylcarbodiimide (DIC). Linking groups that can be an alternative to the traditional amide bond ("peptide bond") linkages include, e.g., ketomethylene (e.g., --C(═O)--CH₂-- for --C(═O)--NH--), aminomethylene (CH₂--NH), ethylene, olefin (CH═CH), ether (CH₂--O), thioether (CH₂--S), tetrazole (CN₄--), thiazole, retroamide, thioamide, or ester (see, e.g., Spatola (1983) in Chemistry and Biochemistry of Amino Acids, Peptides and Proteins, Vol. 7, pp 267-357, "Peptide Backbone Modifications," Marcell Dekker, N.Y.).

[0440] A polypeptide of the invention can also be characterized as a mimetic by containing all or some non-natural residues in place of naturally occurring amino acid residues. Non-natural residues are well described in the scientific and patent literature; a few exemplary non-natural compositions useful as mimetics of natural amino acid residues and guidelines are described below. Mimetics of aromatic amino acids can be generated by replacing by, e.g., D- or L-naphylalanine; D- or L-phenylglycine; D- or L-2 thieneylalanine; D- or L-1, -2, 3-, or 4-pyreneylalanine; D- or L-3 thieneylalanine; D- or L-(2-pyridinyl)-alanine; D- or L-(3-pyridinyl)-alanine; D- or L-(2-pyrazinyl)-alanine; D- or L-(4-isopropyl)-phenylglycine; D-(trifluoromethyl)-phenylglycine; D-(trifluoromethyl)-phenylalanine; D-p-fluoro-phenylalanine; D- or L-p-biphenylphenylalanine; D- or L-p-methoxy-biphenylphenylalanine; D- or L-2-indole(alkyl)alanines; and, D- or L-alkylainines, where alkyl can be substituted or unsubstituted methyl, ethyl, propyl, hexyl, butyl, pentyl, isopropyl, iso-butyl, sec-isotyl, iso-pentyl, or a non-acidic amino acids. Aromatic rings of a non-natural amino acid include, e.g., thiazolyl, thiophenyl, pyrazolyl, benzimidazolyl, naphthyl, furanyl, pyrrolyl, and pyridyl aromatic rings.

[0441] Mimetics of acidic amino acids can be generated by substitution by, e.g., non-carboxylate amino acids while maintaining a negative charge; (phosphono)alanine; sulfated threonine. Carboxyl side groups (e.g., aspartyl or glutamyl) can also be selectively modified by reaction with carbodiimides (R'--N--C--N--R') such as, e.g., 1-cyclohexyl-3(2-morpholinyl-(4-ethyl) carbodiimide or 1-ethyl-3(4-azonia-4,4-dimetholpentyl) carbodiimide. Aspartyl or glutamyl can also be converted to asparaginyl and glutaminyl residues by reaction with ammonium ions. Mimetics of basic amino acids can be generated by substitution with, e.g., (in addition to lysine and arginine) the amino acids ornithine, citrulline, or (guanidino)-acetic acid, or (guanidino)alkyl-acetic acid, where alkyl is defined above. Nitrile derivative (e.g., containing the CN-moiety in place of COOH) can be substituted for asparagine or glutamine. Asparaginyl and glutaminyl residues can be deaminated to the corresponding aspartyl or glutamyl residues. Arginine residue mimetics can be generated by reacting arginyl with, e.g., one or more conventional reagents, including, e.g., phenylglyoxal, 2,3-butanedione, 1,2-cyclo-hexanedione, or ninhydrin, in one aspect under alkaline conditions. Tyrosine residue mimetics can be generated by reacting tyrosyl with, e.g., aromatic diazonium compounds or tetranitromethane. N-acetylimidizol and tetranitromethane can be used to form O-acetyl tyrosyl species and 3-nitro derivatives, respectively. Cysteine residue mimetics can be generated by reacting cysteinyl residues with, e.g., alpha-haloacetates such as 2-chloroacetic acid or chloroacetamide and corresponding amines; to give carboxymethyl or carboxyamidomethyl derivatives. Cysteine residue mimetics can also be generated by reacting cysteinyl residues with, e.g., bromo-trifluoroacetone, alpha-bromo-beta-(5-imidozoyl) propionic acid; chloroacetyl phosphate, N-alkylmaleimides, 3-nitro-2-pyridyl disulfide; methyl 2-pyridyl disulfide; p-chloromercuribenzoate; 2-chloromercuri-4 nitrophenol; or, chloro-7-nitrobenzo-oxa-1,3-diazole. Lysine mimetics can be generated (and amino terminal residues can be altered) by reacting lysinyl with, e.g., succinic or other carboxylic acid anhydrides. Lysine and other alpha-amino-containing residue mimetics can also be generated by reaction with imidoesters, such as methyl picolinimidate, pyridoxal phosphate, pyridoxal, chloroborohydride, trinitro-benzenesulfonic acid, O-methylisourea, 2,4, pentanedione, and transamidase-catalyzed reactions with glyoxylate. Mimetics of methionine can be generated by reaction with, e.g., methionine sulfoxide. Mimetics of proline include, e.g., pipecolic acid, thiazolidine carboxylic acid, 3- or 4-hydroxy proline, dehydroproline, 3- or 4-methylproline, or 3,3,-dimethylproline. Histidine residue mimetics can be generated by reacting histidyl with, e.g., diethylprocarbonate or para-bromophenacyl bromide. Other mimetics include, e.g., those generated by hydroxylation of proline and lysine; phosphorylation of the hydroxyl groups of seryl or threonyl residues; methylation of the alpha-amino groups of lysine, arginine and histidine; acetylation of the N-terminal amine; methylation of main chain amide residues or substitution with N-methyl amino acids; or amidation of C-terminal carboxyl groups.

[0442] In one aspect, a residue, e.g., an amino acid, of a polypeptide of the invention can also be replaced by an amino acid (or peptidomimetic residue) of the opposite chirality. In one aspect, any amino acid naturally occurring in the L-configuration (which can also be referred to as the R or S, depending upon the structure of the chemical entity) can be replaced with the amino acid of the same chemical structural type or a peptidomimetic, but of the opposite chirality, referred to as the D-amino acid, but also can be referred to as the R- or S-form.

[0443] The invention also provides methods for modifying the polypeptides of the invention by either natural processes, such as post-translational processing (e.g., phosphorylation, acylation, etc), or by chemical modification techniques, and the resulting modified polypeptides. Modifications can occur anywhere in the polypeptide, including the peptide backbone, the amino acid side-chains and the amino or carboxyl termini. It will be appreciated that the same type of modification may be present in the same or varying degrees at several sites in a given polypeptide. Also a given polypeptide may have many types of modifications. In one aspect, modifications include acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of a phosphatidylinositol, cross-linking cyclization, disulfide bond formation, demethylation, formation of covalent cross-links, formation of cysteine, formation of pyroglutamate, formylation, gamma-carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristolyation, oxidation, pegylation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, and transfer-RNA mediated addition of amino acids to protein such as arginylation. See, e.g., Creighton, T. E., Proteins--Structure and Molecular Properties 2nd Ed., W.H. Freeman and Company, New York (1993); Posttranslational Covalent Modification of Proteins, B. C. Johnson, Ed., Academic Press, New York, pp. 1-12 (1983).

[0444] Solid-phase chemical peptide synthesis methods can also be used to synthesize the polypeptide or fragments of the invention. Such method have been known in the art since the early 1960's (Merrifield, R. B., J. Am. Chem. Soc., 85:2149-2154, 1963) (See also Stewart, J. M. and Young, J. D., Solid Phase Peptide Synthesis, 2nd Ed., Pierce Chemical Co., Rockford, Ill., pp. 11-12)) and have recently been employed in commercially available laboratory peptide design and synthesis kits (Cambridge Research Biochemicals). Such commercially available laboratory kits have generally utilized the teachings of H. M. Geysen et al, Proc. Natl. Acad. Sci., USA, 81:3998 (1984) and provide for synthesizing peptides upon the tips of a multitude of "rods" or "pins" all of which are connected to a single plate. When such a system is utilized, a plate of rods or pins is inverted and inserted into a second plate of corresponding wells or reservoirs, which contain solutions for attaching or anchoring an appropriate amino acid to the pin's or rod's tips. By repeating such a process step, i.e., inverting and inserting the rod's and pin's tips into appropriate solutions, amino acids are built into desired peptides. In addition, a number of available FMOC peptide synthesis systems are available. For example, assembly of a polypeptide or fragment can be carried out on a solid support using an Applied Biosystems, Inc. Model 431A® automated peptide synthesizer. Such equipment provides ready access to the peptides of the invention, either by direct synthesis or by synthesis of a series of fragments that can be coupled using other known techniques.

[0445] The polypeptides of the invention include cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes in an active or inactive form. For example, the polypeptides of the invention include proproteins before "maturation" or processing of prepro sequences, e.g., by a proprotein-processing enzyme, such as a proprotein convertase to generate an "active" mature protein. The polypeptides of the invention include cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes inactive for other reasons, e.g., before "activation" by a post-translational processing event, e.g., an endo- or exo-peptidase or proteinase action, a phosphorylation event, an amidation, a glycosylation or a sulfation, a dimerization event, and the like. The polypeptides of the invention include all active forms, including active subsequences, e.g., catalytic domains or active sites, of the enzyme.

[0446] The invention includes immobilized cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes, anti-cellulase, e.g., anti-endoglucanase, anti-cellobiohydrolase and/or anti-beta-glucosidase antibodies and fragments thereof. The invention provides methods for inhibiting cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity, e.g., using dominant negative mutants or anti-cellulase, e.g., anti-endoglucanase, anti-cellobiohydrolase and/or anti-beta-glucosidase antibodies of the invention. The invention includes heterocomplexes, e.g., fusion proteins, heterodimers, etc., comprising the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes of the invention.

[0447] Polypeptides of the invention can have a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity under various conditions, e.g., extremes in pH and/or temperature, oxidizing agents, and the like. The invention provides methods leading to alternative cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme preparations with different catalytic efficiencies and stabilities, e.g., towards temperature, oxidizing agents and changing wash conditions. In one aspect, cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme variants can be produced using techniques of site-directed mutagenesis and/or random mutagenesis. In one aspect, directed evolution can be used to produce a great variety of cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme variants with alternative specificities and stability.

[0448] The proteins of the invention are also useful as research reagents to identify cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme modulators, e.g., activators or inhibitors of cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity. Briefly, test samples (compounds, broths, extracts, and the like) are added to cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme assays to determine their ability to inhibit substrate cleavage. Inhibitors identified in this way can be used in industry and research to reduce or prevent undesired proteolysis. As with cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes, inhibitors can be combined to increase the spectrum of activity.

[0449] The enzymes of the invention are also useful as research reagents to digest proteins or in protein sequencing. For example, the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes may be used to break polypeptides into smaller fragments for sequencing using, e.g. an automated sequencer.

[0450] The invention also provides methods of discovering new cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes using the nucleic acids, polypeptides and antibodies of the invention. In one aspect, phagemid libraries are screened for expression-based discovery of cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes. In another aspect, lambda phage libraries are screened for expression-based discovery of cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes. Screening of the phage or phagemid libraries can allow the detection of toxic clones; improved access to substrate; reduced need for engineering a host, by-passing the potential for any bias resulting from mass excision of the library; and, faster growth at low clone densities. Screening of phage or phagemid libraries can be in liquid phase or in solid phase. In one aspect, the invention provides screening in liquid phase. This gives a greater flexibility in assay conditions; additional substrate flexibility; higher sensitivity for weak clones; and ease of automation over solid phase screening.

[0451] The invention provides screening methods using the proteins and nucleic acids of the invention and robotic automation to enable the execution of many thousands of biocatalytic reactions and screening assays in a short period of time, e.g., per day, as well as ensuring a high level of accuracy and reproducibility (see discussion of arrays, below). As a result, a library of derivative compounds can be produced in a matter of weeks. For further teachings on modification of molecules, including small molecules, see PCT/US94/09174; U.S. Pat. No. 6,245,547.

[0452] In one aspect, polypeptides or fragments of the invention are obtained through biochemical enrichment or purification procedures. The sequence of potentially homologous polypeptides or fragments may be determined by cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme assays (see, e.g., Examples 1, 2 and 3, below), gel electrophoresis and/or microsequencing. The sequence of the prospective polypeptide or fragment of the invention can be compared to an exemplary polypeptide of the invention, or a fragment, e.g., comprising at least about 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 or more consecutive amino acids thereof using any of the programs described above.

[0453] Another aspect of the invention is an assay for identifying fragments or variants of the invention, which retain the enzymatic function of the polypeptides of the invention. For example the fragments or variants of said polypeptides, may be used to catalyze biochemical reactions, which indicate that the fragment or variant retains the enzymatic activity of a polypeptide of the invention. An exemplary assay for determining if fragments of variants retain the enzymatic activity of the polypeptides of the invention includes the steps of: contacting the polypeptide fragment or variant with a substrate molecule under conditions which allow the polypeptide fragment or variant to function and detecting either a decrease in the level of substrate or an increase in the level of the specific reaction product of the reaction between the polypeptide and substrate.

[0454] The present invention exploits the unique catalytic properties of enzymes. Whereas the use of biocatalysts (i.e., purified or crude enzymes, non-living or living cells) in chemical transformations normally requires the identification of a particular biocatalyst that reacts with a specific starting compound, the present invention uses selected biocatalysts and reaction conditions that are specific for functional groups that are present in many starting compounds, such as small molecules. Each biocatalyst is specific for one functional group, or several related functional groups and can react with many starting compounds containing this functional group.

[0455] In one aspect, the biocatalytic reactions produce a population of derivatives from a single starting compound. These derivatives can be subjected to another round of biocatalytic reactions to produce a second population of derivative compounds. Thousands of variations of the original small molecule or compound can be produced with each iteration of biocatalytic derivatization.

[0456] Enzymes react at specific sites of a starting compound without affecting the rest of the molecule, a process which is very difficult to achieve using traditional chemical methods. This high degree of biocatalytic specificity provides the means to identify a single active compound within the library. The library is characterized by the series of biocatalytic reactions used to produce it, a so-called "biosynthetic history". Screening the library for biological activities and tracing the biosynthetic history identifies the specific reaction sequence producing the active compound. The reaction sequence is repeated and the structure of the synthesized compound determined. This mode of identification, unlike other synthesis and screening approaches, does not require immobilization technologies and compounds can be synthesized and tested free in solution using virtually any type of screening assay. It is important to note, that the high degree of specificity of enzyme reactions on functional groups allows for the "tracking" of specific enzymatic reactions that make up the biocatalytically produced library.

[0457] In one aspect, procedural steps are performed using robotic automation enabling the execution of many thousands of biocatalytic reactions and/or screening assays per day as well as ensuring a high level of accuracy and reproducibility. Robotic automation can also be used to screen for cellulase activity to determine if a polypeptide is within the scope of the invention. As a result, in one aspect, a library of derivative compounds can be produced in a matter of weeks which would take years to produce using "traditional" chemical or enzymatic screening methods.

[0458] In a particular aspect, the invention provides a method for modifying small molecules, comprising contacting a polypeptide encoded by a polynucleotide described herein or enzymatically active fragments thereof with a small molecule to produce a modified small molecule. A library of modified small molecules is tested to determine if a modified small molecule is present within the library, which exhibits a desired activity. A specific biocatalytic reaction which produces the modified small molecule of desired activity is identified by systematically eliminating each of the biocatalytic reactions used to produce a portion of the library and then testing the small molecules produced in the portion of the library for the presence or absence of the modified small molecule with the desired activity. The specific biocatalytic reactions which produce the modified small molecule of desired activity is optionally repeated. The biocatalytic reactions are conducted with a group of biocatalysts that react with distinct structural moieties found within the structure of a small molecule, each biocatalyst is specific for one structural moiety or a group of related structural moieties; and each biocatalyst reacts with many different small molecules which contain the distinct structural moiety.

[0459] Cellulase, e.g., Endoglucanase, Cellobiohydrolase and/or Beta-Glucosidase Enzyme Signal Sequences, Prepro and Catalytic Domains

[0460] The invention provides cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme signal sequences (e.g., signal peptides (SPs)), prepro domains and catalytic domains (CDs). The SPs, prepro domains and/or CDs of the invention can be isolated or recombinant peptides or can be part of a fusion protein, e.g., as a heterologous domain in a chimeric protein. The invention provides nucleic acids encoding these catalytic domains (CDs), prepro domains and signal sequences (SPs, e.g., a peptide having a sequence comprising/consisting of amino terminal residues of a polypeptide of the invention).

[0461] The invention provides isolated or recombinant signal sequences (e.g., signal peptides) consisting of or comprising a sequence as set forth in residues 1 to 14, 1 to 15, 1 to 16, 1 to 17, 1 to 18, 1 to 19, 1 to 20, 1 to 21, 1 to 22, 1 to 23, 1 to 24, 1 to 25, 1 to 26, 1 to 27, 1 to 28, 1 to 28, 1 to 30, 1 to 31, 1 to 32, 1 to 33, 1 to 34, 1 to 35, 1 to 36, 1 to 37, 1 to 38, 1 to 40, 1 to 41, 1 to 42, 1 to 43, 1 to 44, 1 to 45, 1 to 46, or 1 to 47, or more, of a polypeptide of the invention, e.g., exemplary polypeptides of the invention, see also Table 3, Examples 1 and 4, below, and Sequence Listing. For example, Table 3, above, sets forth exemplary signal (leader) sequences of the invention, e.g., as in the polypeptide having a sequence as set forth in SEQ ID NO:164, encoded, e.g., by SEQ ID NO:163, has a signal sequence comprising (or consisting of) the amino terminal 30 residues, or, MSCRTLMSRRVGWGLLLWGGLFLRTGSVTG. Additional signal sequences are similarly set forth in Table 3.

[0462] In one aspect, the invention provides signal sequences comprising the first 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70 or more amino terminal residues of a polypeptide of the invention.

[0463] The invention includes polypeptides with or without a signal sequence and/or a prepro sequence. The invention includes polypeptides with heterologous signal sequences and/or prepro sequences. The prepro sequence (including a sequence of the invention used as a heterologous prepro domain) can be located on the amino terminal or the carboxy terminal end of the protein. The invention also includes isolated or recombinant signal sequences, prepro sequences and catalytic domains (e.g., "active sites") comprising sequences of the invention. The polypeptide comprising a signal sequence of the invention can be a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme of the invention or another cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme or another enzyme or other polypeptide. Methods for identifying "prepro" domain sequences and signal sequences are well known in the art, see, e.g., Van de Ven (1993) Crit. Rev. Oncog. 4(2):115-136. For example, to identify a prepro sequence, the protein is purified from the extracellular space and the N-terminal protein sequence is determined and compared to the unprocessed form.

[0464] The cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme signal sequences (SPs) and/or prepro sequences of the invention can be isolated or recombinant peptides, or, sequences joined to another cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme or a non-cellulase, e.g., non-endoglucanase, non-cellobiohydrolase and/or non-beta-glucosidase polypeptide, e.g., as a fusion (chimeric) protein. In one aspect, the invention provides polypeptides comprising cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme signal sequences of the invention. In one aspect, polypeptides comprising cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme signal sequences SPs and/or prepro of the invention comprise sequences heterologous to a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme of the invention (e.g., a fusion protein comprising an SP and/or prepro of the invention and sequences from another cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme or a non-cellulase, e.g., non-endoglucanase, non-cellobiohydrolase and/or non-beta-glucosidase protein). In one aspect, the invention provides cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes of the invention with heterologous SPs and/or prepro sequences, e.g., sequences with a yeast signal sequence. A cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme of the invention can comprise a heterologous SP and/or prepro in a vector, e.g., a pPIC series vector (Invitrogen, Carlsbad, Calif.).

[0465] In one aspect, SPs and/or prepro sequences of the invention are identified following identification of novel cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase polypeptides. The pathways by which proteins are sorted and transported to their proper cellular location are often referred to as protein targeting pathways. One of the most important elements in all of these targeting systems is a short amino acid sequence at the amino terminus of a newly synthesized polypeptide called the signal sequence. This signal sequence directs a protein to its appropriate location in the cell and is removed during transport or when the protein reaches its final destination. Most lysosomal, membrane, or secreted proteins have an amino-terminal signal sequence that marks them for translocation into the lumen of the endoplasmic reticulum. The signal sequences can vary in length from about 10 to 65, or more, amino acid residues. Various methods of recognition of signal sequences are known to those of skill in the art. For example, in one aspect, novel cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme signal peptides are identified by a method referred to as SignalP. SignalP uses a combined neural network which recognizes both signal peptides and their cleavage sites. (Nielsen (1997) "Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites." Protein Engineering 10:1-6.

[0466] In some aspects cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes of the invention do not have SPs and/or prepro sequences or "domains." In one aspect, the invention provides the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes of the invention lacking all or part of an SP and/or a prepro domain. In one aspect, the invention provides a nucleic acid sequence encoding a signal sequence (SP) and/or prepro from one cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme operably linked to a nucleic acid sequence of a different cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme or, optionally, a signal sequence (SPs) and/or prepro domain from a non-cellulase, e.g., non-endoglucanase, non-cellobiohydrolase and/or non-beta-glucosidase protein may be desired.

[0467] The invention also provides isolated or recombinant polypeptides comprising signal sequences (SPs), prepro domain and/or catalytic domains (CDs) of the invention and heterologous sequences. The heterologous sequences are sequences not naturally associated (e.g., to a enzyme) with an SP, prepro domain and/or CD. The sequence to which the SP, prepro domain and/or CD are not naturally associated can be on the SP's, prepro domain and/or CD's amino terminal end, carboxy terminal end, and/or on both ends of the SP and/or CD. In one aspect, the invention provides an isolated or recombinant polypeptide comprising (or consisting of) a polypeptide comprising a signal sequence (SP), prepro domain and/or catalytic domain (CD) of the invention with the proviso that it is not associated with any sequence to which it is naturally associated (e.g., a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme sequence). Similarly in one aspect, the invention provides isolated or recombinant nucleic acids encoding these polypeptides. Thus, in one aspect, the isolated or recombinant nucleic acid of the invention comprises coding sequence for a signal sequence (SP), prepro domain and/or catalytic domain (CD) of the invention and a heterologous sequence (i.e., a sequence not naturally associated with the a signal sequence (SP), prepro domain and/or catalytic domain (CD) of the invention). The heterologous sequence can be on the 3' terminal end, 5' terminal end, and/or on both ends of the SP, prepro domain and/or CD coding sequence.

[0468] Hybrid (Chimeric) Cellulase, e.g., Endoglucanase, Cellobiohydrolase and/or Beta-Glucosidase Enzymes and Peptide Libraries

[0469] In one aspect, the invention provides hybrid cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes and fusion proteins, including peptide libraries, comprising sequences of the invention. The peptide libraries of the invention can be used to isolate peptide modulators (e.g., activators or inhibitors) of targets, such as cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme substrates, receptors, enzymes. The peptide libraries of the invention can be used to identify formal binding partners of targets, such as ligands, e.g., cytokines, hormones and the like. In one aspect, the invention provides chimeric proteins comprising a signal sequence (SP), prepro domain and/or catalytic domain (CD) of the invention or a combination thereof and a heterologous sequence (see above).

[0470] In one aspect, the fusion proteins of the invention (e.g., the peptide moiety) are conformationally stabilized (relative to linear peptides) to allow a higher binding affinity for targets. The invention provides fusions of cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes of the invention and other peptides, including known and random peptides. They can be fused in such a manner that the structure of the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes is not significantly perturbed and the peptide is metabolically or structurally conformationally stabilized. This allows the creation of a peptide library that is easily monitored both for its presence within cells and its quantity.

[0471] Amino acid sequence variants of the invention can be characterized by a predetermined nature of the variation, a feature that sets them apart from a naturally occurring form, e.g., an allelic or interspecies variation of a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme sequence. In one aspect, the variants of the invention exhibit the same qualitative biological activity as the naturally occurring analogue. Alternatively, the variants can be selected for having modified characteristics. In one aspect, while the site or region for introducing an amino acid sequence variation is predetermined, the mutation per se need not be predetermined. For example, in order to optimize the performance of a mutation at a given site, random mutagenesis may be conducted at the target codon or region and the expressed cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme variants screened for the optimal combination of desired activity. Techniques for making substitution mutations at predetermined sites in DNA having a known sequence are well known, as discussed herein for example, M13 primer mutagenesis and PCR mutagenesis. Screening of the mutants can be done using, e.g., assays of glucan hydrolysis. In alternative aspects, amino acid substitutions can be single residues; insertions can be on the order of from about 1 to 20 amino acids, although considerably larger insertions can be done. Deletions can range from about 1 to about 20, 30, 40, 50, 60, 70 residues or more. To obtain a final derivative with the optimal properties, substitutions, deletions, insertions or any combination thereof may be used. Generally, these changes are done on a few amino acids to minimize the alteration of the molecule. However, larger changes may be tolerated in certain circumstances.

[0472] The invention provides cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes where the structure of the polypeptide backbone, the secondary or the tertiary structure, e.g., an alpha-helical or beta-sheet structure, has been modified. In one aspect, the charge or hydrophobicity has been modified. In one aspect, the bulk of a side chain has been modified. Substantial changes in function or immunological identity are made by selecting substitutions that are less conservative. For example, substitutions can be made which more significantly affect: the structure of the polypeptide backbone in the area of the alteration, for example a alpha-helical or a beta-sheet structure; a charge or a hydrophobic site of the molecule, which can be at an active site; or a side chain. The invention provides substitutions in polypeptide of the invention where (a) a hydrophilic residues, e.g. seryl or threonyl, is substituted for (or by) a hydrophobic residue, e.g. leucyl, isoleucyl, phenylalanyl, valyl or alanyl; (b) a cysteine or proline is substituted for (or by) any other residue; (c) a residue having an electropositive side chain, e.g. lysyl, arginyl, or histidyl, is substituted for (or by) an electronegative residue, e.g. glutamyl or aspartyl; or (d) a residue having a bulky side chain, e.g. phenylalanine, is substituted for (or by) one not having a side chain, e.g. glycine. The variants can exhibit the same qualitative biological activity (i.e., a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity) although variants can be selected to modify the characteristics of the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes as needed.

[0473] In one aspect, cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes of the invention comprise epitopes or purification tags, signal sequences or other fusion sequences, etc. In one aspect, the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes of the invention can be fused to a random peptide to form a fusion polypeptide. By "fused" or "operably linked" herein is meant that the random peptide and the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme are linked together, in such a manner as to minimize the disruption to the stability of the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme structure, e.g., it retains cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity. The fusion polypeptide (or fusion polynucleotide encoding the fusion polypeptide) can comprise further components as well, including multiple peptides at multiple loops.

[0474] In one aspect, the peptides and nucleic acids encoding them are randomized, either fully randomized or they are biased in their randomization, e.g. in nucleotide/residue frequency generally or per position. "Randomized" means that each nucleic acid and peptide consists of essentially random nucleotides and amino acids, respectively. In one aspect, the nucleic acids which give rise to the peptides can be chemically synthesized, and thus may incorporate any nucleotide at any position. Thus, when the nucleic acids are expressed to form peptides, any amino acid residue may be incorporated at any position. The synthetic process can be designed to generate randomized nucleic acids, to allow the formation of all or most of the possible combinations over the length of the nucleic acid, thus forming a library of randomized nucleic acids. The library can provide a sufficiently structurally diverse population of randomized expression products to affect a probabilistically sufficient range of cellular responses to provide one or more cells exhibiting a desired response. Thus, the invention provides an interaction library large enough so that at least one of its members will have a structure that gives it affinity for some molecule, protein, or other factor.

[0475] In one aspect, a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme of the invention is a multidomain enzyme that comprises a signal peptide, a carbohydrate binding module, a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme catalytic domain, a linker and/or another catalytic domain.

[0476] The invention provides a methods and sequences for generating chimeric polypeptides which may encode biologically active hybrid polypeptides (e.g., hybrid cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes). In one aspect, the original polynucleotides (e.g., an exemplary nucleic acid of the invention) encode biologically active polypeptides. In one aspect, a method of the invention produces new hybrid polypeptides by utilizing cellular processes which integrate the sequence of the original polynucleotides such that the resulting hybrid polynucleotide encodes a polypeptide demonstrating activities derived, but different, from the original biologically active polypeptides (e.g., cellulase or antibody of the invention). For example, the original polynucleotides may encode a particular enzyme (e.g., cellulase) from or found in different microorganisms. An enzyme encoded by a first polynucleotide from one organism or variant may, for example, function effectively under a particular environmental condition, e.g. high salinity. An enzyme encoded by a second polynucleotide from a different organism or variant may function effectively under a different environmental condition, such as extremely high temperatures. A hybrid polynucleotide containing sequences from the first and second original polynucleotides may encode an enzyme which exhibits characteristics of both enzymes encoded by the original polynucleotides. Thus, the enzyme encoded by the hybrid polynucleotide of the invention may function effectively under environmental conditions shared by each of the enzymes encoded by the first and second polynucleotides, e.g., high salinity and extreme temperatures.

[0477] In one aspect, a hybrid polypeptide generated by a method of the invention may exhibit specialized enzyme activity not displayed in the original enzymes. For example, following recombination and/or reductive reassortment of polynucleotides encoding cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes, the resulting hybrid polypeptide encoded by a hybrid polynucleotide can be screened for specialized non-cellulase, e.g., non-endoglucanase, non-cellobiohydrolase and/or non-beta-glucosidase enzyme activities, e.g., hydrolase, peptidase, phosphorylase, etc., activities, obtained from each of the original enzymes. In one aspect, the hybrid polypeptide is screened to ascertain those chemical functionalities which distinguish the hybrid polypeptide from the original parent polypeptides, such as the temperature, pH or salt concentration at which the hybrid polypeptide functions.

[0478] In one aspect, the invention relates to a method for producing a biologically active hybrid polypeptide and screening such a polypeptide for enhanced activity by:

[0479] 1) introducing at least a first polynucleotide in operable linkage and a second polynucleotide in operable linkage, the at least first polynucleotide and second polynucleotide sharing at least one region of partial sequence homology, into a suitable host cell;

[0480] 2) growing the host cell under conditions which promote sequence reorganization resulting in a hybrid polynucleotide in operable linkage;

[0481] 3) expressing a hybrid polypeptide encoded by the hybrid polynucleotide;

[0482] 4) screening the hybrid polypeptide under conditions which promote identification of enhanced biological activity; and

[0483] 5) isolating the a polynucleotide encoding the hybrid polypeptide.

Isolating and Discovering Cellulase Enzymes

[0484] The invention provides methods for isolating and discovering cellulases, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes and the nucleic acids that encode them. Polynucleotides or enzymes may be isolated from individual organisms ("isolates"), collections of organisms that have been grown in defined media ("enrichment cultures"), or, uncultivated organisms ("environmental samples"). The organisms can be isolated by, e.g., in vivo biopanning (see discussion, below). The use of a culture-independent approach to derive polynucleotides encoding novel bioactivities from environmental samples is most preferable since it allows one to access untapped resources of biodiversity. Polynucleotides or enzymes also can be isolated from any one of numerous organisms, e.g. bacteria. In addition to whole cells, polynucleotides or enzymes also can be isolated from crude enzyme preparations derived from cultures of these organisms, e.g., bacteria.

[0485] "Environmental libraries" are generated from environmental samples and represent the collective genomes of naturally occurring organisms archived in cloning vectors that can be propagated in suitable prokaryotic hosts. Because the cloned DNA is initially extracted directly from environmental samples, the libraries are not limited to the small fraction of prokaryotes that can be grown in pure culture. Additionally, a normalization of the environmental DNA present in these samples could allow more equal representation of the DNA from all of the species present in the original sample. This can dramatically increase the efficiency of finding interesting genes from minor constituents of the sample which may be under-represented by several orders of magnitude compared to the dominant species.

[0486] In one aspect, gene libraries generated from one or more uncultivated microorganisms are screened for an activity of interest. Potential pathways encoding bioactive molecules of interest are first captured in prokaryotic cells in the form of gene expression libraries. In one aspect, polynucleotides encoding activities of interest are isolated from such libraries and introduced into a host cell. The host cell is grown under conditions which promote recombination and/or reductive reassortment creating potentially active biomolecules with novel or enhanced activities.

[0487] In vivo biopanning may be performed utilizing a FACS-based and non-optical (e.g., magnetic) based machines. In one aspect, complex gene libraries are constructed with vectors which contain elements which stabilize transcribed RNA. For example, the inclusion of sequences which result in secondary structures such as hairpins which are designed to flank the transcribed regions of the RNA would serve to enhance their stability, thus increasing their half life within the cell. The probe molecules used in the biopanning process consist of oligonucleotides labeled with reporter molecules that only fluoresce upon binding of the probe to a target molecule. These probes are introduced into the recombinant cells from the library using one of several transformation methods. The probe molecules bind to the transcribed target mRNA resulting in DNA/RNA heteroduplex molecules. Binding of the probe to a target will yield a fluorescent signal which is detected and sorted by the FACS machine during the screening process.

[0488] In one aspect, subcloning is performed to further isolate sequences of interest. In subcloning, a portion of DNA is amplified, digested, generally by restriction enzymes, to cut out the desired sequence, the desired sequence is ligated into a recipient vector and is amplified. At each step in subcloning, the portion is examined for the activity of interest, in order to ensure that DNA that encodes the structural protein has not been excluded. The insert may be purified at any step of the subcloning, for example, by gel electrophoresis prior to ligation into a vector or where cells containing the recipient vector and cells not containing the recipient vector are placed on selective media containing, for example, an antibiotic, which will kill the cells not containing the recipient vector. Specific methods of subcloning cDNA inserts into vectors are well-known in the art (Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory Press (1989)). In another aspect, the enzymes of the invention are subclones. Such subclones may differ from the parent clone by, for example, length, a mutation, a tag or a label.

[0489] The microorganisms from which the polynucleotide may be discovered, isolated or prepared include prokaryotic microorganisms, such as Eubacteria and Archaebacteria and lower eukaryotic microorganisms such as fungi, some algae and protozoa. Polynucleotides may be discovered, isolated or prepared from environmental samples in which case the nucleic acid may be recovered without culturing of an organism or recovered from one or more cultured organisms. In one aspect, such microorganisms may be extremophiles, such as hyperthermophiles, psychrophiles, psychrotrophs, halophiles, barophiles and acidophiles. Polynucleotides encoding enzymes isolated from extremophilic microorganisms can be used. Enzymes of this invention can function at temperatures above 100° C., e.g., as those found in terrestrial hot springs and deep sea thermal vents, or at temperatures below 0° C., e.g., as those found in arctic waters, in a saturated salt environment, e.g., as those found in the Dead Sea, at pH values around 0, e.g., as those found in coal deposits and geothermal sulfur-rich springs, or at pH values greater than 11, e.g., as those found in sewage sludge. In one aspect, enzymes of the invention have high activity throughout a wide range of temperatures and pHs.

[0490] Polynucleotides selected and isolated as hereinabove described are introduced into a suitable host cell. A suitable host cell is any cell which is capable of promoting recombination and/or reductive reassortment. The selected polynucleotides are in one aspect already in a vector which includes appropriate control sequences. The host cell can be a higher eukaryotic cell, such as a mammalian cell, or a lower eukaryotic cell, such as a yeast cell, or in one aspect, the host cell can be a prokaryotic cell, such as a bacterial cell. Introduction of the construct into the host cell can be effected by calcium phosphate transfection, DEAE-Dextran mediated transfection, or electroporation.

[0491] Exemplary hosts include bacterial cells, such as E. coli, Streptomyces, Salmonella typhimurium; fungal cells, such as yeast; insect cells such as Drosophila S2 and Spodoptera Sf9; animal cells such as CHO, COS or Bowes melanoma; adenoviruses; and plant cells; see discussion, above. The selection of an appropriate host is deemed to be within the scope of those skilled in the art from the teachings herein.

[0492] Various mammalian cell culture systems can be employed to express recombinant protein; examples of mammalian expression systems include the COS-7 lines of monkey kidney fibroblasts, described in "SV40-transformed simian cells support the replication of early SV40 mutants" (Gluzman, 1981) and other cell lines capable of expressing a compatible vector, for example, the C127, 3T3, CHO, HeLa and BHK cell lines. Mammalian expression vectors can comprise an origin of replication, a suitable promoter and enhancer and also any necessary ribosome binding sites, polyadenylation site, splice donor and acceptor sites, transcriptional termination sequences and 5' flanking nontranscribed sequences. DNA sequences derived from the SV40 splice and polyadenylation sites may be used to provide the required nontranscribed genetic elements.

[0493] In another aspect, nucleic acids, polypeptides and methods of the invention are used in biochemical pathways, or to generate novel polynucleotides encoding biochemical pathways from one or more operons or gene clusters or portions thereof. For example, bacteria and many eukaryotes have a coordinated mechanism for regulating genes whose products are involved in related processes. The genes are clustered, in structures referred to as "gene clusters," on a single chromosome and are transcribed together under the control of a single regulatory sequence, including a single promoter which initiates transcription of the entire cluster. Thus, a gene cluster is a group of adjacent genes that are either identical or related, usually as to their function (an example of a biochemical pathway encoded by gene clusters are polyketides).

[0494] In one aspect, gene cluster DNA is isolated from different organisms and ligated into vectors, e.g., vectors containing expression regulatory sequences which can control and regulate the production of a detectable protein or protein-related array activity from the ligated gene clusters. Use of vectors which have an exceptionally large capacity for exogenous DNA introduction can be appropriate for use with such gene clusters and are described by way of example herein to include the f-factor (or fertility factor) of E. coli. This f-factor of E. coli is a plasmid which affects high-frequency transfer of itself during conjugation and is ideal to achieve and stably propagate large DNA fragments, such as gene clusters from mixed microbial samples. One aspect is to use cloning vectors, referred to as "fosmids" or bacterial artificial chromosome (BAC) vectors. These are derived from E. coli f-factor which is able to stably integrate large segments of genomic DNA. When integrated with DNA from a mixed uncultured environmental sample, this makes it possible to achieve large genomic fragments in the form of a stable "environmental DNA library." Another type of vector for use in the present invention is a cosmid vector. Cosmid vectors were originally designed to clone and propagate large segments of genomic DNA. Cloning into cosmid vectors is described in detail in Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory Press (1989). Once ligated into an appropriate vector, two or more vectors containing different polyketide synthase gene clusters can be introduced into a suitable host cell. Regions of partial sequence homology shared by the gene clusters will promote processes which result in sequence reorganization resulting in a hybrid gene cluster. The novel hybrid gene cluster can then be screened for enhanced activities not found in the original gene clusters.

[0495] Methods for screening for various enzyme activities are known to those of skill in the art and are discussed throughout the present specification, see, e.g., Examples 1, 2 and 3, below. Such methods may be employed when isolating the polypeptides and polynucleotides of the invention.

[0496] In one aspect, the invention provides methods for discovering and isolating cellulases, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase, or compounds to modify the activity of these enzymes, using a whole cell approach (see discussion, below). Putative clones encoding cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase from genomic DNA library can be screened.

Screening Methodologies and "On-Line" Monitoring Devices

[0497] In practicing the methods of the invention, a variety of apparatus and methodologies can be used to in conjunction with the polypeptides and nucleic acids of the invention, e.g., to screen polypeptides for cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity, to screen compounds as potential modulators, e.g., activators or inhibitors, of a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity, for antibodies that bind to a polypeptide of the invention, for nucleic acids that hybridize to a nucleic acid of the invention, to screen for cells expressing a polypeptide of the invention and the like. In addition to the array formats described in detail below for screening samples, alternative formats can also be used to practice the methods of the invention. Such formats include, for example, mass spectrometers, chromatographs, e.g., high-throughput HPLC and other forms of liquid chromatography, and smaller formats, such as 1536-well plates, 384-well plates and so on. High throughput screening apparatus can be adapted and used to practice the methods of the invention, see, e.g., U.S. Patent Application Nos. 20020001809; 20050272044.

[0498] Capillary Arrays

[0499] Nucleic acids or polypeptides of the invention can be immobilized to or applied to an array. Arrays can be used to screen for or monitor libraries of compositions (e.g., small molecules, antibodies, nucleic acids, etc.) for their ability to bind to or modulate the activity of a nucleic acid or a polypeptide of the invention. Capillary arrays, such as the GIGAMATRIX®, Diversa Corporation, San Diego, Calif.; and arrays described in, e.g., U.S. Patent Application No. 20020080350 A1; WO 0231203 A; WO 0244336 A, provide an alternative apparatus for holding and screening samples. In one aspect, the capillary array includes a plurality of capillaries formed into an array of adjacent capillaries, wherein each capillary comprises at least one wall defining a lumen for retaining a sample. The lumen may be cylindrical, square, hexagonal or any other geometric shape so long as the walls form a lumen for retention of a liquid or sample. The capillaries of the capillary array can be held together in close proximity to form a planar structure. The capillaries can be bound together, by being fused (e.g., where the capillaries are made of glass), glued, bonded, or clamped side-by-side. Additionally, the capillary array can include interstitial material disposed between adjacent capillaries in the array, thereby forming a solid planar device containing a plurality of through-holes.

[0500] A capillary array can be formed of any number of individual capillaries, for example, a range from 100 to 4,000,000 capillaries. Further, a capillary array having about 100,000 or more individual capillaries can be formed into the standard size and shape of a Microtiter® plate for fitment into standard laboratory equipment. The lumens are filled manually or automatically using either capillary action or microinjection using a thin needle. Samples of interest may subsequently be removed from individual capillaries for further analysis or characterization. For example, a thin, needle-like probe is positioned in fluid communication with a selected capillary to either add or withdraw material from the lumen.

[0501] In a single-pot screening assay, the assay components are mixed yielding a solution of interest, prior to insertion into the capillary array. The lumen is filled by capillary action when at least a portion of the array is immersed into a solution of interest. Chemical or biological reactions and/or activity in each capillary are monitored for detectable events. A detectable event is often referred to as a "hit", which can usually be distinguished from "non-hit"producing capillaries by optical detection. Thus, capillary arrays allow for massively parallel detection of "hits".

[0502] In a multi-pot screening assay, a polypeptide or nucleic acid, e.g., a ligand, can be introduced into a first component, which is introduced into at least a portion of a capillary of a capillary array. An air bubble can then be introduced into the capillary behind the first component. A second component can then be introduced into the capillary, wherein the second component is separated from the first component by the air bubble. The first and second components can then be mixed by applying hydrostatic pressure to both sides of the capillary array to collapse the bubble. The capillary array is then monitored for a detectable event resulting from reaction or non-reaction of the two components.

[0503] In a binding screening assay, a sample of interest can be introduced as a first liquid labeled with a detectable particle into a capillary of a capillary array, wherein the lumen of the capillary is coated with a binding material for binding the detectable particle to the lumen. The first liquid may then be removed from the capillary tube, wherein the bound detectable particle is maintained within the capillary, and a second liquid may be introduced into the capillary tube. The capillary is then monitored for a detectable event resulting from reaction or non-reaction of the particle with the second liquid.

[0504] Arrays, or "Biochips"

[0505] Nucleic acids or polypeptides of the invention can be immobilized to or applied to an array. Arrays can be used to screen for or monitor libraries of compositions (e.g., small molecules, antibodies, nucleic acids, etc.) for their ability to bind to or modulate the activity of a nucleic acid or a polypeptide of the invention. For example, in one aspect of the invention, a monitored parameter is transcript expression of a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme gene. One or more, or, all the transcripts of a cell can be measured by hybridization of a sample comprising transcripts of the cell, or, nucleic acids representative of or complementary to transcripts of a cell, by hybridization to immobilized nucleic acids on an array, or "biochip." By using an "array" of nucleic acids on a microchip, some or all of the transcripts of a cell can be simultaneously quantified. Alternatively, arrays comprising genomic nucleic acid can also be used to determine the genotype of a newly engineered strain made by the methods of the invention. Polypeptide arrays" can also be used to simultaneously quantify a plurality of proteins. The present invention can be practiced with any known "array," also referred to as a "microarray" or "nucleic acid array" or "polypeptide array" or "antibody array" or "biochip," or variation thereof. Arrays are generically a plurality of "spots" or "target elements," each target element comprising a defined amount of one or more biological molecules, e.g., oligonucleotides, immobilized onto a defined area of a substrate surface for specific binding to a sample molecule, e.g., mRNA transcripts.

[0506] The terms "array" or "microarray" or "biochip" or "chip" as used herein is a plurality of target elements, each target element comprising a defined amount of one or more polypeptides (including antibodies) or nucleic acids immobilized onto a defined area of a substrate surface, as discussed in further detail, below.

[0507] In practicing the methods of the invention, any known array and/or method of making and using arrays can be incorporated in whole or in part, or variations thereof, as described, for example, in U.S. Pat. Nos. 6,277,628; 6,277,489; 6,261,776; 6,258,606; 6,054,270; 6,048,695; 6,045,996; 6,022,963; 6,013,440; 5,965,452; 5,959,098; 5,856,174; 5,830,645; 5,770,456; 5,632,957; 5,556,752; 5,143,854; 5,807,522; 5,800,992; 5,744,305; 5,700,637; 5,556,752; 5,434,049; see also, e.g., WO 99/51773; WO 99/09217; WO 97/46313; WO 96/17958; see also, e.g., Johnston (1998) Curr. Biol. 8:R171-R174; Schummer (1997) Biotechniques 23:1087-1092; Kern (1997) Biotechniques 23:120-124; Solinas-Toldo (1997) Genes, Chromosomes & Cancer 20:399-407; Bowtell (1999) Nature Genetics Supp. 21:25-32. See also published U.S. patent applications Nos. 20010018642; 20010019827; 20010016322; 20010014449; 20010014448; 20010012537; 20010008765.

Antibodies and Antibody-Based Screening Methods

[0508] The invention provides isolated or recombinant antibodies that specifically bind to a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme of the invention. These antibodies can be used to isolate, identify or quantify the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes of the invention or related polypeptides. These antibodies can be used to isolate other polypeptides within the scope the invention or other related cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes. The antibodies can be designed to bind to an active site of a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme. Thus, the invention provides methods of inhibiting cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes using the antibodies of the invention (see discussion above regarding applications for anti-cellulase, e.g., anti-endoglucanase, anti-cellobiohydrolase and/or anti-beta-glucosidase enzyme compositions of the invention).

[0509] The term "antibody" includes a peptide or polypeptide derived from, modeled after or substantially encoded by an immunoglobulin gene or immunoglobulin genes, or fragments thereof, capable of specifically binding an antigen or epitope, see, e.g. Fundamental Immunology, Third Edition, W. E. Paul, ed., Raven Press, N.Y. (1993); Wilson (1994) J. Immunol. Methods 175:267-273; Yarmush (1992) J. Biochem. Biophys. Methods 25:85-97. The term antibody includes antigen-binding portions, i.e., "antigen binding sites," (e.g., fragments, subsequences, complementarity determining regions (CDRs)) that retain capacity to bind antigen, including (i) a Fab fragment, a monovalent fragment consisting of the VL, VH, CL and CH1 domains; (ii) a F(ab')2 fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; (iii) a Fd fragment consisting of the VH and CH1 domains; (iv) a Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (v) a dAb fragment (Ward et al., (1989) Nature 341:544-546), which consists of a VH domain; and (vi) an isolated complementarity determining region (CDR). Single chain antibodies are also included by reference in the term "antibody."

[0510] The invention provides fragments of the enzymes of the invention (e.g., peptides) including immunogenic fragments (e.g., subsequences) of a polypeptide of the invention. The invention provides compositions comprising a polypeptide or peptide of the invention and adjuvants or carriers and the like.

[0511] The antibodies can be used in immunoprecipitation, staining, immunoaffinity columns, and the like. If desired, nucleic acid sequences encoding for specific antigens can be generated by immunization followed by isolation of polypeptide or nucleic acid, amplification or cloning and immobilization of polypeptide onto an array of the invention. Alternatively, the methods of the invention can be used to modify the structure of an antibody produced by a cell to be modified, e.g., an antibody's affinity can be increased or decreased. Furthermore, the ability to make or modify antibodies can be a phenotype engineered into a cell by the methods of the invention.

[0512] Methods of immunization, producing and isolating antibodies (polyclonal and monoclonal) are known to those of skill in the art and described in the scientific and patent literature, see, e.g., Coligan, CURRENT PROTOCOLS IN IMMUNOLOGY, Wiley/Greene, N.Y. (1991); Stites (eds.) BASIC AND CLINICAL IMMUNOLOGY (7th ed.) Lange Medical Publications, Los Altos, Calif. ("Stites"); Goding, MONOCLONAL ANTIBODIES: PRINCIPLES AND PRACTICE (2d ed.) Academic Press, New York, N.Y. (1986); Kohler (1975) Nature 256:495; Harlow (1988) ANTIBODIES, A LABORATORY MANUAL, Cold Spring Harbor Publications, New York. Antibodies also can be generated in vitro, e.g., using recombinant antibody binding site expressing phage display libraries, in addition to the traditional in vivo methods using animals. See, e.g., Hoogenboom (1997) Trends Biotechnol. 15:62-70; Katz (1997) Annu. Rev. Biophys. Biomol. Struct. 26:27-45.

[0513] The polypeptides of the invention or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof, may also be used to generate antibodies which bind specifically to the polypeptides or fragments. The resulting antibodies may be used in immunoaffinity chromatography procedures to isolate or purify the polypeptide or to determine whether the polypeptide is present in a biological sample. In such procedures, a protein preparation, such as an extract, or a biological sample is contacted with an antibody capable of specifically binding to one of the polypeptides of the invention, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof.

[0514] In immunoaffinity procedures, the antibody is attached to a solid support, such as a bead or other column matrix. The protein preparation is placed in contact with the antibody under conditions in which the antibody specifically binds to one of the polypeptides of the invention, or fragment thereof. After a wash to remove non-specifically bound proteins, the specifically bound polypeptides are eluted.

[0515] The ability of proteins in a biological sample to bind to the antibody may be determined using any of a variety of procedures familiar to those skilled in the art. For example, binding may be determined by labeling the antibody with a detectable label such as a fluorescent agent, an enzymatic label, or a radioisotope. Alternatively, binding of the antibody to the sample may be detected using a secondary antibody having such a detectable label thereon. Particular assays include ELISA assays, sandwich assays, radioimmunoassays and Western Blots.

[0516] Polyclonal antibodies generated against the polypeptides of the invention, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof can be obtained by direct injection of the polypeptides into an animal or by administering the polypeptides to an animal, for example, a nonhuman. The antibody so obtained can bind the polypeptide itself. In this manner, even a sequence encoding only a fragment of the polypeptide can be used to generate antibodies which may bind to the whole native polypeptide. Such antibodies can then be used to isolate the polypeptide from cells expressing that polypeptide.

[0517] For preparation of monoclonal antibodies, any technique which provides antibodies produced by continuous cell line cultures can be used. Examples include the hybridoma technique (Kohler and Milstein, Nature, 256:495-497, 1975), the trioma technique, the human B-cell hybridoma technique (Kozbor et al., Immunology Today 4:72, 1983) and the EBV-hybridoma technique (Cole, et al., 1985, in Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96).

[0518] Techniques described for the production of single chain antibodies (U.S. Pat. No. 4,946,778) can be adapted to produce single chain antibodies to the polypeptides of the invention, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof. Alternatively, transgenic mice may be used to express humanized antibodies to these polypeptides or fragments thereof.

[0519] Antibodies generated against the polypeptides of the invention, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof may be used in screening for similar polypeptides from other organisms and samples. In such techniques, polypeptides from the organism are contacted with the antibody and those polypeptides which specifically bind the antibody are detected. Any of the procedures described above may be used to detect antibody binding. One such screening assay is described in "Methods for Measuring Cellulase Activities", Methods in Enzymology, Vol 160, pp. 87-116.

Kits

[0520] The invention provides kits comprising the compositions, e.g., nucleic acids, expression cassettes, vectors, cells, transgenic seeds or plants or plant parts, polypeptides (e.g., a cellulase enzyme) and/or antibodies of the invention. The kits also can contain instructional material teaching the methodologies and industrial, medical and dietary uses of the invention, as described herein.

Whole Cell Engineering and Measuring Metabolic Parameters

[0521] The methods of the invention provide whole cell evolution, or whole cell engineering, of a cell to develop a new cell strain having a new phenotype, e.g., a new or modified cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity, by modifying the genetic composition of the cell. See U.S. patent application no. 20040033975.

[0522] The genetic composition can be modified by addition to the cell of a nucleic acid of the invention, e.g., a coding sequence for an enzyme of the invention. See, e.g., WO0229032; WO0196551.

[0523] To detect the new phenotype, at least one metabolic parameter of a modified cell is monitored in the cell in a "real time" or "on-line" time frame. In one aspect, a plurality of cells, such as a cell culture, is monitored in "real time" or "on-line." In one aspect, a plurality of metabolic parameters is monitored in "real time" or "on-line." Metabolic parameters can be monitored using the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes of the invention.

[0524] Metabolic flux analysis (MFA) is based on a known biochemistry framework. A linearly independent metabolic matrix is constructed based on the law of mass conservation and on the pseudo-steady state hypothesis (PSSH) on the intracellular metabolites. In practicing the methods of the invention, metabolic networks are established, including the:

[0525] identity of all pathway substrates, products and intermediary metabolites

[0526] identity of all the chemical reactions interconverting the pathway metabolites, the stoichiometry of the pathway reactions,

[0527] identity of all the enzymes catalyzing the reactions, the enzyme reaction kinetics,

[0528] the regulatory interactions between pathway components, e.g. allosteric interactions, enzyme-enzyme interactions etc,

[0529] intracellular compartmentalization of enzymes or any other supramolecular organization of the enzymes, and,

[0530] the presence of any concentration gradients of metabolites, enzymes or effector molecules or diffusion barriers to their movement.

[0531] Once the metabolic network for a given strain is built, mathematic presentation by matrix notion can be introduced to estimate the intracellular metabolic fluxes if the on-line metabolome data is available. Metabolic phenotype relies on the changes of the whole metabolic network within a cell. Metabolic phenotype relies on the change of pathway utilization with respect to environmental conditions, genetic regulation, developmental state and the genotype, etc. In one aspect of the methods of the invention, after the on-line MFA calculation, the dynamic behavior of the cells, their phenotype and other properties are analyzed by investigating the pathway utilization. For example, if the glucose supply is increased and the oxygen decreased during the yeast fermentation, the utilization of respiratory pathways will be reduced and/or stopped, and the utilization of the fermentative pathways will dominate. Control of physiological state of cell cultures will become possible after the pathway analysis. The methods of the invention can help determine how to manipulate the fermentation by determining how to change the substrate supply, temperature, use of inducers, etc. to control the physiological state of cells to move along desirable direction. In practicing the methods of the invention, the MFA results can also be compared with transcriptome and proteome data to design experiments and protocols for metabolic engineering or gene shuffling, etc.

[0532] In practicing the methods of the invention, any modified or new phenotype can be conferred and detected, including new or improved characteristics in the cell. Any aspect of metabolism or growth can be monitored.

[0533] Monitoring Expression of an mRNA Transcript

[0534] In one aspect of the invention, the engineered phenotype comprises increasing or decreasing the expression of an mRNA transcript (e.g., a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme message) or generating new (e.g., cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme) transcripts in a cell. This increased or decreased expression can be traced by testing for the presence of a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme of the invention or by cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity assays. mRNA transcripts, or messages, also can be detected and quantified by any method known in the art, including, e.g., Northern blots, quantitative amplification reactions, hybridization to arrays, and the like. Quantitative amplification reactions include, e.g., quantitative PCR, including, e.g., quantitative reverse transcription polymerase chain reaction, or RT-PCR; quantitative real time RT-PCR, or "real-time kinetic RT-PCR" (see, e.g., Kreuzer (2001) Br. J. Haematol. 114:313-318; Xia (2001) Transplantation 72:907-914).

[0535] In one aspect of the invention, the engineered phenotype is generated by knocking out expression of a homologous gene. The gene's coding sequence or one or more transcriptional control elements can be knocked out, e.g., promoters or enhancers. Thus, the expression of a transcript can be completely ablated or only decreased.

[0536] In one aspect of the invention, the engineered phenotype comprises increasing the expression of a homologous gene. This can be effected by knocking out of a negative control element, including a transcriptional regulatory element acting in cis- or trans-, or, mutagenizing a positive control element. One or more, or, all the transcripts of a cell can be measured by hybridization of a sample comprising transcripts of the cell, or, nucleic acids representative of or complementary to transcripts of a cell, by hybridization to immobilized nucleic acids on an array.

[0537] Monitoring Expression of a Polypeptides, Peptides and Amino Acids

[0538] In one aspect of the invention, the engineered phenotype comprises increasing or decreasing the expression of a polypeptide (e.g., a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme) or generating new polypeptides in a cell. This increased or decreased expression can be traced by determining the amount of cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme present or by cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme activity assays. Polypeptides, peptides and amino acids also can be detected and quantified by any method known in the art, including, e.g., nuclear magnetic resonance (NMR), spectrophotometry, radiography (protein radiolabeling), electrophoresis, capillary electrophoresis, high performance liquid chromatography (HPLC), thin layer chromatography (TLC), hyperdiffusion chromatography, various immunological methods, e.g. immunoprecipitation, immunodiffusion, immuno-electrophoresis, radioimmunoassays (RIAs), enzyme-linked immunosorbent assays (ELISAs), immuno-fluorescent assays, gel electrophoresis (e.g., SDS-PAGE), staining with antibodies, fluorescent activated cell sorter (FACS), pyrolysis mass spectrometry, Fourier-Transform Infrared Spectrometry, Raman spectrometry, GC-MS, and LC-Electrospray and cap-LC-tandem-electrospray mass spectrometries, and the like. Novel bioactivities can also be screened using methods, or variations thereof, described in U.S. Pat. No. 6,057,103. Furthermore, as discussed below in detail, one or more, or, all the polypeptides of a cell can be measured using a protein array.

Industrial, Energy, Pharmaceutical and Other Applications

[0539] Polypeptides of the invention (e.g., having cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase) can catalyze the breakdown of cellulose. The enzymes of the invention can be highly selective catalysts. The invention provides industrial processes using enzymes of the invention, e.g., in the pharmaceutical or nutrient (diet) supplement industry, the energy industry (e.g., to make "clean" biofuels), in the food and feed industries, e.g., in methods for making food and feed products and food and feed additives. In one aspect, the invention provides processes using enzymes of the invention in the medical industry, e.g., to make pharmaceuticals or dietary aids or supplements, or food supplements and additives. In addition, the invention provides methods for using the enzymes of the invention in bioethanol, including "clean" fuel, production.

[0540] The enzymes of the invention can catalyze reactions with exquisite stereo-, regio- and chemo-selectivities. The cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes of the invention can be engineered to function in various solvents, operate at extreme pHs (for example, high pHs and low pHs) extreme temperatures (for example, high temperatures and low temperatures), extreme salinity levels (for example, high salinity and low salinity) and catalyze reactions with compounds that are structurally unrelated to their natural, physiological substrates.

[0541] Biomass Conversion and Production of Clean Bio Fuels

[0542] The invention provides enzymes and methods for the conversion of biomass (e.g., lignocellulosic materials) to fuels (e.g., bioethanol) and chemicals. Thus, the compositions and methods of the invention provide effective and sustainable alternatives to use of petroleum-based products. The invention provides organisms expressing enzymes of the invention for participation in chemical cycles involving natural biomass conversion. In one aspect, enzymes and methods for the conversion are used in enzyme ensembles for the efficient depolymerization of cellulosic and hemicellulosic polymers to metabolizable carbon moieties. As discussed above, the invention provides methods for discovering and implementing the most effective of enzymes to enable these important new "biomass conversion" and alternative energy industrial processes.

[0543] In one aspect, the polypeptides of the invention, e.g., proteins having cellulase activity, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity, are used in processes for converting lignocellulosic biomass to ethanol. The invention also provides processes for making ethanol ("bioethanol") from compositions comprising lignocellulosic biomass. The lignocellulose biomass material can be obtained from agricultural crops, as a byproduct of food or feed production, or as lignocellulosic waste products, such as plant residues and waste paper. Examples of suitable plant residues for treatment with polypeptides of the invention include stems, leaves, hulls, husks, cobs and the like, as well as wood, wood chips, wood pulp, and sawdust. Examples of paper waste suitable for treatment with polypeptides of the invention include discard photocopy paper, computer printer paper, notebook paper, notepad paper, typewriter paper, and the like, as well as newspapers, magazines, cardboard, and paper-based packaging materials.

[0544] In one aspect, the enzymes and methods of the invention can be used in conjunction with more "traditional" means of making ethanol from biomass, e.g., as methods comprising hydrolyzing lignocellulosic materials by subjecting dried lignocellulosic material in a reactor to a catalyst comprised of a dilute solution of a strong acid and a metal salt; this can lower the activation energy, or the temperature, of cellulose hydrolysis to obtain higher sugar yields; see, e.g., U.S. Pat. Nos. 6,660,506; 6,423,145.

[0545] Another exemplary method that incorporated use of enzymes of the invention comprises hydrolyzing lignocellulosic material containing hemicellulose, cellulose and lignin by subjecting the material to a first stage hydrolysis step in an aqueous medium at a temperature and a pressure chosen to effect primarily depolymerization of hemicellulose without major depolymerization of cellulose to glucose. This step results in a slurry in which the liquid aqueous phase contains dissolved monosaccharides resulting from depolymerization of hemicellulose and a solid phase containing cellulose and lignin. A second stage hydrolysis step can comprise conditions such that at least a major portion of the cellulose is depolymerized, such step resulting in a liquid aqueous phase containing dissolved/soluble depolymerization products of cellulose. See, e.g., U.S. Pat. No. 5,536,325. Enzymes of the invention can be added at any stage of this exemplary process.

[0546] Another exemplary method that incorporated use of enzymes of the invention comprises processing a lignocellulose-containing biomass material by one or more stages of dilute acid hydrolysis with about 0.4% to 2% strong acid; and treating an unreacted solid lignocellulosic component of the acid hydrolyzed biomass material by alkaline delignification to produce precursors for biodegradable thermoplastics and derivatives. See, e.g., U.S. Pat. No. 6,409,841. Enzymes of the invention can be added at any stage of this exemplary process.

[0547] Another exemplary method that incorporated use of enzymes of the invention comprises prehydrolyzing lignocellulosic material in a prehydrolysis reactor; adding an acidic liquid to the solid lignocellulosic material to make a mixture; heating the mixture to reaction temperature; maintaining reaction temperature for time sufficient to fractionate the lignocellulosic material into a solubilized portion containing at least about 20% of the lignin from the lignocellulosic material and a solid fraction containing cellulose; removing a solubilized portion from the solid fraction while at or near reaction temperature wherein the cellulose in the solid fraction is rendered more amenable to enzymatic digestion; and recovering a solubilized portion. See, e.g., U.S. Pat. No. 5,705,369. Enzymes of the invention can be added at any stage of this exemplary process.

[0548] The invention provides methods for making motor fuel compositions (e.g., for spark ignition motors) based on liquid hydrocarbons blended with a fuel grade alcohol made by using an enzyme or a method of the invention. In one aspect, the fuels made by use of an enzyme of the invention comprise, e.g., coal gas liquid- or natural gas liquid-ethanol blends. In one aspect, a co-solvent is biomass-derived 2-methyltetrahydrofuran (MTHF). See, e.g., U.S. Pat. No. 6,712,866.

[0549] Methods of the invention for the enzymatic degradation of lignocellulose, e.g., for production of ethanol from lignocellulosic material, can also comprise use of ultrasonic treatment of the biomass material; see, e.g., U.S. Pat. No. 6,333,181.

[0550] Another exemplary process for making a biofuel comprising ethanol using enzymes of the invention comprises pretreating a starting material comprising a lignocellulosic feedstock comprising at least hemicellulose and cellulose. In one aspect, the starting material comprises potatoes, soybean (rapeseed), barley, rye, corn, oats, wheat, beets or sugar cane or a component or waste or food or feed production byproduct. The starting material ("feedstock") is reacted at conditions which disrupt the plant's fiber structure to effect at least a partial hydrolysis of the hemicellulose and cellulose. Disruptive conditions can comprise, e.g., subjecting the starting material to an average temperature of 180° C. to 270° C. at pH 0.5 to 2.5 for a period of about 5 seconds to 60 minutes; or, temperature of 220° C. to 270° C., at pH 0.5 to 2.5 for a period of 5 seconds to 120 seconds, or equivalent. This generates a feedstock with increased accessibility to being digested by an enzyme, e.g., a cellulase enzyme of the invention. U.S. Pat. No. 6,090,595.

[0551] Exemplary conditions for cellulase hydrolysis of lignocellulosic material include reactions at temperatures between about 30° C. and 48° C., and/or a pH between about 4.0 and 6.0. Other exemplary conditions include a temperature between about 30° C. and 60° C. and a pH between about 4.0 and 8.0.

[0552] Animal Feeds and Food or Feed Additives

[0553] In addition to providing dietary aids or supplements, or food supplements and additives for human use, the invention also provides compositions and methods for treating animal feeds and foods and food or feed additives using a polypeptide of the invention, e.g., a protein having cellulase activity, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes of the invention, and/or the antibodies of the invention. The invention provides animal feeds, foods, and additives comprising cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes of the invention and/or antibodies of the invention. The animal can be any farm animal or any animal.

[0554] The animal feed additive of the invention may be a granulated enzyme product that may readily be mixed with feed components. Alternatively, feed additives of the invention can form a component of a pre-mix. The granulated enzyme product of the invention may be coated or uncoated. The particle size of the enzyme granulates can be compatible with that of feed and pre-mix components. This provides a safe and convenient mean of incorporating enzymes into feeds. Alternatively, the animal feed additive of the invention may be a stabilized liquid composition. This may be an aqueous or oil-based slurry. See, e.g., U.S. Pat. No. 6,245,546.

[0555] Cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes of the present invention, in the modification of animal feed or a food, can process the food or feed either in vitro (by modifying components of the feed or food) or in vivo. Polypeptides of the invention can be added to animal feed or food compositions.

[0556] In one aspect, an enzyme of the invention is added in combination with another enzyme, e.g., beta-galactosidases, catalases, laccases, other cellulases, endoglycosidases, endo-beta-1,4-laccases, amyloglucosidases, other glucosidases, glucose isomerases, glycosyltransferases, lipases, phospholipases, lipooxygenases, beta-laccases, endo-beta-1,3(4)-laccases, cutinases, peroxidases, amylases, glucoamylases, pectinases, reductases, oxidases, decarboxylases, phenoloxidases, ligninases, pullulanases, arabinanases, hemicellulases, mannanases, xylolaccases, xylanases, pectin acetyl esterases, rhamnogalacturonan acetyl esterases, proteases, peptidases, proteinases, polygalacturonases, rhamnogalacturonases, galactanases, pectin lyases, transglutaminases, pectin methylesterases, other cellobiohydrolases and/or transglutaminases. These enzyme digestion products are more digestible by the animal. Thus, cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes of the invention can contribute to the available energy of the feed or food, or to the digestibility of the food or feed by breaking down cellulose.

[0557] In another aspect, cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme of the invention can be supplied by expressing the enzymes directly in transgenic feed crops (as, e.g., transgenic plants, seeds and the like), such as grains, cereals, corn, soy bean, rape seed, lupin and the like. As discussed above, the invention provides transgenic plants, plant parts and plant cells comprising a nucleic acid sequence encoding a polypeptide of the invention. In one aspect, the nucleic acid is expressed such that the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme of the invention is produced in recoverable quantities. The cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme can be recovered from any plant or plant part. Alternatively, the plant or plant part containing the recombinant polypeptide can be used as such for improving the quality of a food or feed, e.g., improving nutritional value, palatability, etc.

[0558] In one aspect, the enzyme delivery matrix of the invention is in the form of discrete plural particles, pellets or granules. By "granules" is meant particles that are compressed or compacted, such as by a pelletizing, extrusion, or similar compacting to remove water from the matrix. Such compression or compacting of the particles also promotes intraparticle cohesion of the particles. For example, the granules can be prepared by pelletizing the grain-based substrate in a pellet mill. The pellets prepared thereby are ground or crumbled to a granule size suitable for use as an adjuvant in animal feed. Since the matrix is itself approved for use in animal feed, it can be used as a diluent for delivery of enzymes in animal feed.

[0559] In one aspect, the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme contained in the invention enzyme delivery matrix and methods is a thermostable cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme, as described herein, so as to resist inactivation of the cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme during manufacture where elevated temperatures and/or steam may be employed to prepare the palletized enzyme delivery matrix. During digestion of feed containing the invention enzyme delivery matrix, aqueous digestive fluids will cause release of the active enzyme. Other types of thermostable enzymes and nutritional supplements that are thermostable can also be incorporated in the delivery matrix for release under any type of aqueous conditions.

[0560] In one aspect, a coating is applied to the enzyme matrix particles for many different purposes, such as to add a flavor or nutrition supplement to animal feed, to delay release of animal feed supplements and enzymes in gastric conditions, and the like. In one aspect, the coating is applied to achieve a functional goal, for example, whenever it is desirable to slow release of the enzyme from the matrix particles or to control the conditions under which the enzyme will be released. The composition of the coating material can be such that it is selectively broken down by an agent to which it is susceptible (such as heat, acid or base, enzymes or other chemicals). Alternatively, two or more coatings susceptible to different such breakdown agents may be consecutively applied to the matrix particles.

[0561] The invention is also directed towards a process for preparing an enzyme-releasing matrix. In accordance with the invention, the process comprises providing discrete plural particles of a grain-based substrate in a particle size suitable for use as an enzyme-releasing matrix, wherein the particles comprise a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme encoded by an amino acid sequence of the invention. In one aspect, the process includes compacting or compressing the particles of enzyme-releasing matrix into granules, which most in one aspect is accomplished by pelletizing. The mold inhibitor and cohesiveness agent, when used, can be added at any suitable time, and in one aspect are mixed with the grain-based substrate in the desired proportions prior to pelletizing of the grain-based substrate. Moisture content in the pellet mill feed in one aspect is in the ranges set forth above with respect to the moisture content in the finished product, and in one aspect is about 14-15%. In one aspect, moisture is added to the feedstock in the form of an aqueous preparation of the enzyme to bring the feedstock to this moisture content. The temperature in the pellet mill in one aspect is brought to about 82° C. with steam. The pellet mill may be operated under any conditions that impart sufficient work to the feedstock to provide pellets. The pelleting process itself is a cost-effective process for removing water from the enzyme-containing composition.

[0562] The compositions and methods of the invention can be practiced in conjunction with administration of prebiotics, which are high molecular weight sugars, e.g., fructo-oligosaccharides (FOS); galacto-oligosaccharides (GOS), GRAS (Generally Recognized As Safe) material. These prebiotics can be metabolized by some probiotic lactic acid bacteria (LAB). They are non-digestible by the majority of intestinal microbes.

[0563] Treating Foods and Food Processing

[0564] The invention provides foods and feeds comprising enzymes of the invention, and methods for using enzymes of the invention in processing foods and feeds. Cellulases, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes of the invention have numerous applications in food processing industry. The invention provides methods for hydrolyzing cellulose-comprising compositions, including, e.g., a plant cell, a bacterial cell, a yeast cell, an insect cell, or an animal cell, or any plant or plant part, or any food or feed, a waste product and the like.

[0565] For example, the invention provides feeds or foods comprising a cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzyme the invention, e.g., in a feed, a liquid, e.g., a beverage (such as a fruit juice or a beer), a bread or a dough or a bread product, or a drink (e.g., a beer) or a beverage precursor (e.g., a wort).

[0566] The food treatment processes of the invention can also include the use of any combination of other enzymes such as tryptophanases or tyrosine decarboxylases, laccases, catalases, laccases, other cellulases, endoglycosidases, endo-beta-1,4-laccases, amyloglucosidases, other glucosidases, glucose isomerases, glycosyltransferases, lipases, phospholipases, lipooxygenases, beta-laccases, endo-beta-1,3(4)-laccases, cutinases, peroxidases, amylases, glucoamylases, pectinases, reductases, oxidases, decarboxylases, phenoloxidases, ligninases, pullulanases, arabinanases, hemicellulases, mannanases, xylolaccases, xylanases, pectin acetyl esterases, rhamnogalacturonan acetyl esterases, proteases, peptidases, proteinases, polygalacturonases, rhamnogalacturonases, galactanases, pectin lyases, transglutaminases, pectin methylesterases, other cellobiohydrolases and/or transglutaminases.

[0567] In one aspect, the invention provides enzymes and processes for hydrolyzing liquid (liquefied) and granular starch. Such starch can be derived from any source, e.g., beet, cane sugar, potato, corn, wheat, milo, sorghum, rye or bulgher. The invention applies to any plant starch source, e.g., a grain starch source, which is useful in liquefaction (for example, to make bioethanol), including any other grain or vegetable source known to produce starch suitable for liquefaction. The methods of the invention comprise liquefying starch (e.g., making bioethanol) from any natural material, such as rice, germinated rice, corn, barley, milo, wheat, legumes, potato, beet, cane sugar and sweet potato. The liquefying process can substantially hydrolyze the starch to produce a syrup. The temperature range of the liquefaction can be any liquefaction temperature which is known to be effective in liquefying starch. For example, the temperature of the starch can be between about 80° C. to about 115° C., between about 100° C. to about 110° C., and from about 105° C. to about 108° C. The bioethanols made using the enzymes and processes of the invention can be used as fuels or in fuels (e.g., auto fuels), e.g., as discussed below, in addition to their use in (or for making) foods and feeds, including alcoholic beverages.

[0568] Waste Treatment

[0569] The invention provides enzymes for use in waste treatment. Cellulases, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes of the invention can be used in a variety of waste treatment or related industrial applications, e.g., in waste treatment related to biomass conversion to generate fuels. For example, in one aspect, the invention provides a solid and/or liquid waste digestion process using cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes of the invention. The methods can comprise reducing the mass and volume of substantially untreated solid waste. Solid waste can be treated with an enzymatic digestive process in the presence of an enzymatic solution (including cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes of the invention) at a controlled temperature. This results in a reaction without appreciable bacterial fermentation from added microorganisms. The solid waste is converted into a liquefied waste and any residual solid waste. The resulting liquefied waste can be separated from said any residual solidified waste. See e.g., U.S. Pat. No. 5,709,796.

[0570] In one aspect, the compositions and methods of the invention are used for odor removal, odor prevention or odor reduction, e.g., in animal waste lagoons, e.g., on swine farms, in other animal waste management systems, or in any industrial or food processing application.

[0571] The enzymes and methods for the conversion of biomass (e.g., lignocellulosic materials) to fuels (e.g., bioethanol) can incorporate the treatment/recycling of municipal solid waste material, including waste obtained directly from a municipality or municipal solid waste that was previously land-filled and subsequently recovered, or sewage sludge, e.g., in the form of sewage sludge cake which contains substantial amounts of cellulosic material. Since sewage sludge cakes will normally not contain substantial amounts of recyclable materials (aluminum, glass, plastics, etc.), they can be directly treated with concentrated sulfuric acid (to reduce the heavy metal content of the cellulosic component of the waste) and processed in the ethanol production system. See, e.g., U.S. Pat. Nos. 6,267,309; 5,975,439.

[0572] Another exemplary method using enzymes of the invention for recovering organic and inorganic matter from waste material comprises sterilizing a solid organic matter and softening it by subjecting it to heat and pressure. This exemplary process may be carried out by first agitating waste material and then subjecting it to heat and pressure, which sterilizes it and softens the organic matter contained therein. In one aspect, after heating under pressure, the pressure may be suddenly released from a perforated chamber to forces the softened organic matter outwardly through perforations of the container, thus separating the organic matter from the solid inorganic matter. The softened sterilized, organic matter is then fermented in fermentation chamber, e.g., using enzymes of the invention, e.g., to form a mash. The mash may be subjected to further processing by centrifuge, distillation column and/or anaerobic digester to recover fuels such as ethanol and methane, and animal feed supplements. See, e.g., U.S. Pat. No. 6,251,643.

[0573] Enzymes of the invention can also be used in processes, e.g., pretreatments, to reduce the odor of an industrial waste, or a waste generated from an animal production facility, and the like. For example, enzymes of the invention can be used to treat an animal waste in a waste holding facility to enhance efficient degradation of large amounts of organic matter with reduced odor. The process can also include inoculation with sulfide-utilizing bacteria and organic digesting bacteria and lytic enzymes (in addition to an enzyme of the invention). See, e.g., U.S. Pat. No. 5,958,758.

[0574] Enzymes of the invention can also be used in mobile systems, e.g., batch type reactors, for bioremediation of aqueous, hazardous wastes, e.g., as described in U.S. Pat. No. 5,833,857. Batch type reactors can be large vessels having circulatory capability wherein bacteria (e.g., expressing an enzyme of the invention) are maintained in an efficient state by nutrients being feed into the reactor. Such systems can be used where effluent can be delivered to the reactor or the reactor is built into a waste water treatment system. Enzymes of the invention can also be used in treatment systems for use at small or temporary remote locations, e.g., portable, high volume, highly efficient, versatile waste water treatment systems.

[0575] The waste treatment processes of the invention can include the use of any combination of other enzymes such as other cellulase, e.g., endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase enzymes, catalases, laccases, other cellulases, endoglycosidases, endo-beta-1,4-laccases, amyloglucosidases, other glucosidases, glucose isomerases, glycosyltransferases, lipases, phospholipases, lipooxygenases, beta-laccases, endo-beta-1,3(4)-laccases, cutinases, peroxidases, amylases, glucoamylases, pectinases, reductases, oxidases, decarboxylases, phenoloxidases, ligninases, pullulanases, phytases, arabinanases, hemicellulases, mannanases, xylolaccases, xylanases, pectin acetyl esterases, rhamnogalacturonan acetyl esterases, proteases, peptidases, proteinases, polygalacturonases, rhamnogalacturonases, galactanases, pectin lyases, transglutaminases, pectin methylesterases, other cellobiohydrolases and/or transglutaminases.

[0576] Detergent Compositions

[0577] The invention provides detergent compositions comprising one or more polypeptides of the invention (e.g., enzymes having cellulase, endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity) and methods of making and using these compositions. The invention incorporates all methods of making and using detergent compositions, see, e.g., U.S. Pat. Nos. 6,413,928; 6,399,561; 6,365,561; 6,380,147. The detergent compositions can be a one and two part aqueous composition, a non-aqueous liquid composition, a cast solid, a granular form, a particulate form, a compressed tablet, a gel and/or a paste and a slurry form. The invention also provides methods capable of a rapid removal of gross food soils, films of food residue and other minor food compositions using these detergent compositions. Enzymes of the invention can facilitate the removal of starchy stains by means of catalytic hydrolysis of the starch polysaccharide. Enzymes of the invention can be used in dishwashing detergents in textile laundering detergents.

[0578] The actual active enzyme content depends upon the method of manufacture of a detergent composition and is not critical, assuming the detergent solution has the desired enzymatic activity. In one aspect, the amount of glucosidase present in the final solution ranges from about 0.001 mg to 0.5 mg per gram of the detergent composition. The particular enzyme chosen for use in the process and products of this invention depends upon the conditions of final utility, including the physical product form, use pH, use temperature, and soil types to be degraded or altered. The enzyme can be chosen to provide optimum activity and stability for any given set of utility conditions. In one aspect, the polypeptides of the present invention are active in the pH ranges of from about 4 to about 12 and in the temperature range of from about 20° C. to about 95° C. The detergents of the invention can comprise cationic, semi-polar nonionic or zwitterionic surfactants; or, mixtures thereof.

[0579] Enzymes of the present invention (e.g., enzymes having cellulase, endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity) can be formulated into powdered and liquid detergents having pH between 4.0 and 12.0 at levels of about 0.01 to about 5% (preferably 0.1% to 0.5%) by weight. These detergent compositions can also include other enzymes such as known proteases, cellulases, lipases or endoglycosidases, as well as builders and stabilizers. The addition of enzymes of the invention to conventional cleaning compositions does not create any special use limitation. In other words, any temperature and pH suitable for the detergent is also suitable for the present compositions as long as the pH is within the above range, and the temperature is below the described enzyme's denaturing temperature. In addition, the polypeptides of the invention can be used in a cleaning composition without detergents, again either alone or in combination with builders and stabilizers.

[0580] The present invention provides cleaning compositions including detergent compositions for cleaning hard surfaces, detergent compositions for cleaning fabrics, dishwashing compositions, oral cleaning compositions, denture cleaning compositions, and contact lens cleaning solutions.

[0581] In one aspect, the invention provides a method for washing an object comprising contacting the object with a polypeptide of the invention under conditions sufficient for washing. A polypeptide of the invention may be included as a detergent additive. The detergent composition of the invention may, for example, be formulated as a hand or machine laundry detergent composition comprising a polypeptide of the invention. A laundry additive suitable for pre-treatment of stained fabrics can comprise a polypeptide of the invention. A fabric softener composition can comprise a polypeptide of the invention. Alternatively, a polypeptide of the invention can be formulated as a detergent composition for use in general household hard surface cleaning operations. In alternative aspects, detergent additives and detergent compositions of the invention may comprise one or more other enzymes such as a protease, a lipase, a cutinase, another glucosidase, a carbohydrase, another cellulase, a pectinase, a mannanase, an arabinase, a galactanase, a xylanase, an oxidase, e.g., a lactase, and/or a peroxidase. The properties of the enzyme(s) of the invention are chosen to be compatible with the selected detergent (i.e. pH-optimum, compatibility with other enzymatic and non-enzymatic ingredients, etc.) and the enzyme(s) is present in effective amounts. In one aspect, enzymes of the invention are used to remove malodorous materials from fabrics. Various detergent compositions and methods for making them that can be used in practicing the invention are described in, e.g., U.S. Pat. Nos. 6,333,301; 6,329,333; 6,326,341; 6,297,038; 6,309,871; 6,204,232; 6,197,070; 5,856,164.

[0582] The detergents and related processes of the invention can also include the use of any combination of other enzymes such as tryptophanases or tyrosine decarboxylases, laccases, catalases, laccases, other cellulases, endoglycosidases, endo-beta-1,4-laccases, amyloglucosidases, other glucosidases, glucose isomerases, glycosyltransferases, lipases, phospholipases, lipooxygenases, beta-laccases, endo-beta-1,3(4)-laccases, cutinases, peroxidases, amylases, glucoamylases, pectinases, reductases, oxidases, decarboxylases, phenoloxidases, ligninases, pullulanases, arabinanases, hemicellulases, mannanases, xylolaccases, xylanases, pectin acetyl esterases, rhamnogalacturonan acetyl esterases, proteases, peptidases, proteinases, polygalacturonases, rhamnogalacturonases, galactanases, pectin lyases, transglutaminases, pectin methylesterases, other cellobiohydrolases and/or transglutaminases.

[0583] Treating Fabrics and Textiles

[0584] The invention provides methods of treating fabrics and textiles using one or more polypeptides of the invention, e.g., enzymes having cellulase, endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity. The polypeptides of the invention can be used in any fabric-treating method, which are well known in the art, see, e.g., U.S. Pat. No. 6,077,316. For example, in one aspect, the feel and appearance of a fabric is improved by a method comprising contacting the fabric with an enzyme of the invention in a solution. In one aspect, the fabric is treated with the solution under pressure.

[0585] In one aspect, the enzymes of the invention are applied during or after the weaving of textiles, or during the desizing stage, or one or more additional fabric processing steps. During the weaving of textiles, the threads are exposed to considerable mechanical strain. Prior to weaving on mechanical looms, warp yarns are often coated with sizing starch or starch derivatives in order to increase their tensile strength and to prevent breaking. The enzymes of the invention can be applied to remove these sizing starch or starch derivatives. After the textiles have been woven, a fabric can proceed to a desizing stage. This can be followed by one or more additional fabric processing steps. Desizing is the act of removing size from textiles. After weaving, the size coating must be removed before further processing the fabric in order to ensure a homogeneous and wash-proof result. The invention provides a method of desizing comprising enzymatic hydrolysis of the size by the action of an enzyme of the invention.

[0586] The enzymes of the invention (e.g., enzymes having cellulase, endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity) can be used to desize fabrics, including cotton-containing fabrics, as detergent additives, e.g., in aqueous compositions. The invention provides methods for producing a stonewashed look on indigo-dyed denim fabric and garments. For the manufacture of clothes, the fabric can be cut and sewn into clothes or garments, which is afterwards finished. In particular, for the manufacture of denim jeans, different enzymatic finishing methods have been developed. The finishing of denim garment normally is initiated with an enzymatic desizing step, during which garments are subjected to the action of amylolytic enzymes in order to provide softness to the fabric and make the cotton more accessible to the subsequent enzymatic finishing steps. The invention provides methods of finishing denim garments (e.g., a "bio-stoning process"), enzymatic desizing and providing softness to fabrics using the Enzymes of the invention. The invention provides methods for quickly softening denim garments in a desizing and/or finishing process.

[0587] The invention also provides disinfectants comprising enzymes of the invention (e.g., enzymes having cellulase, endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity).

[0588] The fabric or textile treatment processes of the invention can also include the use of any combination of other enzymes such as tryptophanases or tyrosine decarboxylases, laccases, catalases, laccases, other cellulases, endoglycosidases, endo-beta-1,4-laccases, amyloglucosidases, other glucosidases, glucose isomerases, glycosyltransferases, lipases, phospholipases, lipooxygenases, beta-laccases, endo-beta-1,3(4)-laccases, cutinases, peroxidases, amylases, glucoamylases, pectinases, reductases, oxidases, decarboxylases, phenoloxidases, ligninases, pullulanases, arabinanases, hemicellulases, mannanases, xylolaccases, xylanases, pectin acetyl esterases, rhamnogalacturonan acetyl esterases, proteases, peptidases, proteinases, polygalacturonases, rhamnogalacturonases, galactanases, pectin lyases, transglutaminases, pectin methylesterases, other cellobiohydrolases and/or transglutaminases.

[0589] Paper or Pulp Treatment

[0590] The enzymes of the invention (e.g., enzymes having cellulase, endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity) can be in paper or pulp treatment or paper deinking. For example, in one aspect, the invention provides a paper treatment process using enzymes of the invention. In one aspect, the enzymes of the invention can be used to modify starch in the paper thereby converting it into a liquefied form. In another aspect, paper components of recycled photocopied paper during chemical and enzymatic deinking processes. In one aspect, Enzymes of the invention can be used in combination with other enzymes, including other cellulases (including other endoglucanases, cellobiohydrolases and/or beta-glucosidases). The wood, paper, paper product or pulp can be treated by the following three processes: 1) disintegration in the presence of an enzyme of the invention, 2) disintegration with a deinking chemical and an enzyme of the invention, and/or 3) disintegration after soaking with an enzyme of the invention. The recycled paper treated with an enzyme of the invention can have a higher brightness due to removal of toner particles as compared to the paper treated with just cellulase. While the invention is not limited by any particular mechanism, the effect of an enzyme of the invention may be due to its behavior as surface-active agents in pulp suspension.

[0591] The invention provides methods of treating paper and paper pulp using one or more polypeptides of the invention. The polypeptides of the invention can be used in any paper- or pulp-treating method, which are well known in the art, see, e.g., U.S. Pat. Nos. 6,241,849; 6,066,233; 5,582,681. For example, in one aspect, the invention provides a method for deinking and decolorizing a printed paper containing a dye, comprising pulping a printed paper to obtain a pulp slurry, and dislodging an ink from the pulp slurry in the presence of an enzyme of the invention (other enzymes can also be added). In another aspect, the invention provides a method for enhancing the freeness of pulp, e.g., pulp made from secondary fiber, by adding an enzymatic mixture comprising an enzyme of the invention (can also include other enzymes, e.g., pectinase enzymes) to the pulp and treating under conditions to cause a reaction to produce an enzymatically treated pulp. The freeness of the enzymatically treated pulp is increased from the initial freeness of the secondary fiber pulp without a loss in brightness.

[0592] The paper, wood or pulp treatment or recycling processes of the invention can also include the use of any combination of other enzymes such as tryptophanases or tyrosine decarboxylases, laccases, catalases, laccases, other cellulases, endoglycosidases, endo-beta-1,4-laccases, amyloglucosidases, other glucosidases, glucose isomerases, glycosyltransferases, lipases, phospholipases, lipooxygenases, beta-laccases, endo-beta-1,3(4)-laccases, cutinases, peroxidases, amylases, glucoamylases, pectinases, reductases, oxidases, decarboxylases, phenoloxidases, ligninases, pullulanases, arabinanases, hemicellulases, mannanases, xylolaccases, xylanases, pectin acetyl esterases, rhamnogalacturonan acetyl esterases, proteases, peptidases, proteinases, polygalacturonases, rhamnogalacturonases, galactanases, pectin lyases, transglutaminases, pectin methylesterases, other cellobiohydrolases and/or transglutaminases.

[0593] Repulping: Treatment of Lignocellulosic Materials

[0594] The invention also provides a method for the treatment of lignocellulosic fibers, wherein the fibers are treated with a polypeptide of the invention (e.g., enzymes having cellulase, endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity), in an amount which is efficient for improving the fiber properties. The enzymes of the invention may also be used in the production or recycling of lignocellulosic materials such as pulp, paper and cardboard, from starch reinforced waste paper and cardboard, especially where repulping or recycling occurs at pH above 7 and where the enzymes of the invention can facilitate the disintegration of the waste material through degradation of the reinforcing starch. The enzymes of the invention can be useful in a process for producing a papermaking pulp from starch-coated printed paper. The process may be performed as described in, e.g., WO 95/14807. An exemplary process comprises disintegrating the paper to produce a pulp, treating with a starch-degrading enzyme before, during or after the disintegrating, and separating ink particles from the pulp after disintegrating and enzyme treatment. See also U.S. Pat. No. 6,309,871 and other US patents cited herein. Thus, the invention includes a method for enzymatic deinking of recycled paper pulp, wherein the polypeptide is applied in an amount which is efficient for effective de-inking of the fiber surface.

[0595] Brewing and Fermenting

[0596] The invention provides methods of brewing (e.g., fermenting) beer comprising an enzyme of the invention, e.g., enzymes having cellulase, endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity. In one exemplary process, starch-containing raw materials are disintegrated and processed to form a malt. An enzyme of the invention is used at any point in the fermentation process. For example, enzymes of the invention can be used in the processing of barley malt. The major raw material of beer brewing is barley malt. This can be a three stage process. First, the barley grain can be steeped to increase water content, e.g., to around about 40%. Second, the grain can be germinated by incubation at 15-25° C. for 3 to 6 days when enzyme synthesis is stimulated under the control of gibberellins. During this time enzyme levels rise significantly. In one aspect, enzymes of the invention are added at this (or any other) stage of the process. The action of the enzyme results in an increase in fermentable reducing sugars. This can be expressed as the diastatic power, DP, which can rise from around 80 to 190 in 5 days at 12° C.

[0597] Enzymes of the invention can be used in any beer producing process, as described, e.g., in U.S. Pat. Nos. 5,762,991; 5,536,650; 5,405,624; 5,021,246; 4,788,066.

[0598] Increasing the Flow of Production Fluids from a Subterranean Formation

[0599] The invention also includes a method using an enzyme of the invention (e.g., enzymes having cellulase, endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity), wherein the method increases the flow of production fluids from a subterranean formation by removing viscous, starch-containing, damaging fluids formed during production operations; these fluids can be found within the subterranean formation which surrounds a completed well bore. Thus, this method of the invention results in production fluids being able to flow from the well bore. This method of the invention also addresses the problem of damaging fluids reducing the flow of production fluids from a formation below expected flow rates. In one aspect, the invention provides for formulating an enzyme treatment (using an enzyme of the invention) by blending together an aqueous fluid and a polypeptide of the invention; pumping the enzyme treatment to a desired location within the well bore; allowing the enzyme treatment to degrade the viscous, starch-containing, damaging fluid, whereby the fluid can be removed from the subterranean formation to the well surface; and wherein the enzyme treatment is effective to attack the alpha glucosidic linkages in the starch-containing fluid.

[0600] The subterranean formation enzyme treatment processes of the invention can also include the use of any combination of other enzymes such as tryptophanases or tyrosine decarboxylases, laccases, catalases, laccases, other cellulases, endoglycosidases, endo-beta-1,4-laccases, amyloglucosidases, other glucosidases, glucose isomerases, glycosyltransferases, lipases, phospholipases, lipooxygenases, beta-laccases, endo-beta-1,3(4)-laccases, cutinases, peroxidases, amylases, glucoamylases, pectinases, reductases, oxidases, decarboxylases, phenoloxidases, ligninases, pullulanases, arabinanases, hemicellulases, mannanases, xylolaccases, xylanases, pectin acetyl esterases, rhamnogalacturonan acetyl esterases, proteases, peptidases, proteinases, polygalacturonases, rhamnogalacturonases, galactanases, pectin lyases, transglutaminases, pectin methylesterases, other cellobiohydrolases and/or transglutaminases.

[0601] Pharmaceutical Compositions and Dietary Supplements

[0602] The invention also provides pharmaceutical compositions and dietary supplements (e.g., dietary aids) comprising a cellulase of the invention (e.g., enzymes having endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity). The cellulase activity comprises endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity. In one aspect, the pharmaceutical compositions and dietary supplements (e.g., dietary aids) are formulated for oral ingestion, e.g., to improve the digestibility of foods and feeds having a high cellulose or lignocellulosic component.

[0603] Periodontal treatment compounds can comprise an enzyme of the invention, e.g., as described in U.S. Pat. No. 6,776,979. Compositions and methods for the treatment or prophylaxis of acidic gut syndrome can comprise an enzyme of the invention, e.g., as described in U.S. Pat. No. 6,468,964.

[0604] In another aspect, wound dressings, implants and the like comprise antimicrobial (e.g., antibiotic-acting) enzymes, including an enzyme of the invention (including, e.g., exemplary sequences of the invention). Enzymes of the invention can also be used in alginate dressings, antimicrobial barrier dressings, burn dressings, compression bandages, diagnostic tools, gel dressings, hydro-selective dressings, hydrocellular (foam) dressings, hydrocolloid dressings, I.V dressings, incise drapes, low adherent dressings, odor absorbing dressings, paste bandages, post operative dressings, scar management, skin care, transparent film dressings and/or wound closure. Enzymes of the invention can be used in wound cleansing, wound bed preparation, to treat pressure ulcers, leg ulcers, burns, diabetic foot ulcers, scars, IV fixation, surgical wounds and minor wounds. Enzymes of the invention can be used to in sterile enzymatic debriding compositions, e.g., ointments. In various aspects, the cellulase is formulated as a tablet, gel, pill, implant, liquid, spray, powder, food, feed pellet or as an encapsulated formulation.

[0605] Biodefense Applications

[0606] In other aspects, cellulases of the invention (e.g., enzymes having endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity) can be used in biodefense (e.g., destruction of spores or bacteria comprising a lignocellulosic material). Use of cellulases of the invention in biodefense applications offer a significant benefit, in that they can be very rapidly developed against any currently unknown or biological warfare agents of the future. In addition, cellulases of the invention can be used for decontamination of affected environments. In aspect, the invention provides a biodefense or bio-detoxifying agent comprising a polypeptide having a cellulase activity, wherein the polypeptide comprises a sequence of the invention (including, e.g., exemplary sequences of the invention), or a polypeptide encoded by a nucleic acid of the invention (including, e.g., exemplary sequences of the invention), wherein optionally the polypeptide has activity comprising endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity.

REFERENCE LIST

[0607] 1. Sambrook, J. and Russell, D. W. 2001. Molecular Cloning: A Laboratory Manual. Third Edition. Cold Spring Harbor Laboratory Press, New York.

[0608] 2. Benhar, I. Biotechnological applications of phage and cell display. Biotechnology Advances 19, 1-13. 2001.

[0609] 3. Coutinho, P. M. and Henrissat, B. Carbohydrate-Active Enzymes server at URL: http://afmb.cnrs-mrs.fr/˜cazy/CAZY/index.html. 1999.

[0610] 4. Felix, C. R. and L. G. Ljungdahl. 1993. The cellulosome: the exocellular organelle of Clostridium. Annu. Rev. Microbiol 47:791-819:791-819.

[0611] 5. Gray, K. A., T. H. Richardson, K. Kretz, J. M. Short, F. Bartnek, Knowles R., L. Kan, Swanson P. E., and Robertson D. E. 2001. Rapid evolution of reversible denaturation and elevated melting temperature in a microbial haloalkane dehalogenase. Advanced Synthesis and Catalysis 343:607-617.

[0612] 6. Guttman, A., F. T. Chen, R. A. Evangelista, and N. Cooke. 1996. High-resolution capillary gel electrophoresis of reducing oligosaccharides labeled with 1-aminopyrene-3,6,8-trisulfonate. Anal. Biochem 233:234-242.

[0613] 7. Harjunpaa, V., A. Teleman, A. Koivula, L. Ruohonen, T. T. Teeri, O. Teleman, and T. Drakenberg. 1996. Cello-oligosaccharide hydrolysis by cellobiohydrolase II from Trichoderma reesei. Association and rate constants derived from an analysis of progress curves. Eur. J Biochem 240:584-591.

[0614] 8. Himmel, M. E., M. F. Ruth, and C. E. Wyman. 1999. Cellulase for commodity products from cellulosic biomass. Curr. Opin. Biotechnol 10:358-364.

[0615] 9. Kerr, R. A. 1998. GEOLOGY: The Next Oil Crisis Looms Large--and Perhaps Close. Science 281:1128.

[0616] 10. Kerr, R. A. 2000. OIL OUTLOOK:USGS Optimistic on World Oil Prospects. Science 289:237.

[0617] 11. King, R. W., K. D. Lustig, P. T. Stukenberg, T. J. McGarry, and M. W. Kirschner. 1997. Expression cloning in the test tube. Science 277:973-974.

[0618] 12. Kuritz, T. 1999. An easy colorimetric assay for screening and qualitative assessment of deiodination and dehalogenation by bacterial cultures. Lett. Appl Microbiol 28:445-447.

[0619] 13. Lundberg, K. S., P. L. Kretz, G. S. Provost, and J. M. Short. 1993. The use of selection in recovery of transgenic targets for mutation analysis. Mutat. Res. 301:99-105.

[0620] 14. MacKenzie, L. F., G. Sulzenbacher, C. Divne, T. A. Jones, H. F. Woldike, M. Schulein, S. G. Withers, and G. J. Davies. 1998. Crystal structure of the family 7 endoglucanase I (Cel7B) from Humicola insolens at 2.2 A resolution and identification of the catalytic nucleophile by trapping of the covalent glycosyl-enzyme intermediate. Biochem J 335:409-416.

[0621] 15. Richardson, T. H., X. Tan, G. Frey, W. Callen, M. Cabell, D. Lam, J. Macomber, J. M. Short, D. E. Robertson, and C. Miller. 2002. A novel, high performance enzyme for starch liquefaction. Discovery and optimization of a low pH, thermostable alpha-amylase. J Biol Chem 277:26501-26507.

[0622] 16. Sakon, J., D. Irwin, D. B. Wilson, and P. A. Karplus. 1997. Structure and mechanism of endo/exocellulase E4 from Thermomonospora fusca. Nat. Struct. Biol 4:810-818.

[0623] 17. Short, J. M., J. M. Fernandez, J. A. Sorge, and W. D. Huse. 1988. Lambda ZAP: a bacteriophage lambda expression vector with in vivo excision properties. Nucleic Acids Res. 16:7583-7600.

[0624] 18. Snustad, D. P., J. P. Hunsperger, B. M. Chereskin, and J. Messing. 1988. Maize glutamine synthetase cDNAs: isolation by direct genetic selection in Escherichia coli. Genetics 120:1111-1123.

[0625] 19. Varrot, A., S. Hastrup, M. Schulein, and G. J. Davies. 1999. Crystal structure of the catalytic core domain of the family 6 cellobiohydrolase II, Ce16A, from Humicola insolens, at 1.92 A resolution. Biochem J 337:297-304.

[0626] 20. Yano, T., S. Oue, and H. Kagamiyama. 1998. Directed evolution of an aspartate aminotransferase with new substrate specificities. Proc. Natl. Acad. Sci. U.S. A 95:5511-5515.

[0627] 21. Zverlov, V. V., G. A. Velikodvorskaya, and W. H. Schwarz. 2002. A newly described cellulosomal cellobiohydrolase, CelO, from Clostridium thermocellum: investigation of the exo-mode of hydrolysis, and binding capacity to crystalline cellulose. Microbiology 148:247-255.

[0628] The following examples are offered to illustrate, but not to limit the claimed invention.

EXAMPLES

Example 1

GIGAMATRIX® Screen

[0629] In one aspect, the methods of the invention use Diversa Corporation's proprietary GIGAMATRIX® platform; see PCT Patent Publication No. WO 01/38583; U.S. patent application no. 20050046833; 20020080350; U.S. Pat. No. 6,918,738; Design Patent No. D480,814. For example, in one aspect, GIGAMATRIX® is used in methods to determine if a polypeptide has cellulase activity and is within the scope of the invention, or, to identify and isolate a polypeptide having cellulase activity.

[0630] A GIGAMATRIX® platform can include an ultra-high throughput screen based on a 100,000 well microplate with the dimensions of a conventional 96 well plate. In this example, the GIGAMATRIX® screen was implemented using 2 substrates based on previously shown activity by CBHs. Methyl-umbelliferyl cellobioside (MUC) and methylumbelliferyl lactoside (MUL) were tested. Phagemid versions of the different clones were screened because the substrate diffuses into cells and fluorescence was thought to be more easily detectable. A host strain lacking, beta-galactosidase was used in order to decrease activity on the lactoside substrate. The lactoside substrate resulted in fewer hits and was deemed more specific than the cellobiose substrate. In addition, the lactoside substrate resulted in fewer beta-glucosidase hits. In order to test the feasibility of using these substrates in a screen, 14 libraries were chosen for screening based on the fact that these libraries yielded endoglucanase hits from a previous screening program. Of the libraries screened, there were a total of 50 primary hits from 11 of the libraries screened. Secondary screening consisted of plating the clones on agar plates and then colony picking into 384 well plates containing media and MUL. Active clones against MUL are differentiated from a background of inactive clones. Individual clones were then grown overnight and fluorescence was measured and the most active hits were picked for sequencing.

[0631] All genomic clone inserts from hits were sequenced. In general, the hits were from several different glycosyl hydrolase families including 1, 2, 5, 6, 10 and 16. Several other hits were discovered where the open reading frame was not homologous to any known glycosyl hydrolase families. In addition, some of the hits encoded GTP cyclohydrolase genes.

TABLE-US-00002 TABLE 1 Summary of GIGAMATRIX ® hits Enzyme No. Open Reading Frame SEQ ID NO: nearest relevant BLAST 1 SEQ ID NO: 22 (encoded by, e.g. SEQ ID NO: 21) ORF 001 - family 5 (cellulase) 1a SEQ ID NO: 24 (encoded by SEQ ID NO: 23) ORF 003 - Family 16 + CBM 2 SEQ ID NO: 26 (encoded by, e.g. SEQ ID NO: 25) ORF 001 - family 1 (β-glucosidase) 3 SEQ ID NO: 92 (encoded by, e.g. SEQ ID NO: 91) ORF 001 - family 3 3a SEQ ID NO: 94 (encoded by, e.g. SEQ ID NO: 93) ORF 002 - alpha-rhamnosidase 4 SEQ ID NO: 96 (encoded by, e.g. SEQ ID NO: 95) ORF 001 - family 3 4a SEQ ID NO: 98 (encoded by, e.g. SEQ ID NO: 97) ORF 003 - beta-glucuronidase 5 SEQ ID NO: 128 (encoded by, e.g. SEQ ID NO: 127) ORF 004 - short chain dehydrogenase 5a SEQ ID NO: 130 (encoded by, e.g. SEQ ID NO: 129) ORF 010 - short chain dehydrogenase 6 SEQ ID NO: 116 (encoded by, e.g. SEQ ID NO: 115) ORF 004 - short chain dehydrogenase 6a SEQ ID NO: 118 (encoded by, e.g. SEQ ID NO: 117) ORF 011 - short chain dehydrogenase 7 SEQ ID NO: 40 (encoded by, e.g. SEQ ID NO: 39) ORF 004 - putative oxidoreductase 8 SEQ ID NO: 42 (encoded by, e.g. SEQ ID NO: 41) ORF 004 - cysteinyl tRNA synthetase 8a SEQ ID NO: 44 (encoded by, e.g. SEQ ID NO: 43) ORF 011 - hypothetical protein 9 SEQ ID NO: 54 (encoded by, e.g. SEQ ID NO: 53) ORF 002 - Radical SAM family 10 SEQ ID NO: 134 (encoded by, e.g. SEQ ID NO: 133) ORF 006 - family 1 (β-glucosidase) 11 SEQ ID NO: 58 (encoded by, e.g. SEQ ID NO: 57) ORF 001 - subtilisin like protease 12 SEQ ID NO: 46 (encoded by, e.g. SEQ ID NO: 45) ORF 006 - family 1 (β-glucosidase) 13 SEQ ID NO: 8 (encoded by, e.g. SEQ ID NO: 7) ORF 003 - Isocitrate dehydrogenase 13a SEQ ID NO: 10 (encoded by, e.g. SEQ ID NO: 9) ORF 004 - family 10 (xylanase) 14 SEQ ID NO: 48 (encoded by, e.g. SEQ ID NO: 47) ORF 002 - family 1 (β-glucosidase) 14a SEQ ID NO: 50 (encoded by, e.g. SEQ ID NO: 49) ORF 006 - fdhd/narq oxidoreductase 15 SEQ ID NO: 4 (encoded by, e.g. SEQ ID NO: 3) ORF 008 - family 1 (β-glucosidase) 15a SEQ ID NO: 6 (encoded by, e.g. SEQ ID NO: 5) ORF 012 - family 6 (cellulase) 16 SEQ ID NO: 136 (encoded by, e.g. SEQ ID NO: 135) ORF 001 - cellulase (glycosyl hydrolase family 5) 17 SEQ ID NO: 56 (encoded by, e.g. SEQ ID NO: 55) ORF 004 - family 1 (β-glucosidase) 18 SEQ ID NO: 126 (encoded by, e.g. SEQ ID NO: 125) ORF 009 - family 1 (β-glucosidase) 19 SEQ ID NO: 120 (encoded by, e.g. SEQ ID NO: 119) ORF 002 - oxidoreductase 19a SEQ ID NO: 122 (encoded by, e.g. SEQ ID NO: 121) ORF 004 - family 5 (cellulase) 20 SEQ ID NO: 124 (encoded by, e.g. SEQ ID NO: 123) ORF 006 - family 1 (β-glucosidase) 21 SEQ ID NO: 132 (encoded by, e.g. SEQ ID NO: 131) ORF 007 - family 5 (cellulase) 22 SEQ ID NO: 38 (encoded by, e.g. SEQ ID NO: 37) ORF 011 - family 1 (β-glucosidase) 22a SEQ ID NO: 36 (encoded by, e.g. SEQ ID NO: 35) ORF 007 - family 5 (cellulase) 23 SEQ ID NO: 138 (encoded by, e.g. SEQ ID NO: 137) ORF 001 - peptidase.sub.- M37 24 SEQ ID NO: 146 (encoded by, e.g. SEQ ID NO: 145) ORF 002 - family 1 (β-glucosidase) 25 SEQ ID NO: 52 (encoded by, e.g. SEQ ID NO: 51) ORF 001 - family 5 (cellulase) 26 SEQ ID NO: 20 (encoded by, e.g. SEQ ID NO: 19) ORF 008 - family 10 (xylanase) 26a SEQ ID NO: 18 (encoded by, e.g. SEQ ID NO: 17) ORF 005 - β-lactamase 27 SEQ ID NO: 16 (encoded by, e.g. SEQ ID NO: 15) ORF 007 - family 1 (β-glucosidase) 27a SEQ ID NO: 14 (encoded by, e.g. SEQ ID NO: 13) ORF 005 - NADH dependent dehydrogenase 27b SEQ ID NO: 12 (encoded by, e.g. SEQ ID NO: 11) ORF 003 - NAD binding oxidoreductase 28 SEQ ID NO: 28 (encoded by, e.g. SEQ ID NO: 27) ORF 002 - family 1 (β-glucosidase) 29 SEQ ID NO: 114 (encoded by, e.g. SEQ ID NO: 113) ORF 003 - family 10 30 SEQ ID NO: 34 (encoded by, e.g. SEQ ID NO: 33) ORF 006 - family 1 (β-glucosidase) 30a SEQ ID NO: 32 (encoded by, e.g. SEQ ID NO: 31) ORF 002 - cellodextrin phosphorylase 31 SEQ ID NO: 30 (encoded by, e.g. SEQ ID NO: 29) ORF 004 - family 1 (β-glucosidase) 32 SEQ ID NO: 100 (encoded by, e.g. SEQ ID NO: 99) ORF 012 - family 1 (β-glucosidase) 33 SEQ ID NO: 84 (encoded by, e.g. SEQ ID NO: 83) ORF 008 - dehydrogenase 34 SEQ ID NO: 102 (encoded by, e.g. SEQ ID NO: 101) ORF 003 - family 5 (cellulase) 35 SEQ ID NO: 140 (encoded by, e.g. SEQ ID NO: 139) ORF 001 - threonine dehydrogenase 36 SEQ ID NO: 142 (encoded by, e.g. SEQ ID NO: 141) ORF 005 - family 1 (β-glucosidase) 37 SEQ ID NO: 144 (encoded by, e.g. SEQ ID NO: 143) ORF 003 - family 1 (β-glucosidase) 38 SEQ ID NO: 2 (encoded by, e.g. SEQ ID NO: 1) ORF 001 - family 1 (β-glucosidase) 39 SEQ ID NO: 86 (encoded by, e.g. SEQ ID NO: 85) ORF 008 - family 1 (β-glucosidase) Abbreviations: CBM--carbohydrate binding module

Characterization Enzyme and Substrate Activity

[0632] The 39 hits (see Table 1, above) discovered in the GIGAMATRIX® screen were first screened against cellohexaose to determine action pattern on a cellulose oligomer. Genomic clones are defined as clones that have an entire DNA insert potentially containing multiple open reading frames. For example, in Table 1, above, one such genomic clone contains two open reading frames annoted as Enzymes No. 22 and 22a, with said open reading frames having the sequences as depicted in SEQ ID NO:37 and SEQ ID NO:35, respectively. Another such genomic clone is contains three open reading frames, which are annotated as Enzymes 27, 27a and 27b. Subclones are derived from genomic clones and can contain only a single open reading frame. Genomic clones were grown overnight in TB media containing antibiotic, cells were lysed and lysates were clarified by centrifugation. Subclones are grown to an OD600=0.5 induced with an appropriate inducer and then grown an additional 3 h before lysing the cells and clarifying the lysate. Genomic clones will generally have less activity than a subclone, but are a more facile way of assessing activity in a large range of clones. Initial studies were performed using thin layer chromatography (TLC) for endpoint reactions usually run for 24 h. Enzymes were also tested on phosphoric acid swollen cellulose (PASC), which is crystalline cellulose that is made more amorphous through swelling by acid treatment.

[0633] A number of cellulases which were cloned from environmental libraries were active against PASC, but released cellobiose as well as celltriose and/or glucose. The genomic clones from the GIGAMATRIX® discovery effort were also tested against PASC and on cellulosic substrates such as cellohexaose (Seikagaku, Japan). Thin layer chromatography (TLC) experiments showed that several genomic clones were able to hydrolyze the cellohexaose, as illustrated in FIGS. 6 and 7. Of these clones, many were able to generate glucose as the final product which is consistent with the fact that they have sequence identity to glycosyl hydrolase family 1, which includes beta-glucosidases. Several enzymes produced cellobiose and/or larger fragments, but the exact nature of the product pattern could not be discerned from the TLC experiments, so a capillary electrophoresis (CE) method was developed.

Example 2

Capillary Electrophoresis

[0634] In some aspects, Capillary Electrophoresis (CE) is used in assays to screen for enzyme activity, e.g., CE is used in methods to determine if a polypeptide has cellulase activity and is within the scope of the invention, or, to identify and isolate a polypeptide having cellulase activity. Capillary Electrophoresis (CE) offers the advantages of faster run times and greater assay sensitivity. The CE method used 1-aminopyrene-3,6,8-trisulfonate (APTS) as the fluorophore and was optimized for use with sugars and sugar oligomers (Guttman (1996) High-resolution capillary gel electrophoresis of reducing oligosaccharides labeled with 1-aminopyrene-3,6,8-trisulfonate. Anal. Biochem 233:234-242). Enzymes that were shown to be active on cellohexaose were subjected to tests on phosphoric acid swollen cellulose as well as cellohexaose. Genes were subcloned, expressed and partially purified using a nickel-chelating column. Enzymes were incubated with substrate for 1 h and the products were analyzed using a 10 cm or 48 cm capillary. Cellohexaose elutes at 2 and 9 minutes for the 10 and 48 cm capillaries respectively. The 48 cm capillary gives better separation of products in case there are low amounts of sugar or if there are contaminants in the mixture. The CE method was implemented for studies on enzymes from the GIGAMATRIX® discovery that showed good activity on cellohexaose with TLC detection.

[0635] Enzyme 22/22a (see Table, 1 above) showed good performance on PASC (data summarized in graph form in FIG. 8), releasing mainly cellobiose. In addition, enzyme 22/22a was able to release cellobiose from AVICEL® Microcrystalline Cellulose (MCC) (FMC Corporation, Philadelphia, Pa.) (data summarized in graph form in FIG. 9). Sequence analysis showed that enzyme 22 and enzyme 21 are ˜92% identical and belong to glycosyl hydrolase family 5. Family 5 contains mainly endoglucanases, but there are examples of cellobiohydrolases. CelO from Clostridium thermocellum has been characterized as a cellobiohydrolase based on activity on release of only cellobiose from amorphic and crystalline cellulose (Zverlov (2002) A newly described cellulosomal cellobiohydrolase, CelO, from Clostridium thermocellum: investigation of the exo-mode of hydrolysis, and binding capacity to crystalline cellulose. Microbiology 148:247-255).

[0636] All three of these enzymes, when compared to the endoglucanase from Acidothermus cellulolyticus have an insertion that is in close proximity to the substrate binding site. This insertion could form a loop which encloses the substrate binding site thus converting this enzyme from an endoglucanase to a cellobiohydrolase. When these enzymes were tested on cellohexaose they produced mainly cellobiose with a smaller amount of cellotriose. These results are explained by the fact that cellobiohydrolases have the capability to produce both cellobiose and cellotriose from a cellohexaose substrate (Harjunpaa (1996) Cello-oligosaccharide hydrolysis by cellobiohydrolase II from Trichoderma reesei. Association and rate constants derived from an analysis of progress curves. Eur. J Biochem 240:584-591).

Example 3

Sequence Based Discovery

[0637] The invention provides methods for identifying and isolating cellulases, e.g., cellobiohydrolases, using sequences of the invention. In one exemplary method, primers that were homologous to conserved regions of three glycosyl hydrolase families that contain cellobiohydrolases were used to screen either polynucleotide libraries or DNA derived from fungal samples. Primers were designed towards family 48 conserved regions and 96 libraries were screened resulting in 1 confirmed hit. In addition, primers were designed towards family 6 and family 7. Fungal libraries were screened with these primers, resulting in 1 hit for family 6 and 56 hits for family 7. One of the family 7 hits was chosen for studies to extract the full length sequence. The full-length sequence was successfully obtained and showed 73% identity to exo-cellobiohydrolase I of Penicillium janthinellum.

Example 4

Genetic Engineering of an Enzyme with Cellobiohydrolase Activity

[0638] This example described the genetic engineering of an exemplary enzyme of the invention. This enzyme can be used in the conversion of biomass to fuels and chemicals, and for making effective and sustainable alternatives to petroleum-based products. This enzyme can be expressed in organisms (e.g., microorganisms, such as bacteria) for its participation in chemical cycles involving natural biomass conversion. In one aspect, this enzyme is used in "enzyme ensembles" for the efficient depolymerization of cellulosic and hemicellulosic polymers to metabolizable carbon moieties. As discussed above, the invention provides methods for discovering and implementing the most effective of enzymes to enable these important new "biomass conversion" and alternative energy industrial processes.

[0639] Using metagenomic discovery and a non-stochastic method of directed evolution (called "DIRECTEVOLUTION®, as described, e.g., in U.S. Pat. No. 6,939,689, which includes Gene Site Saturation Mutagenesis (GSSM) (as discussed above, see also U.S. Pat. Nos. 6,171,820 and 6,579,258) and Tunable GeneReassembly (TGR) (see, e.g., U.S. Pat. No. 6,537,776) technologies. This effort focused on the discovery and optimization of an important enzyme component for cellulose reduction to glucose, cellobiohydrolase.

[0640] An enzyme discovery screen was implemented using Diversa Corporation's GIGAMATRIX® high throughput expression screening platform (discussed above) to identify cellobiohydrolases using methylumbelliferyl cellobioside as substrate. A total of 100 complex environmental libraries were screened resulting in 25 confirmed cellobiohydrolase hits mainly from glycosyl hydrolase families 5 and 10. These hits were characterized for activity against AVICEL® Microcrystalline Cellulose (MCC) (FMC Corporation, Philadelphia, Pa.). Based on its performance characteristics, one enzyme, SEQ ID NO:162 (encoded by, e.g., SEQ ID NO:161) was chosen as a candidate for optimization using Gene Site Saturation Mutagenesis (GSSM) technology. However, before GSSM evolution was performed, the signal sequence (amino acids 1 through 30) was removed from SEQ ID NO:162 and a starting methionine was added. This signal-free sequence, hereinafter called the "wild-type" and represented by SEQ ID NO:164 (encoded by, e.g., SEQ ID NO:163), was the parental sequence that was optimized using GSSM technology. As discussed above, GSSM technology can rapidly mutate all amino acids in the protein to the 19 other amino acids in a sequential fashion. Mutants were screened using a fiber-based assay and potential upmutants representing single amino acid changes were identified. These upmutants were combined into a new library representing combinations of the upmutants. This library was screened resulting in identification of several candidate enzymes for commercialization.

Research Summary

[0641] GIGAMATRIX® Screen

[0642] The GIGAMATRIX® (GMx) screening platform is an ultra-high throughput method based on a 100,000 well microplate with the dimensions of a conventional 96 well plate (see Phase II application for details). The screen works with fluorescent substrates. The GMx screen was implemented using 2 substrates based on previously shown activity by cellulases. Methylumbelliferyl cellobioside (MUC) was used as the screening substrate. In addition, resorufin-beta-glucopyranoside was also included in the screen in order to eliminate clones that have activity on both substrates and are presumed to be beta-glucosidases.

[0643] Amplified phage or phagemid versions of the target libraries were screened. Two host strains (CEH6 & GAL631) lacking beta-galactosidase genes were used in order to decrease endogenous host activity on the substrates. 100 libraries were chosen for screening based on the fact that these libraries yielded cellulase hits from a previous screening program. Of the libraries screened, there were a total of 355 primary hits from 69 of the libraries screened.

[0644] Secondary screening consisted of plating the clones on agar plates and then colony picking into 384 well plates containing media and methylumbelliferyl cellobioside (MUC) termed a "breakout". FIG. 10 illustrates in graphic form data showing a typical GIGAMATRIX® (GMx) breakout. To generate this data, active clones against MUC (i.e., able to hydrolyze methylumbelliferyl cellobioside) are differentiated from a background of inactive clones. Individual clones were then grown overnight and fluorescence was measured and the most active hits were picked for sequencing. In FIG. 10, the X axis shows sample name; Y axis is relative fluorescent units. Positive "hits" were plated onto agar plates and then colony picked into 384 well plates containing LB+antibiotic plus 50 μM MUC and grown overnight.

TABLE-US-00003 TABLE 2 Summary of GIGAMATRIX ® (GMx) hits Enzyme No. Open Reading Frame SEQ ID NO: Clone Family Characterization 40 SEQ ID NO: 104 (encoded by, e.g., SEQ ID NO: 103) family 5 (cellulase) 41 SEQ ID NO: 108 (encoded by, e.g., SEQ ID NO: 107) family 5 (cellulase) 42 SEQ ID NO: 112 (encoded by, e.g., SEQ ID NO: 111) family 5 (cellulase) H7 SEQ ID NO: 60 (encoded by, e.g., SEQ ID NO: 59) family 5 (cellulase) 43 SEQ ID NO: 82 (encoded by, e.g., SEQ ID NO: 81) family 5 (cellulase) 44 SEQ ID NO: 78 (encoded by, e.g., SEQ ID NO: 77) family 5 (cellulase) 45 SEQ ID NO: 68 (encoded by, e.g., SEQ ID NO: 67) family 5 (cellulase)-ORF 2 45a SEQ ID NO: 70 (encoded by, e.g., SEQ ID NO: 69) family 26 (mannanase)- ORF4 46 SEQ ID NO: 74 (encoded by, e.g., SEQ ID NO: 73) family 10 (xylanase) 47 SEQ ID NO: 110 (encoded by, e.g., SEQ ID NO: 109) family 10 (xylanase) 48 SEQ ID NO: 106 (encoded by, e.g., SEQ ID NO: 105) family 5 (cellulase) 49 SEQ ID NO: 66 (encoded by, e.g., SEQ ID NO: 65) family 10 (xylanase) 50 SEQ ID NO: 72 (encoded by, e.g., SEQ ID NO: 71) family 5 (cellulase) 51 SEQ ID NO: 80 (encoded by, e.g., SEQ ID NO: 79) family 5 (cellulase) H8 SEQ ID NO: 62 (encoded by, e.g., SEQ ID NO: 61) family 5 (cellulase) ORF 1 H8a SEQ ID NO: 64 (encoded by, e.g., SEQ ID NO: 63) family 5 (cellulase) ORF 4 52 SEQ ID NO: 76 (encoded by, e.g., SEQ ID NO: 75) family 5 (cellulase) 53 SEQ ID NO: 160 (encoded by, e.g., SEQ ID NO: 159) family 10 (xylanase) 54 SEQ ID NO: 88 (encoded by, e.g., SEQ ID NO: 87) family 5 (cellulase) 55 SEQ ID NO: 148 (encoded by, e.g., SEQ ID NO: 147) family 10 (xylanase) 56 SEQ ID NO: 90 (encoded by, e.g., SEQ ID NO: 89) family 5 (cellulase) 57 SEQ ID NO: 152 (encoded by, e.g., SEQ ID NO: 151) family 5 (cellulase) 58 SEQ ID NO: 150 (encoded by, e.g., SEQ ID NO: 149) family 5 (cellulase) 59 SEQ ID NO: 154 (encoded by, e.g., SEQ ID NO: 153) family 5 (cellulase) H6 SEQ ID NO: 158 (encoded by, e.g., SEQ ID NO: 157) family 5 (cellulase) 60 SEQ ID NO: 156 (encoded by, e.g., SEQ ID NO: 155) family 5 (cellulase)

[0645] All genomic clone inserts from hits were sequenced. As with Table 1 above, some genomic clones contained more than one open reading frame. For example, one such genomic clone contains two open reading frames annoted as Enzymes No. H8 and H8a, with said open reading frames having the sequences as depicted in SEQ ID NO:67 and SEQ ID NO:69, respectively. There was a total of 25 glycosyl hydrolase hits from 17 of the libraries screened. In general, the hits were from several different glycosyl hydrolase families including 5 and 10. Table 2 (above) lists the hits and their identities. Several other hits were discovered where the open reading frame was not homologous to any known glycosyl hydrolase families. In addition, some of the hits encoded GTP cyclohydrolase genes that are known false positives in this system as they create fluorescence regardless of substrate degradation. Overall the screen was successful in identifying enzymes that were active on MUC.

[0646] Characterization

[0647] Genes discovered in the GIGAMATRIX® screen were sequenced and the data were analyzed. Open reading frames (ORFs) were annotated using a software system. The ORFs were subcloned into the appropriate vector(s) with the introduction of DNA encoding C-terminal His-tags. Construct DNA was transformed into the appropriate E. coli host(s) and expressed for characterization studies. The gene products were screened against phosphoric acid-swollen cellulose (PASC). PASC is crystalline cellulose that is made more amorphous through swelling by acid treatment. PASC was prepared from AVICEL® Microcrystalline Cellulose (MCC). Subclones were grown, expressed and lysed. Lysates were incubated with PASC and the reaction products were analyzed using the bicinchoninic acid (BCA) reducing sugar assay. The most active subclones were selected for larger scale growth and purification. The specific activity of these subclones was determined on PASC.

[0648] The subclones were also analyzed by capillary electrophoresis (CE). Lysates were incubated with substrate for 30 hours. The reaction products were derivatized with the fluorophore 1-aminopyrene-3,6,8-trisulfonate (APTS). The products were analyzed using a 48 cm capillary. Cellobiose elutes at 6 minutes. FIG. 11 illustrates in graph form data showing the activity of selected enzymes against PASC by capillary electrophoresis (CE) analysis. Samples H9 through H1 are individual clones. In FIG. 11, a number of samples had reaction product profiles representative of processive enzymes. A processive enzyme is defined as having a ratio of cellobiose/(glucose+cellotriose)≧10. Two potential processive enzymes that were the most active had specific activities on PASC of 0.35 and 0.04 U/mg, respectively.

[0649] Fungal CBHs in Pichia

[0650] Genes of newly discovered family 6 & 7 fungal cellobiohydrolases were transformed into P. pastoris and the transformations were spread onto solid agar plates. 160 colonies were selected for each construct. The samples were grown and induced and the supernatants were incubated with PASC in the presence of a β-glucosidase. The reaction products were analyzed using the glucose-oxidase assay. A glycosyl hydrolase family 6 cellobiohydrolase, was successfully heterologously expressed in P. pastoris.

[0651] Exo-Endo Acting Cellulase

[0652] The wild-type enzyme, a family 9 glycosyl hydrolase discovered in an enzyme screen, is a homolog of Thermomonospora fusca E4. E4 has been shown to have both endo- and exo-activity. Initial tests of the wild-type enzyme showed it to be active on both PASC and AVICEL® Microcrystalline Cellulose (MCC). HPLC analysis of the reaction products showed the primary products to be glucose and cellobiose. The wild-type enzyme is a multi-domain protein which includes a glycosyl hydrolase family 9 catalytic domain, a family 3 cellulose binding domain, and three bacterial Ig-like domains that are believed to be involved in cell adhesion. Three additional subclone variants of the wild-type enzyme were tested to determine the effects of the domains on activity. The wild-type enzyme was subcloned with: 1) the catalytic domain alone (CD); 2) the catalytic and carbohydrate domain (CCD); and 3) the catalytic and carbohydrate binding domain plus the 11 downstream amino acids (CCD+11). The full-length protein and the 3 subclone variants were assayed on AVICEL® Microcrystalline Cellulose (MCC) and the reaction products were analyzed by the BCA reducing sugar assay, and the data is summarized in graphic form in FIG. 12. The data illustrated in FIG. 12 was generated by BCA of the wild-type enzyme and truncation mutants incubated with AVICEL® Microcrystalline Cellulose (MCC) for 74 hours, 37° C., pH 5. CBH1 is a positive control. The negative control is the host without insert.

[0653] The wild-type enzyme, the full-length protein (SEQ ID NO:164, encoded by, e.g., SEQ ID NO:163), was the most active. The full length protein was selected for GSSM evolution. The catalytic and the carbohydrate binding domain were evolved.

[0654] GSSM Screening

[0655] GSSM technology (discussed above) was used to rapidly and sequentially mutate the amino acids of the catalytic and carbohydrate binding domain of the target protein into the 19 other amino acids. The goal of the GSSM screen was to identify mutants that increased the extent of hydrolysis on insoluble microcrystalline cellulose. A robotic screening method was developed to facilitate the GSSM screening process.

[0656] DNA from the mutation constructs was transformed into DH10b host cells. Individual colonies were picked into 96 well (shallow) plates containing 150 uL LB/Ampicillin using the automatic colony picking system. The plates were incubated for 24 hours at 37° C., 400 rpm. 15 uL of culture was transferred from each well into an induction plate. Each well of the induction plate contained 135 uL LB/Ampicillin with 1.1 mM IPTG. The induction plates were incubated for 24 hours at 37° C., 400 rpm. The plates were centrifuged and the supernatant was discarded.

[0657] The automated portion of the assay began at this point. The cells were lysed and resuspended by the robot. 150 uL of lysis buffer (125 uL water plus 25 uL BPER containing 0.2 mg/ml lysozyme and 20 unit/ml DNase I) was added to each well. 15 uL lysate was transferred from each well to a reaction plate. Each well of the reaction plate contained 185 uL of a reaction mix (1% AVICEL® Microcrystalline Cellulose (MCC), 50 mM sodium acetate buffer pH5.0). The reaction plates were incubated at 37° C. for 30 hours with 95% humidity. After incubation, the plates were centrifuged and 15 uL supernatant was transferred to BCA plates. The BCA plates contained 50 uL reagent A, 50 uL reagent B, and 80 uL 400 mM Carbonate buffer, pH 10 per well. The plates were covered with rubber seals and incubated at 80° C. for 30 minutes, then cooled by centrifugation and the absorbance read at A560.

[0658] Results

[0659] At least 80 random mutation colonies were screened for each amino acid site. An example of the primary GSSM® screening data is graphically illustrated in FIG. 13. Column 6 contained the wildtype samples and column 12 contained the host/vector negative controls. After a 30 hour incubation with AVICEL® Microcrystalline Cellulose (MCC), the signal produced from the wildtype samples was around 0.53, with a standard deviation at 0.07. The negative control had an average signal at 0.29. Samples with signal higher than the average of positive controls plus 2 times the standard deviation were deemed primary hits. From this screening plate, about ten primary hits were selected for the secondary confirmation screening.

[0660] Primary hits were reconfirmed in a secondary assay. This assay was the same as the primary screen. Samples were run in quadruplicate however. An example of the secondary GSSM screening data is graphically illustrated in FIG. 14. Samples in wells E3-H3, A4-D4, A7-D7 on average, had higher activity than the wildtype. These 12 wells correspond to 3 hits since the samples were run in quadruplicate. These samples were the primary hits shown in wells E4, G2, and H3 in FIG. 13 (plate 29805-AA89 BCA plate).

[0661] There were 77 hits from the secondary screening. These samples were sequenced. Thirty five of the samples had amino acid changes, 22 had transposon insertions, and the rest were wildtype or had deletions.

[0662] Hits from the secondary screen were further analyzed. The GSSM upmutants were mapped onto the crystal structure of T. fusca E4. Samples were prioritized based on amino acid location, amino acid change and the fold improvement score. Eight upmutants were selected from the GSSM screening and selected for gene reassembly evolution, i.e., Tunable GeneReassembly (TGR), discussed above, and also see, e.g., U.S. Pat. No. 6,537,776.

TABLE-US-00004 TABLE 2 Up-mutants selected for site directed mutagenesis reassembly. Residue OLD AA NEW AA 89 M R 103 F G 110 P G 114 Y L 157 A S 481 W F 550 P N 590 G R

Blending of Upmutants

[0663] Using gene reassembly (Tunable GeneReassembly (TGR)) technology, the upmutants shown in Table 2, above, were blended in order to identify the candidate with the best activity. Activity assays were the same as for the GSSM screening except reactions were further diluted to account for increased activity of upmutants over the wildtype enzyme. FIG. 15 illustrates in graph form data from mixed, or "blended", GSSM® screening assays.

[0664] In summary, the invention provides enzymes having cellulase activity having the following sequences based on SEQ ID NO:164 (encoded by, e.g., SEQ ID NO:163):

TABLE-US-00005 Codons Encoding New Amino Original Original Acid (after Codons Encoding Residue Amino Acid Amino Acid GSSM Evolution) New Amino Acid 89 M ATG R CGT, CGC, CGA, CGG, AGA, AGG 103 F TTT, TTC G GGT, GGC, GGA, GGG 110 P CCA, CCC, CCG, CCT G GGT, GGC, GGA, GGG 114 Y TAT, TAC L TTA, TTG, CTT, CTC, CTA, CTG 157 A GCT, GCC, GCA, GCG S TCT, TCC, TCA, TCG, AGT, AGC 481 W TGG F TTT, TTC 550 P CCA, CCC, CCG, CCT N AAT, AAC 590 G GGT, GGC, GGA, GGG R CGT, CGC, CGA, CGG, AGA, AGG

[0665] A number of aspects of the invention have been described. Nevertheless, it will be understood that various modifications may be made without departing from the spirit and scope of the invention. Accordingly, other aspects are within the scope of the following claims.

Sequence CWU 1

1

16611323DNAUnknownObtained from environmental sample 1atgtcaacct ataaatttcc gcacaacttt ttttggggag ccgcaaccgc gtcttatcag 60atcgaaggcg catggaacga ggatggcaaa ggcgaatcca tttgggatcg cttcagccat 120acgcccggaa aggtcaccaa tgccgatacc ggtgacatcg cctgtgacca ctatcaccgt 180tgggaggaag atatcgccct tatgcgccaa cttgggttga aggcgtaccg cttttccact 240tcatggcccc gtgtgatccc ggcgggccgc agacgggtga atgtcaaagg gctggatttc 300tacgatcgcc tggtggatgg tctgtgcgcc gcgaacatcg aaccgttcct caccctgtat 360cactgggacc tgccgcaggc tcttcaagac gaaggcggct gggataatcg caacaccgcc 420catgcctttg ccgattatgc cgcattgatg gtgaaacgac ttggcgaccg tatccgctat 480tggacgacgt tcaacgaacc cagcgttgtg gcgttcaatg gtcattactc aggctcgcac 540gccccgggca ttcaagatgc ccgtgttacc cgccaggtgg tgcatcattt gctggtggcg 600catgggttgg ctgtgcaggc gatccgcggc gcaaactcca aagtggatgt gggcatcgtg 660cttaatttat ggcccgccga acccgattcg gactcccccg aagatgccgc cgccgccgaa 720gccgcctgga accggcacga gaccctgttc cttgacccca tctttaaggc gcattatccc 780gtatctgccc ttgatgcgat tggggaggat atgccccgca tccacgacgg cgatctggcg 840ttgatctctc aggaattgga ttttgtcggc atcaactatt actcccgcca tgtggtcagt 900gccacaaaag aaataggcag gcttcccgaa tcggaataca ctgaaatggg ctgggaagta 960tgcgcccccg cactccgccg cctgctggtc aagatccata acgattaccg tttgccgccc 1020atctatatca ccgaaaacgg atcggcattc aaggacgaag ttaacgcaga cggaaaggtt 1080catgacccgc ggcggttgga ttacctgaaa caacacctga ttcaactttg ccttgccatg 1140caggacggcg tggatgtgcg cggctacatg gcttggtccc tgctggataa tttcgagtgg 1200ggtcacggct tttccaagcg ctttggcttg gtccatgtgg attacgagag ccagaagcgg 1260attattaaag actcgggtga atggtatgca agtgtgatac ggaagaacga ggttgttgaa 1320taa 13232440PRTUnknownObtained from environmental sample 2Met Ser Thr Tyr Lys Phe Pro His Asn Phe Phe Trp Gly Ala Ala Thr 1 5 10 15 Ala Ser Tyr Gln Ile Glu Gly Ala Trp Asn Glu Asp Gly Lys Gly Glu 20 25 30 Ser Ile Trp Asp Arg Phe Ser His Thr Pro Gly Lys Val Thr Asn Ala 35 40 45 Asp Thr Gly Asp Ile Ala Cys Asp His Tyr His Arg Trp Glu Glu Asp 50 55 60 Ile Ala Leu Met Arg Gln Leu Gly Leu Lys Ala Tyr Arg Phe Ser Thr 65 70 75 80 Ser Trp Pro Arg Val Ile Pro Ala Gly Arg Arg Arg Val Asn Val Lys 85 90 95 Gly Leu Asp Phe Tyr Asp Arg Leu Val Asp Gly Leu Cys Ala Ala Asn 100 105 110 Ile Glu Pro Phe Leu Thr Leu Tyr His Trp Asp Leu Pro Gln Ala Leu 115 120 125 Gln Asp Glu Gly Gly Trp Asp Asn Arg Asn Thr Ala His Ala Phe Ala 130 135 140 Asp Tyr Ala Ala Leu Met Val Lys Arg Leu Gly Asp Arg Ile Arg Tyr 145 150 155 160 Trp Thr Thr Phe Asn Glu Pro Ser Val Val Ala Phe Asn Gly His Tyr 165 170 175 Ser Gly Ser His Ala Pro Gly Ile Gln Asp Ala Arg Val Thr Arg Gln 180 185 190 Val Val His His Leu Leu Val Ala His Gly Leu Ala Val Gln Ala Ile 195 200 205 Arg Gly Ala Asn Ser Lys Val Asp Val Gly Ile Val Leu Asn Leu Trp 210 215 220 Pro Ala Glu Pro Asp Ser Asp Ser Pro Glu Asp Ala Ala Ala Ala Glu 225 230 235 240 Ala Ala Trp Asn Arg His Glu Thr Leu Phe Leu Asp Pro Ile Phe Lys 245 250 255 Ala His Tyr Pro Val Ser Ala Leu Asp Ala Ile Gly Glu Asp Met Pro 260 265 270 Arg Ile His Asp Gly Asp Leu Ala Leu Ile Ser Gln Glu Leu Asp Phe 275 280 285 Val Gly Ile Asn Tyr Tyr Ser Arg His Val Val Ser Ala Thr Lys Glu 290 295 300 Ile Gly Arg Leu Pro Glu Ser Glu Tyr Thr Glu Met Gly Trp Glu Val 305 310 315 320 Cys Ala Pro Ala Leu Arg Arg Leu Leu Val Lys Ile His Asn Asp Tyr 325 330 335 Arg Leu Pro Pro Ile Tyr Ile Thr Glu Asn Gly Ser Ala Phe Lys Asp 340 345 350 Glu Val Asn Ala Asp Gly Lys Val His Asp Pro Arg Arg Leu Asp Tyr 355 360 365 Leu Lys Gln His Leu Ile Gln Leu Cys Leu Ala Met Gln Asp Gly Val 370 375 380 Asp Val Arg Gly Tyr Met Ala Trp Ser Leu Leu Asp Asn Phe Glu Trp 385 390 395 400 Gly His Gly Phe Ser Lys Arg Phe Gly Leu Val His Val Asp Tyr Glu 405 410 415 Ser Gln Lys Arg Ile Ile Lys Asp Ser Gly Glu Trp Tyr Ala Ser Val 420 425 430 Ile Arg Lys Asn Glu Val Val Glu 435 440 31389DNAUnknownObtained from environmental sample 3atgagcgctc cgagtcccgc ccgccccgtg tcctttcctc cccgcttcgt gtggggagcc 60gcggccgcat cctatcaaat cgagggcgcc gtccgggagg acggcaaggg cccttcggtg 120tgggacatgt tctgcgagaa gccgggagcc gtcttcgagg ggcacgacgg ggcggtggct 180tgcgatcact accaccgtta ccgggaagac gtggccctga tgcggcagat tgggctccag 240gcttaccgcc tgagcgtgtg ctggcccagg gtgctgcccg aggggaccgg gcagcccaac 300gagaaggggc tcgacttcta ctcccggctc gtcgacgcct tgctcgaggc ggggatcacg 360ccttgggtca ccctttttca ctgggactac ccactagccc tatatcaccg gggaggctgg 420ctcaatcggg atagctcaga ctggttcggc gagtacgcgg gtctgattgc ggagcgcctc 480tccgatcggg tgagccactt cttcacccag aacgagcccc aggtgtacat cggcttcggg 540cacctcgagg ggaaacacgc gccgggcgat acccttcccc tgtcgcagat gctgctggcc 600ggtcaccaca gcctgctcgc ccatggaaag gccgtgcagg cgctgcgcgc ccacggcaag 660cagcagctgc gggttggata cgctccggtg gggatgccgc tgcatccggt cagcgagtcc 720gccgaagacg tggcggctgc acgcaccgcc actttccgcg tccgagagaa gaattcctgg 780aacaacgctt ggtggatgga cccggtgtac ctcggtgagt accccgccca agggctcgag 840ttctacgggc gagacgtccc cgcgatccgg tccggagaca tggaactcat ccggcaaccc 900ttggactttt tcggcgtcaa catctaccag agcacgcccg tgcgcgccgc gggggcgccc 960caggggttcg aggtcgtccg gcatccgacg ggccacccca tcaccgcgtt caactggccg 1020gttacgccac aggccttgta ttgggggccg cggttcttct acgagcgcta tggcaagccc 1080atcgtcatta cggaaaacgg gctttcctgc cgagacgtga tcgcccttga cggcaaggtg 1140cacgatccgt cccgcatcga cttcaccacg cgctacctgc gcgagctcca ccgcgccatc 1200gccgaaggca acgaggtgga gggctacttc cactggtcca tcatggacaa cttcgaatgg 1260gctgccggat accgagaacg cttcgggctc gttcacgtgg attacgagac cctggtgagg 1320acacccaagg actctgcggc gtggtaccgc caggtcatcc agagcaacgg ggccgtgctg 1380ttcgattga 13894462PRTUnknownObtained from environmental sample 4Met Ser Ala Pro Ser Pro Ala Arg Pro Val Ser Phe Pro Pro Arg Phe 1 5 10 15 Val Trp Gly Ala Ala Ala Ala Ser Tyr Gln Ile Glu Gly Ala Val Arg 20 25 30 Glu Asp Gly Lys Gly Pro Ser Val Trp Asp Met Phe Cys Glu Lys Pro 35 40 45 Gly Ala Val Phe Glu Gly His Asp Gly Ala Val Ala Cys Asp His Tyr 50 55 60 His Arg Tyr Arg Glu Asp Val Ala Leu Met Arg Gln Ile Gly Leu Gln 65 70 75 80 Ala Tyr Arg Leu Ser Val Cys Trp Pro Arg Val Leu Pro Glu Gly Thr 85 90 95 Gly Gln Pro Asn Glu Lys Gly Leu Asp Phe Tyr Ser Arg Leu Val Asp 100 105 110 Ala Leu Leu Glu Ala Gly Ile Thr Pro Trp Val Thr Leu Phe His Trp 115 120 125 Asp Tyr Pro Leu Ala Leu Tyr His Arg Gly Gly Trp Leu Asn Arg Asp 130 135 140 Ser Ser Asp Trp Phe Gly Glu Tyr Ala Gly Leu Ile Ala Glu Arg Leu 145 150 155 160 Ser Asp Arg Val Ser His Phe Phe Thr Gln Asn Glu Pro Gln Val Tyr 165 170 175 Ile Gly Phe Gly His Leu Glu Gly Lys His Ala Pro Gly Asp Thr Leu 180 185 190 Pro Leu Ser Gln Met Leu Leu Ala Gly His His Ser Leu Leu Ala His 195 200 205 Gly Lys Ala Val Gln Ala Leu Arg Ala His Gly Lys Gln Gln Leu Arg 210 215 220 Val Gly Tyr Ala Pro Val Gly Met Pro Leu His Pro Val Ser Glu Ser 225 230 235 240 Ala Glu Asp Val Ala Ala Ala Arg Thr Ala Thr Phe Arg Val Arg Glu 245 250 255 Lys Asn Ser Trp Asn Asn Ala Trp Trp Met Asp Pro Val Tyr Leu Gly 260 265 270 Glu Tyr Pro Ala Gln Gly Leu Glu Phe Tyr Gly Arg Asp Val Pro Ala 275 280 285 Ile Arg Ser Gly Asp Met Glu Leu Ile Arg Gln Pro Leu Asp Phe Phe 290 295 300 Gly Val Asn Ile Tyr Gln Ser Thr Pro Val Arg Ala Ala Gly Ala Pro 305 310 315 320 Gln Gly Phe Glu Val Val Arg His Pro Thr Gly His Pro Ile Thr Ala 325 330 335 Phe Asn Trp Pro Val Thr Pro Gln Ala Leu Tyr Trp Gly Pro Arg Phe 340 345 350 Phe Tyr Glu Arg Tyr Gly Lys Pro Ile Val Ile Thr Glu Asn Gly Leu 355 360 365 Ser Cys Arg Asp Val Ile Ala Leu Asp Gly Lys Val His Asp Pro Ser 370 375 380 Arg Ile Asp Phe Thr Thr Arg Tyr Leu Arg Glu Leu His Arg Ala Ile 385 390 395 400 Ala Glu Gly Asn Glu Val Glu Gly Tyr Phe His Trp Ser Ile Met Asp 405 410 415 Asn Phe Glu Trp Ala Ala Gly Tyr Arg Glu Arg Phe Gly Leu Val His 420 425 430 Val Asp Tyr Glu Thr Leu Val Arg Thr Pro Lys Asp Ser Ala Ala Trp 435 440 445 Tyr Arg Gln Val Ile Gln Ser Asn Gly Ala Val Leu Phe Asp 450 455 460 51098DNAUnknownObtained from environmental sample 5atgactcgga ggtctatcgt gcgttcttct tccaacaagt ggcttgtcct tgccggtgcg 60gcgctgctcg cctgcaccgc cctcgggtgc aagaaaaaag gcgagagcgg tgacgtcgcc 120tcggccccgg ggcaggccca ggcgggcggc aagcagccgt ttcccgacga tgcgccgatc 180accgaaccgc ccgctccgcc ccctcgtagc ggcaatcctc tggtgggcgc caagctcttc 240gtcgacccgg aatctttggc catgttgcag gcgaacaagc tgcggcgcac cgacccggag 300aaggcggcga ttttggatcg catcgcccag cagccccagg ctttgtggat gggcgagtgg 360aacacgaaca tcttccgcgc ggtcgagcat ttcgtggctc gcgccaaggc ggagggcgcc 420gtgcccgtca tgatcgccta caacatcccc caccgcgact gcgggcagta ctctcagggt 480gggctttcct ccaaggaggc ttaccagcgc tggattcgga acgtcgccgc ggggattggc 540agcgatgcag cggtcgtcgt gctcgagccc gacgcgctcg gccacttcca ggagtgtttg 600accgaggagc agagcgccga gcgcatgttc ctgctcagcg acgccgtcaa ggtgctgcgc 660caaaatccga agacggccgt gtacctggat gccgggcacg cgcgctgggt gccggtggag 720gagatggccg agcgcctcaa gctcgcgggc atcgagcacg cccatggctt ttcgctcaac 780acctcgaact acgtgggcac cgaggagaac gccgcttacg gccacaagct cgtcgaggcc 840ctgggtggga acgtgcgctt cgtcatcgac acgagccgca atggggcggg cccctacgag 900gaggccaaga acgccgagga gagctggtgc aacccgcccg gtcgcaagat cggcaagccg 960ccgaccaccg agacggggga tcccctcatc gacggattcc tttggctgaa gcgcccgggc 1020gagtcggacg gtcagtgcaa cggcgggccc aaggccggtg tgttctggct ggagcaggct 1080ctccagcagg cccagtaa 10986365PRTUnknownObtained from environmental sample 6Met Thr Arg Arg Ser Ile Val Arg Ser Ser Ser Asn Lys Trp Leu Val 1 5 10 15 Leu Ala Gly Ala Ala Leu Leu Ala Cys Thr Ala Leu Gly Cys Lys Lys 20 25 30 Lys Gly Glu Ser Gly Asp Val Ala Ser Ala Pro Gly Gln Ala Gln Ala 35 40 45 Gly Gly Lys Gln Pro Phe Pro Asp Asp Ala Pro Ile Thr Glu Pro Pro 50 55 60 Ala Pro Pro Pro Arg Ser Gly Asn Pro Leu Val Gly Ala Lys Leu Phe 65 70 75 80 Val Asp Pro Glu Ser Leu Ala Met Leu Gln Ala Asn Lys Leu Arg Arg 85 90 95 Thr Asp Pro Glu Lys Ala Ala Ile Leu Asp Arg Ile Ala Gln Gln Pro 100 105 110 Gln Ala Leu Trp Met Gly Glu Trp Asn Thr Asn Ile Phe Arg Ala Val 115 120 125 Glu His Phe Val Ala Arg Ala Lys Ala Glu Gly Ala Val Pro Val Met 130 135 140 Ile Ala Tyr Asn Ile Pro His Arg Asp Cys Gly Gln Tyr Ser Gln Gly 145 150 155 160 Gly Leu Ser Ser Lys Glu Ala Tyr Gln Arg Trp Ile Arg Asn Val Ala 165 170 175 Ala Gly Ile Gly Ser Asp Ala Ala Val Val Val Leu Glu Pro Asp Ala 180 185 190 Leu Gly His Phe Gln Glu Cys Leu Thr Glu Glu Gln Ser Ala Glu Arg 195 200 205 Met Phe Leu Leu Ser Asp Ala Val Lys Val Leu Arg Gln Asn Pro Lys 210 215 220 Thr Ala Val Tyr Leu Asp Ala Gly His Ala Arg Trp Val Pro Val Glu 225 230 235 240 Glu Met Ala Glu Arg Leu Lys Leu Ala Gly Ile Glu His Ala His Gly 245 250 255 Phe Ser Leu Asn Thr Ser Asn Tyr Val Gly Thr Glu Glu Asn Ala Ala 260 265 270 Tyr Gly His Lys Leu Val Glu Ala Leu Gly Gly Asn Val Arg Phe Val 275 280 285 Ile Asp Thr Ser Arg Asn Gly Ala Gly Pro Tyr Glu Glu Ala Lys Asn 290 295 300 Ala Glu Glu Ser Trp Cys Asn Pro Pro Gly Arg Lys Ile Gly Lys Pro 305 310 315 320 Pro Thr Thr Glu Thr Gly Asp Pro Leu Ile Asp Gly Phe Leu Trp Leu 325 330 335 Lys Arg Pro Gly Glu Ser Asp Gly Gln Cys Asn Gly Gly Pro Lys Ala 340 345 350 Gly Val Phe Trp Leu Glu Gln Ala Leu Gln Gln Ala Gln 355 360 365 72649DNAUnknownObtained from environmental sample 7atgcaaggaa agaaaattga tttcattaac tcaaggttgt tagttcctga ttatccaatc 60gttcccttca ttgagggaga tggtaccggc cctgatatct ggcgtgcttc agtcagggtg 120ctggatgttg ctgttgacag ggcatattcc ggcaagcgaa aacttctctg gaaagaggtg 180ctggctggcg aaaaggcatt tacaaatacc gggtcctggc ttccggagga aactcttaga 240gcatttcgtg aatatcatgt tggaattaaa gggccactca ctacgccagt tggtggggga 300attcgttctc tcaatgtagc cctcaggcaa gagcttgact tgtatgtttg cctgaggcca 360gtcaaatggt ttaagggtgt accaagtcct ctaaaagatc cttccaaagt ggatatgcat 420attttccgcg aaaacactga agatatttat gcaggtattg aatttatgca tggtgaaccg 480gaggccctga aagttaagaa atttcttacc gaagaaatgg gaatcaagaa gtttcggttt 540cccgatacat cctccattgg tatcaagcct atctcactcg aaggaacaga gcgtcttgta 600agagcttcca ttcaatatgc acttgacagg aagttgcctt ccgtaacatt ggttcataaa 660ggcaatatca tgaaattcac cgagggggca ttcaaaaaat ggggttatga acttgccgaa 720agagaatttg gcgacagggt ttttacatgg tcaatgtatg accgtatcgc cgatgaacat 780ggaacggaag aagctggcaa agtgcaatcc gaagcgattg caaaaggtaa actcctgata 840aaggatgtga ttgctgatgc ttttctgcag caaatactac tcaggcctgc cgagtacagc 900gttatcgcaa ccatgaacct gaatggcgat tatatcagcg atgcactggc agctatggtg 960gggggtatag gaattgctcc cggagccaat attaaccatc aaactggcca tgcagtcttt 1020gaagcaacac acggcacggc tcccaaatat gccaaccttg atcaggtaaa ccctggctca 1080gtaatactaa gtggcgcgct gatgctcgaa tacatgggct ggaacgaagc cgctcagctc 1140attaccaatg gattggaggc taccattcaa cagaaactgg taacctatga tttccatcgc 1200ttaatggaag gtgctacaaa gttgaagact tcagaatttg gcgatgctgt gatccggccg 1260gcacgttccg cctgggcgga cacggctgcc gatgccctct ccgggcggcg gcgtcgtgcg 1320cggaacggcg ggcttgttgc cccgcccgcg gcctgtcgcc gggggcgggt acgggactca 1380gcgcttgcgc gcctccttca gggtggactg cagggcgaag aaggccggct tgcggacgaa 1440cttctccgtc atgaccgtgg cgctgccctc accctcgaag aagaccggca cccacgagta 1500cttgtcggtg aagccccaga tggtgaagga gttgcagtcg ttcacggcca ggcaggccga 1560cagtgcctgc tggtagtagt cggcctgctg ccgcagctgc tccttggtgg gcttgccgct 1620cgccgggagg tccatgcgga cgtcgatctc ggtgatggcg gtctccagac cgaggtcggc 1680gaaccgctgc aggttctgct gcaggtcgcc cgggaagccg tagcgggtgc tcaggtggcc 1740ctgggcgccg aatccgtgga gcggcacgcc ctgctccagc atctcctggg cgagctcgta 1800gtaggcgtcg ctcttggcgt tgatgccctc gacgttgtag tcgttgagga acagcttggc 1860ctcggggtcg gcctcgtggg cccagcggaa ggcgtccgcg acgatctccg ggccgagctc 1920acgtatccag atgttctcgt cggtgcgcag ctcggcctgg tcgttgaaga tctcgttggc 1980cacgtcccac tgctggatct tgccggcgta gcggccgacg accgtgtcga tgtggtcctt 2040gaggatggcg cgcagttcct ccttggtgaa gtcgccctcc tccagccatt cggggttctg 2100gctgtgccac aggagggtgt gcccgcgcac ggcctggcgg ttccgctggg cgaactcgac 2160gatggcgtcg gcctcctcga agcggtactg gtcgcgctcg gggtggatga actcccactt 2220catctggttc tcggcggaga ccgagttgaa ctgctggccc aggatcttcc ggtacttctt 2280gtcgaaggtg aaggggtccg ggtagtcctg ttcgaggtgg tggccgccgc cggccgccgc 2340ggagcctatg aagaaccctt cgggggcggc ccagcgcagg cggtcgaact tggcgttgga 2400gtggggcgcg gcctcgtggt cggcggacgg cttggccgtg gccgtcgacg tcaccagcgg 2460gacggccagc gcggcggcga gagcaaaggt gacgatgcgg acggatctca tcagaggtcc

2520ctcattcgat cgcggctccg aaagttttcg gaggattacc ggaatgtttc agggacctta 2580aggcgcccgg agccgggtcg tcaacggttt ggcccggccc ggtcgaagct tctcccgacc 2640aggcgttga 26498882PRTUnknownObtained from environmental sample 8Met Gln Gly Lys Lys Ile Asp Phe Ile Asn Ser Arg Leu Leu Val Pro 1 5 10 15 Asp Tyr Pro Ile Val Pro Phe Ile Glu Gly Asp Gly Thr Gly Pro Asp 20 25 30 Ile Trp Arg Ala Ser Val Arg Val Leu Asp Val Ala Val Asp Arg Ala 35 40 45 Tyr Ser Gly Lys Arg Lys Leu Leu Trp Lys Glu Val Leu Ala Gly Glu 50 55 60 Lys Ala Phe Thr Asn Thr Gly Ser Trp Leu Pro Glu Glu Thr Leu Arg 65 70 75 80 Ala Phe Arg Glu Tyr His Val Gly Ile Lys Gly Pro Leu Thr Thr Pro 85 90 95 Val Gly Gly Gly Ile Arg Ser Leu Asn Val Ala Leu Arg Gln Glu Leu 100 105 110 Asp Leu Tyr Val Cys Leu Arg Pro Val Lys Trp Phe Lys Gly Val Pro 115 120 125 Ser Pro Leu Lys Asp Pro Ser Lys Val Asp Met His Ile Phe Arg Glu 130 135 140 Asn Thr Glu Asp Ile Tyr Ala Gly Ile Glu Phe Met His Gly Glu Pro 145 150 155 160 Glu Ala Leu Lys Val Lys Lys Phe Leu Thr Glu Glu Met Gly Ile Lys 165 170 175 Lys Phe Arg Phe Pro Asp Thr Ser Ser Ile Gly Ile Lys Pro Ile Ser 180 185 190 Leu Glu Gly Thr Glu Arg Leu Val Arg Ala Ser Ile Gln Tyr Ala Leu 195 200 205 Asp Arg Lys Leu Pro Ser Val Thr Leu Val His Lys Gly Asn Ile Met 210 215 220 Lys Phe Thr Glu Gly Ala Phe Lys Lys Trp Gly Tyr Glu Leu Ala Glu 225 230 235 240 Arg Glu Phe Gly Asp Arg Val Phe Thr Trp Ser Met Tyr Asp Arg Ile 245 250 255 Ala Asp Glu His Gly Thr Glu Glu Ala Gly Lys Val Gln Ser Glu Ala 260 265 270 Ile Ala Lys Gly Lys Leu Leu Ile Lys Asp Val Ile Ala Asp Ala Phe 275 280 285 Leu Gln Gln Ile Leu Leu Arg Pro Ala Glu Tyr Ser Val Ile Ala Thr 290 295 300 Met Asn Leu Asn Gly Asp Tyr Ile Ser Asp Ala Leu Ala Ala Met Val 305 310 315 320 Gly Gly Ile Gly Ile Ala Pro Gly Ala Asn Ile Asn His Gln Thr Gly 325 330 335 His Ala Val Phe Glu Ala Thr His Gly Thr Ala Pro Lys Tyr Ala Asn 340 345 350 Leu Asp Gln Val Asn Pro Gly Ser Val Ile Leu Ser Gly Ala Leu Met 355 360 365 Leu Glu Tyr Met Gly Trp Asn Glu Ala Ala Gln Leu Ile Thr Asn Gly 370 375 380 Leu Glu Ala Thr Ile Gln Gln Lys Leu Val Thr Tyr Asp Phe His Arg 385 390 395 400 Leu Met Glu Gly Ala Thr Lys Leu Lys Thr Ser Glu Phe Gly Asp Ala 405 410 415 Val Ile Arg Pro Ala Arg Ser Ala Trp Ala Asp Thr Ala Ala Asp Ala 420 425 430 Leu Ser Gly Arg Arg Arg Arg Ala Arg Asn Gly Gly Leu Val Ala Pro 435 440 445 Pro Ala Ala Cys Arg Arg Gly Arg Val Arg Asp Ser Ala Leu Ala Arg 450 455 460 Leu Leu Gln Gly Gly Leu Gln Gly Glu Glu Gly Arg Leu Ala Asp Glu 465 470 475 480 Leu Leu Arg His Asp Arg Gly Ala Ala Leu Thr Leu Glu Glu Asp Arg 485 490 495 His Pro Arg Val Leu Val Gly Glu Ala Pro Asp Gly Glu Gly Val Ala 500 505 510 Val Val His Gly Gln Ala Gly Arg Gln Cys Leu Leu Val Val Val Gly 515 520 525 Leu Leu Pro Gln Leu Leu Leu Gly Gly Leu Ala Ala Arg Arg Glu Val 530 535 540 His Ala Asp Val Asp Leu Gly Asp Gly Gly Leu Gln Thr Glu Val Gly 545 550 555 560 Glu Pro Leu Gln Val Leu Leu Gln Val Ala Arg Glu Ala Val Ala Gly 565 570 575 Ala Gln Val Ala Leu Gly Ala Glu Ser Val Glu Arg His Ala Leu Leu 580 585 590 Gln His Leu Leu Gly Glu Leu Val Val Gly Val Ala Leu Gly Val Asp 595 600 605 Ala Leu Asp Val Val Val Val Glu Glu Gln Leu Gly Leu Gly Val Gly 610 615 620 Leu Val Gly Pro Ala Glu Gly Val Arg Asp Asp Leu Arg Ala Glu Leu 625 630 635 640 Thr Tyr Pro Asp Val Leu Val Gly Ala Gln Leu Gly Leu Val Val Glu 645 650 655 Asp Leu Val Gly His Val Pro Leu Leu Asp Leu Ala Gly Val Ala Ala 660 665 670 Asp Asp Arg Val Asp Val Val Leu Glu Asp Gly Ala Gln Phe Leu Leu 675 680 685 Gly Glu Val Ala Leu Leu Gln Pro Phe Gly Val Leu Ala Val Pro Gln 690 695 700 Glu Gly Val Pro Ala His Gly Leu Ala Val Pro Leu Gly Glu Leu Asp 705 710 715 720 Asp Gly Val Gly Leu Leu Glu Ala Val Leu Val Ala Leu Gly Val Asp 725 730 735 Glu Leu Pro Leu His Leu Val Leu Gly Gly Asp Arg Val Glu Leu Leu 740 745 750 Ala Gln Asp Leu Pro Val Leu Leu Val Glu Gly Glu Gly Val Arg Val 755 760 765 Val Leu Phe Glu Val Val Ala Ala Ala Gly Arg Arg Gly Ala Tyr Glu 770 775 780 Glu Pro Phe Gly Gly Gly Pro Ala Gln Ala Val Glu Leu Gly Val Gly 785 790 795 800 Val Gly Arg Gly Leu Val Val Gly Gly Arg Leu Gly Arg Gly Arg Arg 805 810 815 Arg His Gln Arg Asp Gly Gln Arg Gly Gly Glu Ser Lys Gly Asp Asp 820 825 830 Ala Asp Gly Ser His Gln Arg Ser Leu Ile Arg Ser Arg Leu Arg Lys 835 840 845 Phe Ser Glu Asp Tyr Arg Asn Val Ser Gly Thr Leu Arg Arg Pro Glu 850 855 860 Pro Gly Arg Gln Arg Phe Gly Pro Ala Arg Ser Lys Leu Leu Pro Thr 865 870 875 880 Arg Arg 91134DNAUnknownObtained from environmental sample 9atgagatccg tccgcatcgt cacctttgct ctcgccgccg cgctggccgt cccgctggtg 60acgtcgacgg ccacggccaa gccgtccgcc gaccacgagg ccgcgcccca ctccaacgcc 120aagttcgacc gcctgcgctg ggccgccccc gaagggttct tcataggctc cgcggcggcc 180ggcggcggcc accacctcga acaggactac ccggacccct tcaccttcga caagaagtac 240cggaagatcc tgggccagca gttcaactcg gtctccgccg agaaccagat gaagtgggag 300ttcatccacc ccgagcgcga ccagtaccgc ttcgaggagg ccgacgccat cgtcgagttc 360gcccagcgga accgccaggc cgtgcgcggg cacaccctcc tgtggcacag ccagaacccc 420gaatggctgg aggagggcga cttcaccaag gaggaactgc gcgccatcct caaggaccac 480atcgacacgg tcgtcggccg ctacgccggc aagatccagc agtgggacgt ggccaacgag 540atcttcaacg accaggccga gctgcgcacc gacgagaaca tctggatacg tgagctcggc 600ccggagatcg tcgcggacgc cttccgctgg gcccacgagg ccgaccccga ggccaagctg 660ttcctcaacg actacaacgt cgagggcatc aacgccaaga gcgacgccta ctacgagctc 720gcccaggaga tgctggagca gggcgtgccg ctccacggat tcggcgccca gggccacctg 780agcacccgct acggcttccc gggcgacctg cagcagaacc tgcagcggtt cgccgacctc 840ggtctggaga ccgccatcac cgagatcgac gtccgcatgg acctcccggc gagcggcaag 900cccaccaagg agcagctgcg gcagcaggcc gactactacc agcaggcact gtcggcctgc 960ctggccgtga acgactgcaa ctccttcacc atctggggct tcaccgacaa gtactcgtgg 1020gtgccggtct tcttcgaggg tgagggcagc gccacggtca tgacggagaa gttcgtccgc 1080aagccggcct tcttcgccct gcagtccacc ctgaaggagg cgcgcaagcg ctga 113410377PRTUnknownObtained from environmental sample 10Met Arg Ser Val Arg Ile Val Thr Phe Ala Leu Ala Ala Ala Leu Ala 1 5 10 15 Val Pro Leu Val Thr Ser Thr Ala Thr Ala Lys Pro Ser Ala Asp His 20 25 30 Glu Ala Ala Pro His Ser Asn Ala Lys Phe Asp Arg Leu Arg Trp Ala 35 40 45 Ala Pro Glu Gly Phe Phe Ile Gly Ser Ala Ala Ala Gly Gly Gly His 50 55 60 His Leu Glu Gln Asp Tyr Pro Asp Pro Phe Thr Phe Asp Lys Lys Tyr 65 70 75 80 Arg Lys Ile Leu Gly Gln Gln Phe Asn Ser Val Ser Ala Glu Asn Gln 85 90 95 Met Lys Trp Glu Phe Ile His Pro Glu Arg Asp Gln Tyr Arg Phe Glu 100 105 110 Glu Ala Asp Ala Ile Val Glu Phe Ala Gln Arg Asn Arg Gln Ala Val 115 120 125 Arg Gly His Thr Leu Leu Trp His Ser Gln Asn Pro Glu Trp Leu Glu 130 135 140 Glu Gly Asp Phe Thr Lys Glu Glu Leu Arg Ala Ile Leu Lys Asp His 145 150 155 160 Ile Asp Thr Val Val Gly Arg Tyr Ala Gly Lys Ile Gln Gln Trp Asp 165 170 175 Val Ala Asn Glu Ile Phe Asn Asp Gln Ala Glu Leu Arg Thr Asp Glu 180 185 190 Asn Ile Trp Ile Arg Glu Leu Gly Pro Glu Ile Val Ala Asp Ala Phe 195 200 205 Arg Trp Ala His Glu Ala Asp Pro Glu Ala Lys Leu Phe Leu Asn Asp 210 215 220 Tyr Asn Val Glu Gly Ile Asn Ala Lys Ser Asp Ala Tyr Tyr Glu Leu 225 230 235 240 Ala Gln Glu Met Leu Glu Gln Gly Val Pro Leu His Gly Phe Gly Ala 245 250 255 Gln Gly His Leu Ser Thr Arg Tyr Gly Phe Pro Gly Asp Leu Gln Gln 260 265 270 Asn Leu Gln Arg Phe Ala Asp Leu Gly Leu Glu Thr Ala Ile Thr Glu 275 280 285 Ile Asp Val Arg Met Asp Leu Pro Ala Ser Gly Lys Pro Thr Lys Glu 290 295 300 Gln Leu Arg Gln Gln Ala Asp Tyr Tyr Gln Gln Ala Leu Ser Ala Cys 305 310 315 320 Leu Ala Val Asn Asp Cys Asn Ser Phe Thr Ile Trp Gly Phe Thr Asp 325 330 335 Lys Tyr Ser Trp Val Pro Val Phe Phe Glu Gly Glu Gly Ser Ala Thr 340 345 350 Val Met Thr Glu Lys Phe Val Arg Lys Pro Ala Phe Phe Ala Leu Gln 355 360 365 Ser Thr Leu Lys Glu Ala Arg Lys Arg 370 375 111080DNAUnknownObtained from environmental sample 11atgccctgga gctcatcaac gggacctgca cctatgacga gtaacccgcc cctcaaacgc 60cccctgcgta tcggtctggt cggcacgggc atcggctcac tgcacgccgc cggaatttcc 120cggatgcctc agcttgccac gctgggggcc atctgtgggc ttgataccca cgccgtgaat 180gccctagcca cacgctacgg ggtagaaaaa accacatctc gctatgagga tttactgaac 240gatcccggcc ttgatgtcat cgatctgtgc gttcctcacg atgaacacat gcccatggcc 300attgccgccg cccgggccgg aaaacatctc ctcatcgaaa aacctttggc ccgcaccctg 360gaagaggccg atgcaatcct cgaggccgtg aaaagcgccg gtgtaacgct gatgatggga 420cacaaccagc gttactacgc ccatcacgcc agggctaaag cattggtcga cgccggggtc 480atcggaaaac cctacatgat cgtagcttcg gttcatgtgc acgggcagat tgatggtttt 540cgccgctttc ttaagcacgc cgggggtggc acgttgatcg attcgggagt gcaccgcttc 600gacctcattc gctggatcat gggtgaagtc gagaccgtct tcgctcaaac gggtcgcttc 660ctccagatgc aaatggaagg agaagactgc gcggtggtca ccctccgctt ccgcagcgga 720gccatcggga gcttctcatg cagctggagc gccaaaggcc ctgttccaga agaaacattg 780caaattttcg gcccctatgg ttcgatttat accgaagacc acacccgcac cttacgcctt 840tacaccgaaa gacccacccc cgaactggaa gacgtaaggc agtttgtctt cccggtcgat 900caggctgagt ccatccgccg catgattgaa gcgcacttca ccagcctgca acaggggtta 960ccccctccga tcaccggtat ggacggacgc gcttcccttg agctcagcat ggcctcctat 1020cgctcggctc aaaccggcca gcctgttcat cttccccttc agagaggaaa ccagaaatga 108012359PRTUnknownObtained from environmental sample 12Met Pro Trp Ser Ser Ser Thr Gly Pro Ala Pro Met Thr Ser Asn Pro 1 5 10 15 Pro Leu Lys Arg Pro Leu Arg Ile Gly Leu Val Gly Thr Gly Ile Gly 20 25 30 Ser Leu His Ala Ala Gly Ile Ser Arg Met Pro Gln Leu Ala Thr Leu 35 40 45 Gly Ala Ile Cys Gly Leu Asp Thr His Ala Val Asn Ala Leu Ala Thr 50 55 60 Arg Tyr Gly Val Glu Lys Thr Thr Ser Arg Tyr Glu Asp Leu Leu Asn 65 70 75 80 Asp Pro Gly Leu Asp Val Ile Asp Leu Cys Val Pro His Asp Glu His 85 90 95 Met Pro Met Ala Ile Ala Ala Ala Arg Ala Gly Lys His Leu Leu Ile 100 105 110 Glu Lys Pro Leu Ala Arg Thr Leu Glu Glu Ala Asp Ala Ile Leu Glu 115 120 125 Ala Val Lys Ser Ala Gly Val Thr Leu Met Met Gly His Asn Gln Arg 130 135 140 Tyr Tyr Ala His His Ala Arg Ala Lys Ala Leu Val Asp Ala Gly Val 145 150 155 160 Ile Gly Lys Pro Tyr Met Ile Val Ala Ser Val His Val His Gly Gln 165 170 175 Ile Asp Gly Phe Arg Arg Phe Leu Lys His Ala Gly Gly Gly Thr Leu 180 185 190 Ile Asp Ser Gly Val His Arg Phe Asp Leu Ile Arg Trp Ile Met Gly 195 200 205 Glu Val Glu Thr Val Phe Ala Gln Thr Gly Arg Phe Leu Gln Met Gln 210 215 220 Met Glu Gly Glu Asp Cys Ala Val Val Thr Leu Arg Phe Arg Ser Gly 225 230 235 240 Ala Ile Gly Ser Phe Ser Cys Ser Trp Ser Ala Lys Gly Pro Val Pro 245 250 255 Glu Glu Thr Leu Gln Ile Phe Gly Pro Tyr Gly Ser Ile Tyr Thr Glu 260 265 270 Asp His Thr Arg Thr Leu Arg Leu Tyr Thr Glu Arg Pro Thr Pro Glu 275 280 285 Leu Glu Asp Val Arg Gln Phe Val Phe Pro Val Asp Gln Ala Glu Ser 290 295 300 Ile Arg Arg Met Ile Glu Ala His Phe Thr Ser Leu Gln Gln Gly Leu 305 310 315 320 Pro Pro Pro Ile Thr Gly Met Asp Gly Arg Ala Ser Leu Glu Leu Ser 325 330 335 Met Ala Ser Tyr Arg Ser Ala Gln Thr Gly Gln Pro Val His Leu Pro 340 345 350 Leu Gln Arg Gly Asn Gln Lys 355 131038DNAUnknownObtained from environmental sample 13atgagcccgg tgcgcgttgc tgtcatcggc gccgggcaaa ttgcccagcg cgggcattta 60cccgggcttc tggaagctgg cgccgaaatt accgttctgt gcgataattc ccttcctcag 120cttgaagaaa ttggggccaa atttcacgtt caccgggtct accgcgactg gcacgccatg 180ctggatgccg gcggattcga agccgtcacc atttgtaccc cgcccttcct ccatgccgag 240atggccatcg aatgtgcccg cagagggttg catgtactgg tagaaaaacc catggctgta 300aatctccaac aatgcgatca aatgatcgcc gcgtctgaac aggccggaac catcttaatg 360gtctcgcata accagcgctt tatggaggca catcgtctgg ccaaagaaat ccttgatgcc 420ggcctcctcg gcaggctcta cctggcgcac ggggtctttg gccacggcgg cccggaggtt 480tggagcccaa cccagcaatg gtacttccga cctgaccgcg ccggcgctgg cgtgatcgct 540gacctggggt atcataaact tgacctgatc cgctggctca ccgggcaaga aattaccgcg 600gtgggagcac tgggcgccac ctttgaaaag caaacctcgc ttgaagactc tgctgtgatg 660ctggttcacc tttcggaggg tactctcgcc accatccagg taagctgggt gttcaggcct 720gactgggaaa acagcctggt ccttcgagga gaacgggggg tgctcgccat ccccactgat 780gcctcgcaac ccctgcgggt ctcttacata tcttcttcgg gtcaggtcat tgaaagtacg 840catcgttgcg actccggcga tacctccggc tggttcggag cgatccgggc atttctcacc 900gcgatcgaaa aaagcgctcc cgctcccatt gacggaaaag aagggcgtgc tgtcatggcg 960gcagttctgg cggccacacg ctccattcaa aaacatacga tcatttctat aaccgaggta 1020gaaaccatcc atgactga 103814345PRTUnknownObtained from environmental sample 14Met Ser Pro Val Arg Val Ala Val Ile Gly Ala Gly Gln Ile Ala Gln 1 5 10 15 Arg Gly His Leu Pro Gly Leu Leu Glu Ala Gly Ala Glu Ile Thr Val 20 25 30 Leu Cys Asp Asn Ser Leu Pro Gln Leu Glu Glu Ile Gly Ala Lys Phe 35 40 45 His Val His Arg Val Tyr Arg Asp Trp His Ala Met Leu Asp Ala Gly 50 55 60 Gly Phe Glu Ala Val Thr Ile Cys Thr Pro Pro Phe Leu His Ala Glu 65 70 75 80 Met Ala Ile Glu Cys Ala Arg Arg Gly Leu His Val Leu Val Glu Lys 85 90 95 Pro Met Ala Val Asn Leu Gln Gln Cys Asp Gln Met Ile Ala Ala

Ser 100 105 110 Glu Gln Ala Gly Thr Ile Leu Met Val Ser His Asn Gln Arg Phe Met 115 120 125 Glu Ala His Arg Leu Ala Lys Glu Ile Leu Asp Ala Gly Leu Leu Gly 130 135 140 Arg Leu Tyr Leu Ala His Gly Val Phe Gly His Gly Gly Pro Glu Val 145 150 155 160 Trp Ser Pro Thr Gln Gln Trp Tyr Phe Arg Pro Asp Arg Ala Gly Ala 165 170 175 Gly Val Ile Ala Asp Leu Gly Tyr His Lys Leu Asp Leu Ile Arg Trp 180 185 190 Leu Thr Gly Gln Glu Ile Thr Ala Val Gly Ala Leu Gly Ala Thr Phe 195 200 205 Glu Lys Gln Thr Ser Leu Glu Asp Ser Ala Val Met Leu Val His Leu 210 215 220 Ser Glu Gly Thr Leu Ala Thr Ile Gln Val Ser Trp Val Phe Arg Pro 225 230 235 240 Asp Trp Glu Asn Ser Leu Val Leu Arg Gly Glu Arg Gly Val Leu Ala 245 250 255 Ile Pro Thr Asp Ala Ser Gln Pro Leu Arg Val Ser Tyr Ile Ser Ser 260 265 270 Ser Gly Gln Val Ile Glu Ser Thr His Arg Cys Asp Ser Gly Asp Thr 275 280 285 Ser Gly Trp Phe Gly Ala Ile Arg Ala Phe Leu Thr Ala Ile Glu Lys 290 295 300 Ser Ala Pro Ala Pro Ile Asp Gly Lys Glu Gly Arg Ala Val Met Ala 305 310 315 320 Ala Val Leu Ala Ala Thr Arg Ser Ile Gln Lys His Thr Ile Ile Ser 325 330 335 Ile Thr Glu Val Glu Thr Ile His Asp 340 345 151347DNAUnknownObtained from environmental sample 15atgactgacc atcgttttcc aaaaggattc atctggggaa ccgctacggc gtctttccag 60attgaaggcg ccacccgcga agatggccgg ggcgaatcca tctgggaccg cttctgcgcc 120acgccgggga aaattgtcac gggcgaaacc ggcgatcctg cctgcgactc ctatcatcgt 180taccctgaag acatcgccct gatgaaggct atgtcgctca atggttaccg cttttcaatc 240gcctggcctc gcgtcattcc tgacggagac ggtaaagtct gtcaggccgg gctcgactac 300tacgatcgtg tggtagatgc tctcctggcg gagaatatcc aaccttttat caccctgtac 360cactgggacc tgccccaggc attacaggat cggggtggct ggggcaaccg tgccacggtt 420gaggcgttca ctcgctacgt agatattgtg gtttctcgcc tgggtgaccg cgtaaagtac 480tggatgacac acaacgaacc ctggtgtgta tccattttga gccatgagct tggtgaacat 540gcccccgggt tgaaggaccg aaaactggcc ctccaggtgg cgcaccatgt cctcgtttct 600cacggcctgg ccgtgcccat catccgccag cgttgtaaag aggcgcaggt tggcatcgtg 660ttgaattttt cacctgctta cccggccacc gatagcctgg ccgaccagat ggccacccgt 720cagcaccacg cccggtttaa cctctggttc ctcgatccca tcgccgggcg cggctacccg 780caggatgcct gggaagggta cggagccgat gttcccgcca tgaggcctga tgacatgcag 840atcatcgccg cccccatcga cttcctgggc gtcaatttct acagtcgggc ggtctgccac 900gatccggccg ggggcgaagg ttcccgggtg ctcaatgtgc gcagtaaaac cgaggccacc 960gatcgagact gggagattta ccctcaggcg ctctacgatt tactcatctg gatccacaat 1020ggataccagt tcagagatat ttacattacc gagaatggcg cctcatacaa cgatgtggtc 1080tccccggatg ggaaagtgca cgatcctaaa cgtctggact atctgaaacg ccatctggcc 1140atggctctgc gggccatcga agcgggcgtt ccactgcgtg gttatttctg ctggagcttg 1200atggacaact tcgaatgggc catgggcacc agcagccgat tcgggttggc ctacaccgac 1260ttcactaccc agaagcgtat tctcaaagac agtgggctct ggtttggcga agtggcacgg 1320gcaaacgcct taatcgacct tccctga 134716448PRTUnknownObtained from environmental sample 16Met Thr Asp His Arg Phe Pro Lys Gly Phe Ile Trp Gly Thr Ala Thr 1 5 10 15 Ala Ser Phe Gln Ile Glu Gly Ala Thr Arg Glu Asp Gly Arg Gly Glu 20 25 30 Ser Ile Trp Asp Arg Phe Cys Ala Thr Pro Gly Lys Ile Val Thr Gly 35 40 45 Glu Thr Gly Asp Pro Ala Cys Asp Ser Tyr His Arg Tyr Pro Glu Asp 50 55 60 Ile Ala Leu Met Lys Ala Met Ser Leu Asn Gly Tyr Arg Phe Ser Ile 65 70 75 80 Ala Trp Pro Arg Val Ile Pro Asp Gly Asp Gly Lys Val Cys Gln Ala 85 90 95 Gly Leu Asp Tyr Tyr Asp Arg Val Val Asp Ala Leu Leu Ala Glu Asn 100 105 110 Ile Gln Pro Phe Ile Thr Leu Tyr His Trp Asp Leu Pro Gln Ala Leu 115 120 125 Gln Asp Arg Gly Gly Trp Gly Asn Arg Ala Thr Val Glu Ala Phe Thr 130 135 140 Arg Tyr Val Asp Ile Val Val Ser Arg Leu Gly Asp Arg Val Lys Tyr 145 150 155 160 Trp Met Thr His Asn Glu Pro Trp Cys Val Ser Ile Leu Ser His Glu 165 170 175 Leu Gly Glu His Ala Pro Gly Leu Lys Asp Arg Lys Leu Ala Leu Gln 180 185 190 Val Ala His His Val Leu Val Ser His Gly Leu Ala Val Pro Ile Ile 195 200 205 Arg Gln Arg Cys Lys Glu Ala Gln Val Gly Ile Val Leu Asn Phe Ser 210 215 220 Pro Ala Tyr Pro Ala Thr Asp Ser Leu Ala Asp Gln Met Ala Thr Arg 225 230 235 240 Gln His His Ala Arg Phe Asn Leu Trp Phe Leu Asp Pro Ile Ala Gly 245 250 255 Arg Gly Tyr Pro Gln Asp Ala Trp Glu Gly Tyr Gly Ala Asp Val Pro 260 265 270 Ala Met Arg Pro Asp Asp Met Gln Ile Ile Ala Ala Pro Ile Asp Phe 275 280 285 Leu Gly Val Asn Phe Tyr Ser Arg Ala Val Cys His Asp Pro Ala Gly 290 295 300 Gly Glu Gly Ser Arg Val Leu Asn Val Arg Ser Lys Thr Glu Ala Thr 305 310 315 320 Asp Arg Asp Trp Glu Ile Tyr Pro Gln Ala Leu Tyr Asp Leu Leu Ile 325 330 335 Trp Ile His Asn Gly Tyr Gln Phe Arg Asp Ile Tyr Ile Thr Glu Asn 340 345 350 Gly Ala Ser Tyr Asn Asp Val Val Ser Pro Asp Gly Lys Val His Asp 355 360 365 Pro Lys Arg Leu Asp Tyr Leu Lys Arg His Leu Ala Met Ala Leu Arg 370 375 380 Ala Ile Glu Ala Gly Val Pro Leu Arg Gly Tyr Phe Cys Trp Ser Leu 385 390 395 400 Met Asp Asn Phe Glu Trp Ala Met Gly Thr Ser Ser Arg Phe Gly Leu 405 410 415 Ala Tyr Thr Asp Phe Thr Thr Gln Lys Arg Ile Leu Lys Asp Ser Gly 420 425 430 Leu Trp Phe Gly Glu Val Ala Arg Ala Asn Ala Leu Ile Asp Leu Pro 435 440 445 171215DNAUnknownObtained from environmental sample 17atgcggtacg tgctgatttc ctgccttgcg ctggcttccc tgtgcgcgca gcctcttcct 60gtttccacgc ctgaaaaaga gggcttctcg gcggagcgcc tcgggcggat gcaccggtat 120ttcgagaacc tgacgaaaac cggagagcgg cctggcgcga tcacgctgat cgtgcgcaac 180gggcgcatcg tggactggcg cacgttcggg ctgcgcgacg tcgagaacaa tctgccgatg 240gagaaggaca cgatcgtcca catctactcg atgacgaagc cggtgacgtc cgtggccgtg 300atgatgctgg tggaggaggg caggctggcg ctggacgacc gggtggacaa gttcattccc 360gagttcaagg ggatgaaggt gtacaagggc ggcacggtgg agcggccgga gctggaggac 420gcggcgcggc cgatcacggt gaagcatctg ctgacgcaca cgagcgggct gagctacggc 480tggggcaacg acaacgtctc cgcgatgtac cgcaaggccg acccgctcgg cgcgccgagc 540ctgaaagagt ttatcgacag gctggtgaaa ctgccgctgg cattccaccc gggcgagcgt 600tacgagtatt cgatgtcgat cgacgtgctg ggctacctgg tggaggctgt ctccggcgag 660ccgttcgatc agttcgtgga gaagcggatc acggggccgc tgaagatgaa cgacacgcat 720ttcagactgc cggaggcgaa gcgggcgcgg ctggcgaaga tctactcgcg gcgcgagggg 780aagctgacgg cgcagcgcgg cctgcagacg ggaggcgttc cgtacggcgg catggggctg 840tactcgacga tcggcgacta tgcgcggttc gcgcagatgc tgttgaacgg cggccatctc 900gacggagtgc gcctgctggg gcggaagacg gtggatctga tgatgatgaa ccatctgggc 960ggactgtcga agccgacgat cggcggcgat gattcagcgg gattcggact gggcggagcg 1020gtgcggatcg atccggcgaa atcgggccgt ccgggcacgg aaggactctt cggctgggac 1080ggggcggctt cgacgtattt ccgggtggac cggaaagaga agctggcgat gctgctgttc 1140ctgcaatgga tgccgtttga tcaggggacg ctgaacctgt acgagacgct ggtctaccaa 1200gctctggtgg actga 121518404PRTUnknownObtained from environmental sample 18Met Arg Tyr Val Leu Ile Ser Cys Leu Ala Leu Ala Ser Leu Cys Ala 1 5 10 15 Gln Pro Leu Pro Val Ser Thr Pro Glu Lys Glu Gly Phe Ser Ala Glu 20 25 30 Arg Leu Gly Arg Met His Arg Tyr Phe Glu Asn Leu Thr Lys Thr Gly 35 40 45 Glu Arg Pro Gly Ala Ile Thr Leu Ile Val Arg Asn Gly Arg Ile Val 50 55 60 Asp Trp Arg Thr Phe Gly Leu Arg Asp Val Glu Asn Asn Leu Pro Met 65 70 75 80 Glu Lys Asp Thr Ile Val His Ile Tyr Ser Met Thr Lys Pro Val Thr 85 90 95 Ser Val Ala Val Met Met Leu Val Glu Glu Gly Arg Leu Ala Leu Asp 100 105 110 Asp Arg Val Asp Lys Phe Ile Pro Glu Phe Lys Gly Met Lys Val Tyr 115 120 125 Lys Gly Gly Thr Val Glu Arg Pro Glu Leu Glu Asp Ala Ala Arg Pro 130 135 140 Ile Thr Val Lys His Leu Leu Thr His Thr Ser Gly Leu Ser Tyr Gly 145 150 155 160 Trp Gly Asn Asp Asn Val Ser Ala Met Tyr Arg Lys Ala Asp Pro Leu 165 170 175 Gly Ala Pro Ser Leu Lys Glu Phe Ile Asp Arg Leu Val Lys Leu Pro 180 185 190 Leu Ala Phe His Pro Gly Glu Arg Tyr Glu Tyr Ser Met Ser Ile Asp 195 200 205 Val Leu Gly Tyr Leu Val Glu Ala Val Ser Gly Glu Pro Phe Asp Gln 210 215 220 Phe Val Glu Lys Arg Ile Thr Gly Pro Leu Lys Met Asn Asp Thr His 225 230 235 240 Phe Arg Leu Pro Glu Ala Lys Arg Ala Arg Leu Ala Lys Ile Tyr Ser 245 250 255 Arg Arg Glu Gly Lys Leu Thr Ala Gln Arg Gly Leu Gln Thr Gly Gly 260 265 270 Val Pro Tyr Gly Gly Met Gly Leu Tyr Ser Thr Ile Gly Asp Tyr Ala 275 280 285 Arg Phe Ala Gln Met Leu Leu Asn Gly Gly His Leu Asp Gly Val Arg 290 295 300 Leu Leu Gly Arg Lys Thr Val Asp Leu Met Met Met Asn His Leu Gly 305 310 315 320 Gly Leu Ser Lys Pro Thr Ile Gly Gly Asp Asp Ser Ala Gly Phe Gly 325 330 335 Leu Gly Gly Ala Val Arg Ile Asp Pro Ala Lys Ser Gly Arg Pro Gly 340 345 350 Thr Glu Gly Leu Phe Gly Trp Asp Gly Ala Ala Ser Thr Tyr Phe Arg 355 360 365 Val Asp Arg Lys Glu Lys Leu Ala Met Leu Leu Phe Leu Gln Trp Met 370 375 380 Pro Phe Asp Gln Gly Thr Leu Asn Leu Tyr Glu Thr Leu Val Tyr Gln 385 390 395 400 Ala Leu Val Asp 191794DNAUnknownObtained from environmental sample 19atgcccgttt tgttcgccct gtttcttgtt gcctcgtcct gcgcggcgca gtcgctggcc 60gggccggttt ccctgcttgg cggagatgcg ggcgcggcgt tccgctatac cgggccatcg 120gcgggcgcgg cgagcggctc ggccgaatgg gtggcggtgg agaacatgcc gttcacgcac 180gcctggcggc tgcgcacgaa tccgctgccg gagagcggcg gcaacgaatg ggacctgcgc 240atccgcgccc gcggagcggc ggctgtttcg gcaggggaca agatcctggc cgagttctgg 300atgcgctgcg tggagcccga aaacggcgac tgcattctgc gcctgaacgt ggagcgcgac 360gggtcgccgt ggaccaaatc catcagcaac ccctacccgg tgggccggga gtggcggcgg 420ttccgcgtgc tgttcgagat gcgggagagc tacgccgccg gcggctacat gatcgatttc 480tggatgggcc agcaggtgca gacggcggaa gtgggcggga tttccctgct gaattacggt 540ccgcaggcca cggccgagca gcttggcctg gaccggtttt atgagggcgc ggcggcggac 600gccgcgtggc ggcaggcggc cgagcagcgg atcgaggaga tccggaaagc gggcatgatc 660atcgtggcgg tgacgccgga cggcgagccg atcgagggcg ctgaaatccg ggcgaagctg 720aagcggcacg cgttcgggtg gggcacggct gtggcggcat cacggcttct ggggacggga 780acggacagcg agcgctaccg caacttcatc cgcgagaact tcaacatggc ggtgctcgag 840aacgacctga aatggggccc gttcgaagag aaccgcaacc gcgcgatgaa cgcgctgcgc 900tggctgcatg agaacgggat cacgtggatc cgcgggcaca atctcgtctg gccgggctgg 960cggtggatgc cgaacgacgt gcgcaacctg gcgaacaatc ccgaggcgct gcggcagcgg 1020attctggacc gcatccggga cacggccacg gccacgcgcg ggctggtggt gcactgggac 1080gtcgtcaacg agccggtggc cgagcgcgac gtgctgaaca ttctgggcga cgaggtgatg 1140gcggactggt tccgcgccgc gaaggagtgc gatcccgagg cgaggatgtt catcaatgag 1200tacgacattc tggcggcgaa cggggccaat ctgcggaagc agaacgcgta ttaccgcatg 1260atcgagatgc tgttgaagct cgaggcgccg gtggagggca tcggcttcca gggccacttc 1320gacacggcca cgccgccgga gcggatgctg gagatcatga accggtacgc ccggctcggg 1380ctgccgatcg ccatcaccga gtacgatttc gccacggcgg acgaggagct gcaggcgcag 1440ttcacgcgcg acctgatgat tctcgccttc agccatccgg cggtttcgga cttcctgatg 1500tggggcttct gggaagggag ccactggaag ccgctgggcg ccatgatccg gcgcgactgg 1560agcgagaagc cgatgtaccg cgtctggcgc gagctgatct tcgagcgctg gcagacggat 1620gaaacaggcg tgacgccgga gcacggtgcc atctacgtgc ggggcttcaa gggcgactac 1680gagatcacgg tgaaggcggg cgggcaggaa gtccgggtgc cgtacacgct gaaagaagac 1740ggccaggtgc tgtgggtgac ggtgggcggg gcttctgaag agcgcgtgca gtaa 179420597PRTUnknownObtained from environmental sample 20Met Pro Val Leu Phe Ala Leu Phe Leu Val Ala Ser Ser Cys Ala Ala 1 5 10 15 Gln Ser Leu Ala Gly Pro Val Ser Leu Leu Gly Gly Asp Ala Gly Ala 20 25 30 Ala Phe Arg Tyr Thr Gly Pro Ser Ala Gly Ala Ala Ser Gly Ser Ala 35 40 45 Glu Trp Val Ala Val Glu Asn Met Pro Phe Thr His Ala Trp Arg Leu 50 55 60 Arg Thr Asn Pro Leu Pro Glu Ser Gly Gly Asn Glu Trp Asp Leu Arg 65 70 75 80 Ile Arg Ala Arg Gly Ala Ala Ala Val Ser Ala Gly Asp Lys Ile Leu 85 90 95 Ala Glu Phe Trp Met Arg Cys Val Glu Pro Glu Asn Gly Asp Cys Ile 100 105 110 Leu Arg Leu Asn Val Glu Arg Asp Gly Ser Pro Trp Thr Lys Ser Ile 115 120 125 Ser Asn Pro Tyr Pro Val Gly Arg Glu Trp Arg Arg Phe Arg Val Leu 130 135 140 Phe Glu Met Arg Glu Ser Tyr Ala Ala Gly Gly Tyr Met Ile Asp Phe 145 150 155 160 Trp Met Gly Gln Gln Val Gln Thr Ala Glu Val Gly Gly Ile Ser Leu 165 170 175 Leu Asn Tyr Gly Pro Gln Ala Thr Ala Glu Gln Leu Gly Leu Asp Arg 180 185 190 Phe Tyr Glu Gly Ala Ala Ala Asp Ala Ala Trp Arg Gln Ala Ala Glu 195 200 205 Gln Arg Ile Glu Glu Ile Arg Lys Ala Gly Met Ile Ile Val Ala Val 210 215 220 Thr Pro Asp Gly Glu Pro Ile Glu Gly Ala Glu Ile Arg Ala Lys Leu 225 230 235 240 Lys Arg His Ala Phe Gly Trp Gly Thr Ala Val Ala Ala Ser Arg Leu 245 250 255 Leu Gly Thr Gly Thr Asp Ser Glu Arg Tyr Arg Asn Phe Ile Arg Glu 260 265 270 Asn Phe Asn Met Ala Val Leu Glu Asn Asp Leu Lys Trp Gly Pro Phe 275 280 285 Glu Glu Asn Arg Asn Arg Ala Met Asn Ala Leu Arg Trp Leu His Glu 290 295 300 Asn Gly Ile Thr Trp Ile Arg Gly His Asn Leu Val Trp Pro Gly Trp 305 310 315 320 Arg Trp Met Pro Asn Asp Val Arg Asn Leu Ala Asn Asn Pro Glu Ala 325 330 335 Leu Arg Gln Arg Ile Leu Asp Arg Ile Arg Asp Thr Ala Thr Ala Thr 340 345 350 Arg Gly Leu Val Val His Trp Asp Val Val Asn Glu Pro Val Ala Glu 355 360 365 Arg Asp Val Leu Asn Ile Leu Gly Asp Glu Val Met Ala Asp Trp Phe 370 375 380 Arg Ala Ala Lys Glu Cys Asp Pro Glu Ala Arg Met Phe Ile Asn Glu 385 390 395 400 Tyr Asp Ile Leu Ala Ala Asn Gly Ala Asn Leu Arg Lys Gln Asn Ala 405 410 415 Tyr Tyr Arg Met Ile Glu Met Leu Leu Lys Leu Glu Ala Pro Val Glu 420 425 430 Gly Ile Gly Phe Gln Gly His Phe Asp Thr Ala Thr Pro Pro Glu Arg 435 440 445 Met Leu Glu Ile Met Asn Arg Tyr Ala Arg Leu Gly Leu Pro Ile Ala 450 455 460 Ile Thr Glu Tyr Asp Phe Ala Thr Ala Asp Glu Glu Leu Gln Ala Gln 465 470 475 480 Phe Thr Arg Asp Leu Met Ile Leu Ala Phe Ser His Pro Ala Val Ser

485 490 495 Asp Phe Leu Met Trp Gly Phe Trp Glu Gly Ser His Trp Lys Pro Leu 500 505 510 Gly Ala Met Ile Arg Arg Asp Trp Ser Glu Lys Pro Met Tyr Arg Val 515 520 525 Trp Arg Glu Leu Ile Phe Glu Arg Trp Gln Thr Asp Glu Thr Gly Val 530 535 540 Thr Pro Glu His Gly Ala Ile Tyr Val Arg Gly Phe Lys Gly Asp Tyr 545 550 555 560 Glu Ile Thr Val Lys Ala Gly Gly Gln Glu Val Arg Val Pro Tyr Thr 565 570 575 Leu Lys Glu Asp Gly Gln Val Leu Trp Val Thr Val Gly Gly Ala Ser 580 585 590 Glu Glu Arg Val Gln 595 211032DNAClostridium thermocellum 21atggtgagtt ttaaagcagg tataaattta ggcggatgga tatcacaata tcaagttttc 60agcaaagagc atttcgatac attcattacg gagaaggaca ttgaaactat tgcagaagca 120gggtttgacc atgtcagact gccttttgat tatccaatta tcgagtctga tgacaatgtg 180ggagaatata aagaagatgg gctttcttat attgaccggt gccttgagtg gtgtaaaaaa 240tacaatttgg ggcttgtgtt ggatatgcat cacgctcccg ggtaccgctt tcaagatttt 300aagacaagca ccttgtttga agatccgaac cagcaaaaga gatttgttga catatggaga 360tttttagcca agcgttacat aaatgaacgg gaacatattg cctttgaact gttaaatgaa 420gttgttgagc ctgacagtac ccgctggaac aagttgatgc ttgagtgtgt aaaagcaatc 480agggaaattg attccaccag gtggctttac attgggggca ataactataa cagtcctgat 540gagcttaaaa accttgcaga tattgatgat gattacatag tttacaattt ccatttttac 600aatccttttt tctttacgca tcagaaagcc cactggtcgg aaagtgccat ggcgtacaac 660aggactgtaa aatatccggg acaatatgag ggaattgaag agtttgtgaa aaataatcct 720aagtacagtt ttatgatgga attgaataac ctgaagctga ataaagagct tttgcgcaaa 780gatttaaaac cagcaattga gttcagggaa aagaaaaaat gcaaactata ttgcggggag 840tttggcgtaa ttgccattgc tgacctggag tccaggataa aatggcatga agattatata 900agtcttctag aggagtatga tatcggcggc gcggtgtgga actacaaaaa aatggatttt 960gaaatttata atgaggatag aaaacctgtc tcgcaagaat tggtaaatat actggcgaga 1020agaaaaactt ga 103222343PRTClostridium thermocellumDOMAIN(1)...(323)Cellulase (glycosyl hydrolase family 5) 22Met Val Ser Phe Lys Ala Gly Ile Asn Leu Gly Gly Trp Ile Ser Gln 1 5 10 15 Tyr Gln Val Phe Ser Lys Glu His Phe Asp Thr Phe Ile Thr Glu Lys 20 25 30 Asp Ile Glu Thr Ile Ala Glu Ala Gly Phe Asp His Val Arg Leu Pro 35 40 45 Phe Asp Tyr Pro Ile Ile Glu Ser Asp Asp Asn Val Gly Glu Tyr Lys 50 55 60 Glu Asp Gly Leu Ser Tyr Ile Asp Arg Cys Leu Glu Trp Cys Lys Lys 65 70 75 80 Tyr Asn Leu Gly Leu Val Leu Asp Met His His Ala Pro Gly Tyr Arg 85 90 95 Phe Gln Asp Phe Lys Thr Ser Thr Leu Phe Glu Asp Pro Asn Gln Gln 100 105 110 Lys Arg Phe Val Asp Ile Trp Arg Phe Leu Ala Lys Arg Tyr Ile Asn 115 120 125 Glu Arg Glu His Ile Ala Phe Glu Leu Leu Asn Glu Val Val Glu Pro 130 135 140 Asp Ser Thr Arg Trp Asn Lys Leu Met Leu Glu Cys Val Lys Ala Ile 145 150 155 160 Arg Glu Ile Asp Ser Thr Arg Trp Leu Tyr Ile Gly Gly Asn Asn Tyr 165 170 175 Asn Ser Pro Asp Glu Leu Lys Asn Leu Ala Asp Ile Asp Asp Asp Tyr 180 185 190 Ile Val Tyr Asn Phe His Phe Tyr Asn Pro Phe Phe Phe Thr His Gln 195 200 205 Lys Ala His Trp Ser Glu Ser Ala Met Ala Tyr Asn Arg Thr Val Lys 210 215 220 Tyr Pro Gly Gln Tyr Glu Gly Ile Glu Glu Phe Val Lys Asn Asn Pro 225 230 235 240 Lys Tyr Ser Phe Met Met Glu Leu Asn Asn Leu Lys Leu Asn Lys Glu 245 250 255 Leu Leu Arg Lys Asp Leu Lys Pro Ala Ile Glu Phe Arg Glu Lys Lys 260 265 270 Lys Cys Lys Leu Tyr Cys Gly Glu Phe Gly Val Ile Ala Ile Ala Asp 275 280 285 Leu Glu Ser Arg Ile Lys Trp His Glu Asp Tyr Ile Ser Leu Leu Glu 290 295 300 Glu Tyr Asp Ile Gly Gly Ala Val Trp Asn Tyr Lys Lys Met Asp Phe 305 310 315 320 Glu Ile Tyr Asn Glu Asp Arg Lys Pro Val Ser Gln Glu Leu Val Asn 325 330 335 Ile Leu Ala Arg Arg Lys Thr 340 233966DNAClostridium thermocellum 23atgtataaaa gattattgtc gtcagtactg ataattatgc tgttattatc agcctggtcg 60ccaatatccg tacaagcttc tgatggaatc aatgacatta gaggtcattg ggctgaagaa 120gacttgaaca aatggatgga aaaaggtatt ttggtgggct accaggatgg gacgataagg 180cccgataata atatcacaag agccgaattt gtcacattaa ttaacaaggt tttcgggctt 240tatgaattaa gccgggagca attcgcagat gttgaagact caaaatggta ttcccgtgaa 300atattaaaag ccagggctgc gggatatatt gcaggttatg gaagcaatgt tttcaaacct 360gacaattata ttacaagaca agaagccgtt gttataatcg cgaaagtttt tgaacttcaa 420agcggcagca attatacaag caagtttaaa gatggaagtc tggtaaagga atacgcaaaa 480gattccgtta gcgcgttggt tgaaaaaggc tacatagcag gttatgaaga tggcactttc 540aggccggaca actacattac ccgtgcagaa acaataaaaa ttctgaataa aattattcct 600tccttgtata acgagaaagg agattataaa aatgaagaag tagccggaaa cgctctgatt 660aacaccgaag gagttatttt aaaagatacc gtaataaacg gggatttgta tcttgctcag 720ggaattcaga acggcgatgt tacccttgac ggtgtgaatg taaaaggaac ggttttcgta 780aatggtggag gaagcgacag catacatttt ataaatacga aaataaacag ggttgttgtc 840aataaaacag gagttagaat tgtaacttcc ggcaatacct cggttgaaag tgttgtcgtt 900aaatccggtg caaaacttga agaaaaagaa ttgacgggcg acggctttaa aaacgttaca 960gtcgattctc aactttcagc cggcaatgaa ataatatttg tcggggattt tgaacaggtc 1020gatgttctgg cggatgatgc cttgctggaa accaaagagg caaaaatgaa actgagaata 1080ttcggccaaa ggattaaagt aaatggaaag gcaatagaaa aatcatcaaa gaactatatt 1140gtaaacgggg aacttatatc aactgaggaa gaacccggtc cttccgacgc acccggtgcg 1200gaagacgatc aaaattcagg tagtccgggc tcatcgacta atcctgcacc aaccaagaat 1260ccgaatgaag agtggcgtct ggtttggagc gatgagttta acggttctga aataaatatg 1320gctaattgga gctatgacga cccgaccaac ggaagatgga acggggaagt acaatcctac 1380acacaaaaca atgcctatat caaagacggc gcgttggtta ttgaagcaag aaaagaagac 1440attacggaac caagcggtga gacttatcat tatacatcgt caaagctgat taccaaaggc 1500aaaaagtcat ggaagtacgg aaaatttgaa ataagggcaa aaatgccaca gggacaaggt 1560atatggcctg caatctggat gatgccggaa gacgaaccct tctacggaac atggccaaag 1620tgcggcgaaa tagatattat ggagcttttg ggccacgagc ctgataaaat ttatggaacg 1680atccattttg gagagcctca taaagaatcc cagggaacgt ataccttgcc ggaaggccag 1740acttttgctg atgatttcca cgtttattcg attgaatggg aaccgggaga aatacgctgg 1800tatatagacg gcaagctgta tcatgtcgct aatgactggt actcgaggga cccgtacctt 1860gccgatgact acacttatcc cgcacctttt gaccagaatt tcttcttgat tctcaatata 1920tccgttggtg gcggctggcc gggatatcct gacgaaacga cagttttccc gcagcaaatg 1980gttgtggact atgtgagagt atatcaaaaa gataaatatc ctcacaggga aaaaccggca 2040aaggaagaag tgaagccaag agagcctctt gaggacggca attatatcta taacggcggt 2100tttgatgtgg atgattctgc agcagttggt gtggacggtg ttccctatac gtcttactgg 2160acattcttaa cagcatccgg tggagctgcg acagtcaatg tagaggaagg tgttatgcac 2220gtacagatag aaaacggagg gacaaccgac tacggcgtac aattgcttca agctccgatt 2280catcttgaaa aaggcgcaaa atataaagca tcttttgaca tgaaagctga aaatccaagg 2340caggtaaaac tgaaaatagg cggagacggc gacaggggat ggaaagatta tgcggctatt 2400ccaccgttta cggtctcaac agagatgacc aactatgagt ttgagtttac tatgaaagat 2460gataccgatg ttaaggcacg gtttgagttt aatatgggtt tggacgataa tgatgtctgg 2520attgacaatg ttaaactgat taaaacagaa gatgcgccgg ttatagatcc ttccgaaata 2580gcaagacctc cgcttctttc cggcaactat atatacaacg gtacctttga ccaaggtccg 2640aacagaatgg gattctggaa ttttgttgtg gatagcactg caaaggctac atactatatt 2700ggaagcgatg ttaatgagcg caggtttgaa acaagaatag aaaaaggcgg aacatcgagg 2760ggagccataa gattggttca gccgggaatt aacattgaaa acggcaaaac atacaaggtt 2820agcttcgaag ccagtgcggc aaatacaaga actattgagg tggaaattgc aagcaatctt 2880cacaacagca gcatttttgc gacaactttt gaaataagca aagagagcaa gatatacgaa 2940tttgagttta caatggacaa agattcggac aagaacggag aacttaggtt caatctgggc 3000ggaagcaacg tgaacgtcta tattgataat gtcgttatga aaagagtaag taccgatgaa 3060gttgaaggaa acctgatttt aaacggcgta tttaacggcc tggcaggctg gggatatgga 3120gcgtatgaac ctggatcggc agattttgaa agtcatgagg aacaatttag ggcaattatt 3180agctctgtcg gtaatgaagg ttggaatgta cagttgtatc aggataatgt tccgctggaa 3240caagggcaaa cctacgaagt ttcttttgat gcaaaatcaa cgattgacag aaagataatt 3300gttcagctgc aaaggaacgg tacttcggat aataattggg actcctattt ctatcaagaa 3360gttgaactta ctaatgaact taaaacattc aaatatgaat ttacaatgag taaacctaca 3420gattcggcgt caagatttaa ttttgctttg ggtaatactg aaaacaaaac ttatgctcct 3480catgaaataa taattgacaa tgttgtagta agaaaagttg cgactccttc tgcgctgata 3540ttgaacggaa cctttgacga tggaatggat cattggctgc tatactgggg agacggtgaa 3600ggcaattgcg atgtaactga cggagagctt gaaattaaca ttaccaaggt aggtaccgcg 3660gattacatgc cgcagattaa acaggaaaac atagcgttgc aagagggtgt gacgtatact 3720ttgtctctta aagcgagagc gcttgaggca agaagtatta aagtggacat attggattct 3780tcttataact ggtatggcgg aactattttc gatttaacaa cggaagatgc cgtatacacg 3840tttacattta cccaaagcaa gtcgataaat aacggtgtct taactataaa tttaggtacc 3900atagaaggta agacatccgc cgcaactact gtctatcttg atgatatttt gctggaacaa 3960cagtaa 3966241321PRTClostridium thermocellumSIGNAL(1)...(26)DOMAIN(30)...(71)S-layer homology domain 24Met Tyr Lys Arg Leu Leu Ser Ser Val Leu Ile Ile Met Leu Leu Leu 1 5 10 15 Ser Ala Trp Ser Pro Ile Ser Val Gln Ala Ser Asp Gly Ile Asn Asp 20 25 30 Ile Arg Gly His Trp Ala Glu Glu Asp Leu Asn Lys Trp Met Glu Lys 35 40 45 Gly Ile Leu Val Gly Tyr Gln Asp Gly Thr Ile Arg Pro Asp Asn Asn 50 55 60 Ile Thr Arg Ala Glu Phe Val Thr Leu Ile Asn Lys Val Phe Gly Leu 65 70 75 80 Tyr Glu Leu Ser Arg Glu Gln Phe Ala Asp Val Glu Asp Ser Lys Trp 85 90 95 Tyr Ser Arg Glu Ile Leu Lys Ala Arg Ala Ala Gly Tyr Ile Ala Gly 100 105 110 Tyr Gly Ser Asn Val Phe Lys Pro Asp Asn Tyr Ile Thr Arg Gln Glu 115 120 125 Ala Val Val Ile Ile Ala Lys Val Phe Glu Leu Gln Ser Gly Ser Asn 130 135 140 Tyr Thr Ser Lys Phe Lys Asp Gly Ser Leu Val Lys Glu Tyr Ala Lys 145 150 155 160 Asp Ser Val Ser Ala Leu Val Glu Lys Gly Tyr Ile Ala Gly Tyr Glu 165 170 175 Asp Gly Thr Phe Arg Pro Asp Asn Tyr Ile Thr Arg Ala Glu Thr Ile 180 185 190 Lys Ile Leu Asn Lys Ile Ile Pro Ser Leu Tyr Asn Glu Lys Gly Asp 195 200 205 Tyr Lys Asn Glu Glu Val Ala Gly Asn Ala Leu Ile Asn Thr Glu Gly 210 215 220 Val Ile Leu Lys Asp Thr Val Ile Asn Gly Asp Leu Tyr Leu Ala Gln 225 230 235 240 Gly Ile Gln Asn Gly Asp Val Thr Leu Asp Gly Val Asn Val Lys Gly 245 250 255 Thr Val Phe Val Asn Gly Gly Gly Ser Asp Ser Ile His Phe Ile Asn 260 265 270 Thr Lys Ile Asn Arg Val Val Val Asn Lys Thr Gly Val Arg Ile Val 275 280 285 Thr Ser Gly Asn Thr Ser Val Glu Ser Val Val Val Lys Ser Gly Ala 290 295 300 Lys Leu Glu Glu Lys Glu Leu Thr Gly Asp Gly Phe Lys Asn Val Thr 305 310 315 320 Val Asp Ser Gln Leu Ser Ala Gly Asn Glu Ile Ile Phe Val Gly Asp 325 330 335 Phe Glu Gln Val Asp Val Leu Ala Asp Asp Ala Leu Leu Glu Thr Lys 340 345 350 Glu Ala Lys Met Lys Leu Arg Ile Phe Gly Gln Arg Ile Lys Val Asn 355 360 365 Gly Lys Ala Ile Glu Lys Ser Ser Lys Asn Tyr Ile Val Asn Gly Glu 370 375 380 Leu Ile Ser Thr Glu Glu Glu Pro Gly Pro Ser Asp Ala Pro Gly Ala 385 390 395 400 Glu Asp Asp Gln Asn Ser Gly Ser Pro Gly Ser Ser Thr Asn Pro Ala 405 410 415 Pro Thr Lys Asn Pro Asn Glu Glu Trp Arg Leu Val Trp Ser Asp Glu 420 425 430 Phe Asn Gly Ser Glu Ile Asn Met Ala Asn Trp Ser Tyr Asp Asp Pro 435 440 445 Thr Asn Gly Arg Trp Asn Gly Glu Val Gln Ser Tyr Thr Gln Asn Asn 450 455 460 Ala Tyr Ile Lys Asp Gly Ala Leu Val Ile Glu Ala Arg Lys Glu Asp 465 470 475 480 Ile Thr Glu Pro Ser Gly Glu Thr Tyr His Tyr Thr Ser Ser Lys Leu 485 490 495 Ile Thr Lys Gly Lys Lys Ser Trp Lys Tyr Gly Lys Phe Glu Ile Arg 500 505 510 Ala Lys Met Pro Gln Gly Gln Gly Ile Trp Pro Ala Ile Trp Met Met 515 520 525 Pro Glu Asp Glu Pro Phe Tyr Gly Thr Trp Pro Lys Cys Gly Glu Ile 530 535 540 Asp Ile Met Glu Leu Leu Gly His Glu Pro Asp Lys Ile Tyr Gly Thr 545 550 555 560 Ile His Phe Gly Glu Pro His Lys Glu Ser Gln Gly Thr Tyr Thr Leu 565 570 575 Pro Glu Gly Gln Thr Phe Ala Asp Asp Phe His Val Tyr Ser Ile Glu 580 585 590 Trp Glu Pro Gly Glu Ile Arg Trp Tyr Ile Asp Gly Lys Leu Tyr His 595 600 605 Val Ala Asn Asp Trp Tyr Ser Arg Asp Pro Tyr Leu Ala Asp Asp Tyr 610 615 620 Thr Tyr Pro Ala Pro Phe Asp Gln Asn Phe Phe Leu Ile Leu Asn Ile 625 630 635 640 Ser Val Gly Gly Gly Trp Pro Gly Tyr Pro Asp Glu Thr Thr Val Phe 645 650 655 Pro Gln Gln Met Val Val Asp Tyr Val Arg Val Tyr Gln Lys Asp Lys 660 665 670 Tyr Pro His Arg Glu Lys Pro Ala Lys Glu Glu Val Lys Pro Arg Glu 675 680 685 Pro Leu Glu Asp Gly Asn Tyr Ile Tyr Asn Gly Gly Phe Asp Val Asp 690 695 700 Asp Ser Ala Ala Val Gly Val Asp Gly Val Pro Tyr Thr Ser Tyr Trp 705 710 715 720 Thr Phe Leu Thr Ala Ser Gly Gly Ala Ala Thr Val Asn Val Glu Glu 725 730 735 Gly Val Met His Val Gln Ile Glu Asn Gly Gly Thr Thr Asp Tyr Gly 740 745 750 Val Gln Leu Leu Gln Ala Pro Ile His Leu Glu Lys Gly Ala Lys Tyr 755 760 765 Lys Ala Ser Phe Asp Met Lys Ala Glu Asn Pro Arg Gln Val Lys Leu 770 775 780 Lys Ile Gly Gly Asp Gly Asp Arg Gly Trp Lys Asp Tyr Ala Ala Ile 785 790 795 800 Pro Pro Phe Thr Val Ser Thr Glu Met Thr Asn Tyr Glu Phe Glu Phe 805 810 815 Thr Met Lys Asp Asp Thr Asp Val Lys Ala Arg Phe Glu Phe Asn Met 820 825 830 Gly Leu Asp Asp Asn Asp Val Trp Ile Asp Asn Val Lys Leu Ile Lys 835 840 845 Thr Glu Asp Ala Pro Val Ile Asp Pro Ser Glu Ile Ala Arg Pro Pro 850 855 860 Leu Leu Ser Gly Asn Tyr Ile Tyr Asn Gly Thr Phe Asp Gln Gly Pro 865 870 875 880 Asn Arg Met Gly Phe Trp Asn Phe Val Val Asp Ser Thr Ala Lys Ala 885 890 895 Thr Tyr Tyr Ile Gly Ser Asp Val Asn Glu Arg Arg Phe Glu Thr Arg 900 905 910 Ile Glu Lys Gly Gly Thr Ser Arg Gly Ala Ile Arg Leu Val Gln Pro 915 920 925 Gly Ile Asn Ile Glu Asn Gly Lys Thr Tyr Lys Val Ser Phe Glu Ala 930 935 940 Ser Ala Ala Asn Thr Arg Thr Ile Glu Val Glu Ile Ala Ser Asn Leu 945 950 955 960 His Asn Ser Ser Ile Phe Ala Thr Thr Phe Glu Ile Ser Lys Glu Ser 965 970 975 Lys Ile Tyr Glu Phe Glu Phe Thr Met Asp Lys Asp Ser Asp Lys Asn 980 985 990 Gly Glu Leu Arg Phe Asn Leu Gly Gly Ser Asn Val Asn Val Tyr Ile 995 1000 1005 Asp Asn Val Val Met Lys Arg Val Ser Thr Asp Glu Val Glu Gly 1010 1015 1020 Asn Leu Ile Leu Asn Gly Val Phe Asn Gly

Leu Ala Gly Trp Gly 1025 1030 1035 Tyr Gly Ala Tyr Glu Pro Gly Ser Ala Asp Phe Glu Ser His Glu 1040 1045 1050 Glu Gln Phe Arg Ala Ile Ile Ser Ser Val Gly Asn Glu Gly Trp 1055 1060 1065 Asn Val Gln Leu Tyr Gln Asp Asn Val Pro Leu Glu Gln Gly Gln 1070 1075 1080 Thr Tyr Glu Val Ser Phe Asp Ala Lys Ser Thr Ile Asp Arg Lys 1085 1090 1095 Ile Ile Val Gln Leu Gln Arg Asn Gly Thr Ser Asp Asn Asn Trp 1100 1105 1110 Asp Ser Tyr Phe Tyr Gln Glu Val Glu Leu Thr Asn Glu Leu Lys 1115 1120 1125 Thr Phe Lys Tyr Glu Phe Thr Met Ser Lys Pro Thr Asp Ser Ala 1130 1135 1140 Ser Arg Phe Asn Phe Ala Leu Gly Asn Thr Glu Asn Lys Thr Tyr 1145 1150 1155 Ala Pro His Glu Ile Ile Ile Asp Asn Val Val Val Arg Lys Val 1160 1165 1170 Ala Thr Pro Ser Ala Leu Ile Leu Asn Gly Thr Phe Asp Asp Gly 1175 1180 1185 Met Asp His Trp Leu Leu Tyr Trp Gly Asp Gly Glu Gly Asn Cys 1190 1195 1200 Asp Val Thr Asp Gly Glu Leu Glu Ile Asn Ile Thr Lys Val Gly 1205 1210 1215 Thr Ala Asp Tyr Met Pro Gln Ile Lys Gln Glu Asn Ile Ala Leu 1220 1225 1230 Gln Glu Gly Val Thr Tyr Thr Leu Ser Leu Lys Ala Arg Ala Leu 1235 1240 1245 Glu Ala Arg Ser Ile Lys Val Asp Ile Leu Asp Ser Ser Tyr Asn 1250 1255 1260 Trp Tyr Gly Gly Thr Ile Phe Asp Leu Thr Thr Glu Asp Ala Val 1265 1270 1275 Tyr Thr Phe Thr Phe Thr Gln Ser Lys Ser Ile Asn Asn Gly Val 1280 1285 1290 Leu Thr Ile Asn Leu Gly Thr Ile Glu Gly Lys Thr Ser Ala Ala 1295 1300 1305 Thr Thr Val Tyr Leu Asp Asp Ile Leu Leu Glu Gln Gln 1310 1315 1320 251347DNAClostridium thermocellum 25atgtcaaaga taactttccc aaaagatttc atatggggtt ctgcaacagc agcatatcag 60attgaaggtg catacaacga agacggcaaa ggtgaatcta tatgggaccg tttttcccac 120acgccaggaa atatagcaga cggacatacc ggcgatgttg catgcgacca ctatcatcgt 180tatgaagaag atatcaaaat aatgaaagaa atcggtatta aatcatacag gttttccatc 240tcatggccca gaatctttcc tgaaggaaca ggtaaattaa atcaaaaggg actggatttt 300tacaaaaggc tcacaaatct gcttctggaa aacggaatta tgcctgcaat cactctttat 360cactgggacc ttccccaaaa gcttcaggat aaaggcggat ggaaaaaccg ggacaccacc 420gattatttta cagaatactc tgaagtaata tttaaaaatc tcggagatat cgttccaata 480tggtttactc acaatgaacc cggtgttgtt tctttgcttg gccacttttt aggaattcat 540gcccctggga taaaagacct ccgcacttca ttggaagtct cgcacaatct tcttttgtcc 600cacggcaagg ccgtgaaact gtttagagaa atgaatattg acgcccaaat tggaatagct 660ctcaatttat cttaccatta tcccgcatcc gaaaaagctg aggatattga agcagcggaa 720ttgtcatttt ctctggcggg aaggtggtat ctggatcctg tgctaaaagg ccggtatcct 780gaaaacgcat tgaaacttta taaaaagaag ggtattgagc tttctttccc tgaagatgac 840ctgaaactta tcagtcagcc aatagacttc atagcattca acaattattc ttcggaattt 900ataaaatatg atccgtccag tgagtcaggt ttttcacctg caaactccat attagaaaag 960ttcgaaaaaa cagatatggg ctggatcata tatcctgaag gcttgtatga tctgcttatg 1020ctccttgaca gggattatgg aaagccaaac attgttatca gcgaaaacgg agccgccttc 1080aaagatgaaa taggtagcaa cggaaagata gaagacacaa agagaatcca atatcttaaa 1140gattatctga cccaggctca cagggcaatt caggacggtg taaacttaaa agcatactac 1200ttgtggtcgc ttttggacaa ctttgaatgg gcttacgggt acaacaagag attcggaatc 1260gttcacgtaa attttgatac gttggaaaga aaaataaagg atagcggcta ctggtacaaa 1320gaagtaatca aaaacaacgg tttttaa 134726448PRTClostridium thermocellumDOMAIN(2)...(448)Glycosyl hydrolase family 1 26Met Ser Lys Ile Thr Phe Pro Lys Asp Phe Ile Trp Gly Ser Ala Thr 1 5 10 15 Ala Ala Tyr Gln Ile Glu Gly Ala Tyr Asn Glu Asp Gly Lys Gly Glu 20 25 30 Ser Ile Trp Asp Arg Phe Ser His Thr Pro Gly Asn Ile Ala Asp Gly 35 40 45 His Thr Gly Asp Val Ala Cys Asp His Tyr His Arg Tyr Glu Glu Asp 50 55 60 Ile Lys Ile Met Lys Glu Ile Gly Ile Lys Ser Tyr Arg Phe Ser Ile 65 70 75 80 Ser Trp Pro Arg Ile Phe Pro Glu Gly Thr Gly Lys Leu Asn Gln Lys 85 90 95 Gly Leu Asp Phe Tyr Lys Arg Leu Thr Asn Leu Leu Leu Glu Asn Gly 100 105 110 Ile Met Pro Ala Ile Thr Leu Tyr His Trp Asp Leu Pro Gln Lys Leu 115 120 125 Gln Asp Lys Gly Gly Trp Lys Asn Arg Asp Thr Thr Asp Tyr Phe Thr 130 135 140 Glu Tyr Ser Glu Val Ile Phe Lys Asn Leu Gly Asp Ile Val Pro Ile 145 150 155 160 Trp Phe Thr His Asn Glu Pro Gly Val Val Ser Leu Leu Gly His Phe 165 170 175 Leu Gly Ile His Ala Pro Gly Ile Lys Asp Leu Arg Thr Ser Leu Glu 180 185 190 Val Ser His Asn Leu Leu Leu Ser His Gly Lys Ala Val Lys Leu Phe 195 200 205 Arg Glu Met Asn Ile Asp Ala Gln Ile Gly Ile Ala Leu Asn Leu Ser 210 215 220 Tyr His Tyr Pro Ala Ser Glu Lys Ala Glu Asp Ile Glu Ala Ala Glu 225 230 235 240 Leu Ser Phe Ser Leu Ala Gly Arg Trp Tyr Leu Asp Pro Val Leu Lys 245 250 255 Gly Arg Tyr Pro Glu Asn Ala Leu Lys Leu Tyr Lys Lys Lys Gly Ile 260 265 270 Glu Leu Ser Phe Pro Glu Asp Asp Leu Lys Leu Ile Ser Gln Pro Ile 275 280 285 Asp Phe Ile Ala Phe Asn Asn Tyr Ser Ser Glu Phe Ile Lys Tyr Asp 290 295 300 Pro Ser Ser Glu Ser Gly Phe Ser Pro Ala Asn Ser Ile Leu Glu Lys 305 310 315 320 Phe Glu Lys Thr Asp Met Gly Trp Ile Ile Tyr Pro Glu Gly Leu Tyr 325 330 335 Asp Leu Leu Met Leu Leu Asp Arg Asp Tyr Gly Lys Pro Asn Ile Val 340 345 350 Ile Ser Glu Asn Gly Ala Ala Phe Lys Asp Glu Ile Gly Ser Asn Gly 355 360 365 Lys Ile Glu Asp Thr Lys Arg Ile Gln Tyr Leu Lys Asp Tyr Leu Thr 370 375 380 Gln Ala His Arg Ala Ile Gln Asp Gly Val Asn Leu Lys Ala Tyr Tyr 385 390 395 400 Leu Trp Ser Leu Leu Asp Asn Phe Glu Trp Ala Tyr Gly Tyr Asn Lys 405 410 415 Arg Phe Gly Ile Val His Val Asn Phe Asp Thr Leu Glu Arg Lys Ile 420 425 430 Lys Asp Ser Gly Tyr Trp Tyr Lys Glu Val Ile Lys Asn Asn Gly Phe 435 440 445 271362DNAUnknownObtained from environmental sample 27atggcaaaca agataacctt tcctgaaaat tttctgtggg gcgcggcaac ggcttcgtac 60cagatcgaag gcgcctggaa caaacatggt aaaggcgaat ccacctggga tcgcttttca 120cacacgcccg gtaagatcag gaacaacgat acgggcgatg tagcaaatga ccattatcgc 180ctctggaaaa aagacattgg cttgatgaag aagatcgggt tgaaggctta tcgattttcc 240atttcgtggc cgcgtattct tcctgctgga agaggcaagg tcaatcaaag agggctggat 300ttttacaaca agatcgtaga tgagctgctg aaagcagata tcatcccatt tgttactctc 360aatcactggg acctgcccca aaaactggaa gatgagggcg gctggccggc ccgttctact 420gccgatgctt ttattgaata cacagatgtg atcacccgct cccttggcga ccgcgcaaag 480aattggatca ctcacaatga acctgccgtc gttgcctgga tgggatactc cactggccaa 540cacgcacccg gactgaagga ctatgggctt ggtgcccgcg ccgcgcatca cctgttgctc 600tcacatggac aggctgtacc ggtcattcgc agcaatagcg cgggggcaga agtgggaatt 660acgctcgata ttagctggcg gatcgctgcc tcaaacagcc gcgccgaccg ggagctggtc 720cgtgaggatg atgggaggtg gttccgctgg tttgccgacc cgctttacgg gcgcggatat 780ccctccgata aggtgtctga tttcactaag ttgggagcac tgcccaacgg acttgatttt 840gtgcaggcag gcgacatgga cacgatcgcg acaccgactg attttatggg gctaaactac 900tactcccgaa atgtctaccg cgcggacggt gcagataatg atccgcaaac tgttttccca 960caaccgaaga tgcccgaaca ctggaccgag atgggctggg aaatttaccc ggatgggctg 1020accaacattc tgggacgcgt ctatttcaac tatcagccgc gcaaactata cgtcacagaa 1080aacggcgcca gttactccac gcctcctgat gataagggga atgtcgcgga tgaactccgc 1140atccattatc tgaggacaca ttttgcagct gcctatcggg ccattcaaat gggcgtgcct 1200ctggcaggat acttcgtctg gtccctcatg gacaactttg agtggtcatg gggctatatg 1260caacgctttg gactcatctg ggtggattat gagacccaaa aacgcacttt aaaggatagc 1320gcaaaatggt ataagcgcgt gatcaagaag aatgggctct aa 136228453PRTUnknownObtained from environmental sample 28Met Ala Asn Lys Ile Thr Phe Pro Glu Asn Phe Leu Trp Gly Ala Ala 1 5 10 15 Thr Ala Ser Tyr Gln Ile Glu Gly Ala Trp Asn Lys His Gly Lys Gly 20 25 30 Glu Ser Thr Trp Asp Arg Phe Ser His Thr Pro Gly Lys Ile Arg Asn 35 40 45 Asn Asp Thr Gly Asp Val Ala Asn Asp His Tyr Arg Leu Trp Lys Lys 50 55 60 Asp Ile Gly Leu Met Lys Lys Ile Gly Leu Lys Ala Tyr Arg Phe Ser 65 70 75 80 Ile Ser Trp Pro Arg Ile Leu Pro Ala Gly Arg Gly Lys Val Asn Gln 85 90 95 Arg Gly Leu Asp Phe Tyr Asn Lys Ile Val Asp Glu Leu Leu Lys Ala 100 105 110 Asp Ile Ile Pro Phe Val Thr Leu Asn His Trp Asp Leu Pro Gln Lys 115 120 125 Leu Glu Asp Glu Gly Gly Trp Pro Ala Arg Ser Thr Ala Asp Ala Phe 130 135 140 Ile Glu Tyr Thr Asp Val Ile Thr Arg Ser Leu Gly Asp Arg Ala Lys 145 150 155 160 Asn Trp Ile Thr His Asn Glu Pro Ala Val Val Ala Trp Met Gly Tyr 165 170 175 Ser Thr Gly Gln His Ala Pro Gly Leu Lys Asp Tyr Gly Leu Gly Ala 180 185 190 Arg Ala Ala His His Leu Leu Leu Ser His Gly Gln Ala Val Pro Val 195 200 205 Ile Arg Ser Asn Ser Ala Gly Ala Glu Val Gly Ile Thr Leu Asp Ile 210 215 220 Ser Trp Arg Ile Ala Ala Ser Asn Ser Arg Ala Asp Arg Glu Leu Val 225 230 235 240 Arg Glu Asp Asp Gly Arg Trp Phe Arg Trp Phe Ala Asp Pro Leu Tyr 245 250 255 Gly Arg Gly Tyr Pro Ser Asp Lys Val Ser Asp Phe Thr Lys Leu Gly 260 265 270 Ala Leu Pro Asn Gly Leu Asp Phe Val Gln Ala Gly Asp Met Asp Thr 275 280 285 Ile Ala Thr Pro Thr Asp Phe Met Gly Leu Asn Tyr Tyr Ser Arg Asn 290 295 300 Val Tyr Arg Ala Asp Gly Ala Asp Asn Asp Pro Gln Thr Val Phe Pro 305 310 315 320 Gln Pro Lys Met Pro Glu His Trp Thr Glu Met Gly Trp Glu Ile Tyr 325 330 335 Pro Asp Gly Leu Thr Asn Ile Leu Gly Arg Val Tyr Phe Asn Tyr Gln 340 345 350 Pro Arg Lys Leu Tyr Val Thr Glu Asn Gly Ala Ser Tyr Ser Thr Pro 355 360 365 Pro Asp Asp Lys Gly Asn Val Ala Asp Glu Leu Arg Ile His Tyr Leu 370 375 380 Arg Thr His Phe Ala Ala Ala Tyr Arg Ala Ile Gln Met Gly Val Pro 385 390 395 400 Leu Ala Gly Tyr Phe Val Trp Ser Leu Met Asp Asn Phe Glu Trp Ser 405 410 415 Trp Gly Tyr Met Gln Arg Phe Gly Leu Ile Trp Val Asp Tyr Glu Thr 420 425 430 Gln Lys Arg Thr Leu Lys Asp Ser Ala Lys Trp Tyr Lys Arg Val Ile 435 440 445 Lys Lys Asn Gly Leu 450 291362DNAUnknownObtained from environmental sample 29atggcgaaca aaattacctt tcccgaaaat tttctttggg gcgcggcaac agcctcctac 60cagatcgaag gtgcgtggga caaacatggc aagggtgaat ccatctggga tcgcttttcg 120catacccctg gcaagatcag aaataatgat acgggcgatg ttgccaatga tcattatcgt 180ctctggaaaa aagacattgg cttgatgaag aagatcggct tgaaggcata tcgtttttcc 240atttcgtggc cgcgtgttct tcccgccgga cgcggcaaag tcaatcagaa gggactggat 300ttctataaca ggctggtaga tgctctgttg aaagaagata tcatcccatt tgtgactctc 360aatcactggg acctgcccca aaagctggag gaggaaggcg gttggccggt tcgctccacc 420gcagatgcct ttgtggaata cacagacgtg gtcacacgtt ccctcggcga ccgcgtaaag 480aattggatca cgcataatga gcctgccgtc gttgcctgga tgggatattc cacaggtcaa 540cacgcacccg gtttgaagga ctatgggctt ggtgtgcgcg ccgcgcatca tctgctgctc 600tcccacgggc aggcggtgcc agtcatccgc agtaacagcg ccgatgcaga agtgggcatt 660acgctggata ttagctggcg gattcctgcc tccaatagcc gagcagaccg ggaattggtc 720cgtaaagatg acggactatg gttccgctgg ttcgccgatc cgctttatgg gcgcggatac 780ccctcggata aagtcaccga ttttacaaag atcggcgcgc tgcccaatgg tctggacttt 840atgcaagccg gtgatatgga tgcgatcgcc acgccaaccg atttcatggg gctgaactat 900tatttccgaa atgtctaccg cgcgaatggc gaagacaatg atccgcaggt cgttttccca 960caaccaaaga tgcccgaaca ctggacggag atgggctggg aaatctatcc ggatggactg 1020acgaacatcc tgggacgcgt ttatttcaat taccagccac ataaactgta tatcacagag 1080aacggcgcga gctactccac cccgcccgat gaaaagggga atgtcgccga tgagctccgc 1140actcattatt tacggacaca cttcgcggct gcctaccggg cgattcagat gggcgtgcct 1200ctggcaggat actttgtctg gtccctcatg gacaactttg agtggtcctg gggatatatg 1260cagcgctttg ggctcatctg ggtggactac gagacacaga aacgcaccct gaaggatagc 1320gccaagtggt acaaacgtgt gatcaggaag aatgggtttt ag 136230453PRTUnknownObtained from environmental sample 30Met Ala Asn Lys Ile Thr Phe Pro Glu Asn Phe Leu Trp Gly Ala Ala 1 5 10 15 Thr Ala Ser Tyr Gln Ile Glu Gly Ala Trp Asp Lys His Gly Lys Gly 20 25 30 Glu Ser Ile Trp Asp Arg Phe Ser His Thr Pro Gly Lys Ile Arg Asn 35 40 45 Asn Asp Thr Gly Asp Val Ala Asn Asp His Tyr Arg Leu Trp Lys Lys 50 55 60 Asp Ile Gly Leu Met Lys Lys Ile Gly Leu Lys Ala Tyr Arg Phe Ser 65 70 75 80 Ile Ser Trp Pro Arg Val Leu Pro Ala Gly Arg Gly Lys Val Asn Gln 85 90 95 Lys Gly Leu Asp Phe Tyr Asn Arg Leu Val Asp Ala Leu Leu Lys Glu 100 105 110 Asp Ile Ile Pro Phe Val Thr Leu Asn His Trp Asp Leu Pro Gln Lys 115 120 125 Leu Glu Glu Glu Gly Gly Trp Pro Val Arg Ser Thr Ala Asp Ala Phe 130 135 140 Val Glu Tyr Thr Asp Val Val Thr Arg Ser Leu Gly Asp Arg Val Lys 145 150 155 160 Asn Trp Ile Thr His Asn Glu Pro Ala Val Val Ala Trp Met Gly Tyr 165 170 175 Ser Thr Gly Gln His Ala Pro Gly Leu Lys Asp Tyr Gly Leu Gly Val 180 185 190 Arg Ala Ala His His Leu Leu Leu Ser His Gly Gln Ala Val Pro Val 195 200 205 Ile Arg Ser Asn Ser Ala Asp Ala Glu Val Gly Ile Thr Leu Asp Ile 210 215 220 Ser Trp Arg Ile Pro Ala Ser Asn Ser Arg Ala Asp Arg Glu Leu Val 225 230 235 240 Arg Lys Asp Asp Gly Leu Trp Phe Arg Trp Phe Ala Asp Pro Leu Tyr 245 250 255 Gly Arg Gly Tyr Pro Ser Asp Lys Val Thr Asp Phe Thr Lys Ile Gly 260 265 270 Ala Leu Pro Asn Gly Leu Asp Phe Met Gln Ala Gly Asp Met Asp Ala 275 280 285 Ile Ala Thr Pro Thr Asp Phe Met Gly Leu Asn Tyr Tyr Phe Arg Asn 290 295 300 Val Tyr Arg Ala Asn Gly Glu Asp Asn Asp Pro Gln Val Val Phe Pro 305 310 315 320 Gln Pro Lys Met Pro Glu His Trp Thr Glu Met Gly Trp Glu Ile Tyr 325 330 335 Pro Asp Gly Leu Thr Asn Ile Leu Gly Arg Val Tyr Phe Asn Tyr Gln 340 345 350 Pro His Lys Leu Tyr Ile Thr Glu Asn Gly Ala Ser Tyr Ser Thr Pro 355 360 365 Pro Asp Glu Lys Gly Asn Val Ala Asp Glu Leu Arg Thr His Tyr Leu 370 375 380 Arg Thr His Phe Ala Ala Ala Tyr Arg Ala Ile Gln Met Gly Val Pro 385 390 395 400 Leu Ala Gly Tyr Phe Val Trp Ser Leu Met Asp Asn Phe Glu Trp Ser 405 410

415 Trp Gly Tyr Met Gln Arg Phe Gly Leu Ile Trp Val Asp Tyr Glu Thr 420 425 430 Gln Lys Arg Thr Leu Lys Asp Ser Ala Lys Trp Tyr Lys Arg Val Ile 435 440 445 Arg Lys Asn Gly Phe 450 311167DNAUnknownObtained from environmental sample 31atggaagacc gcccgcacta ttacagcgac gaccatctct ggggtgtact gtgcgtgacc 60gcctacatca aggaaactgg ggactttgca ttcctggacg agaaagttca cttttacgag 120aaggacccgg tcgagggcgt gtctgtgctg gatcacgtta aacgggcctt gacctttacc 180cgcaacaaca tcgggaaaca tggtctgcct ctcctcggct ttgcggattg gaacgacacg 240atcaatctgg cgaagggcgc cgagtctctt ttcacgtcgc atctatatgg acgcgcgctg 300ctggagttta ttgatctgct cacatatctt ggcaagaacg atgaagccga tgaatggcag 360cgagcccacg ttgagatgca gtcccgcgtc gaaaaacatg cctgggatgg cgaatggtat 420ttcatgtact ttgaccacga cggcagcccg gttgggtctc acacgaatca gtatggaaag 480atccatctca acggacagag ctgggctgtg ctttcgggct ttgcctctcc gcagcgcgcc 540cgccaggcca tggactcggt ttacaagcat ctcaacacaa agcacggcat caagctctcc 600acgccgggct acaatggcta tgaccccaac tacggcggcg tgaccaccta cccaccggga 660gcaaaggaaa acggcggcat cttcctgcac ccgaatccct gggccatgat cgcagagacc 720atgctcgggg atggcgatcg cgcctacgag tattactcgc agatcaaccc ggccggcaag 780aacgatgaca tcgacctgta cgaggtcgag ccatatgttt acgctcaaaa catcctgggc 840gatgagcatc cgcagttcgg gctgggacgc aactcgtggc tctcgggtac ggcatcctgg 900tgctatcagg ctgccacaca gtggatcctc ggaatccgcg ccgactatga agggctgcgc 960atcgacccgt gcattccgtc caagtgggat gggttcaagg caacgcgcct gtatcgcggc 1020gtgaagtaca acattacggt caccaacccg aagcacatct gcaaaggcgt ggaaaaagtt 1080ctggtcaacg gcaaaccggt tgaggggaat gtggtccggg cagacgtggg tttgcgcgaa 1140gtgaacgtgg aagttacctt aggataa 116732388PRTUnknownObtained from environmental sample 32Met Glu Asp Arg Pro His Tyr Tyr Ser Asp Asp His Leu Trp Gly Val 1 5 10 15 Leu Cys Val Thr Ala Tyr Ile Lys Glu Thr Gly Asp Phe Ala Phe Leu 20 25 30 Asp Glu Lys Val His Phe Tyr Glu Lys Asp Pro Val Glu Gly Val Ser 35 40 45 Val Leu Asp His Val Lys Arg Ala Leu Thr Phe Thr Arg Asn Asn Ile 50 55 60 Gly Lys His Gly Leu Pro Leu Leu Gly Phe Ala Asp Trp Asn Asp Thr 65 70 75 80 Ile Asn Leu Ala Lys Gly Ala Glu Ser Leu Phe Thr Ser His Leu Tyr 85 90 95 Gly Arg Ala Leu Leu Glu Phe Ile Asp Leu Leu Thr Tyr Leu Gly Lys 100 105 110 Asn Asp Glu Ala Asp Glu Trp Gln Arg Ala His Val Glu Met Gln Ser 115 120 125 Arg Val Glu Lys His Ala Trp Asp Gly Glu Trp Tyr Phe Met Tyr Phe 130 135 140 Asp His Asp Gly Ser Pro Val Gly Ser His Thr Asn Gln Tyr Gly Lys 145 150 155 160 Ile His Leu Asn Gly Gln Ser Trp Ala Val Leu Ser Gly Phe Ala Ser 165 170 175 Pro Gln Arg Ala Arg Gln Ala Met Asp Ser Val Tyr Lys His Leu Asn 180 185 190 Thr Lys His Gly Ile Lys Leu Ser Thr Pro Gly Tyr Asn Gly Tyr Asp 195 200 205 Pro Asn Tyr Gly Gly Val Thr Thr Tyr Pro Pro Gly Ala Lys Glu Asn 210 215 220 Gly Gly Ile Phe Leu His Pro Asn Pro Trp Ala Met Ile Ala Glu Thr 225 230 235 240 Met Leu Gly Asp Gly Asp Arg Ala Tyr Glu Tyr Tyr Ser Gln Ile Asn 245 250 255 Pro Ala Gly Lys Asn Asp Asp Ile Asp Leu Tyr Glu Val Glu Pro Tyr 260 265 270 Val Tyr Ala Gln Asn Ile Leu Gly Asp Glu His Pro Gln Phe Gly Leu 275 280 285 Gly Arg Asn Ser Trp Leu Ser Gly Thr Ala Ser Trp Cys Tyr Gln Ala 290 295 300 Ala Thr Gln Trp Ile Leu Gly Ile Arg Ala Asp Tyr Glu Gly Leu Arg 305 310 315 320 Ile Asp Pro Cys Ile Pro Ser Lys Trp Asp Gly Phe Lys Ala Thr Arg 325 330 335 Leu Tyr Arg Gly Val Lys Tyr Asn Ile Thr Val Thr Asn Pro Lys His 340 345 350 Ile Cys Lys Gly Val Glu Lys Val Leu Val Asn Gly Lys Pro Val Glu 355 360 365 Gly Asn Val Val Arg Ala Asp Val Gly Leu Arg Glu Val Asn Val Glu 370 375 380 Val Thr Leu Gly 385 331362DNAUnknownObtained from environmental sample 33atggcaaata aaattctctt ccccgagaac tttctctggg gcacggcgac cgcatcctac 60cagatcgagg gggcttggga taaacatggt aagggcgagt cgacctggga ccgttttacg 120catacacctg gaaagatcaa aaacaatgat acgggcgatg tagcagatga ccattatcga 180ttatggaaaa aagatatcgg cttgatgaag aagctcggct tgaaggctta tcgtttttcg 240acttcctggc cgcgggtgct gccggccggg cgcggtaaga gcaatcaaaa aggactcgat 300ttctacagca agctggttga tgagttgcta aaagcaaata tcatcccatt cgtgacattg 360aatcactggg acatcccaca aaagttggag gacgagggtg gctgggccgt gcgctcaacg 420gctgaggcat ttgtggaata tgccgatctc atgtcgcgca cgcttggaga ccgcgtcaag 480aactggatca cgcacaacga accggccgtc gtcgcctgga tgggatacgg gatgggcatc 540cacgcgccgg gcttaacgga tttctcgatt gcggtgccgg tctcgcatca tctgctcctt 600tcgcacggat gggccgtgcc tgtgattcgc ggtaacagcc cggatgccga ggtgggcatt 660accctcaaca ttcaatgggg cgaagcagca tccaacagcc gggccgacct aaacgccctg 720cgcctgaacg atggacagtg gttccgctgg tttgccgatc cggtttatgg ccgcggctat 780ccttccgacg tggtggctga tttcgagaaa atgggcgcgc tgccgaacgg catgaatttc 840gtgcaacctg gcgatatgga tgtcatcgcc acgccaaccg atttcctcgg gctcaattat 900tattcccgcc atgtgcatcg cgtcaacaca ccggataacg atcaacaggt tgtgtttgcc 960aaacagcagg gtcccgagaa ctggaccgag atgggctggg agatccatcc tgatggattg 1020gccggaattt tatccagagc gtatttcaat taccagccgc gcaaagtata tgtgactgaa 1080aacggtgcca gctattccac cgcgcccgat gagaatggta ttgtcaacga cattcaccgc 1140gtcaattatc tacggacgca cttcgcggct gcccatcgcg ccctgcaggc gggcgtgcca 1200ttggcaggat acttcgtctg gtcaatgctc gataacttcg aatggagtca cgggtacagc 1260cagcgctttg gcatcgttta tgtggactat caaacccaga agcgttactt gaaagacagc 1320gccaagtggt acaaaggtgt catcaaaaag aatgggttct aa 136234453PRTUnknownObtained from environmental sample 34Met Ala Asn Lys Ile Leu Phe Pro Glu Asn Phe Leu Trp Gly Thr Ala 1 5 10 15 Thr Ala Ser Tyr Gln Ile Glu Gly Ala Trp Asp Lys His Gly Lys Gly 20 25 30 Glu Ser Thr Trp Asp Arg Phe Thr His Thr Pro Gly Lys Ile Lys Asn 35 40 45 Asn Asp Thr Gly Asp Val Ala Asp Asp His Tyr Arg Leu Trp Lys Lys 50 55 60 Asp Ile Gly Leu Met Lys Lys Leu Gly Leu Lys Ala Tyr Arg Phe Ser 65 70 75 80 Thr Ser Trp Pro Arg Val Leu Pro Ala Gly Arg Gly Lys Ser Asn Gln 85 90 95 Lys Gly Leu Asp Phe Tyr Ser Lys Leu Val Asp Glu Leu Leu Lys Ala 100 105 110 Asn Ile Ile Pro Phe Val Thr Leu Asn His Trp Asp Ile Pro Gln Lys 115 120 125 Leu Glu Asp Glu Gly Gly Trp Ala Val Arg Ser Thr Ala Glu Ala Phe 130 135 140 Val Glu Tyr Ala Asp Leu Met Ser Arg Thr Leu Gly Asp Arg Val Lys 145 150 155 160 Asn Trp Ile Thr His Asn Glu Pro Ala Val Val Ala Trp Met Gly Tyr 165 170 175 Gly Met Gly Ile His Ala Pro Gly Leu Thr Asp Phe Ser Ile Ala Val 180 185 190 Pro Val Ser His His Leu Leu Leu Ser His Gly Trp Ala Val Pro Val 195 200 205 Ile Arg Gly Asn Ser Pro Asp Ala Glu Val Gly Ile Thr Leu Asn Ile 210 215 220 Gln Trp Gly Glu Ala Ala Ser Asn Ser Arg Ala Asp Leu Asn Ala Leu 225 230 235 240 Arg Leu Asn Asp Gly Gln Trp Phe Arg Trp Phe Ala Asp Pro Val Tyr 245 250 255 Gly Arg Gly Tyr Pro Ser Asp Val Val Ala Asp Phe Glu Lys Met Gly 260 265 270 Ala Leu Pro Asn Gly Met Asn Phe Val Gln Pro Gly Asp Met Asp Val 275 280 285 Ile Ala Thr Pro Thr Asp Phe Leu Gly Leu Asn Tyr Tyr Ser Arg His 290 295 300 Val His Arg Val Asn Thr Pro Asp Asn Asp Gln Gln Val Val Phe Ala 305 310 315 320 Lys Gln Gln Gly Pro Glu Asn Trp Thr Glu Met Gly Trp Glu Ile His 325 330 335 Pro Asp Gly Leu Ala Gly Ile Leu Ser Arg Ala Tyr Phe Asn Tyr Gln 340 345 350 Pro Arg Lys Val Tyr Val Thr Glu Asn Gly Ala Ser Tyr Ser Thr Ala 355 360 365 Pro Asp Glu Asn Gly Ile Val Asn Asp Ile His Arg Val Asn Tyr Leu 370 375 380 Arg Thr His Phe Ala Ala Ala His Arg Ala Leu Gln Ala Gly Val Pro 385 390 395 400 Leu Ala Gly Tyr Phe Val Trp Ser Met Leu Asp Asn Phe Glu Trp Ser 405 410 415 His Gly Tyr Ser Gln Arg Phe Gly Ile Val Tyr Val Asp Tyr Gln Thr 420 425 430 Gln Lys Arg Tyr Leu Lys Asp Ser Ala Lys Trp Tyr Lys Gly Val Ile 435 440 445 Lys Lys Asn Gly Phe 450 351116DNAUnknownObtained from environmental sample 35atgaataaaa tcctcaaact cttcagcagc ctgctgcttt ttgcaggcat ctgtcccgcg 60cttcaggcag agccagtaga aacctacttt cccctgtccc gcgggatcaa catgagccac 120tggctctctc aagtgaatga aaacattccc gaccgttcca cctatgtgac ggagcgggat 180ttgcaatttc tgcgggcagc cggtttcgac catgtgcgtc tgccaatcga tgaggtcgaa 240ctctgggatg aagagggcaa tcagatcgag gaggcctggc aatacatgca taactttctc 300cgttggagcc gaaagaacga tctccgggtc attctcgacc tgcacacggt attgtcccac 360cacttcaacg cggtaaatat gggagaggtc aatacactct tcaatgatcc cagggaacag 420gaaaagttcc tcaacctatg ggaacaaatc atggatgccg tgggtcacca tccgaatgag 480tttctcgcct atgaaatgct caatgaggcg gtcgcggaag atgatgaaga ctggaatctg 540ctcctcaacc gcgccattgt ccgcatccgg gaccgtgagc cttatcgggt gctgattgcg 600gggtcgaact ggtggcagca tgccgaccgg gtccccaacc tgaggctccc gaaaggagac 660cccaatatca tcatcagttt tcatttttat tccccttttc tcttcaccca ctaccgcagt 720agctggactg cgatgcaggc gtaccagggc ttcgtccaat accctggcaa aaccatacct 780tccatacatc tcgaaggcat gaactacccg gagtccttcg ttcatatgtg ggaagcgcac 840aatcggtact atgacatcca ttccatgtat gccgaaatgg tcccggcggt gcgttttgcc 900gaaaagttgg gacttcggct ctattgcgga gaattcgggg ccatgaagac cgttgatcgc 960gcccagatgc tgcagtggta tcgggatgtt gtcactgtat ttaataaatt gggtattccc 1020tatactgcct gggattatca gggaaccttc ggaatccgcg atgagctgac cggtgagccc 1080gatcatgaaa tgatcgatat tctcctcggg cgctga 111636371PRTUnknownObtained from environmental sample 36Met Asn Lys Ile Leu Lys Leu Phe Ser Ser Leu Leu Leu Phe Ala Gly 1 5 10 15 Ile Cys Pro Ala Leu Gln Ala Glu Pro Val Glu Thr Tyr Phe Pro Leu 20 25 30 Ser Arg Gly Ile Asn Met Ser His Trp Leu Ser Gln Val Asn Glu Asn 35 40 45 Ile Pro Asp Arg Ser Thr Tyr Val Thr Glu Arg Asp Leu Gln Phe Leu 50 55 60 Arg Ala Ala Gly Phe Asp His Val Arg Leu Pro Ile Asp Glu Val Glu 65 70 75 80 Leu Trp Asp Glu Glu Gly Asn Gln Ile Glu Glu Ala Trp Gln Tyr Met 85 90 95 His Asn Phe Leu Arg Trp Ser Arg Lys Asn Asp Leu Arg Val Ile Leu 100 105 110 Asp Leu His Thr Val Leu Ser His His Phe Asn Ala Val Asn Met Gly 115 120 125 Glu Val Asn Thr Leu Phe Asn Asp Pro Arg Glu Gln Glu Lys Phe Leu 130 135 140 Asn Leu Trp Glu Gln Ile Met Asp Ala Val Gly His His Pro Asn Glu 145 150 155 160 Phe Leu Ala Tyr Glu Met Leu Asn Glu Ala Val Ala Glu Asp Asp Glu 165 170 175 Asp Trp Asn Leu Leu Leu Asn Arg Ala Ile Val Arg Ile Arg Asp Arg 180 185 190 Glu Pro Tyr Arg Val Leu Ile Ala Gly Ser Asn Trp Trp Gln His Ala 195 200 205 Asp Arg Val Pro Asn Leu Arg Leu Pro Lys Gly Asp Pro Asn Ile Ile 210 215 220 Ile Ser Phe His Phe Tyr Ser Pro Phe Leu Phe Thr His Tyr Arg Ser 225 230 235 240 Ser Trp Thr Ala Met Gln Ala Tyr Gln Gly Phe Val Gln Tyr Pro Gly 245 250 255 Lys Thr Ile Pro Ser Ile His Leu Glu Gly Met Asn Tyr Pro Glu Ser 260 265 270 Phe Val His Met Trp Glu Ala His Asn Arg Tyr Tyr Asp Ile His Ser 275 280 285 Met Tyr Ala Glu Met Val Pro Ala Val Arg Phe Ala Glu Lys Leu Gly 290 295 300 Leu Arg Leu Tyr Cys Gly Glu Phe Gly Ala Met Lys Thr Val Asp Arg 305 310 315 320 Ala Gln Met Leu Gln Trp Tyr Arg Asp Val Val Thr Val Phe Asn Lys 325 330 335 Leu Gly Ile Pro Tyr Thr Ala Trp Asp Tyr Gln Gly Thr Phe Gly Ile 340 345 350 Arg Asp Glu Leu Thr Gly Glu Pro Asp His Glu Met Ile Asp Ile Leu 355 360 365 Leu Gly Arg 370 371383DNAUnknownObtained from environmental sample 37atgagcaaac tccccaaatt cctctttgga gccggcacct caagttatca gatcgaaggt 60gcctggaata tagatggcaa aggtccctcc atttgggatt tccacactcg ccatcccggc 120gcggtttatc ggatgcacaa cggggatatg gcctgcgatc attatcatcg gtatcgaacg 180gatatcgagc tgatgcagaa gatcggccta gaggcttacc gcttttccat aaactggccc 240cgggttctgc cggaagggac cggtgccgcc aatgaagcag gtctggactt ttacgaccgg 300ctggtggacg cactgttgga agcgggaatt cagccttgga tcacccttta tcactgggaa 360ctcccctggg ctctccacct gcgcgggggt tggctcaatc gggacatgcc cgaccacatt 420gagaactacg ccgccttggt cgccaggtgc ctcggtgacc gggtgaaaaa ctggattact 480ttgaatgagc ctcaggtttt catcgggctt ggctatgcca gcggggttca tgcccccggc 540tataagttgt ccttgcggga gtgcctggtc ggttcccacc atgccgtgct ttcccaccac 600cgggcagtca aggcgatccg ggccaactgc gaaggcagcg tccagatcgg ctcagccccg 660gtgggtgttg tctgccgacc ggaaacggag tcggcagcag acattgaggc tgcccgccag 720gccacctacc atatcaacac tcccagcacc cacactcccg acaatctgat cggctgcctc 780tggaacagca cttggtggat agatccaatg gttctgggga agtatccgga acacgggctg 840aaagcctttg aaagctatct gccggacaac attcaggccg aactggatgc cgtattcgaa 900ccgacggact ttgtcggttc caacatctac cacggccgca cggtgcgggc caagcaggat 960ggtggttttg agtttatcga ccttccgccc ggcagccccc gcaccaccat gggctgggac 1020atcaccccgg acatcctcta ctggggagga aagtatcttt acgaacgcta tggcaagccg 1080atgtttatca cggaaaacgg cattgccgtc ccggaactgg tgaatgatga aggccaggtc 1140gaggataccg tccgtgagca atacatgaag ctgcacctgc gtgggctgca gcgggcccgc 1200gatgaaggca tcccctatgc cggatacttc cactggtccc tgctcgacaa cttcgagtgg 1260gaacaaggct actcccagcg ctttggcatg gtctacgtcg actaccagac ccaggaacgt 1320atcctcaaac gttcgggcca gcatttcgct gccatcgtcc gggaaatcac cggaaccgcc 1380taa 138338460PRTUnknownObtained from environmental sample 38Met Ser Lys Leu Pro Lys Phe Leu Phe Gly Ala Gly Thr Ser Ser Tyr 1 5 10 15 Gln Ile Glu Gly Ala Trp Asn Ile Asp Gly Lys Gly Pro Ser Ile Trp 20 25 30 Asp Phe His Thr Arg His Pro Gly Ala Val Tyr Arg Met His Asn Gly 35 40 45 Asp Met Ala Cys Asp His Tyr His Arg Tyr Arg Thr Asp Ile Glu Leu 50 55 60 Met Gln Lys Ile Gly Leu Glu Ala Tyr Arg Phe Ser Ile Asn Trp Pro 65 70 75 80 Arg Val Leu Pro Glu Gly Thr Gly Ala Ala Asn Glu Ala Gly Leu Asp 85 90 95 Phe Tyr Asp Arg Leu Val Asp Ala Leu Leu Glu Ala Gly Ile Gln Pro 100 105 110 Trp Ile Thr Leu Tyr His Trp Glu Leu Pro Trp Ala Leu His Leu Arg 115 120 125 Gly Gly Trp Leu Asn Arg Asp Met Pro Asp His Ile Glu Asn Tyr Ala 130 135 140 Ala Leu Val Ala Arg Cys Leu Gly Asp Arg Val Lys Asn Trp Ile Thr 145 150 155 160 Leu Asn Glu Pro Gln Val Phe Ile Gly Leu Gly Tyr Ala Ser Gly Val 165 170 175 His Ala Pro Gly Tyr Lys Leu Ser Leu Arg Glu Cys Leu Val Gly Ser 180 185 190 His His Ala Val Leu Ser His His Arg Ala Val Lys Ala Ile Arg Ala 195 200

205 Asn Cys Glu Gly Ser Val Gln Ile Gly Ser Ala Pro Val Gly Val Val 210 215 220 Cys Arg Pro Glu Thr Glu Ser Ala Ala Asp Ile Glu Ala Ala Arg Gln 225 230 235 240 Ala Thr Tyr His Ile Asn Thr Pro Ser Thr His Thr Pro Asp Asn Leu 245 250 255 Ile Gly Cys Leu Trp Asn Ser Thr Trp Trp Ile Asp Pro Met Val Leu 260 265 270 Gly Lys Tyr Pro Glu His Gly Leu Lys Ala Phe Glu Ser Tyr Leu Pro 275 280 285 Asp Asn Ile Gln Ala Glu Leu Asp Ala Val Phe Glu Pro Thr Asp Phe 290 295 300 Val Gly Ser Asn Ile Tyr His Gly Arg Thr Val Arg Ala Lys Gln Asp 305 310 315 320 Gly Gly Phe Glu Phe Ile Asp Leu Pro Pro Gly Ser Pro Arg Thr Thr 325 330 335 Met Gly Trp Asp Ile Thr Pro Asp Ile Leu Tyr Trp Gly Gly Lys Tyr 340 345 350 Leu Tyr Glu Arg Tyr Gly Lys Pro Met Phe Ile Thr Glu Asn Gly Ile 355 360 365 Ala Val Pro Glu Leu Val Asn Asp Glu Gly Gln Val Glu Asp Thr Val 370 375 380 Arg Glu Gln Tyr Met Lys Leu His Leu Arg Gly Leu Gln Arg Ala Arg 385 390 395 400 Asp Glu Gly Ile Pro Tyr Ala Gly Tyr Phe His Trp Ser Leu Leu Asp 405 410 415 Asn Phe Glu Trp Glu Gln Gly Tyr Ser Gln Arg Phe Gly Met Val Tyr 420 425 430 Val Asp Tyr Gln Thr Gln Glu Arg Ile Leu Lys Arg Ser Gly Gln His 435 440 445 Phe Ala Ala Ile Val Arg Glu Ile Thr Gly Thr Ala 450 455 460 391521DNAUnknownObtained from environmental sample 39gtgctcgccc ataaccgctc gcaccgtgaa gaactcctca atcgccggcc ggttgaattc 60atcagcgccc tggaggcccg gggcgagctc cagcgcatca ccgccgaggt ggacccctac 120ctcgagatca ccgagatctg cgatcgcacc ctgcgcgccg gcggcccggc gctgctgttc 180gagaacgtca aggggcacga catgcctctg ctcggcaacc tcttcggcac gccgaagcgg 240gttgccctcg gcatgggcca ggactccgtg gccgccctgc gcgaagtggg cgagctgctc 300gccttcctca aggagccgga gcctcccaag ggctttcgcg acgcctggga caagctgccg 360atcttcaagc aggtgatgag catggggccg aagaaggtcc gctcggcgcc ggtgcaggaa 420aaggtgtacg agggcgacga ggtcgacctc gaccgcctgc cgatccagca ctgctggccc 480ggcgacgccg cgcccctggt cacctggccg ctggtgatca cccgcgggcc ccacaagaag 540cgccagaacc tcggcatcta ccgccagcag aagctgtcga agaaccggct gatcatgcgc 600tggctctccc accgcggcgg ggcgctggac ttcctggagt tccagaaggc ccaccccggc 660gagcccttcc cggtggcggt ggcgctgggc gccgacccgg cgaccatcct cggcgcggtg 720accccggtgc cggattcgct ctccgagtac gccttcgccg ggctgctgcg cggctcgcgc 780accgagctgg tcaagtgcgg ccacgccgac ctggacgtgc cggcctcggc ggagatcatc 840ctggaggggt tcatctaccc ggatgacatg gcccccgagg gcccctacgg cgaccatacc 900ggctactaca acgaggtgga taccttcccg gtcttcacgg tgacgcgtat gaccatgcgc 960cgcgatgcca tctatcactc cacctacacc ggccggccgc ccgacgagcc ggcgatcctt 1020gggctggcgc tcaacgaggt gttcgtgccg atcctgcgcc gccagttccc ggagatcgtc 1080gacttctacc tgccgccgga gggctgctcc taccgcatgg cggtggtgac catgaagaag 1140cagtacccgg gccacgccaa gcgggtgatg atgggcgtgt ggagcttcct gcgccagttc 1200atgtacacca agttcgtggt ggtgctcgac gacgacgtca gcgcccggga ctgggaggac 1260gtgatctggg ccatcaccac ccgcatggac ccggcccggg acaccgtggt ggtggagaac 1320acccccatcg actacctgga cttcgcctcg ccggtctccg gcctcggttc caagatgggc 1380ctggatgcca ccagcaagtg gcccggcgag accgaccgcg agtggggggt gcccatcgtc 1440atggacgagg ccgtcaaggc ccgcgtcagc gagcgctgga acgagctggg catcgagctc 1500cccgacaaca cgaccccctg a 152140506PRTUnknownObtained from environmental sample 40Met Leu Ala His Asn Arg Ser His Arg Glu Glu Leu Leu Asn Arg Arg 1 5 10 15 Pro Val Glu Phe Ile Ser Ala Leu Glu Ala Arg Gly Glu Leu Gln Arg 20 25 30 Ile Thr Ala Glu Val Asp Pro Tyr Leu Glu Ile Thr Glu Ile Cys Asp 35 40 45 Arg Thr Leu Arg Ala Gly Gly Pro Ala Leu Leu Phe Glu Asn Val Lys 50 55 60 Gly His Asp Met Pro Leu Leu Gly Asn Leu Phe Gly Thr Pro Lys Arg 65 70 75 80 Val Ala Leu Gly Met Gly Gln Asp Ser Val Ala Ala Leu Arg Glu Val 85 90 95 Gly Glu Leu Leu Ala Phe Leu Lys Glu Pro Glu Pro Pro Lys Gly Phe 100 105 110 Arg Asp Ala Trp Asp Lys Leu Pro Ile Phe Lys Gln Val Met Ser Met 115 120 125 Gly Pro Lys Lys Val Arg Ser Ala Pro Val Gln Glu Lys Val Tyr Glu 130 135 140 Gly Asp Glu Val Asp Leu Asp Arg Leu Pro Ile Gln His Cys Trp Pro 145 150 155 160 Gly Asp Ala Ala Pro Leu Val Thr Trp Pro Leu Val Ile Thr Arg Gly 165 170 175 Pro His Lys Lys Arg Gln Asn Leu Gly Ile Tyr Arg Gln Gln Lys Leu 180 185 190 Ser Lys Asn Arg Leu Ile Met Arg Trp Leu Ser His Arg Gly Gly Ala 195 200 205 Leu Asp Phe Leu Glu Phe Gln Lys Ala His Pro Gly Glu Pro Phe Pro 210 215 220 Val Ala Val Ala Leu Gly Ala Asp Pro Ala Thr Ile Leu Gly Ala Val 225 230 235 240 Thr Pro Val Pro Asp Ser Leu Ser Glu Tyr Ala Phe Ala Gly Leu Leu 245 250 255 Arg Gly Ser Arg Thr Glu Leu Val Lys Cys Gly His Ala Asp Leu Asp 260 265 270 Val Pro Ala Ser Ala Glu Ile Ile Leu Glu Gly Phe Ile Tyr Pro Asp 275 280 285 Asp Met Ala Pro Glu Gly Pro Tyr Gly Asp His Thr Gly Tyr Tyr Asn 290 295 300 Glu Val Asp Thr Phe Pro Val Phe Thr Val Thr Arg Met Thr Met Arg 305 310 315 320 Arg Asp Ala Ile Tyr His Ser Thr Tyr Thr Gly Arg Pro Pro Asp Glu 325 330 335 Pro Ala Ile Leu Gly Leu Ala Leu Asn Glu Val Phe Val Pro Ile Leu 340 345 350 Arg Arg Gln Phe Pro Glu Ile Val Asp Phe Tyr Leu Pro Pro Glu Gly 355 360 365 Cys Ser Tyr Arg Met Ala Val Val Thr Met Lys Lys Gln Tyr Pro Gly 370 375 380 His Ala Lys Arg Val Met Met Gly Val Trp Ser Phe Leu Arg Gln Phe 385 390 395 400 Met Tyr Thr Lys Phe Val Val Val Leu Asp Asp Asp Val Ser Ala Arg 405 410 415 Asp Trp Glu Asp Val Ile Trp Ala Ile Thr Thr Arg Met Asp Pro Ala 420 425 430 Arg Asp Thr Val Val Val Glu Asn Thr Pro Ile Asp Tyr Leu Asp Phe 435 440 445 Ala Ser Pro Val Ser Gly Leu Gly Ser Lys Met Gly Leu Asp Ala Thr 450 455 460 Ser Lys Trp Pro Gly Glu Thr Asp Arg Glu Trp Gly Val Pro Ile Val 465 470 475 480 Met Asp Glu Ala Val Lys Ala Arg Val Ser Glu Arg Trp Asn Glu Leu 485 490 495 Gly Ile Glu Leu Pro Asp Asn Thr Thr Pro 500 505 411410DNAUnknownObtained from environmental sample 41atgaagacgc cttcgatcta cgataccatg acgcggtcgg tgcagccgtt gacacccgcc 60gacggcgaca ccttccgctt ttattgctgc ggccccaccg tctacgggcc ggcgcatgtc 120ggcaatttcc gcaccttcat cattcaggac gtgctgcgac gcgttatcga agggtcgggc 180ctcaaaacga gacacgtacg caacatcacc gatgtggacg acaaaaccat ccgccaatcg 240caagcggaag gaaaatctct gaaaatcttc acagggtact ggctggaacg gttccacgcc 300gattgcgacg cgctgaatct gctgcgcccg cacgtcgagc ccggcgccgt tgaccatatc 360ccggcgcaaa tccggatgat cgaacaactg atcgaaaaag gccacgccta cgtggcggac 420gacaactcgg tctattatcg cgttgcttcg ttcgaagcgt acggccggtt gtcacgcctg 480caagaacgac acatcaccac cggctgcgcc gaacacgcgc ataccgacga tgaatacgag 540cgcgaatcgg ccgccgactt cgccttgtgg aaagcgcata aatccgagga cggcccgaac 600gcgtggccga gcccgtgggg cgacggacga cccggctggc acatcgagtg cagcgccatg 660tccgtcgagt atctgggcga gacattcgat ctgcacggcg gcggcgtgga cctgaccttc 720ccccaccacg aaaacgaaat cgcgcaaagc gaagccgcca ccggcaagcc cttcgcgcgt 780atctggttcc attccgcgca tctcatggtc gaaggccaca agatgtccaa gagcctcggc 840aacctgttta cgctcgacga tatccgcgcg cgcggattcg acgccatgac cctgcgctat 900gtcctgcttt cgggcaatta ccgccaaccc ctcaatttca cgtgggactc ccttaacgcc 960gcgcaaagcg ccttacgccg cctgcgtcag ctcaaccacg atctccagca ggcggcgggc 1020aagacggtcg cgcccgctga tacttcgtgg gggccgttcg aaccggtgta cgacgcgctt 1080gccgacaacc tgaacacgcc cgacgccctc ggccgcttat tctccgccct gcacagcatc 1140gagcgcgcgc ttaacggcaa ggaaaggacg gccgaagagg ccgccctcgc ccgtgcgcag 1200ttcctgcggg tcatggacct tttcggtttc agcctggacg cgccgccgac cgccgaagcg 1260cccgaagaag tgcgtgcgct ggcgcagcag cgatgggacg ctaaacaagc gcgcgatttc 1320gtccgcgccg acgccttgcg caaacaggtc accgacctcg gctggaccat ccgcgacgcc 1380aaagacggct acgaactcgt ccaagagtaa 141042469PRTUnknownObtained from environmental sample 42Met Lys Thr Pro Ser Ile Tyr Asp Thr Met Thr Arg Ser Val Gln Pro 1 5 10 15 Leu Thr Pro Ala Asp Gly Asp Thr Phe Arg Phe Tyr Cys Cys Gly Pro 20 25 30 Thr Val Tyr Gly Pro Ala His Val Gly Asn Phe Arg Thr Phe Ile Ile 35 40 45 Gln Asp Val Leu Arg Arg Val Ile Glu Gly Ser Gly Leu Lys Thr Arg 50 55 60 His Val Arg Asn Ile Thr Asp Val Asp Asp Lys Thr Ile Arg Gln Ser 65 70 75 80 Gln Ala Glu Gly Lys Ser Leu Lys Ile Phe Thr Gly Tyr Trp Leu Glu 85 90 95 Arg Phe His Ala Asp Cys Asp Ala Leu Asn Leu Leu Arg Pro His Val 100 105 110 Glu Pro Gly Ala Val Asp His Ile Pro Ala Gln Ile Arg Met Ile Glu 115 120 125 Gln Leu Ile Glu Lys Gly His Ala Tyr Val Ala Asp Asp Asn Ser Val 130 135 140 Tyr Tyr Arg Val Ala Ser Phe Glu Ala Tyr Gly Arg Leu Ser Arg Leu 145 150 155 160 Gln Glu Arg His Ile Thr Thr Gly Cys Ala Glu His Ala His Thr Asp 165 170 175 Asp Glu Tyr Glu Arg Glu Ser Ala Ala Asp Phe Ala Leu Trp Lys Ala 180 185 190 His Lys Ser Glu Asp Gly Pro Asn Ala Trp Pro Ser Pro Trp Gly Asp 195 200 205 Gly Arg Pro Gly Trp His Ile Glu Cys Ser Ala Met Ser Val Glu Tyr 210 215 220 Leu Gly Glu Thr Phe Asp Leu His Gly Gly Gly Val Asp Leu Thr Phe 225 230 235 240 Pro His His Glu Asn Glu Ile Ala Gln Ser Glu Ala Ala Thr Gly Lys 245 250 255 Pro Phe Ala Arg Ile Trp Phe His Ser Ala His Leu Met Val Glu Gly 260 265 270 His Lys Met Ser Lys Ser Leu Gly Asn Leu Phe Thr Leu Asp Asp Ile 275 280 285 Arg Ala Arg Gly Phe Asp Ala Met Thr Leu Arg Tyr Val Leu Leu Ser 290 295 300 Gly Asn Tyr Arg Gln Pro Leu Asn Phe Thr Trp Asp Ser Leu Asn Ala 305 310 315 320 Ala Gln Ser Ala Leu Arg Arg Leu Arg Gln Leu Asn His Asp Leu Gln 325 330 335 Gln Ala Ala Gly Lys Thr Val Ala Pro Ala Asp Thr Ser Trp Gly Pro 340 345 350 Phe Glu Pro Val Tyr Asp Ala Leu Ala Asp Asn Leu Asn Thr Pro Asp 355 360 365 Ala Leu Gly Arg Leu Phe Ser Ala Leu His Ser Ile Glu Arg Ala Leu 370 375 380 Asn Gly Lys Glu Arg Thr Ala Glu Glu Ala Ala Leu Ala Arg Ala Gln 385 390 395 400 Phe Leu Arg Val Met Asp Leu Phe Gly Phe Ser Leu Asp Ala Pro Pro 405 410 415 Thr Ala Glu Ala Pro Glu Glu Val Arg Ala Leu Ala Gln Gln Arg Trp 420 425 430 Asp Ala Lys Gln Ala Arg Asp Phe Val Arg Ala Asp Ala Leu Arg Lys 435 440 445 Gln Val Thr Asp Leu Gly Trp Thr Ile Arg Asp Ala Lys Asp Gly Tyr 450 455 460 Glu Leu Val Gln Glu 465 43984DNAUnknownObtained from environmental sample 43atgacgactg aaaccaaatc caaactgtac ttgcataaag tgaacggcca gaaaggactg 60gacctgcgcc agacctatca gcgcgacttc accgtgaccg aggcgtatcg cgatacgctg 120ccggatatgc agaacgcttc cgaggcgttg cagggggcca atgtcgccat ccagaaagtc 180ggcgtatcca atttcaagct gccactcaag taccgcaccc acacgggcga accgaccacg 240ctggaaacca gcgtaaccgg cagcgtatcc ctgaagccgg gcctgaaggg catcaacatg 300tcccgcgtca tgcggacctt ctacgacttc caggacgacg tgttcacgct cgacacgctg 360gcccgtatac tggaagcgta caaacgggat gtcgacagca acgacgcaca tcttcggctg 420agtttctcct acccgctgct tcaaaaaagt ctgcgcagcg aattattcgg ctggcaatat 480taccaggtcg cattcgaggg acggatcgat gccgaaaatc gagtccgcac gttcattcat 540tttgacttcg tgtattcctc cgcctgtccc tgttcggctg aactggccga acacgcgcgg 600gaagtgcgcg gcctatacag catcccccac tcgcaacgca gcaaggcgcg cgtcttcgtg 660gaagttcagc ccggcgccga actcaccatc gaagacgtgc acatgcactg cctgaacgcg 720ctccaaacgg aaacgcaagt gatggtcaaa cgcgaagacg agcaggcgtt cgctgaaatg 780aacggcgccg ccatcaaatt cgtcgaagac gccgcccgtc tgatctatga gcagttcgac 840caggatccgc gcatcaagga tttcgaaatc gcctgcgcgc atctggaatc cttgcactcg 900cacgacgccg tatcggtcat cgccaaaggc gtgcccggcg gcttccgcgc cgacttctcg 960gacttcaaga gtctgatctg ctaa 98444327PRTUnknownObtained from environmental sample 44Met Thr Thr Glu Thr Lys Ser Lys Leu Tyr Leu His Lys Val Asn Gly 1 5 10 15 Gln Lys Gly Leu Asp Leu Arg Gln Thr Tyr Gln Arg Asp Phe Thr Val 20 25 30 Thr Glu Ala Tyr Arg Asp Thr Leu Pro Asp Met Gln Asn Ala Ser Glu 35 40 45 Ala Leu Gln Gly Ala Asn Val Ala Ile Gln Lys Val Gly Val Ser Asn 50 55 60 Phe Lys Leu Pro Leu Lys Tyr Arg Thr His Thr Gly Glu Pro Thr Thr 65 70 75 80 Leu Glu Thr Ser Val Thr Gly Ser Val Ser Leu Lys Pro Gly Leu Lys 85 90 95 Gly Ile Asn Met Ser Arg Val Met Arg Thr Phe Tyr Asp Phe Gln Asp 100 105 110 Asp Val Phe Thr Leu Asp Thr Leu Ala Arg Ile Leu Glu Ala Tyr Lys 115 120 125 Arg Asp Val Asp Ser Asn Asp Ala His Leu Arg Leu Ser Phe Ser Tyr 130 135 140 Pro Leu Leu Gln Lys Ser Leu Arg Ser Glu Leu Phe Gly Trp Gln Tyr 145 150 155 160 Tyr Gln Val Ala Phe Glu Gly Arg Ile Asp Ala Glu Asn Arg Val Arg 165 170 175 Thr Phe Ile His Phe Asp Phe Val Tyr Ser Ser Ala Cys Pro Cys Ser 180 185 190 Ala Glu Leu Ala Glu His Ala Arg Glu Val Arg Gly Leu Tyr Ser Ile 195 200 205 Pro His Ser Gln Arg Ser Lys Ala Arg Val Phe Val Glu Val Gln Pro 210 215 220 Gly Ala Glu Leu Thr Ile Glu Asp Val His Met His Cys Leu Asn Ala 225 230 235 240 Leu Gln Thr Glu Thr Gln Val Met Val Lys Arg Glu Asp Glu Gln Ala 245 250 255 Phe Ala Glu Met Asn Gly Ala Ala Ile Lys Phe Val Glu Asp Ala Ala 260 265 270 Arg Leu Ile Tyr Glu Gln Phe Asp Gln Asp Pro Arg Ile Lys Asp Phe 275 280 285 Glu Ile Ala Cys Ala His Leu Glu Ser Leu His Ser His Asp Ala Val 290 295 300 Ser Val Ile Ala Lys Gly Val Pro Gly Gly Phe Arg Ala Asp Phe Ser 305 310 315 320 Asp Phe Lys Ser Leu Ile Cys 325 451377DNAUnknownObtained from environmental sample 45atgacacaac tggcttttcc atctaacttc atctggggaa cagctacttc cgcttaccaa 60atcgaaggcg cctggaacgc agacggcaag ggcgaatcta tttgggatcg cttttcccat 120acgcagggga agatcattga cggcagcaac ggcgatgtgg cctgcgatca ctaccaccgc 180tggcgcgagg acgtggccct catgagagac ttgggtatgc aggcatatcg cttctccatc 240tcctggccac gcatcctgcc caccggtcat ggacagatca atcaggctgg gctggacttt 300tacaatcgcc tggtggacgg gttgctggaa gctggcatca agccctttgc caccctctac 360cactgggacc tgccgctggc gctacaggct gacggcggct ggccggagcg ctccacggcc 420aaggcctttg tcgaatacgc cgacgtggtc agccgcgcgc tgggcgatcg ggtgaagagc 480tggatcaccc

ataacgaacc gtggtgcatc agcatgctga gccatcaaat tggggagcat 540gcgcccggct ggcgggactg gcaggctgcg ttggcggccg cgcaccacgt cctcctttcg 600catggttggg ccgtgccgga actgcgtcgc aacagccgcg atgcagaaat cggcatcacg 660ttgaacttta ccccggcgga gccagcttcg aacagcgcag ccgatttcaa ggcctatcgc 720cagttcgatg gctacttcaa ccgctggttc ctggacccgc tctatggccg ccactatccg 780gcagatatgg tgcacgatta catcgcgcaa ggctacctgc catcacaggg tttgactttc 840gtggaagctg gtgacctgga cgcgatcgcg acgcgcaccg atttcctggg tgtgaactat 900tacacgcgcg aagtggtccg tagccaggaa atcccagaga gtgagaacgc gccgcgcaca 960gtcttgcgcg cgccacagga agagtggaca gagatgggct gggaagtgta tcctgagggc 1020ctctacaggt tgctcaatcg gttgcacttt gaataccagc cgcgcaagct ctacgtgacc 1080gagagcggtt gcagctactc cgatggaccc ggccccaacg gtcggatacc ggaccaacgc 1140cgtatcaact acctgcgcga tcacttcgca gcggcgcatc aggcgataca atgcggcgtc 1200ccgctggccg gctacttcgt ctggtcgttc atggacaact tcgagtgggc caaagggtac 1260acccaacgtt ttggtatcgt atgggtggat tatcaatcgc aacgacggat accgaaagac 1320agcgcctact ggtatcgcga tgtcgtcgcc gccaacgcgg tgcaagttcc tgattag 137746458PRTUnknownObtained from environmental sample 46Met Thr Gln Leu Ala Phe Pro Ser Asn Phe Ile Trp Gly Thr Ala Thr 1 5 10 15 Ser Ala Tyr Gln Ile Glu Gly Ala Trp Asn Ala Asp Gly Lys Gly Glu 20 25 30 Ser Ile Trp Asp Arg Phe Ser His Thr Gln Gly Lys Ile Ile Asp Gly 35 40 45 Ser Asn Gly Asp Val Ala Cys Asp His Tyr His Arg Trp Arg Glu Asp 50 55 60 Val Ala Leu Met Arg Asp Leu Gly Met Gln Ala Tyr Arg Phe Ser Ile 65 70 75 80 Ser Trp Pro Arg Ile Leu Pro Thr Gly His Gly Gln Ile Asn Gln Ala 85 90 95 Gly Leu Asp Phe Tyr Asn Arg Leu Val Asp Gly Leu Leu Glu Ala Gly 100 105 110 Ile Lys Pro Phe Ala Thr Leu Tyr His Trp Asp Leu Pro Leu Ala Leu 115 120 125 Gln Ala Asp Gly Gly Trp Pro Glu Arg Ser Thr Ala Lys Ala Phe Val 130 135 140 Glu Tyr Ala Asp Val Val Ser Arg Ala Leu Gly Asp Arg Val Lys Ser 145 150 155 160 Trp Ile Thr His Asn Glu Pro Trp Cys Ile Ser Met Leu Ser His Gln 165 170 175 Ile Gly Glu His Ala Pro Gly Trp Arg Asp Trp Gln Ala Ala Leu Ala 180 185 190 Ala Ala His His Val Leu Leu Ser His Gly Trp Ala Val Pro Glu Leu 195 200 205 Arg Arg Asn Ser Arg Asp Ala Glu Ile Gly Ile Thr Leu Asn Phe Thr 210 215 220 Pro Ala Glu Pro Ala Ser Asn Ser Ala Ala Asp Phe Lys Ala Tyr Arg 225 230 235 240 Gln Phe Asp Gly Tyr Phe Asn Arg Trp Phe Leu Asp Pro Leu Tyr Gly 245 250 255 Arg His Tyr Pro Ala Asp Met Val His Asp Tyr Ile Ala Gln Gly Tyr 260 265 270 Leu Pro Ser Gln Gly Leu Thr Phe Val Glu Ala Gly Asp Leu Asp Ala 275 280 285 Ile Ala Thr Arg Thr Asp Phe Leu Gly Val Asn Tyr Tyr Thr Arg Glu 290 295 300 Val Val Arg Ser Gln Glu Ile Pro Glu Ser Glu Asn Ala Pro Arg Thr 305 310 315 320 Val Leu Arg Ala Pro Gln Glu Glu Trp Thr Glu Met Gly Trp Glu Val 325 330 335 Tyr Pro Glu Gly Leu Tyr Arg Leu Leu Asn Arg Leu His Phe Glu Tyr 340 345 350 Gln Pro Arg Lys Leu Tyr Val Thr Glu Ser Gly Cys Ser Tyr Ser Asp 355 360 365 Gly Pro Gly Pro Asn Gly Arg Ile Pro Asp Gln Arg Arg Ile Asn Tyr 370 375 380 Leu Arg Asp His Phe Ala Ala Ala His Gln Ala Ile Gln Cys Gly Val 385 390 395 400 Pro Leu Ala Gly Tyr Phe Val Trp Ser Phe Met Asp Asn Phe Glu Trp 405 410 415 Ala Lys Gly Tyr Thr Gln Arg Phe Gly Ile Val Trp Val Asp Tyr Gln 420 425 430 Ser Gln Arg Arg Ile Pro Lys Asp Ser Ala Tyr Trp Tyr Arg Asp Val 435 440 445 Val Ala Ala Asn Ala Val Gln Val Pro Asp 450 455 471353DNAUnknownObtained from environmental sample 47atgaaaaaat acctttttcc tgaaaatttt ttatggggtg ctgccacagc ttcgtatcaa 60atcgaaggtt ctccctctgc tgatggcaaa ggtgaatcga tatgggaccg tttttctcac 120acaccgggga acatttggaa cgctgaaacc ggggatatcg cctgcgatca ttaccggcgt 180tacgtggatg atgtaaagct gatttcacaa atcgggctta acgcgtaccg tttttcaatt 240tcctggccca gggtatttcc agaggggaga ggaaaagcaa atgaaaaagg actcgatttt 300taccgcaggt tgattgaaca gctgcagcaa catcgaatca aaacggcagt gacactttac 360cactgggatc ttccacaagt tctgcaggat cgcggcgggt gggcaaaccg tgatacggcg 420aagtattttt ctgagtatgc cacctttctc tttgaaaaac tcgatctccc cgttgacatg 480tggattactc ttaacgaacc atgggttatc gctattctgg ggcatgcttt tggtatccac 540gctccaggga tgagtgactt cagcacagcc ctccaggtct cgcataacct gcttctgggg 600cacgggttgg cggttaaagc atttcgggag tctaagaggg gtgatgaacc ggtaggtatt 660acccttaacc ttgccccggt tgaaccgctg accgaaaagc ccgccgatct aaaggcagct 720ttactttctg acggttttat gaaccgctgg taccttgatc ccctgttcaa aggtggttac 780cctgaagata tgatggatat ctattcccgg aactttgaac tgcccaaaat tgaaaagggg 840gatgctcagg ttattgccga accgatcgac ttcctgggca taaataacta taccagggtt 900ctcgtggaag ccagcggtga tgaaaatgcc tttatgggca accctgtcaa cccccagggc 960tctgaatata ctgaaatggg ttgggaggtt tatccgcagg gtctctacga cctgctgacc 1020agggttcacc gggattacgg gccaatgccg ctatatataa ctgaaaacgg ggcagccttt 1080cccgatgaac ttgacagcaa tgggcagata gatgatccaa ggcggataaa ttacctggaa 1140acttatcttc atcagtgctg gaaggcagtt caggacggtg tgcctctaaa aggctatttt 1200gtctggaccc tgatggataa cttcgagtgg gctttcggtt tcagcaagcg atttgggctc 1260atatacgtag attaccagga tcagaaacgt tacttgaaaa acagcgccta ctggtatagc 1320aaggttattg ggcgaaacgg cctcgagcta taa 135348450PRTUnknownObtained from environmental sample 48Met Lys Lys Tyr Leu Phe Pro Glu Asn Phe Leu Trp Gly Ala Ala Thr 1 5 10 15 Ala Ser Tyr Gln Ile Glu Gly Ser Pro Ser Ala Asp Gly Lys Gly Glu 20 25 30 Ser Ile Trp Asp Arg Phe Ser His Thr Pro Gly Asn Ile Trp Asn Ala 35 40 45 Glu Thr Gly Asp Ile Ala Cys Asp His Tyr Arg Arg Tyr Val Asp Asp 50 55 60 Val Lys Leu Ile Ser Gln Ile Gly Leu Asn Ala Tyr Arg Phe Ser Ile 65 70 75 80 Ser Trp Pro Arg Val Phe Pro Glu Gly Arg Gly Lys Ala Asn Glu Lys 85 90 95 Gly Leu Asp Phe Tyr Arg Arg Leu Ile Glu Gln Leu Gln Gln His Arg 100 105 110 Ile Lys Thr Ala Val Thr Leu Tyr His Trp Asp Leu Pro Gln Val Leu 115 120 125 Gln Asp Arg Gly Gly Trp Ala Asn Arg Asp Thr Ala Lys Tyr Phe Ser 130 135 140 Glu Tyr Ala Thr Phe Leu Phe Glu Lys Leu Asp Leu Pro Val Asp Met 145 150 155 160 Trp Ile Thr Leu Asn Glu Pro Trp Val Ile Ala Ile Leu Gly His Ala 165 170 175 Phe Gly Ile His Ala Pro Gly Met Ser Asp Phe Ser Thr Ala Leu Gln 180 185 190 Val Ser His Asn Leu Leu Leu Gly His Gly Leu Ala Val Lys Ala Phe 195 200 205 Arg Glu Ser Lys Arg Gly Asp Glu Pro Val Gly Ile Thr Leu Asn Leu 210 215 220 Ala Pro Val Glu Pro Leu Thr Glu Lys Pro Ala Asp Leu Lys Ala Ala 225 230 235 240 Leu Leu Ser Asp Gly Phe Met Asn Arg Trp Tyr Leu Asp Pro Leu Phe 245 250 255 Lys Gly Gly Tyr Pro Glu Asp Met Met Asp Ile Tyr Ser Arg Asn Phe 260 265 270 Glu Leu Pro Lys Ile Glu Lys Gly Asp Ala Gln Val Ile Ala Glu Pro 275 280 285 Ile Asp Phe Leu Gly Ile Asn Asn Tyr Thr Arg Val Leu Val Glu Ala 290 295 300 Ser Gly Asp Glu Asn Ala Phe Met Gly Asn Pro Val Asn Pro Gln Gly 305 310 315 320 Ser Glu Tyr Thr Glu Met Gly Trp Glu Val Tyr Pro Gln Gly Leu Tyr 325 330 335 Asp Leu Leu Thr Arg Val His Arg Asp Tyr Gly Pro Met Pro Leu Tyr 340 345 350 Ile Thr Glu Asn Gly Ala Ala Phe Pro Asp Glu Leu Asp Ser Asn Gly 355 360 365 Gln Ile Asp Asp Pro Arg Arg Ile Asn Tyr Leu Glu Thr Tyr Leu His 370 375 380 Gln Cys Trp Lys Ala Val Gln Asp Gly Val Pro Leu Lys Gly Tyr Phe 385 390 395 400 Val Trp Thr Leu Met Asp Asn Phe Glu Trp Ala Phe Gly Phe Ser Lys 405 410 415 Arg Phe Gly Leu Ile Tyr Val Asp Tyr Gln Asp Gln Lys Arg Tyr Leu 420 425 430 Lys Asn Ser Ala Tyr Trp Tyr Ser Lys Val Ile Gly Arg Asn Gly Leu 435 440 445 Glu Leu 450 49591DNAUnknownObtained from environmental sample 49atggactttg agcgggcagt tgacaggaat atcattagat tacgctcttc gttaaaggaa 60gaaatgaagg atctagttgc agttgaagct ccggtaacaa tatttttaaa tggcagcgag 120ctggtaaccc tgctctgcac cccggagaaa attgatcgtt tggccctcgg tttccttcat 180tcagaagggc tgcttaactc acttgatgat cttagtatga tcaggaccag ggagagcgaa 240ggcctggttg aaattgaact taaagaggcc tcgccggcac ttgataaatt atacgggaag 300aggacaatta cttccggttg cggtaaggga acaatttttt ttaatgttct cgattctctg 360cgcagtaaac cactcgacgg aaagcttgtg attacaaccg aagagattca taaattaatg 420gatgacctgc aggggcgggc ggaactgttc aaggctaccg ggggtgttca cagcgctgcg 480cttgccgaca gaaaggaaat actctttttc agtgaagata tcggccgcca taatgctatc 540gataaaattg tgggagagtg tttgctggag ggggtatctc ctgaagataa g 59150197PRTUnknownObtained from environmental sample 50Met Asp Phe Glu Arg Ala Val Asp Arg Asn Ile Ile Arg Leu Arg Ser 1 5 10 15 Ser Leu Lys Glu Glu Met Lys Asp Leu Val Ala Val Glu Ala Pro Val 20 25 30 Thr Ile Phe Leu Asn Gly Ser Glu Leu Val Thr Leu Leu Cys Thr Pro 35 40 45 Glu Lys Ile Asp Arg Leu Ala Leu Gly Phe Leu His Ser Glu Gly Leu 50 55 60 Leu Asn Ser Leu Asp Asp Leu Ser Met Ile Arg Thr Arg Glu Ser Glu 65 70 75 80 Gly Leu Val Glu Ile Glu Leu Lys Glu Ala Ser Pro Ala Leu Asp Lys 85 90 95 Leu Tyr Gly Lys Arg Thr Ile Thr Ser Gly Cys Gly Lys Gly Thr Ile 100 105 110 Phe Phe Asn Val Leu Asp Ser Leu Arg Ser Lys Pro Leu Asp Gly Lys 115 120 125 Leu Val Ile Thr Thr Glu Glu Ile His Lys Leu Met Asp Asp Leu Gln 130 135 140 Gly Arg Ala Glu Leu Phe Lys Ala Thr Gly Gly Val His Ser Ala Ala 145 150 155 160 Leu Ala Asp Arg Lys Glu Ile Leu Phe Phe Ser Glu Asp Ile Gly Arg 165 170 175 His Asn Ala Ile Asp Lys Ile Val Gly Glu Cys Leu Leu Glu Gly Val 180 185 190 Ser Pro Glu Asp Lys 195 511014DNAUnknownObtained from environmental sample 51atgtccaggg gcatcctgat cctcgtcatg ctgtctgttc tgagcggcgc ggcgctggcc 60caaccggccg ggctgccgcc gcgttcgccg gtgcagcgct gcatcaacct gggcaatatg 120ctggaagcgc cggaggaggg ctggtggggg ctgcgcgtcg agcgcgacta cctgacgacg 180atcgccgggg ccgggttcga tgcggtgcgc atcccgataa gctggtcaac ccatgctgcc 240agcgagccgc cctacaccat cgatccggct ttcttcgccc gcgttgatga agtcgtcggc 300tgggcgctgg cggacgggct gaaggccatc atcaacgtgc accactacga ggagatgatg 360agcgatccgg cggggcattt cccccggctg cgcgcgctgt gggcgcagat cgcggagcac 420tacgccgact acccgcccgc gctgatgttc gagctgctca acgaaccgtt cgaggcgctg 480acgccgctgc ggtggaacga gtacgccgcc gatctgatcg cgctgatccg ccagaccaac 540ccggggcgca ccctgatcgt cggcgggggc tggtggaaca gtgtggaagg gctgatgcag 600ctccgcctgc cggatgatcc cgatctgctg gcgacgttcc attactacca cccgttcgag 660ttcacgcatc agggggcgga gtggtcaccg gaagtgactg acctgagcgg gatcgcctgg 720gggacgggcg aggaacggct cgatctggag tccaatatcc gtattgcggc ggcctgggcg 780gtgtacaacc ggcgcccgct gctgttgggc gaattcggcg tctatggccg ggtggccgat 840ctcgattcgc gcctgcgctg gacgacggcg gtgcgcgccg aggccgaggc gcagggcatc 900ggctggtgct actgggaatt cgccgccggc ttcggcattt acgacccgga aagccggacg 960ttcaacccgc tgtaccgcgc gctgatcccg caggccgggc cggcgcgccc ctga 101452337PRTUnknownObtained from environmental sample 52Met Ser Arg Gly Ile Leu Ile Leu Val Met Leu Ser Val Leu Ser Gly 1 5 10 15 Ala Ala Leu Ala Gln Pro Ala Gly Leu Pro Pro Arg Ser Pro Val Gln 20 25 30 Arg Cys Ile Asn Leu Gly Asn Met Leu Glu Ala Pro Glu Glu Gly Trp 35 40 45 Trp Gly Leu Arg Val Glu Arg Asp Tyr Leu Thr Thr Ile Ala Gly Ala 50 55 60 Gly Phe Asp Ala Val Arg Ile Pro Ile Ser Trp Ser Thr His Ala Ala 65 70 75 80 Ser Glu Pro Pro Tyr Thr Ile Asp Pro Ala Phe Phe Ala Arg Val Asp 85 90 95 Glu Val Val Gly Trp Ala Leu Ala Asp Gly Leu Lys Ala Ile Ile Asn 100 105 110 Val His His Tyr Glu Glu Met Met Ser Asp Pro Ala Gly His Phe Pro 115 120 125 Arg Leu Arg Ala Leu Trp Ala Gln Ile Ala Glu His Tyr Ala Asp Tyr 130 135 140 Pro Pro Ala Leu Met Phe Glu Leu Leu Asn Glu Pro Phe Glu Ala Leu 145 150 155 160 Thr Pro Leu Arg Trp Asn Glu Tyr Ala Ala Asp Leu Ile Ala Leu Ile 165 170 175 Arg Gln Thr Asn Pro Gly Arg Thr Leu Ile Val Gly Gly Gly Trp Trp 180 185 190 Asn Ser Val Glu Gly Leu Met Gln Leu Arg Leu Pro Asp Asp Pro Asp 195 200 205 Leu Leu Ala Thr Phe His Tyr Tyr His Pro Phe Glu Phe Thr His Gln 210 215 220 Gly Ala Glu Trp Ser Pro Glu Val Thr Asp Leu Ser Gly Ile Ala Trp 225 230 235 240 Gly Thr Gly Glu Glu Arg Leu Asp Leu Glu Ser Asn Ile Arg Ile Ala 245 250 255 Ala Ala Trp Ala Val Tyr Asn Arg Arg Pro Leu Leu Leu Gly Glu Phe 260 265 270 Gly Val Tyr Gly Arg Val Ala Asp Leu Asp Ser Arg Leu Arg Trp Thr 275 280 285 Thr Ala Val Arg Ala Glu Ala Glu Ala Gln Gly Ile Gly Trp Cys Tyr 290 295 300 Trp Glu Phe Ala Ala Gly Phe Gly Ile Tyr Asp Pro Glu Ser Arg Thr 305 310 315 320 Phe Asn Pro Leu Tyr Arg Ala Leu Ile Pro Gln Ala Gly Pro Ala Arg 325 330 335 Pro 531377DNAUnknownObtained from environmental sample 53atgtggatgg ttcaagcgac atctttaatt caaaaataca atgtgcctgg cccacgctac 60accagttatc caacggttcc ttattgggaa agtgagaatt tttcactaaa gcagtggcaa 120caaacgctca aaaaatcctt tgatgagtcg aatcaaagtg aaggcatcag tctgtatatc 180catttgccat tttgcgaaag tttatgcacc ttctgtggtt gccataaacg tgtgactaaa 240aagcatgaga tggaaaagcc ttatatccaa gcggtattaa aagaatggga tttatattgc 300caacttttgg tggataaacc tgtcattaaa gaaattcatt tgggtggggg aactccgaca 360ttttttagtc ctgaacattt aacgcagctg attaagggga tattggctaa agccgaagtt 420gcagatgagc atgagtttag ttttgaagga catcccaaca atacgacacg tgaacatttg 480caagcgctct atgatgttgg atttcgacgt gtcagttatg gcgtgcagga ctataacgaa 540actgtgcaaa aagccattca ccgcattcag ccctatgaaa atgttaaaaa tgtcaccgag 600tgggcgcgtg agattggcta tacctctatt tcgcatgatt tggtctttgg cctgccgttt 660caaagtttag acgatgtctt aaatacgatt gatcaaacca ataccttaat gccggatcgt 720ttggctttgt atagctatgc ccatgtgcca tggattaaag gcaatggtca acgcggtttt 780aaagatgctg atgtcccgaa agacgagatt aaacgtcaat gttatgagga aggcaaaaaa 840aaattattag aacatggcta tcatgaaatt ggtatggatc attttgctct agaacaagac 900agtatgtatc agtcttttaa agcagggagc ttgcatcgta atttcatggg ttataccgca 960tcgaaaacgc aagtgatgat tgggcttggg atttcatcaa ttagtgacag ttggtacagc 1020tttgcgcaaa acgtgaaaac attagatgaa tattatacct tgctagaaaa aaatcagatt 1080cccgtgttta aagggcatgt cttgaatcag gaagatttga tcatccgtaa acatatttta 1140aatttgatgt gtggcttcca aacctcatgg gcaaatcccg atatgcaatt tcctgaaatt 1200cagtctgttt tggcacaatt agcagaaatg cagcaagatg gtttgattca aattgaagac 1260gcatcggtca cagttttaga agcgggcaag ccttttgttc gaaatatttg tatggccttt 1320gatttaagac tcaagcgcaa caagcctgag aatcggattt tttcgatgac gatttaa

137754458PRTUnknownObtained from environmental sample 54Met Trp Met Val Gln Ala Thr Ser Leu Ile Gln Lys Tyr Asn Val Pro 1 5 10 15 Gly Pro Arg Tyr Thr Ser Tyr Pro Thr Val Pro Tyr Trp Glu Ser Glu 20 25 30 Asn Phe Ser Leu Lys Gln Trp Gln Gln Thr Leu Lys Lys Ser Phe Asp 35 40 45 Glu Ser Asn Gln Ser Glu Gly Ile Ser Leu Tyr Ile His Leu Pro Phe 50 55 60 Cys Glu Ser Leu Cys Thr Phe Cys Gly Cys His Lys Arg Val Thr Lys 65 70 75 80 Lys His Glu Met Glu Lys Pro Tyr Ile Gln Ala Val Leu Lys Glu Trp 85 90 95 Asp Leu Tyr Cys Gln Leu Leu Val Asp Lys Pro Val Ile Lys Glu Ile 100 105 110 His Leu Gly Gly Gly Thr Pro Thr Phe Phe Ser Pro Glu His Leu Thr 115 120 125 Gln Leu Ile Lys Gly Ile Leu Ala Lys Ala Glu Val Ala Asp Glu His 130 135 140 Glu Phe Ser Phe Glu Gly His Pro Asn Asn Thr Thr Arg Glu His Leu 145 150 155 160 Gln Ala Leu Tyr Asp Val Gly Phe Arg Arg Val Ser Tyr Gly Val Gln 165 170 175 Asp Tyr Asn Glu Thr Val Gln Lys Ala Ile His Arg Ile Gln Pro Tyr 180 185 190 Glu Asn Val Lys Asn Val Thr Glu Trp Ala Arg Glu Ile Gly Tyr Thr 195 200 205 Ser Ile Ser His Asp Leu Val Phe Gly Leu Pro Phe Gln Ser Leu Asp 210 215 220 Asp Val Leu Asn Thr Ile Asp Gln Thr Asn Thr Leu Met Pro Asp Arg 225 230 235 240 Leu Ala Leu Tyr Ser Tyr Ala His Val Pro Trp Ile Lys Gly Asn Gly 245 250 255 Gln Arg Gly Phe Lys Asp Ala Asp Val Pro Lys Asp Glu Ile Lys Arg 260 265 270 Gln Cys Tyr Glu Glu Gly Lys Lys Lys Leu Leu Glu His Gly Tyr His 275 280 285 Glu Ile Gly Met Asp His Phe Ala Leu Glu Gln Asp Ser Met Tyr Gln 290 295 300 Ser Phe Lys Ala Gly Ser Leu His Arg Asn Phe Met Gly Tyr Thr Ala 305 310 315 320 Ser Lys Thr Gln Val Met Ile Gly Leu Gly Ile Ser Ser Ile Ser Asp 325 330 335 Ser Trp Tyr Ser Phe Ala Gln Asn Val Lys Thr Leu Asp Glu Tyr Tyr 340 345 350 Thr Leu Leu Glu Lys Asn Gln Ile Pro Val Phe Lys Gly His Val Leu 355 360 365 Asn Gln Glu Asp Leu Ile Ile Arg Lys His Ile Leu Asn Leu Met Cys 370 375 380 Gly Phe Gln Thr Ser Trp Ala Asn Pro Asp Met Gln Phe Pro Glu Ile 385 390 395 400 Gln Ser Val Leu Ala Gln Leu Ala Glu Met Gln Gln Asp Gly Leu Ile 405 410 415 Gln Ile Glu Asp Ala Ser Val Thr Val Leu Glu Ala Gly Lys Pro Phe 420 425 430 Val Arg Asn Ile Cys Met Ala Phe Asp Leu Arg Leu Lys Arg Asn Lys 435 440 445 Pro Glu Asn Arg Ile Phe Ser Met Thr Ile 450 455 551389DNAUnknownObtained from environmental sample 55atgagcgctt cgagtccctc ccgccccctg tccttcccag agcagttcgt ctggggtgct 60gccgcggcct cctaccaagt cgagggcgcc gtccacgagg acgggaaggg cccctccgtc 120tgggacatgt tctgcgagaa gcccggagcg gtcttccagg ggcacgacgg ggcggtggct 180tgcgaccact atcaccgcta ccgagaggac gtggcgttga tgcgacaggt gggcctgcac 240gcctaccgcc tgagcgtgtg ctggccccga gtgctcccgg agggcgtcgg gcagcccaac 300gagaagggcc tcgacttcta ctcgcggttg gtggacgcgc tgctcgaggc agggattacg 360ccctgggtaa cgctttttca ttgggactac cccttggctc tctatcaccg ggggggctgg 420ctcaaccggg atagcgcgga ttggtttgcc gagtacgcgg gcctaatcgc cgatcgcctc 480tccgaccggg tgcagcattt cttcactcag aacgagcccc aggtctatat cggcttcgga 540cacctcgagg gtaagcatgc tccaggagac accttgccca tgtcccaggt gctgcttgcg 600gggcatcata gcctactggc gcacggcaag gccgtgcagg cgctccgcgc ccaggcgaag 660cagcagctgc gcgtcggcta cgctcccgtc ggcatgcccc tccatccctt cacggactcg 720gccgaggacg tggccgctgc gcggaaggcg accttttggg ttcgggagaa gaactcctgg 780aacaacgcct ggtggatgga cccggtgttc ttgggtgagt acccggctca gggcctcgcc 840ttcttcggcc gggacgtgcc gcaggtgcgc gagggagaca tgcagctcat cgcgcagccc 900ttggacttct ttggggtcaa catctaccag agcacccccg tgcgcgcgtc tagcgccgaa 960agcggcttcg aggtcgtccc ccatccaacg ggctatccta tcactgcctt caactggccg 1020atcacgcccc aggccctcta ctggggtccg cgcttcttct acgagcgcta ccagaagccg 1080atcgtcatca cggagaacgg actgtcctgt cgggacgtcg tcgctgtgga cgggaaggtt 1140cacgatccgg ctcgcatcga tttcaccacc cgctatctgc gcgagctcca ccgagccgtc 1200gcggacggcg tcgcggtcga gggctacttc cactggtcca tcatggacaa cttcgaatgg 1260gctgccggct accgcgagcg gttcgggctc attcacgtcg actacgagac cctggcgcgg 1320acgcccaagg cgtccgctgc gtggtatcgc aaggtaatcg agagcaacgg agcgaccctt 1380ttcggatga 138956462PRTUnknownObtained from environmental sample 56Met Ser Ala Ser Ser Pro Ser Arg Pro Leu Ser Phe Pro Glu Gln Phe 1 5 10 15 Val Trp Gly Ala Ala Ala Ala Ser Tyr Gln Val Glu Gly Ala Val His 20 25 30 Glu Asp Gly Lys Gly Pro Ser Val Trp Asp Met Phe Cys Glu Lys Pro 35 40 45 Gly Ala Val Phe Gln Gly His Asp Gly Ala Val Ala Cys Asp His Tyr 50 55 60 His Arg Tyr Arg Glu Asp Val Ala Leu Met Arg Gln Val Gly Leu His 65 70 75 80 Ala Tyr Arg Leu Ser Val Cys Trp Pro Arg Val Leu Pro Glu Gly Val 85 90 95 Gly Gln Pro Asn Glu Lys Gly Leu Asp Phe Tyr Ser Arg Leu Val Asp 100 105 110 Ala Leu Leu Glu Ala Gly Ile Thr Pro Trp Val Thr Leu Phe His Trp 115 120 125 Asp Tyr Pro Leu Ala Leu Tyr His Arg Gly Gly Trp Leu Asn Arg Asp 130 135 140 Ser Ala Asp Trp Phe Ala Glu Tyr Ala Gly Leu Ile Ala Asp Arg Leu 145 150 155 160 Ser Asp Arg Val Gln His Phe Phe Thr Gln Asn Glu Pro Gln Val Tyr 165 170 175 Ile Gly Phe Gly His Leu Glu Gly Lys His Ala Pro Gly Asp Thr Leu 180 185 190 Pro Met Ser Gln Val Leu Leu Ala Gly His His Ser Leu Leu Ala His 195 200 205 Gly Lys Ala Val Gln Ala Leu Arg Ala Gln Ala Lys Gln Gln Leu Arg 210 215 220 Val Gly Tyr Ala Pro Val Gly Met Pro Leu His Pro Phe Thr Asp Ser 225 230 235 240 Ala Glu Asp Val Ala Ala Ala Arg Lys Ala Thr Phe Trp Val Arg Glu 245 250 255 Lys Asn Ser Trp Asn Asn Ala Trp Trp Met Asp Pro Val Phe Leu Gly 260 265 270 Glu Tyr Pro Ala Gln Gly Leu Ala Phe Phe Gly Arg Asp Val Pro Gln 275 280 285 Val Arg Glu Gly Asp Met Gln Leu Ile Ala Gln Pro Leu Asp Phe Phe 290 295 300 Gly Val Asn Ile Tyr Gln Ser Thr Pro Val Arg Ala Ser Ser Ala Glu 305 310 315 320 Ser Gly Phe Glu Val Val Pro His Pro Thr Gly Tyr Pro Ile Thr Ala 325 330 335 Phe Asn Trp Pro Ile Thr Pro Gln Ala Leu Tyr Trp Gly Pro Arg Phe 340 345 350 Phe Tyr Glu Arg Tyr Gln Lys Pro Ile Val Ile Thr Glu Asn Gly Leu 355 360 365 Ser Cys Arg Asp Val Val Ala Val Asp Gly Lys Val His Asp Pro Ala 370 375 380 Arg Ile Asp Phe Thr Thr Arg Tyr Leu Arg Glu Leu His Arg Ala Val 385 390 395 400 Ala Asp Gly Val Ala Val Glu Gly Tyr Phe His Trp Ser Ile Met Asp 405 410 415 Asn Phe Glu Trp Ala Ala Gly Tyr Arg Glu Arg Phe Gly Leu Ile His 420 425 430 Val Asp Tyr Glu Thr Leu Ala Arg Thr Pro Lys Ala Ser Ala Ala Trp 435 440 445 Tyr Arg Lys Val Ile Glu Ser Asn Gly Ala Thr Leu Phe Gly 450 455 460 57414DNAUnknownObtained from environmental sample 57atgattgctt catctatgtt ctatggaacg gttcgtggaa tacaagagct aactcaaaac 60gttattgcat tggataccgc aatggtttcg cttaccagag ttgctgacgg aagtgatttt 120gagtttgata gagttattga acgctcgatt gaaaacgtaa ccgaactatc aggtaagcta 180actgattaca tggatttagt aacggagttt gctagaactg gtaaaacaat agatgaatct 240tttaatttag ctaatacaac acaaatgtta atgaatattt ctgaattaac agcagatgaa 300tcagtaaata gtttaactgc cgcaatgatt gcttttaata ttaacgcaga tgatagtatt 360agaattgctg ataagttgaa tgaggttaac aatatcagcc tccttttgtg gtaa 41458137PRTUnknownObtained from environmental sample 58Met Ile Ala Ser Ser Met Phe Tyr Gly Thr Val Arg Gly Ile Gln Glu 1 5 10 15 Leu Thr Gln Asn Val Ile Ala Leu Asp Thr Ala Met Val Ser Leu Thr 20 25 30 Arg Val Ala Asp Gly Ser Asp Phe Glu Phe Asp Arg Val Ile Glu Arg 35 40 45 Ser Ile Glu Asn Val Thr Glu Leu Ser Gly Lys Leu Thr Asp Tyr Met 50 55 60 Asp Leu Val Thr Glu Phe Ala Arg Thr Gly Lys Thr Ile Asp Glu Ser 65 70 75 80 Phe Asn Leu Ala Asn Thr Thr Gln Met Leu Met Asn Ile Ser Glu Leu 85 90 95 Thr Ala Asp Glu Ser Val Asn Ser Leu Thr Ala Ala Met Ile Ala Phe 100 105 110 Asn Ile Asn Ala Asp Asp Ser Ile Arg Ile Ala Asp Lys Leu Asn Glu 115 120 125 Val Asn Asn Ile Ser Leu Leu Leu Trp 130 135 591044DNAUnknownObtained from environmental sample 59atgagaattt ttgaaggatt tcagcgaggt gtaaaccttg gcggctggat ctcccagttc 60gacaagtacg accatgagca tttccgcagc tttattacgg aaaatgacat cgccgccatt 120gcagctcttg gttttgacca tgtccgcgtg ccggtggatt ataacgtgct ggaggatgag 180gagggcaacc gcatcgacag cggatttgtc tacctgagaa gctgctacga gtggtgccgc 240aaacacgacc tgaacatgct ggtggatctt cacgagtgct acggctactc cttcgatccg 300ctgaaaaaag atatggaccg caaacgcttc ttctatgccg aagctctgca ggagcgtttt 360ctgaagctct gggagcagat ctgtgaaacc tttaaagacg atcctgtgca cgtggcattc 420gagccgctga atgagatcgt tttaggagag gtcgcagacg cctggaacgt gatgatccgc 480aaatatatca agaccgtccg cgccatctgc ccggagcact atctggtcct tggaagcgtg 540cactacagcc acgttaccac catccctctt cttgaggcac cggcagatga caagatcgtc 600ttcaacttcc actgctacga gccgctggtc ttcacccacc agggcgcata ctggctggag 660gatatgattc cggatttccg catgacctat cctgccacca tggaagagtt ctacgaagca 720acaaagaaga tcctgccaaa catgagtccg gatggattta aggatttcga tcaggagatg 780ggtccgggct tctttgagaa gatcttcaca ccggccctga aacgtgccga gcaggacaat 840gtagccctct actgcggcga gtacggcgtc attgatctgg cagataacca tgccaagatc 900cgctggctca aagacatcca caccaccttc tccaaatacg gcatcggaag tgccctctgg 960aactacaagg gcaaggattt cggctatgta gatgatcgct tcgccgagtg cagagaagca 1020tttatcgagt gcctgaaggc ctga 104460347PRTUnknownObtained from environmental sample 60Met Arg Ile Phe Glu Gly Phe Gln Arg Gly Val Asn Leu Gly Gly Trp 1 5 10 15 Ile Ser Gln Phe Asp Lys Tyr Asp His Glu His Phe Arg Ser Phe Ile 20 25 30 Thr Glu Asn Asp Ile Ala Ala Ile Ala Ala Leu Gly Phe Asp His Val 35 40 45 Arg Val Pro Val Asp Tyr Asn Val Leu Glu Asp Glu Glu Gly Asn Arg 50 55 60 Ile Asp Ser Gly Phe Val Tyr Leu Arg Ser Cys Tyr Glu Trp Cys Arg 65 70 75 80 Lys His Asp Leu Asn Met Leu Val Asp Leu His Glu Cys Tyr Gly Tyr 85 90 95 Ser Phe Asp Pro Leu Lys Lys Asp Met Asp Arg Lys Arg Phe Phe Tyr 100 105 110 Ala Glu Ala Leu Gln Glu Arg Phe Leu Lys Leu Trp Glu Gln Ile Cys 115 120 125 Glu Thr Phe Lys Asp Asp Pro Val His Val Ala Phe Glu Pro Leu Asn 130 135 140 Glu Ile Val Leu Gly Glu Val Ala Asp Ala Trp Asn Val Met Ile Arg 145 150 155 160 Lys Tyr Ile Lys Thr Val Arg Ala Ile Cys Pro Glu His Tyr Leu Val 165 170 175 Leu Gly Ser Val His Tyr Ser His Val Thr Thr Ile Pro Leu Leu Glu 180 185 190 Ala Pro Ala Asp Asp Lys Ile Val Phe Asn Phe His Cys Tyr Glu Pro 195 200 205 Leu Val Phe Thr His Gln Gly Ala Tyr Trp Leu Glu Asp Met Ile Pro 210 215 220 Asp Phe Arg Met Thr Tyr Pro Ala Thr Met Glu Glu Phe Tyr Glu Ala 225 230 235 240 Thr Lys Lys Ile Leu Pro Asn Met Ser Pro Asp Gly Phe Lys Asp Phe 245 250 255 Asp Gln Glu Met Gly Pro Gly Phe Phe Glu Lys Ile Phe Thr Pro Ala 260 265 270 Leu Lys Arg Ala Glu Gln Asp Asn Val Ala Leu Tyr Cys Gly Glu Tyr 275 280 285 Gly Val Ile Asp Leu Ala Asp Asn His Ala Lys Ile Arg Trp Leu Lys 290 295 300 Asp Ile His Thr Thr Phe Ser Lys Tyr Gly Ile Gly Ser Ala Leu Trp 305 310 315 320 Asn Tyr Lys Gly Lys Asp Phe Gly Tyr Val Asp Asp Arg Phe Ala Glu 325 330 335 Cys Arg Glu Ala Phe Ile Glu Cys Leu Lys Ala 340 345 611230DNAUnknownObtained from environmental sample 61ttggtatgga caccagctcg atcaacgctt gctggatctt ctgaaatccc actaatgaca 60atgaatatat tccccaatag aaaagactca cgaatgtccc tctggatcaa gcttggcata 120ctttgtatga tggctggaac ggtgatggtt cacggagcgc agactggtca aggagaagca 180acaatgaatc aagcaaatgg cttcaaggta agcaacggga ccaatatcag ccattggttg 240tcccagtgtt ttgaaacaat gccaccccgg cgcggatttt tctccgaact ggatgttatc 300ttcatccgct cgctggggat ggatcatttc cgtcttccgg tggacgagaa ggaactttgg 360acggaggatc ttgagaagat tcccgaagcg tgggattacc tcaggaatgc tctaagctgg 420gctagaaagc atgagcttcg tgtgattgtg gatcttcacg tcgtgcggtc ccatcacttt 480aatgcggcaa atgaaggggg aaccaacact ctgtgggatg atccggaggc gcaggaaagt 540ttcctcaacc tttggaggca gctttcggca gagctcgcct acaccgatgt ggactgggtg 600gcctatgaga tcatgaatga ggccgtcgcg gatgatccgg aggactggaa tcgtctcatc 660gccaaagccc actccttgat ccgcgagcgt gagccaaggc gcacactcgt catcggatcc 720aaccggtggc aaattccgtc aacgttcccg gatctgaaga ttccggacgg agatccgaac 780atcctcctga gtttccattt ctacgcgcct ctgcttttca cccactatcg ggcaacctgg 840gttgcctttt acgattatga tgggccggtt tcctatcctg gcaggatcgt tgatgatgca 900gctcttgaga aaaatgatta tactcctgca ttcaaagaca agattcgtgc gttgaatggt 960gtgtatgaca tcgacgctct cgaaaaagaa atgcagccgg ctatcgaata cgcaaaacag 1020aaagggttac cactgtattg cggagagtgg ggatgttttc atgctgtgga aagaaaacaa 1080cgcttgcaat ggtacaaaga tatatccact attttgaaac gcaatgggat cgcccatgcc 1140acatgggatt acaagggcga gttcggcatt gtggacactt ggacactagg tgttgattgg 1200aatttggtag gagcaatcct gtcagagtag 123062409PRTUnknownObtained from environmental sample 62Met Val Trp Thr Pro Ala Arg Ser Thr Leu Ala Gly Ser Ser Glu Ile 1 5 10 15 Pro Leu Met Thr Met Asn Ile Phe Pro Asn Arg Lys Asp Ser Arg Met 20 25 30 Ser Leu Trp Ile Lys Leu Gly Ile Leu Cys Met Met Ala Gly Thr Val 35 40 45 Met Val His Gly Ala Gln Thr Gly Gln Gly Glu Ala Thr Met Asn Gln 50 55 60 Ala Asn Gly Phe Lys Val Ser Asn Gly Thr Asn Ile Ser His Trp Leu 65 70 75 80 Ser Gln Cys Phe Glu Thr Met Pro Pro Arg Arg Gly Phe Phe Ser Glu 85 90 95 Leu Asp Val Ile Phe Ile Arg Ser Leu Gly Met Asp His Phe Arg Leu 100 105 110 Pro Val Asp Glu Lys Glu Leu Trp Thr Glu Asp Leu Glu Lys Ile Pro 115 120 125 Glu Ala Trp Asp Tyr Leu Arg Asn Ala Leu Ser Trp Ala Arg Lys His 130 135 140 Glu Leu Arg Val Ile Val Asp Leu His Val Val Arg Ser His His Phe 145 150 155 160 Asn Ala Ala Asn Glu Gly Gly Thr Asn Thr Leu Trp Asp Asp Pro Glu 165 170 175 Ala Gln Glu Ser Phe Leu Asn Leu Trp Arg Gln Leu Ser Ala Glu Leu 180 185 190

Ala Tyr Thr Asp Val Asp Trp Val Ala Tyr Glu Ile Met Asn Glu Ala 195 200 205 Val Ala Asp Asp Pro Glu Asp Trp Asn Arg Leu Ile Ala Lys Ala His 210 215 220 Ser Leu Ile Arg Glu Arg Glu Pro Arg Arg Thr Leu Val Ile Gly Ser 225 230 235 240 Asn Arg Trp Gln Ile Pro Ser Thr Phe Pro Asp Leu Lys Ile Pro Asp 245 250 255 Gly Asp Pro Asn Ile Leu Leu Ser Phe His Phe Tyr Ala Pro Leu Leu 260 265 270 Phe Thr His Tyr Arg Ala Thr Trp Val Ala Phe Tyr Asp Tyr Asp Gly 275 280 285 Pro Val Ser Tyr Pro Gly Arg Ile Val Asp Asp Ala Ala Leu Glu Lys 290 295 300 Asn Asp Tyr Thr Pro Ala Phe Lys Asp Lys Ile Arg Ala Leu Asn Gly 305 310 315 320 Val Tyr Asp Ile Asp Ala Leu Glu Lys Glu Met Gln Pro Ala Ile Glu 325 330 335 Tyr Ala Lys Gln Lys Gly Leu Pro Leu Tyr Cys Gly Glu Trp Gly Cys 340 345 350 Phe His Ala Val Glu Arg Lys Gln Arg Leu Gln Trp Tyr Lys Asp Ile 355 360 365 Ser Thr Ile Leu Lys Arg Asn Gly Ile Ala His Ala Thr Trp Asp Tyr 370 375 380 Lys Gly Glu Phe Gly Ile Val Asp Thr Trp Thr Leu Gly Val Asp Trp 385 390 395 400 Asn Leu Val Gly Ala Ile Leu Ser Glu 405 631152DNAUnknownObtained from environmental sample 63atgaaacgga gggaattcat gttggggggt gcgggtgttg ctgcgttggc atcgactctt 60ggagtctccg ccggttccac ttccgggcag ggagtgaacg agaatgtgag ggtataccgg 120aatgcgattc cccgttggag ggggttcaac ctcatgccct ttttctcggc aatgagcacc 180aacccggaat acaatggtct gacggtgccg gaggatgacc taaactggat ccgcgactgg 240ggttttgact atgtccggct tccgattgat tactggattc tggttgattc cgattggcga 300gatgcaaagc gcatgcgggt agaggatgtt cgcaaggccg accagaaggg atattcacgg 360ctggacgctg tgattgaagc ctgtatcgcg aagggtttgc acctcaacct gaatatgcat 420cggtgtcccg ggtattgcat caatggctgg gaactggagc cctataacct cttcaaggat 480gagcaggcgg aggatgattt tgtctaccat tgggagttgc tcgcgagacg ctataaggga 540atcgatcctt cgctgctgag tttcaatctg ctgaatgagg ctcccaatcc tggagacaag 600atgtcgtcgg aggattatcg tcgggtgatg cttcgatccg ctgctgttat tcgggggata 660agcccggacc gcatgattat tgtggacggg ctggaaatcg gtaaatcagt tgttccaggg 720ctgatgcatg agccatttgc ccaagctgtt catgcctacg agccccacga gttgagccat 780tataatgcgc cttggacgtc ggtgtttatg ggtattcctg agccatcctg gccgacagtt 840cgtttggatg gttctctgtt cgaccgcaag cgactggagt tgtatttcgc gccgtggggg 900gagttggtcc gccagggggt aggggtccac tgtggggaga ccggttgcta cattcatacg 960ccccatcggg tgtttctgtc ctggttcgaa gatgttttgg atatcctgac cggatacgac 1020atagggtggg ctctatggaa tttccgggga gatttcggaa tacttgattc caaacgcaag 1080gatgtgcaat atgtcgattg gtatggacac cagctcgatc aacgcttgct ggatcttctg 1140aaatcccact aa 115264383PRTUnknownObtained from environmental sample 64Met Lys Arg Arg Glu Phe Met Leu Gly Gly Ala Gly Val Ala Ala Leu 1 5 10 15 Ala Ser Thr Leu Gly Val Ser Ala Gly Ser Thr Ser Gly Gln Gly Val 20 25 30 Asn Glu Asn Val Arg Val Tyr Arg Asn Ala Ile Pro Arg Trp Arg Gly 35 40 45 Phe Asn Leu Met Pro Phe Phe Ser Ala Met Ser Thr Asn Pro Glu Tyr 50 55 60 Asn Gly Leu Thr Val Pro Glu Asp Asp Leu Asn Trp Ile Arg Asp Trp 65 70 75 80 Gly Phe Asp Tyr Val Arg Leu Pro Ile Asp Tyr Trp Ile Leu Val Asp 85 90 95 Ser Asp Trp Arg Asp Ala Lys Arg Met Arg Val Glu Asp Val Arg Lys 100 105 110 Ala Asp Gln Lys Gly Tyr Ser Arg Leu Asp Ala Val Ile Glu Ala Cys 115 120 125 Ile Ala Lys Gly Leu His Leu Asn Leu Asn Met His Arg Cys Pro Gly 130 135 140 Tyr Cys Ile Asn Gly Trp Glu Leu Glu Pro Tyr Asn Leu Phe Lys Asp 145 150 155 160 Glu Gln Ala Glu Asp Asp Phe Val Tyr His Trp Glu Leu Leu Ala Arg 165 170 175 Arg Tyr Lys Gly Ile Asp Pro Ser Leu Leu Ser Phe Asn Leu Leu Asn 180 185 190 Glu Ala Pro Asn Pro Gly Asp Lys Met Ser Ser Glu Asp Tyr Arg Arg 195 200 205 Val Met Leu Arg Ser Ala Ala Val Ile Arg Gly Ile Ser Pro Asp Arg 210 215 220 Met Ile Ile Val Asp Gly Leu Glu Ile Gly Lys Ser Val Val Pro Gly 225 230 235 240 Leu Met His Glu Pro Phe Ala Gln Ala Val His Ala Tyr Glu Pro His 245 250 255 Glu Leu Ser His Tyr Asn Ala Pro Trp Thr Ser Val Phe Met Gly Ile 260 265 270 Pro Glu Pro Ser Trp Pro Thr Val Arg Leu Asp Gly Ser Leu Phe Asp 275 280 285 Arg Lys Arg Leu Glu Leu Tyr Phe Ala Pro Trp Gly Glu Leu Val Arg 290 295 300 Gln Gly Val Gly Val His Cys Gly Glu Thr Gly Cys Tyr Ile His Thr 305 310 315 320 Pro His Arg Val Phe Leu Ser Trp Phe Glu Asp Val Leu Asp Ile Leu 325 330 335 Thr Gly Tyr Asp Ile Gly Trp Ala Leu Trp Asn Phe Arg Gly Asp Phe 340 345 350 Gly Ile Leu Asp Ser Lys Arg Lys Asp Val Gln Tyr Val Asp Trp Tyr 355 360 365 Gly His Gln Leu Asp Gln Arg Leu Leu Asp Leu Leu Lys Ser His 370 375 380 651131DNAUnknownObtained from environmental sample 65atgaacacac tcctaccacg gcggcgactg tggtcctcca cggcgatcct gcgcacgctg 60gcggccgggg cgctggcggc cggtatggtc ctggcacccg tcagtgccgc caacgcggcc 120accaccctcg gtgcctcggc ggcggagaag ggccggtact tcggtgcggc cgtcgggacg 180tacaagttca acgacagcac ctacatgtcg gtgctgaacc gcgagttcaa cagcctggtc 240gccgagaacg agatgaagtg ggacgcgacc gagccccagc gcggcgtgtt caactacagc 300gccggggacc gcatcgtcaa ccacgcccga tcccagggca tgaaggtacg cggacacgcc 360ctgttgtggc acgcccagca gccacgctgg acggagggcc tgtccggcgg cgacctgcgc 420aacgccgcga tcaaccatgt cacccaggtg gccagccact tccgggggca gatctactcc 480tgggacgtgg tgaacgaggc tttcgccgac ggtggcagcg gtgcccggcg ggactcgaac 540ctccagcgca ccggcaacga ctggatcgag gcggcgttcc gtgccgcccg ggcagccgat 600cccaacgcca agctctgcta caacgactac aacaccgacg ggatcaacgc gaagtccacc 660ggcgtctaca acatggtgcg tgacttcaag tcccgtgggg tgccgatcga ctgcgtgggc 720ttccagtcac acctgggcac caccctcccc ggtgactacc aggccaacct tcagcgcttc 780gccgacctgg gcgtcgacgt ggagatcacc gagctggaca tcacccaggg cggaaaccag 840gccaacatgt acggcgccgt cacccgcgcc tgcctggcga tctcgcgctg caccggcatc 900accgtgtggg gggtacggga ctgcgactcc tggcgtggtg gggacaacgc cctgctgttc 960gactgcgccg gcaacaagaa gcccgcgtac acggccgtcc tcgacgccct caacagcggc 1020tcgaacccga accccaaccc caccggcaac cggctgcgca acgaggcctc cggtcgatgc 1080ctggacgtca acggcgcaag ctccgccaac gggtcacaaa tgatccaaag a 113166377PRTUnknownObtained from environmental sample 66Met Asn Thr Leu Leu Pro Arg Arg Arg Leu Trp Ser Ser Thr Ala Ile 1 5 10 15 Leu Arg Thr Leu Ala Ala Gly Ala Leu Ala Ala Gly Met Val Leu Ala 20 25 30 Pro Val Ser Ala Ala Asn Ala Ala Thr Thr Leu Gly Ala Ser Ala Ala 35 40 45 Glu Lys Gly Arg Tyr Phe Gly Ala Ala Val Gly Thr Tyr Lys Phe Asn 50 55 60 Asp Ser Thr Tyr Met Ser Val Leu Asn Arg Glu Phe Asn Ser Leu Val 65 70 75 80 Ala Glu Asn Glu Met Lys Trp Asp Ala Thr Glu Pro Gln Arg Gly Val 85 90 95 Phe Asn Tyr Ser Ala Gly Asp Arg Ile Val Asn His Ala Arg Ser Gln 100 105 110 Gly Met Lys Val Arg Gly His Ala Leu Leu Trp His Ala Gln Gln Pro 115 120 125 Arg Trp Thr Glu Gly Leu Ser Gly Gly Asp Leu Arg Asn Ala Ala Ile 130 135 140 Asn His Val Thr Gln Val Ala Ser His Phe Arg Gly Gln Ile Tyr Ser 145 150 155 160 Trp Asp Val Val Asn Glu Ala Phe Ala Asp Gly Gly Ser Gly Ala Arg 165 170 175 Arg Asp Ser Asn Leu Gln Arg Thr Gly Asn Asp Trp Ile Glu Ala Ala 180 185 190 Phe Arg Ala Ala Arg Ala Ala Asp Pro Asn Ala Lys Leu Cys Tyr Asn 195 200 205 Asp Tyr Asn Thr Asp Gly Ile Asn Ala Lys Ser Thr Gly Val Tyr Asn 210 215 220 Met Val Arg Asp Phe Lys Ser Arg Gly Val Pro Ile Asp Cys Val Gly 225 230 235 240 Phe Gln Ser His Leu Gly Thr Thr Leu Pro Gly Asp Tyr Gln Ala Asn 245 250 255 Leu Gln Arg Phe Ala Asp Leu Gly Val Asp Val Glu Ile Thr Glu Leu 260 265 270 Asp Ile Thr Gln Gly Gly Asn Gln Ala Asn Met Tyr Gly Ala Val Thr 275 280 285 Arg Ala Cys Leu Ala Ile Ser Arg Cys Thr Gly Ile Thr Val Trp Gly 290 295 300 Val Arg Asp Cys Asp Ser Trp Arg Gly Gly Asp Asn Ala Leu Leu Phe 305 310 315 320 Asp Cys Ala Gly Asn Lys Lys Pro Ala Tyr Thr Ala Val Leu Asp Ala 325 330 335 Leu Asn Ser Gly Ser Asn Pro Asn Pro Asn Pro Thr Gly Asn Arg Leu 340 345 350 Arg Asn Glu Ala Ser Gly Arg Cys Leu Asp Val Asn Gly Ala Ser Ser 355 360 365 Ala Asn Gly Ser Gln Met Ile Gln Arg 370 375 671023DNAUnknownObtained from environmental sample 67atgaaatata tattttcgta tataataatg atgattttaa tcggttttat accggtctat 60ggattcggcg attcacctga ccaaacatac tctctcccct tcctcagcgt agaaggaaat 120tcattcgtcg atgaaaacgg tgaggaggtt attttgcggg gtgtatcgtt tcccgatccc 180aatcgattgg atgatgctac tcaatggaac aaacggtatt tccaggcagc aaaagattgg 240aactgtaatg tcgtcagaat accggttcat ccgcaaagat ggcgggaaag gggaaaagaa 300aattatctga aacttttaga taagggtatc gagtgggccg gtgaactcgg tatgtacgtg 360atcattgact ggcacactat cggcaatccg attaccgaag tgttcttcgg cgagctctat 420aatacgaccc agaccgaaac gttccggttc tggagaacaa tagcggagcg atatgcaggt 480aatcccgttg ttgcatttta tgaattgttt aatgaaccga ccgattataa cggtcggctc 540gggaggatga cctgggatca atataaagaa ttcatcgaag agatcattta tataatttat 600gcacacgacg aaaccgtgat accgcttgta ggcggtttcg attggggata tgatctcagg 660aatgttagag ataatccgat aaatgccccg ggtatcgcgt atgttactca cccgtatccg 720caaaagcggg accaaccgtg ggaagaaaaa tgggaaaggg atttcggttt cgtagccgac 780acctaccctg tgtttgctac cgagttcgga tttatgagtg aggatggttt gggtgcacat 840attcccgtta tcggtgatga aacatacggt gaagcgatca tcagttactt caatgagaaa 900ggtatatcgt ggacggcctg ggtgttcgat ccgctctggt cgccgcagct tattaaagac 960tggtatttta ccccgacccg gcagggacag ttttttaaag agaagctaat ggagttgaat 1020taa 102368340PRTUnknownObtained from environmental sample 68Met Lys Tyr Ile Phe Ser Tyr Ile Ile Met Met Ile Leu Ile Gly Phe 1 5 10 15 Ile Pro Val Tyr Gly Phe Gly Asp Ser Pro Asp Gln Thr Tyr Ser Leu 20 25 30 Pro Phe Leu Ser Val Glu Gly Asn Ser Phe Val Asp Glu Asn Gly Glu 35 40 45 Glu Val Ile Leu Arg Gly Val Ser Phe Pro Asp Pro Asn Arg Leu Asp 50 55 60 Asp Ala Thr Gln Trp Asn Lys Arg Tyr Phe Gln Ala Ala Lys Asp Trp 65 70 75 80 Asn Cys Asn Val Val Arg Ile Pro Val His Pro Gln Arg Trp Arg Glu 85 90 95 Arg Gly Lys Glu Asn Tyr Leu Lys Leu Leu Asp Lys Gly Ile Glu Trp 100 105 110 Ala Gly Glu Leu Gly Met Tyr Val Ile Ile Asp Trp His Thr Ile Gly 115 120 125 Asn Pro Ile Thr Glu Val Phe Phe Gly Glu Leu Tyr Asn Thr Thr Gln 130 135 140 Thr Glu Thr Phe Arg Phe Trp Arg Thr Ile Ala Glu Arg Tyr Ala Gly 145 150 155 160 Asn Pro Val Val Ala Phe Tyr Glu Leu Phe Asn Glu Pro Thr Asp Tyr 165 170 175 Asn Gly Arg Leu Gly Arg Met Thr Trp Asp Gln Tyr Lys Glu Phe Ile 180 185 190 Glu Glu Ile Ile Tyr Ile Ile Tyr Ala His Asp Glu Thr Val Ile Pro 195 200 205 Leu Val Gly Gly Phe Asp Trp Gly Tyr Asp Leu Arg Asn Val Arg Asp 210 215 220 Asn Pro Ile Asn Ala Pro Gly Ile Ala Tyr Val Thr His Pro Tyr Pro 225 230 235 240 Gln Lys Arg Asp Gln Pro Trp Glu Glu Lys Trp Glu Arg Asp Phe Gly 245 250 255 Phe Val Ala Asp Thr Tyr Pro Val Phe Ala Thr Glu Phe Gly Phe Met 260 265 270 Ser Glu Asp Gly Leu Gly Ala His Ile Pro Val Ile Gly Asp Glu Thr 275 280 285 Tyr Gly Glu Ala Ile Ile Ser Tyr Phe Asn Glu Lys Gly Ile Ser Trp 290 295 300 Thr Ala Trp Val Phe Asp Pro Leu Trp Ser Pro Gln Leu Ile Lys Asp 305 310 315 320 Trp Tyr Phe Thr Pro Thr Arg Gln Gly Gln Phe Phe Lys Glu Lys Leu 325 330 335 Met Glu Leu Asn 340 691182DNAUnknownObtained from environmental sample 69atgagtttta aaaaccacat acttttgtcg ctcctcatag tattgctttt cttttcagcg 60tgcgatatcg aagaaccgat cgccggagat tatcatacac ttgtggatca aaacgctata 120tcgcacaccc gcgcattatt caccaacctc gaacgtatcc gtcacgatca tatcctcttc 180ggtcatcagg atgcgcttgc atacggtgtt cactggcgca acgatgagcc gggtcgatcg 240gatgtattcg aagtaaccgg ttcgtatcct gcggtgtatg gctgggagat tggcgatatt 300gaacttggtg caccggaaaa tctggataac gtaaacttcg atcaaatgca gggctggatt 360cgcgaagggt acgaacgcgg cggtataatt acgattagct ggcatatgaa caatccggca 420tcgggtggtg attcgtggga tgtgaatgga ggtcataaag cggtaactaa gatacttccc 480ggcggagaac ttcacgatac gtttaaagaa tggctggata cgtttgcaaa attcgcgaag 540agccagattg cttttcccga aacaaataat gaacacctta tcccggtcat attccggccg 600tatcatgaaa acaccggaag ctggttctgg tggggcgccg accactgtac acctgaagaa 660tataaaaagt tatggcgatt taccgtcgaa tacctgcgcg atgtaaaagg tgttcacaat 720ctcctctggg cgtattcacc tgccggcaat gctgcggatt cagaggaagc atattttgct 780cggtatcccg gcgacgacta tgttgatatt attggattcg acgattacgg cagtgtgcgg 840aaaccgtatc aaatcgaacg ttttactaac cggattcgaa cgattgtaaa cttcgccgaa 900gcacgaaata aaatcccggc aataacggaa accggctatg aaactatccc cgatccgcaa 960tggtggacgg gtacattgct tagtgcactt gatcacgatt tgacaacccg gagaatagca 1020tacgtacttg tgtggcgaaa ttcaaacaat gctaccgacc ggcagaatca ttattacgct 1080ccgtatcccg gacatccaag tgctgacgat tttatcgcgt tcaggaatca cccgttgata 1140gttttcgaag atgatctgcc gggtatgtat acactaccgt aa 118270393PRTUnknownObtained from environmental sample 70Met Ser Phe Lys Asn His Ile Leu Leu Ser Leu Leu Ile Val Leu Leu 1 5 10 15 Phe Phe Ser Ala Cys Asp Ile Glu Glu Pro Ile Ala Gly Asp Tyr His 20 25 30 Thr Leu Val Asp Gln Asn Ala Ile Ser His Thr Arg Ala Leu Phe Thr 35 40 45 Asn Leu Glu Arg Ile Arg His Asp His Ile Leu Phe Gly His Gln Asp 50 55 60 Ala Leu Ala Tyr Gly Val His Trp Arg Asn Asp Glu Pro Gly Arg Ser 65 70 75 80 Asp Val Phe Glu Val Thr Gly Ser Tyr Pro Ala Val Tyr Gly Trp Glu 85 90 95 Ile Gly Asp Ile Glu Leu Gly Ala Pro Glu Asn Leu Asp Asn Val Asn 100 105 110 Phe Asp Gln Met Gln Gly Trp Ile Arg Glu Gly Tyr Glu Arg Gly Gly 115 120 125 Ile Ile Thr Ile Ser Trp His Met Asn Asn Pro Ala Ser Gly Gly Asp 130 135 140 Ser Trp Asp Val Asn Gly Gly His Lys Ala Val Thr Lys Ile Leu Pro 145 150 155 160 Gly Gly Glu Leu His Asp Thr Phe Lys Glu Trp Leu Asp Thr Phe Ala 165 170 175 Lys Phe Ala Lys Ser Gln Ile Ala Phe Pro Glu Thr Asn Asn Glu His 180 185 190 Leu Ile Pro Val Ile Phe Arg Pro Tyr His Glu Asn Thr Gly Ser Trp 195 200 205 Phe Trp Trp Gly Ala Asp His Cys Thr Pro Glu Glu

Tyr Lys Lys Leu 210 215 220 Trp Arg Phe Thr Val Glu Tyr Leu Arg Asp Val Lys Gly Val His Asn 225 230 235 240 Leu Leu Trp Ala Tyr Ser Pro Ala Gly Asn Ala Ala Asp Ser Glu Glu 245 250 255 Ala Tyr Phe Ala Arg Tyr Pro Gly Asp Asp Tyr Val Asp Ile Ile Gly 260 265 270 Phe Asp Asp Tyr Gly Ser Val Arg Lys Pro Tyr Gln Ile Glu Arg Phe 275 280 285 Thr Asn Arg Ile Arg Thr Ile Val Asn Phe Ala Glu Ala Arg Asn Lys 290 295 300 Ile Pro Ala Ile Thr Glu Thr Gly Tyr Glu Thr Ile Pro Asp Pro Gln 305 310 315 320 Trp Trp Thr Gly Thr Leu Leu Ser Ala Leu Asp His Asp Leu Thr Thr 325 330 335 Arg Arg Ile Ala Tyr Val Leu Val Trp Arg Asn Ser Asn Asn Ala Thr 340 345 350 Asp Arg Gln Asn His Tyr Tyr Ala Pro Tyr Pro Gly His Pro Ser Ala 355 360 365 Asp Asp Phe Ile Ala Phe Arg Asn His Pro Leu Ile Val Phe Glu Asp 370 375 380 Asp Leu Pro Gly Met Tyr Thr Leu Pro 385 390 711089DNAUnknownObtained from environmental sample 71atgaaacttt taaaactttt aatctttctc cttattacgg taattttttc tgatgtttcg 60gctcaaactt ttcaaataca aaaaggcaag aacattagcc attggctgtc ccaaagtaaa 120agaaggggag aagagcgaaa agagttcttt actaagaatg acgtagaatt tattgcaggc 180atcggcttcg atcatattcg tattcctatt gacgaggagc aaatgtggga tgaaaaaggc 240aacaaagagc ctgaagcgtt tcagttgctg cacaacgcga tagaatggag caggcaatcg 300aacttaaaag ttattgtgga cctgcatatt ttgaggtcgc attatttcaa cgcggaagaa 360aaaccgcttt ttacggaccc taaagctcag gaacgttttt accaatgttg ggcggatctg 420tctggtgaat tgaaaaaata tccgaataca ctggtggctt atgaattaat gaacgaacct 480gtagccgatg atccggaaga ctggaataga attgtaagag aatcagtaaa aaggctaagg 540gtgcttgagc ccaatagggt tattgtaatc gggtctaacc gatggcagca ttatgacact 600ctgaaggatt tatacgtgcc ggaaaacgac aaaaacatca ttttaagctt tcatttttat 660aaccctatgt tgcttacgca ttacagggcc agctgggtaa atttcggcga ttaccagggt 720cccgttaact acccgggaca gttggtagac tcaaagcatt tgtcgggact gagcgaagat 780ttaagaaaga aagtcgagca aaacaatggc gtttataata aggctcggat tgagaaaatg 840atagccgaag ccgttgctgt agcaaaaaag cacaacctcc ctttgtattg tggtgaatgg 900ggtgcctacg aaaaagcgcc aagggagccc aggctacaat ggtacagaga catggtggat 960gtgttgaaca aaaacaatat tgcctggact acctgggact ataaaggagg cttcggcata 1020gttgacgcca aaggaaacaa agacgaacag ttgatcaatg tattaacagg aaaagagaaa 1080aaaatgtaa 108972362PRTUnknownObtained from environmental sample 72Met Lys Leu Leu Lys Leu Leu Ile Phe Leu Leu Ile Thr Val Ile Phe 1 5 10 15 Ser Asp Val Ser Ala Gln Thr Phe Gln Ile Gln Lys Gly Lys Asn Ile 20 25 30 Ser His Trp Leu Ser Gln Ser Lys Arg Arg Gly Glu Glu Arg Lys Glu 35 40 45 Phe Phe Thr Lys Asn Asp Val Glu Phe Ile Ala Gly Ile Gly Phe Asp 50 55 60 His Ile Arg Ile Pro Ile Asp Glu Glu Gln Met Trp Asp Glu Lys Gly 65 70 75 80 Asn Lys Glu Pro Glu Ala Phe Gln Leu Leu His Asn Ala Ile Glu Trp 85 90 95 Ser Arg Gln Ser Asn Leu Lys Val Ile Val Asp Leu His Ile Leu Arg 100 105 110 Ser His Tyr Phe Asn Ala Glu Glu Lys Pro Leu Phe Thr Asp Pro Lys 115 120 125 Ala Gln Glu Arg Phe Tyr Gln Cys Trp Ala Asp Leu Ser Gly Glu Leu 130 135 140 Lys Lys Tyr Pro Asn Thr Leu Val Ala Tyr Glu Leu Met Asn Glu Pro 145 150 155 160 Val Ala Asp Asp Pro Glu Asp Trp Asn Arg Ile Val Arg Glu Ser Val 165 170 175 Lys Arg Leu Arg Val Leu Glu Pro Asn Arg Val Ile Val Ile Gly Ser 180 185 190 Asn Arg Trp Gln His Tyr Asp Thr Leu Lys Asp Leu Tyr Val Pro Glu 195 200 205 Asn Asp Lys Asn Ile Ile Leu Ser Phe His Phe Tyr Asn Pro Met Leu 210 215 220 Leu Thr His Tyr Arg Ala Ser Trp Val Asn Phe Gly Asp Tyr Gln Gly 225 230 235 240 Pro Val Asn Tyr Pro Gly Gln Leu Val Asp Ser Lys His Leu Ser Gly 245 250 255 Leu Ser Glu Asp Leu Arg Lys Lys Val Glu Gln Asn Asn Gly Val Tyr 260 265 270 Asn Lys Ala Arg Ile Glu Lys Met Ile Ala Glu Ala Val Ala Val Ala 275 280 285 Lys Lys His Asn Leu Pro Leu Tyr Cys Gly Glu Trp Gly Ala Tyr Glu 290 295 300 Lys Ala Pro Arg Glu Pro Arg Leu Gln Trp Tyr Arg Asp Met Val Asp 305 310 315 320 Val Leu Asn Lys Asn Asn Ile Ala Trp Thr Thr Trp Asp Tyr Lys Gly 325 330 335 Gly Phe Gly Ile Val Asp Ala Lys Gly Asn Lys Asp Glu Gln Leu Ile 340 345 350 Asn Val Leu Thr Gly Lys Glu Lys Lys Met 355 360 731146DNAUnknownObtained from environmental sample 73gtggatatta ccggacatcc cgaccacatc gccttcgcgc gggaagttgc cgagcaaagc 60atggtcttgc tgcaaaaccg tgcgaacctc gccccccttt cggtatctga ctattccacc 120attgccgtga tcggcccgaa tgccaatgac actttgctgg gttcttacag cggcgttccg 180aaaacctact acacggtact cgacgggata cggtcctatg tcggtgaccg ggcgaatgtg 240gtttacgctc aggggccgaa gataaccaaa cccggccatc gggaggacaa tgaagtattt 300ccaccggatc ctgaaaacga ccggagacga ctggccgaag cgatagctgt cgccgagaac 360gccgacctga tcatcctcgc gatcggcggc aatgaactga cgggacgaga ggcatgggcg 420gcgcatcatc ccggtgatcg accggatctg tcgttgctcg gtttgcagga ggatcttgtt 480gacgcagttg gagcgatggg ggttccatct gtcgcattgg ttttcggtgc acggccgctg 540gacctcggca atgtcgccga aaaaattgat gtggtcttcc aaaactggta cctgggccag 600gaaaccggca atgccgtcgc caatgtgctg tttggcgagg tgtcaccgtc cgccaaactc 660cccatcagct tcccgcggac tgccgggcac attcctgcct actacaatta caaaccatcg 720gctcgacggg tctacctttt tgacgatgtc actccgcgtt accatttcgg gtacggcctc 780agctatacga cgtttgaata cggggaaccg cagctatcgg atacactact gtctggcgat 840ggtgaaataa ccctctacgt tgaagttacc aacaccggag agcgaggcgg ttcggaagtc 900gtgcaactgt acatcaacca cgaatacaga tccgtcaccc ggccggtaaa ggagctcaag 960ggattcgaaa aggtgtatct cgagccgaat gaaactgccg gtgtatcgtt caccatcact 1020tcagatcagt tgaggttctg gaatatcgac atggagttta ccgctgaatc cggtaaagtg 1080aacctgatgg tcggctcatc cagccgtgac gaagacctgc agacgacggc aatttttctt 1140gaataa 114674381PRTUnknownObtained from environmental sample 74Met Asp Ile Thr Gly His Pro Asp His Ile Ala Phe Ala Arg Glu Val 1 5 10 15 Ala Glu Gln Ser Met Val Leu Leu Gln Asn Arg Ala Asn Leu Ala Pro 20 25 30 Leu Ser Val Ser Asp Tyr Ser Thr Ile Ala Val Ile Gly Pro Asn Ala 35 40 45 Asn Asp Thr Leu Leu Gly Ser Tyr Ser Gly Val Pro Lys Thr Tyr Tyr 50 55 60 Thr Val Leu Asp Gly Ile Arg Ser Tyr Val Gly Asp Arg Ala Asn Val 65 70 75 80 Val Tyr Ala Gln Gly Pro Lys Ile Thr Lys Pro Gly His Arg Glu Asp 85 90 95 Asn Glu Val Phe Pro Pro Asp Pro Glu Asn Asp Arg Arg Arg Leu Ala 100 105 110 Glu Ala Ile Ala Val Ala Glu Asn Ala Asp Leu Ile Ile Leu Ala Ile 115 120 125 Gly Gly Asn Glu Leu Thr Gly Arg Glu Ala Trp Ala Ala His His Pro 130 135 140 Gly Asp Arg Pro Asp Leu Ser Leu Leu Gly Leu Gln Glu Asp Leu Val 145 150 155 160 Asp Ala Val Gly Ala Met Gly Val Pro Ser Val Ala Leu Val Phe Gly 165 170 175 Ala Arg Pro Leu Asp Leu Gly Asn Val Ala Glu Lys Ile Asp Val Val 180 185 190 Phe Gln Asn Trp Tyr Leu Gly Gln Glu Thr Gly Asn Ala Val Ala Asn 195 200 205 Val Leu Phe Gly Glu Val Ser Pro Ser Ala Lys Leu Pro Ile Ser Phe 210 215 220 Pro Arg Thr Ala Gly His Ile Pro Ala Tyr Tyr Asn Tyr Lys Pro Ser 225 230 235 240 Ala Arg Arg Val Tyr Leu Phe Asp Asp Val Thr Pro Arg Tyr His Phe 245 250 255 Gly Tyr Gly Leu Ser Tyr Thr Thr Phe Glu Tyr Gly Glu Pro Gln Leu 260 265 270 Ser Asp Thr Leu Leu Ser Gly Asp Gly Glu Ile Thr Leu Tyr Val Glu 275 280 285 Val Thr Asn Thr Gly Glu Arg Gly Gly Ser Glu Val Val Gln Leu Tyr 290 295 300 Ile Asn His Glu Tyr Arg Ser Val Thr Arg Pro Val Lys Glu Leu Lys 305 310 315 320 Gly Phe Glu Lys Val Tyr Leu Glu Pro Asn Glu Thr Ala Gly Val Ser 325 330 335 Phe Thr Ile Thr Ser Asp Gln Leu Arg Phe Trp Asn Ile Asp Met Glu 340 345 350 Phe Thr Ala Glu Ser Gly Lys Val Asn Leu Met Val Gly Ser Ser Ser 355 360 365 Arg Asp Glu Asp Leu Gln Thr Thr Ala Ile Phe Leu Glu 370 375 380 751014DNAUnknownObtained from environmental sample 75atgctgcgca agttgatcgt ctcggtcttc ggcttcgtca tgctgactag tgcggcagcg 60gcgcagactc ctcccgcctt agcggaatcc gcgcctgctc tccggcgcgg aatgaacgtt 120ctgggctacg acccaatctg gcacgacccg aagaaaggtc ggttcgaaga gcggcacttc 180gccgagattc gcaagggcgg cttcgacttc gttcgggtga acctccacgg gttcaaacat 240atgaacgccg cggacaaact cagtccggag ttcctgagcc gcgtggactg gatcgtgaag 300cacgccagtg cggcgggcct gtcggtcatc ctagacgagc atgaatatga ggaatgctcg 360gacgacgtcg caatgtgccg gcggcgtttg gcggcattct ggacgcaggt cgcgccgcgc 420tacaagggcg cgcccgatac ggttctgttc gagcttctca atgagccgca cgacaagttg 480gatgccgaca cctggaacgc cttgtttccc gacatcctgg ccatcgtgcg gcagtcgaac 540ccgaagcgcc gcgtggtgat cggcccgact cagtggaaca acttcagcca gctggacacg 600ctcaagctgc cggcagacga ccggaacatc gtcgtcacct tccattatta cgatccgttc 660ccgtttaccc accagggcgc gccgtgggtt ccggacatgc tcaaggtgaa aggcatcgag 720tggaagcccg agcagagggc gaagatcgcc gaggacttcg gcaaggtcgc ggaatggtcg 780cagaaaaccg gccgcgaaat cttgctcggc gagttcgggg cctacgatgt gagcggtacg 840ccaaccgcca tgcgttcagc ttatacggaa gcggtggcgc gcgaggcgga acgccacggc 900ttcgcttggg cctactggca gttcgacagc aatttcctgg cttgggacat gaagacaaac 960ggctgggtcg agccgatcca caaggcactc atccccgagg cgaagcagcc ttag 101476337PRTUnknownObtained from environmental sample 76Met Leu Arg Lys Leu Ile Val Ser Val Phe Gly Phe Val Met Leu Thr 1 5 10 15 Ser Ala Ala Ala Ala Gln Thr Pro Pro Ala Leu Ala Glu Ser Ala Pro 20 25 30 Ala Leu Arg Arg Gly Met Asn Val Leu Gly Tyr Asp Pro Ile Trp His 35 40 45 Asp Pro Lys Lys Gly Arg Phe Glu Glu Arg His Phe Ala Glu Ile Arg 50 55 60 Lys Gly Gly Phe Asp Phe Val Arg Val Asn Leu His Gly Phe Lys His 65 70 75 80 Met Asn Ala Ala Asp Lys Leu Ser Pro Glu Phe Leu Ser Arg Val Asp 85 90 95 Trp Ile Val Lys His Ala Ser Ala Ala Gly Leu Ser Val Ile Leu Asp 100 105 110 Glu His Glu Tyr Glu Glu Cys Ser Asp Asp Val Ala Met Cys Arg Arg 115 120 125 Arg Leu Ala Ala Phe Trp Thr Gln Val Ala Pro Arg Tyr Lys Gly Ala 130 135 140 Pro Asp Thr Val Leu Phe Glu Leu Leu Asn Glu Pro His Asp Lys Leu 145 150 155 160 Asp Ala Asp Thr Trp Asn Ala Leu Phe Pro Asp Ile Leu Ala Ile Val 165 170 175 Arg Gln Ser Asn Pro Lys Arg Arg Val Val Ile Gly Pro Thr Gln Trp 180 185 190 Asn Asn Phe Ser Gln Leu Asp Thr Leu Lys Leu Pro Ala Asp Asp Arg 195 200 205 Asn Ile Val Val Thr Phe His Tyr Tyr Asp Pro Phe Pro Phe Thr His 210 215 220 Gln Gly Ala Pro Trp Val Pro Asp Met Leu Lys Val Lys Gly Ile Glu 225 230 235 240 Trp Lys Pro Glu Gln Arg Ala Lys Ile Ala Glu Asp Phe Gly Lys Val 245 250 255 Ala Glu Trp Ser Gln Lys Thr Gly Arg Glu Ile Leu Leu Gly Glu Phe 260 265 270 Gly Ala Tyr Asp Val Ser Gly Thr Pro Thr Ala Met Arg Ser Ala Tyr 275 280 285 Thr Glu Ala Val Ala Arg Glu Ala Glu Arg His Gly Phe Ala Trp Ala 290 295 300 Tyr Trp Gln Phe Asp Ser Asn Phe Leu Ala Trp Asp Met Lys Thr Asn 305 310 315 320 Gly Trp Val Glu Pro Ile His Lys Ala Leu Ile Pro Glu Ala Lys Gln 325 330 335 Pro 771125DNAUnknownObtained from environmental sample 77atgaaaagga aacgggtttt tattcattct ctaatcgtat tttttttaat gattggttct 60tttacttctt gtggatcagt cgccgatgat gccgaagaag ggtttgatat ttttagagga 120accaatatcg ctcattggtt atcacaaagt aatgcaaggg gcgaagagcg aaaaaatttc 180tttaccgaaa atgatataaa atttattgct gatgctggtt ttgatcatat tcgtttgcca 240attgacgagg ttcatttctg ggatgagaat atgaaccggc accaagatgc atttgatctt 300atgcatgact gtattaagtg gtcagagaaa catggtctta gggttgtagt ggatttgcat 360attattcgtt cacattattt tgttggagat gataatacac tatgggatga aagacatgaa 420caggaaaagt ttgttgatat ttggatggag ttatcatctg aactatctca atattcaaac 480tcattagtag cttatgagtt aatgaatgaa cctgtagccc cttctcatga tgattggaat 540agtttggttg cggaaactat agaggcaatt cgtaaagttg aacctgagag atatattgta 600gttggatcaa atatgtggca aggtattgat acatttgagt atttggaagt tcccgaaaat 660gatgatagaa taattcttag ttttcatttt tatgatccct ttattttgac tcattatact 720gcatcttggg ggtatttaag agattactca gggcctgtta actatccggg atatcttgtt 780acaaatgacc agctgttgga tatgtcaaac gaaatgcaaa agttaattag ggagtttcag 840acaaattttg atatttatac cattgaagaa ctgatatcta ttccatatag tattgcaaag 900gaaaaagggt tgaaattata ttgtggagag tttggtgcaa ttgatcaggc tccaagagat 960gcgagattgg catggtacag agatgttgtt caggtttttg agcgatatgg tatagctcat 1020gccaactgga attacaaaga ttatggtacg tttgggataa agaactatag cgaggagata 1080gatcaggaac tgtttgaaat cttaattgga acaaaacata aatag 112578374PRTUnknownObtained from environmental sample 78Met Lys Arg Lys Arg Val Phe Ile His Ser Leu Ile Val Phe Phe Leu 1 5 10 15 Met Ile Gly Ser Phe Thr Ser Cys Gly Ser Val Ala Asp Asp Ala Glu 20 25 30 Glu Gly Phe Asp Ile Phe Arg Gly Thr Asn Ile Ala His Trp Leu Ser 35 40 45 Gln Ser Asn Ala Arg Gly Glu Glu Arg Lys Asn Phe Phe Thr Glu Asn 50 55 60 Asp Ile Lys Phe Ile Ala Asp Ala Gly Phe Asp His Ile Arg Leu Pro 65 70 75 80 Ile Asp Glu Val His Phe Trp Asp Glu Asn Met Asn Arg His Gln Asp 85 90 95 Ala Phe Asp Leu Met His Asp Cys Ile Lys Trp Ser Glu Lys His Gly 100 105 110 Leu Arg Val Val Val Asp Leu His Ile Ile Arg Ser His Tyr Phe Val 115 120 125 Gly Asp Asp Asn Thr Leu Trp Asp Glu Arg His Glu Gln Glu Lys Phe 130 135 140 Val Asp Ile Trp Met Glu Leu Ser Ser Glu Leu Ser Gln Tyr Ser Asn 145 150 155 160 Ser Leu Val Ala Tyr Glu Leu Met Asn Glu Pro Val Ala Pro Ser His 165 170 175 Asp Asp Trp Asn Ser Leu Val Ala Glu Thr Ile Glu Ala Ile Arg Lys 180 185 190 Val Glu Pro Glu Arg Tyr Ile Val Val Gly Ser Asn Met Trp Gln Gly 195 200 205 Ile Asp Thr Phe Glu Tyr Leu Glu Val Pro Glu Asn Asp Asp Arg Ile 210 215 220 Ile Leu Ser Phe His Phe Tyr Asp Pro Phe Ile Leu Thr His Tyr Thr 225 230 235 240 Ala Ser Trp Gly Tyr Leu Arg Asp Tyr Ser Gly Pro Val Asn Tyr Pro 245 250 255 Gly Tyr Leu Val Thr Asn Asp Gln Leu Leu Asp Met Ser Asn Glu Met 260 265 270 Gln Lys Leu Ile Arg Glu Phe Gln Thr Asn Phe Asp Ile Tyr Thr Ile 275 280 285 Glu Glu Leu Ile Ser Ile Pro Tyr Ser Ile Ala Lys Glu Lys Gly Leu 290

295 300 Lys Leu Tyr Cys Gly Glu Phe Gly Ala Ile Asp Gln Ala Pro Arg Asp 305 310 315 320 Ala Arg Leu Ala Trp Tyr Arg Asp Val Val Gln Val Phe Glu Arg Tyr 325 330 335 Gly Ile Ala His Ala Asn Trp Asn Tyr Lys Asp Tyr Gly Thr Phe Gly 340 345 350 Ile Lys Asn Tyr Ser Glu Glu Ile Asp Gln Glu Leu Phe Glu Ile Leu 355 360 365 Ile Gly Thr Lys His Lys 370 791017DNAUnknownObtained from environmental sample 79atgaaatata aagctatttt tatatacctt attgttttga ttctatttta ctcaattaat 60atttatgcta atgcagaaaa caaccccctc cccttcctca gtgtcgaagg aaacaggttc 120gtcgatgaag atggaaatac ggtaatcctg cgaggtgtat cgttccccga tcccgaccgg 180ctggctgagg caactcaatg gaacaagcga tacttccagg cggcaaaaga ctggaactgt 240aatgtcgtcc ggattcctgt ccatccacag aaatggcggg aaagaggcga ggaaaattat 300ctgaaacttt tagataaggg aattcaatgg gcgggtgaac tcgggatgta tgtaatcatc 360gactggcata ccatcggtaa tccgataacc gaagtatttt tccgcgaact atacaatacg 420tcacgtgcgg agaccttcca gttctggaga acaatcgctg agcgctatgc cggtaacccg 480gttgttgctt tctatgaact gttcaatgaa ccgaccgact acaacggccg tctcggaaga 540atgaactggg atcagtataa agagtttatc gaggagataa ttcacatcat ctattctcac 600gacgatacag ttatccctct cgttgccggt ttcgactggg cgtatgaact ccgccatata 660aaagataaac ctatagattt tcccggcatc gcttatgtga ctcaccccta tccccagaaa 720cgcgatccgc catgggaaga aaaatgggaa gaggatttcg ggtttgccgc cgatatgtat 780ccggtgtttg caaccgagtt cggtttcatg ggggaggatg aattaggtgc acacataccc 840gtcatcggcg atgaaacata cggcgaagcc attatcgatt acttttataa aaaggggata 900tcgtggactg catgggtatt cgatccgctt tggtcgccgc agcttattag agactggtat 960tttaccccgt cccgacaggg gcagtttttt aaagagaagt tgatggagtt gaattag 101780338PRTUnknownObtained from environmental sample 80Met Lys Tyr Lys Ala Ile Phe Ile Tyr Leu Ile Val Leu Ile Leu Phe 1 5 10 15 Tyr Ser Ile Asn Ile Tyr Ala Asn Ala Glu Asn Asn Pro Leu Pro Phe 20 25 30 Leu Ser Val Glu Gly Asn Arg Phe Val Asp Glu Asp Gly Asn Thr Val 35 40 45 Ile Leu Arg Gly Val Ser Phe Pro Asp Pro Asp Arg Leu Ala Glu Ala 50 55 60 Thr Gln Trp Asn Lys Arg Tyr Phe Gln Ala Ala Lys Asp Trp Asn Cys 65 70 75 80 Asn Val Val Arg Ile Pro Val His Pro Gln Lys Trp Arg Glu Arg Gly 85 90 95 Glu Glu Asn Tyr Leu Lys Leu Leu Asp Lys Gly Ile Gln Trp Ala Gly 100 105 110 Glu Leu Gly Met Tyr Val Ile Ile Asp Trp His Thr Ile Gly Asn Pro 115 120 125 Ile Thr Glu Val Phe Phe Arg Glu Leu Tyr Asn Thr Ser Arg Ala Glu 130 135 140 Thr Phe Gln Phe Trp Arg Thr Ile Ala Glu Arg Tyr Ala Gly Asn Pro 145 150 155 160 Val Val Ala Phe Tyr Glu Leu Phe Asn Glu Pro Thr Asp Tyr Asn Gly 165 170 175 Arg Leu Gly Arg Met Asn Trp Asp Gln Tyr Lys Glu Phe Ile Glu Glu 180 185 190 Ile Ile His Ile Ile Tyr Ser His Asp Asp Thr Val Ile Pro Leu Val 195 200 205 Ala Gly Phe Asp Trp Ala Tyr Glu Leu Arg His Ile Lys Asp Lys Pro 210 215 220 Ile Asp Phe Pro Gly Ile Ala Tyr Val Thr His Pro Tyr Pro Gln Lys 225 230 235 240 Arg Asp Pro Pro Trp Glu Glu Lys Trp Glu Glu Asp Phe Gly Phe Ala 245 250 255 Ala Asp Met Tyr Pro Val Phe Ala Thr Glu Phe Gly Phe Met Gly Glu 260 265 270 Asp Glu Leu Gly Ala His Ile Pro Val Ile Gly Asp Glu Thr Tyr Gly 275 280 285 Glu Ala Ile Ile Asp Tyr Phe Tyr Lys Lys Gly Ile Ser Trp Thr Ala 290 295 300 Trp Val Phe Asp Pro Leu Trp Ser Pro Gln Leu Ile Arg Asp Trp Tyr 305 310 315 320 Phe Thr Pro Ser Arg Gln Gly Gln Phe Phe Lys Glu Lys Leu Met Glu 325 330 335 Leu Asn 811119DNAUnknownObtained from environmental sample 81atgaatttac ttgctcaata cttttccgga ctatttctga tttttttgat ctcaattttt 60ttcgttagtt ctgcagcgaa tcatcattat gaaaaaaata cagtcaacga attttctgat 120gatgtaaatc aaacaacatt agtccttcaa cccgggatat ccgaagccca gaatactcaa 180aacctgccgc ggatttcggt tgaaggaaac caatttgtgg atgaatcggg aaacacagtc 240acatttcagg gtgtcagtgt tgccgatccg cacaggctta ataatgccgg ccaatggaaa 300cgggaactgt ttgaagaaat cgcaaactgg ggagcaaacg tcgttcgtct gcccatacac 360ccgctctggt ggcgggaacg gggagaggag caatacctcg aatggattga tgaagccgtg 420gagtgggcca aagagctgga gatgtacctc atcatcgact ggcacagtat cgggaacctg 480cggacagaac tctttttcag ggatatctac aacaccaccc gccgtgaaac ttatgaattc 540tggaggctga tttcggatcg ctatgctgat gaaaccacaa ttgcctttta cgaaatcttt 600aatgaaccca cacggcagca gggcaggctg ggaaccatga cctggaagca atggaaggaa 660attctaaccg acattatcac aatcatttat gcccacaatc ctgatgcgat tccgctggta 720gcaggtttta actgggcgta tgaccttact ccggtccgcc actcacccct cgattttgaa 780ggtattgcct atgttaccca cccatatccg caaaaaagaa gcaggccctg ggttccaaaa 840tgggaagaag atttcggttt tgtggctgac aaatatcctg tatttgccac tgaattcggc 900tatatgaggg agtatgagcg gggcgctcat gtgcccgtaa tcggggacga agaatatggg 960gaaatcctca tcaattattt ccgcgaaaaa gggatttcgt ggacagcctg ggtattcgat 1020ccaagctggt cgccacagct cattcaggat tgggattata cacccacacg ctcaggtgag 1080tttttcagaa atgcgatgag aacgaaaaac aatgaataa 111982372PRTUnknownObtained from environmental sample 82Met Asn Leu Leu Ala Gln Tyr Phe Ser Gly Leu Phe Leu Ile Phe Leu 1 5 10 15 Ile Ser Ile Phe Phe Val Ser Ser Ala Ala Asn His His Tyr Glu Lys 20 25 30 Asn Thr Val Asn Glu Phe Ser Asp Asp Val Asn Gln Thr Thr Leu Val 35 40 45 Leu Gln Pro Gly Ile Ser Glu Ala Gln Asn Thr Gln Asn Leu Pro Arg 50 55 60 Ile Ser Val Glu Gly Asn Gln Phe Val Asp Glu Ser Gly Asn Thr Val 65 70 75 80 Thr Phe Gln Gly Val Ser Val Ala Asp Pro His Arg Leu Asn Asn Ala 85 90 95 Gly Gln Trp Lys Arg Glu Leu Phe Glu Glu Ile Ala Asn Trp Gly Ala 100 105 110 Asn Val Val Arg Leu Pro Ile His Pro Leu Trp Trp Arg Glu Arg Gly 115 120 125 Glu Glu Gln Tyr Leu Glu Trp Ile Asp Glu Ala Val Glu Trp Ala Lys 130 135 140 Glu Leu Glu Met Tyr Leu Ile Ile Asp Trp His Ser Ile Gly Asn Leu 145 150 155 160 Arg Thr Glu Leu Phe Phe Arg Asp Ile Tyr Asn Thr Thr Arg Arg Glu 165 170 175 Thr Tyr Glu Phe Trp Arg Leu Ile Ser Asp Arg Tyr Ala Asp Glu Thr 180 185 190 Thr Ile Ala Phe Tyr Glu Ile Phe Asn Glu Pro Thr Arg Gln Gln Gly 195 200 205 Arg Leu Gly Thr Met Thr Trp Lys Gln Trp Lys Glu Ile Leu Thr Asp 210 215 220 Ile Ile Thr Ile Ile Tyr Ala His Asn Pro Asp Ala Ile Pro Leu Val 225 230 235 240 Ala Gly Phe Asn Trp Ala Tyr Asp Leu Thr Pro Val Arg His Ser Pro 245 250 255 Leu Asp Phe Glu Gly Ile Ala Tyr Val Thr His Pro Tyr Pro Gln Lys 260 265 270 Arg Ser Arg Pro Trp Val Pro Lys Trp Glu Glu Asp Phe Gly Phe Val 275 280 285 Ala Asp Lys Tyr Pro Val Phe Ala Thr Glu Phe Gly Tyr Met Arg Glu 290 295 300 Tyr Glu Arg Gly Ala His Val Pro Val Ile Gly Asp Glu Glu Tyr Gly 305 310 315 320 Glu Ile Leu Ile Asn Tyr Phe Arg Glu Lys Gly Ile Ser Trp Thr Ala 325 330 335 Trp Val Phe Asp Pro Ser Trp Ser Pro Gln Leu Ile Gln Asp Trp Asp 340 345 350 Tyr Thr Pro Thr Arg Ser Gly Glu Phe Phe Arg Asn Ala Met Arg Thr 355 360 365 Lys Asn Asn Glu 370 831089DNAUnknownObtained from environmental sample 83atgagccttg gcctgactgc aatcgagttg atcaatcgcg cccgcgccga tctgcgactg 60ggcgtgccga tcgttctgcg cgagggcgac gtgcaggcgc tggtgctggc ggtcgagcca 120gtaaccgagg cgcggctggg tgggctgcgc gggctggggc cagggctggt gcttgcaatc 180acgcagcgcc gcgccacgac actgaaggcg cgcgcctatg atgaggatct tgcgcgagtg 240gtggtgcccg agggggtagg ctgcgactgg ctgcgggcgg tggcggaccc ctccgacgat 300ctgcgctttc cgatgaaggg cccgctgatg accgctcgcg agggcacggc cgcgctgcat 360cgcgctgcac ttcaactggt gaaatccgcg cagcttcttc cggccgcact tgttcagccg 420cttgcggatc ccgaggcgct gcccgtcacg gggctgacag tgctcgatat cgccgatgtc 480agccgtgaat tggcgcgcga gacagtgttg tatccagtgg tgcatgcgcg cttgccgatg 540ctggcggcgc aagcgggccg cgtgcatatc ttccgacccc gcgacggcgg cgttgagcat 600tacgccatcg agatcggcca gcccgaccgt gccgcgcccg tgctcacgcg gctgcattcg 660gcctgtttca caggcgatgt gctgggctcg ctcaaatgcg attgcggccc gcaactgcag 720gcagcactcg cgcagatggg cgaggaaggc gcgggggtgc tgctctatct caatcaggag 780ggtcgcggca tcgggcttgc caacaagatg cgcgcctatt cgctgcagga tcagggcttt 840gacacggtcg aggccaatca ccgtctgggg ttcgaggatg acgagcggga tttccgcatc 900ggggccgcgc ttctgcggcg gatggggttc tctcgggcgc ggctgctgac caacaaccct 960cggaaggtga acatgctgaa tgcgcatcgg gtcgaagtgg tggaacgggt gccgcttcgg 1020gtgggcgaga cggtcgagaa ccgcgcctat cttgccacca aggccgccaa atccgggcat 1080ctgttgtga 108984362PRTUnknownObtained from environmental sample 84Met Ser Leu Gly Leu Thr Ala Ile Glu Leu Ile Asn Arg Ala Arg Ala 1 5 10 15 Asp Leu Arg Leu Gly Val Pro Ile Val Leu Arg Glu Gly Asp Val Gln 20 25 30 Ala Leu Val Leu Ala Val Glu Pro Val Thr Glu Ala Arg Leu Gly Gly 35 40 45 Leu Arg Gly Leu Gly Pro Gly Leu Val Leu Ala Ile Thr Gln Arg Arg 50 55 60 Ala Thr Thr Leu Lys Ala Arg Ala Tyr Asp Glu Asp Leu Ala Arg Val 65 70 75 80 Val Val Pro Glu Gly Val Gly Cys Asp Trp Leu Arg Ala Val Ala Asp 85 90 95 Pro Ser Asp Asp Leu Arg Phe Pro Met Lys Gly Pro Leu Met Thr Ala 100 105 110 Arg Glu Gly Thr Ala Ala Leu His Arg Ala Ala Leu Gln Leu Val Lys 115 120 125 Ser Ala Gln Leu Leu Pro Ala Ala Leu Val Gln Pro Leu Ala Asp Pro 130 135 140 Glu Ala Leu Pro Val Thr Gly Leu Thr Val Leu Asp Ile Ala Asp Val 145 150 155 160 Ser Arg Glu Leu Ala Arg Glu Thr Val Leu Tyr Pro Val Val His Ala 165 170 175 Arg Leu Pro Met Leu Ala Ala Gln Ala Gly Arg Val His Ile Phe Arg 180 185 190 Pro Arg Asp Gly Gly Val Glu His Tyr Ala Ile Glu Ile Gly Gln Pro 195 200 205 Asp Arg Ala Ala Pro Val Leu Thr Arg Leu His Ser Ala Cys Phe Thr 210 215 220 Gly Asp Val Leu Gly Ser Leu Lys Cys Asp Cys Gly Pro Gln Leu Gln 225 230 235 240 Ala Ala Leu Ala Gln Met Gly Glu Glu Gly Ala Gly Val Leu Leu Tyr 245 250 255 Leu Asn Gln Glu Gly Arg Gly Ile Gly Leu Ala Asn Lys Met Arg Ala 260 265 270 Tyr Ser Leu Gln Asp Gln Gly Phe Asp Thr Val Glu Ala Asn His Arg 275 280 285 Leu Gly Phe Glu Asp Asp Glu Arg Asp Phe Arg Ile Gly Ala Ala Leu 290 295 300 Leu Arg Arg Met Gly Phe Ser Arg Ala Arg Leu Leu Thr Asn Asn Pro 305 310 315 320 Arg Lys Val Asn Met Leu Asn Ala His Arg Val Glu Val Val Glu Arg 325 330 335 Val Pro Leu Arg Val Gly Glu Thr Val Glu Asn Arg Ala Tyr Leu Ala 340 345 350 Thr Lys Ala Ala Lys Ser Gly His Leu Leu 355 360 851284DNAUnknownObtained from environmental sample 85gtgaacaccg cgcatcgcat cgaattccct cggcaattta tcttcggttc cgccactgct 60gctcaccaag tggagggcaa caacgttcac aatgattggt gggcccacga gcatgccacc 120gacacgaatg ccgtggagcc gtcgggcctc gcctgcgacc actttcggcg ctttgccgac 180gacttccgcc tcttacgcca actcggacag ccagcgcacc gcctgtcgct ggaatggagc 240cgcatcgaac cggcacccgg tgaaatcgat cgttcggcat tgtcccacta ccgccgagtc 300ctgggtactt tgcgagacct cggaatcgag ccatgggtca ccatccacca cttcacttgc 360cctcgctggt tcgtggaaca gggagggttt acacgcatgg attcagcgcg ctctctcgtt 420cgccataccg aacgcgtggc gagggagttc tccgacctag tcacaaactg gtgcaccata 480aatgagccaa acgtcgtggc agaactcggt tatcgcttcg gatactttcc gccgcggttg 540caggacgatg agctggcagc ggaagtgctc accaacttct ttcgcttaca cgctgaaatg 600gcagaagttt tgcgcgctca cgcgcagaga tcggcgcaaa tcggtatcac ccttgcgatg 660caagcacacg agccgctgcg catcgaaagc gaagcggacc gcgcactggc ggcgcggcgc 720gacgccgaga ccaacggcgt catgctcaac gccttgcgaa ccggtgtatt cgcctacccg 780ggacgggagc cggtggaaat ccctggactg aaaacgtcat cgaccttcgt gggggtccag 840tactattcgc gggtccgcta cgacgccgag tcgcaaggtc cagcaatgcc cgacttcgag 900cgcaccctca gccaaatggg atgggaggtg tatcctgagg ggttcggccc cttgctcgag 960cgcgcagcag aaactggact cgaagtgatc gtcacagaga acgggatggc gcacgacgat 1020gaccgtgtgc gcgtgcgttt tatcgccgac cacttgcggg tcgttcaccg ccttctggaa 1080cgcggtgtgc gcatcggagg gtacttttac tggtcgacca tggacaactt cgaatggaac 1140ttcgggtacg gaccgaagtt cggcctgatc gaagtggacc gttctaccct ggaacgcagg 1200ccgcggcgaa gcgcgtattt cttccgtgac atgatccagc agcgagtgct cgacgacgac 1260ctggtcgagc actggactcg ctga 128486427PRTUnknownObtained from environmental sample 86Met Asn Thr Ala His Arg Ile Glu Phe Pro Arg Gln Phe Ile Phe Gly 1 5 10 15 Ser Ala Thr Ala Ala His Gln Val Glu Gly Asn Asn Val His Asn Asp 20 25 30 Trp Trp Ala His Glu His Ala Thr Asp Thr Asn Ala Val Glu Pro Ser 35 40 45 Gly Leu Ala Cys Asp His Phe Arg Arg Phe Ala Asp Asp Phe Arg Leu 50 55 60 Leu Arg Gln Leu Gly Gln Pro Ala His Arg Leu Ser Leu Glu Trp Ser 65 70 75 80 Arg Ile Glu Pro Ala Pro Gly Glu Ile Asp Arg Ser Ala Leu Ser His 85 90 95 Tyr Arg Arg Val Leu Gly Thr Leu Arg Asp Leu Gly Ile Glu Pro Trp 100 105 110 Val Thr Ile His His Phe Thr Cys Pro Arg Trp Phe Val Glu Gln Gly 115 120 125 Gly Phe Thr Arg Met Asp Ser Ala Arg Ser Leu Val Arg His Thr Glu 130 135 140 Arg Val Ala Arg Glu Phe Ser Asp Leu Val Thr Asn Trp Cys Thr Ile 145 150 155 160 Asn Glu Pro Asn Val Val Ala Glu Leu Gly Tyr Arg Phe Gly Tyr Phe 165 170 175 Pro Pro Arg Leu Gln Asp Asp Glu Leu Ala Ala Glu Val Leu Thr Asn 180 185 190 Phe Phe Arg Leu His Ala Glu Met Ala Glu Val Leu Arg Ala His Ala 195 200 205 Gln Arg Ser Ala Gln Ile Gly Ile Thr Leu Ala Met Gln Ala His Glu 210 215 220 Pro Leu Arg Ile Glu Ser Glu Ala Asp Arg Ala Leu Ala Ala Arg Arg 225 230 235 240 Asp Ala Glu Thr Asn Gly Val Met Leu Asn Ala Leu Arg Thr Gly Val 245 250 255 Phe Ala Tyr Pro Gly Arg Glu Pro Val Glu Ile Pro Gly Leu Lys Thr 260 265 270 Ser Ser Thr Phe Val Gly Val Gln Tyr Tyr Ser Arg Val Arg Tyr Asp 275 280 285 Ala Glu Ser Gln Gly Pro Ala Met Pro Asp Phe Glu Arg Thr Leu Ser 290 295 300 Gln Met Gly Trp Glu Val Tyr Pro Glu Gly Phe Gly Pro Leu Leu Glu 305 310 315 320 Arg Ala Ala Glu Thr Gly Leu Glu Val Ile Val Thr Glu Asn Gly Met 325 330 335 Ala His Asp Asp Asp Arg Val Arg Val Arg Phe Ile Ala Asp His Leu 340 345 350 Arg Val Val His Arg Leu Leu Glu Arg Gly Val Arg Ile Gly Gly Tyr 355 360 365 Phe Tyr Trp Ser Thr Met Asp Asn Phe Glu Trp Asn Phe Gly Tyr Gly 370 375 380 Pro Lys Phe Gly Leu Ile Glu Val

Asp Arg Ser Thr Leu Glu Arg Arg 385 390 395 400 Pro Arg Arg Ser Ala Tyr Phe Phe Arg Asp Met Ile Gln Gln Arg Val 405 410 415 Leu Asp Asp Asp Leu Val Glu His Trp Thr Arg 420 425 871167DNAUnknownObtained from environmental sample 87atgagaaaga gtgtgttcac cctcgccgtg tttttgtcgg cactgtttgc attcacgtct 60tgtcagaaca agagccagaa cgaggctcaa gaccaggcag gacaagtcaa taacttccgc 120atcaagcgcg gcacgaacat cagccactgg ctgtcgcagt cggagcagcg cggtgaggct 180cgcagactgc atatccagga ggacgacttc gcccgtctgg aagagctggg cttcgacttc 240gtgcgcatcc ccatcgacga ggtgcagttc tgggacgagc agggcaacaa gctgcccgag 300gcgtgggatc tgctgaacaa cgccctcgac tggagcaaga agcacaacct gcgtgccatc 360gtcgacctgc acatcatccg tgcgcactat ttcaatgccg tgaatgaggc agaccaggcc 420gccaataccc tcttcacctc tgaggaggca caggaaggac tccttaacct gtggcgccag 480ctctccgagt tcctgaagga ccgcagcaac gactgggtgg cctacgagtt catgaacgag 540ccggtagccc ctgagcacga gatgtggaac cagctggtag ccaaggtaca caaggccctg 600cgcgaactgg aaccccagcg tacactcgtc gtcggctcga acatgtggca gggacacgag 660acgatgaagt atctgaaagt gcccgagggc gataagaaca tcatcctctc gttccactac 720tacaacccga tgctgctgac gcactacggt gcctggtggt cgccgctgtg tgctgcctac 780aagggtaagg tgaactatcc cggtgtgctc gtgtcgaagg aagactacga tgccgctcct 840gctgccatca aggatcagct gaagcccttt accgaggaag tatggaacat cgacaagatc 900cgtgagcagt tcaaggatgc catcgaggcc gccaagaaat atgacctgca actgttctgc 960ggcgagtggg gtgtctatga gcccgtggac cgtgagctgg cctacaaatg gtatcgtgac 1020gtgctgacgg tgttcgacga gttcaacatc gcctggacga cctggtgcta cgatgctgac 1080ttcggtttct gggatcagca gcgccactgc tacaaagact atccgctggt ggagctcctg 1140atgtcaggaa agaaactggg agaatag 116788388PRTUnknownObtained from environmental sample 88Met Arg Lys Ser Val Phe Thr Leu Ala Val Phe Leu Ser Ala Leu Phe 1 5 10 15 Ala Phe Thr Ser Cys Gln Asn Lys Ser Gln Asn Glu Ala Gln Asp Gln 20 25 30 Ala Gly Gln Val Asn Asn Phe Arg Ile Lys Arg Gly Thr Asn Ile Ser 35 40 45 His Trp Leu Ser Gln Ser Glu Gln Arg Gly Glu Ala Arg Arg Leu His 50 55 60 Ile Gln Glu Asp Asp Phe Ala Arg Leu Glu Glu Leu Gly Phe Asp Phe 65 70 75 80 Val Arg Ile Pro Ile Asp Glu Val Gln Phe Trp Asp Glu Gln Gly Asn 85 90 95 Lys Leu Pro Glu Ala Trp Asp Leu Leu Asn Asn Ala Leu Asp Trp Ser 100 105 110 Lys Lys His Asn Leu Arg Ala Ile Val Asp Leu His Ile Ile Arg Ala 115 120 125 His Tyr Phe Asn Ala Val Asn Glu Ala Asp Gln Ala Ala Asn Thr Leu 130 135 140 Phe Thr Ser Glu Glu Ala Gln Glu Gly Leu Leu Asn Leu Trp Arg Gln 145 150 155 160 Leu Ser Glu Phe Leu Lys Asp Arg Ser Asn Asp Trp Val Ala Tyr Glu 165 170 175 Phe Met Asn Glu Pro Val Ala Pro Glu His Glu Met Trp Asn Gln Leu 180 185 190 Val Ala Lys Val His Lys Ala Leu Arg Glu Leu Glu Pro Gln Arg Thr 195 200 205 Leu Val Val Gly Ser Asn Met Trp Gln Gly His Glu Thr Met Lys Tyr 210 215 220 Leu Lys Val Pro Glu Gly Asp Lys Asn Ile Ile Leu Ser Phe His Tyr 225 230 235 240 Tyr Asn Pro Met Leu Leu Thr His Tyr Gly Ala Trp Trp Ser Pro Leu 245 250 255 Cys Ala Ala Tyr Lys Gly Lys Val Asn Tyr Pro Gly Val Leu Val Ser 260 265 270 Lys Glu Asp Tyr Asp Ala Ala Pro Ala Ala Ile Lys Asp Gln Leu Lys 275 280 285 Pro Phe Thr Glu Glu Val Trp Asn Ile Asp Lys Ile Arg Glu Gln Phe 290 295 300 Lys Asp Ala Ile Glu Ala Ala Lys Lys Tyr Asp Leu Gln Leu Phe Cys 305 310 315 320 Gly Glu Trp Gly Val Tyr Glu Pro Val Asp Arg Glu Leu Ala Tyr Lys 325 330 335 Trp Tyr Arg Asp Val Leu Thr Val Phe Asp Glu Phe Asn Ile Ala Trp 340 345 350 Thr Thr Trp Cys Tyr Asp Ala Asp Phe Gly Phe Trp Asp Gln Gln Arg 355 360 365 His Cys Tyr Lys Asp Tyr Pro Leu Val Glu Leu Leu Met Ser Gly Lys 370 375 380 Lys Leu Gly Glu 385 891500DNAUnknownObtained from environmental sample 89atgaaacgtt cagtctctat ctttatcgca tgtttattaa tgacagtatt aacaattagc 60ggtgtcgcgg caccagaagc atctgcagca ggggcgaaaa cgcctgtagc ccttaatggc 120cagcttagca ttaaaggtac tcagctagtc aatcaaaacg gaaaaccggt gcagctgaag 180gggatcagct cacacggttt gcagtggttc ggcgattatg tcaataaaga cactttaaaa 240tggctaagag acgattgggg aattaccgtc ttccgggcgg caatgtacac ggctgacggc 300ggttatatcg agaatccgtc tgtgaaaaat aaagtcaaag aagctgttga agcggcaaaa 360gagctcggga tatatgtcat cattgactgg catattttaa atgacggcaa tccaaatcaa 420aataaagaga aggcgaagga attctttaag gaaatgtcaa gcctttacgg aagctcacca 480aacgttatat atgaaattgc taatgaaccg aacggtgatg taaattggaa gcgcgatatc 540aaaccgtatg cggaagaagt gatttctgtt atccgtaaaa atgacccgga taacatcatt 600attaccggaa caggcacttg gagccaggat gtcaacgatg ctgcggatga tcagcttaag 660gatgcaaacg tcatgtacgc gcttcatttt tatgccggta cacacggcca gtttttaagg 720gataaagcgg actatgcgct cagcaaagga gctccgattt ttgtaacgga atgggggacg 780agtgacgctt ccggaaatgg aggggtatac cttgaccagt cgagggaatg gctgaattat 840ctcgacagca agaaaatcag ctgggtaaac tggaaccttt ctgataagca ggaatcatcc 900tcagctttaa agccgggggc atctaaaaca ggcggctggc cgttatcaga tttatccgct 960tcagggacat ttgtaagaga aaacattcgc ggctcccaaa attcgagtga agacagatct 1020gagacaccaa agcaagagaa acccgcacag gaaaacagca tctctgtgca atacagaaca 1080ggggatggaa gtgtgaacag caaccaaatc cgtcctcaga tcaatgtgaa aaacaacagc 1140aagaccaccg ttaacttaaa aaatgtaact gtccgctact ggtataacac gaaaaacaaa 1200ggccaaaact tcgactgtga ttacgcgaag atcggatgca gcaatgtgac gcacaagttt 1260gtgacattac ataaacctgt aaaaggtgca gatgcctatc tggaacttgg gtttagaaac 1320gggacgctgt caccgggagc aagcaccgga gaaattcaaa ttcgtcttca caatgaggac 1380tggagcaatt attcacaagc cggggattat tcttttttcc agtcgaatac gtttaaagat 1440acaaaaaaaa tcacattata taataacgga aaactgattt ggggaacaga acccaaatag 150090499PRTUnknownObtained from environmental sample 90Met Lys Arg Ser Val Ser Ile Phe Ile Ala Cys Leu Leu Met Thr Val 1 5 10 15 Leu Thr Ile Ser Gly Val Ala Ala Pro Glu Ala Ser Ala Ala Gly Ala 20 25 30 Lys Thr Pro Val Ala Leu Asn Gly Gln Leu Ser Ile Lys Gly Thr Gln 35 40 45 Leu Val Asn Gln Asn Gly Lys Pro Val Gln Leu Lys Gly Ile Ser Ser 50 55 60 His Gly Leu Gln Trp Phe Gly Asp Tyr Val Asn Lys Asp Thr Leu Lys 65 70 75 80 Trp Leu Arg Asp Asp Trp Gly Ile Thr Val Phe Arg Ala Ala Met Tyr 85 90 95 Thr Ala Asp Gly Gly Tyr Ile Glu Asn Pro Ser Val Lys Asn Lys Val 100 105 110 Lys Glu Ala Val Glu Ala Ala Lys Glu Leu Gly Ile Tyr Val Ile Ile 115 120 125 Asp Trp His Ile Leu Asn Asp Gly Asn Pro Asn Gln Asn Lys Glu Lys 130 135 140 Ala Lys Glu Phe Phe Lys Glu Met Ser Ser Leu Tyr Gly Ser Ser Pro 145 150 155 160 Asn Val Ile Tyr Glu Ile Ala Asn Glu Pro Asn Gly Asp Val Asn Trp 165 170 175 Lys Arg Asp Ile Lys Pro Tyr Ala Glu Glu Val Ile Ser Val Ile Arg 180 185 190 Lys Asn Asp Pro Asp Asn Ile Ile Ile Thr Gly Thr Gly Thr Trp Ser 195 200 205 Gln Asp Val Asn Asp Ala Ala Asp Asp Gln Leu Lys Asp Ala Asn Val 210 215 220 Met Tyr Ala Leu His Phe Tyr Ala Gly Thr His Gly Gln Phe Leu Arg 225 230 235 240 Asp Lys Ala Asp Tyr Ala Leu Ser Lys Gly Ala Pro Ile Phe Val Thr 245 250 255 Glu Trp Gly Thr Ser Asp Ala Ser Gly Asn Gly Gly Val Tyr Leu Asp 260 265 270 Gln Ser Arg Glu Trp Leu Asn Tyr Leu Asp Ser Lys Lys Ile Ser Trp 275 280 285 Val Asn Trp Asn Leu Ser Asp Lys Gln Glu Ser Ser Ser Ala Leu Lys 290 295 300 Pro Gly Ala Ser Lys Thr Gly Gly Trp Pro Leu Ser Asp Leu Ser Ala 305 310 315 320 Ser Gly Thr Phe Val Arg Glu Asn Ile Arg Gly Ser Gln Asn Ser Ser 325 330 335 Glu Asp Arg Ser Glu Thr Pro Lys Gln Glu Lys Pro Ala Gln Glu Asn 340 345 350 Ser Ile Ser Val Gln Tyr Arg Thr Gly Asp Gly Ser Val Asn Ser Asn 355 360 365 Gln Ile Arg Pro Gln Ile Asn Val Lys Asn Asn Ser Lys Thr Thr Val 370 375 380 Asn Leu Lys Asn Val Thr Val Arg Tyr Trp Tyr Asn Thr Lys Asn Lys 385 390 395 400 Gly Gln Asn Phe Asp Cys Asp Tyr Ala Lys Ile Gly Cys Ser Asn Val 405 410 415 Thr His Lys Phe Val Thr Leu His Lys Pro Val Lys Gly Ala Asp Ala 420 425 430 Tyr Leu Glu Leu Gly Phe Arg Asn Gly Thr Leu Ser Pro Gly Ala Ser 435 440 445 Thr Gly Glu Ile Gln Ile Arg Leu His Asn Glu Asp Trp Ser Asn Tyr 450 455 460 Ser Gln Ala Gly Asp Tyr Ser Phe Phe Gln Ser Asn Thr Phe Lys Asp 465 470 475 480 Thr Lys Lys Ile Thr Leu Tyr Asn Asn Gly Lys Leu Ile Trp Gly Thr 485 490 495 Glu Pro Lys 911725DNAUnknownObtained from environmental sample 91atgctgaaat taagtgataa cctaactttc ttgaaaagca aaccattttt tcttaatgaa 60aaagaaatga agtgggtgga gaaaacactt caatccatgt ccttacatga aaaagtaggg 120caattatttt gtcccattgg cggttcagat aataaacaag aattagaagc ctttattaag 180gaatatcatc ctggcggcat catgtaccgt cctaatacag gagcaaaaat acaggaaaca 240catcggttgt tacaagagct atccccggta cctttattaa tttctgctaa cttagaggcc 300ggtggtaatg ggattgctac ggatggtact tacttcggaa agcaaatgca ggtggctgca 360acagataatg aagaaatggc ctataaatta ggattagttg ctggccgtga aggccgtgtg 420gccggttgta actgggcttt tgcaccaatt gttgatattg atatgaacta tcgaaaccca 480attacaaacg taagaacgta tgggtctgac ccaattagag ttgcccaaat gtctaaagct 540tttatgaagg gaattcatga aagcggactc gcagcagctg ttaagcattt cccaggggat 600ggagtggatg atagagatca gcatctttta tcatctgtaa acaccttatc taccgaagaa 660tgggatcaaa cctttgggat ggtttatcaa gaaatgatag acagtggggc aaaatcgatt 720atggcgggcc atatcatgct ccctgaatat tcaagagaac tattgccggg tattgaagac 780gaacaaatca tgcccgccac actagcacca gagttactta atggtttatt aagggaaaag 840ttaggtttta atggtttaat cgtgactgat gcatccccta tgttagggtt cactacttcg 900gaaagaagag aaattgctgt tcctaaggcg attgcttcgg gctgtgatat gtttctcttc 960aaccgtaaca taaaagaaga ttatgagttc atgctgaatg gaattgaaac tggaattcta 1020accttggaaa gagtagatga agctgttact agagtacttg ctcttaaagc atctctaggt 1080ctgaatgtac aaaaggaatt gggaatatta gtacctgaag aagcggaatt gtcggtatta 1140caatctgaag aacatttgga ttgggcaaga gaatgtgcag accaatcggt tacattagta 1200aaggatacac aaaaactgct gcctattagt gctgatcagt ataaacgggt tcgactttat 1260gtattgggtg atcaagaagg agggctaaag gaaggcggct ccgtcactca accgtttatc 1320gattctctta aaaatgctgg ctttgaagta gatttatata atgacaagca agttaatttc 1380caagaactgt ttatgagtgt aaacgagttt aaaaagaact atgatctgat catttatgtc 1440gccaaccttg aaaccgctag taaccaaacg acagtcagaa ttaattggca gcagccgcta 1500aatgccaacg ctccatggtt tgttaaagat ataccgacat tatttatttc ggttgctaac 1560ccataccatc tacaggacgt accaatggtt aagacctata taaatgctta ttcatctaat 1620gaatatgtgg tagaagcaat tgtagataaa atcttaggaa aatcagagtt taaagggaag 1680aatcccgtcg atccgttttg tgggaaatgg gataccagac tttaa 172592574PRTUnknownObtained from environmental sample 92Met Leu Lys Leu Ser Asp Asn Leu Thr Phe Leu Lys Ser Lys Pro Phe 1 5 10 15 Phe Leu Asn Glu Lys Glu Met Lys Trp Val Glu Lys Thr Leu Gln Ser 20 25 30 Met Ser Leu His Glu Lys Val Gly Gln Leu Phe Cys Pro Ile Gly Gly 35 40 45 Ser Asp Asn Lys Gln Glu Leu Glu Ala Phe Ile Lys Glu Tyr His Pro 50 55 60 Gly Gly Ile Met Tyr Arg Pro Asn Thr Gly Ala Lys Ile Gln Glu Thr 65 70 75 80 His Arg Leu Leu Gln Glu Leu Ser Pro Val Pro Leu Leu Ile Ser Ala 85 90 95 Asn Leu Glu Ala Gly Gly Asn Gly Ile Ala Thr Asp Gly Thr Tyr Phe 100 105 110 Gly Lys Gln Met Gln Val Ala Ala Thr Asp Asn Glu Glu Met Ala Tyr 115 120 125 Lys Leu Gly Leu Val Ala Gly Arg Glu Gly Arg Val Ala Gly Cys Asn 130 135 140 Trp Ala Phe Ala Pro Ile Val Asp Ile Asp Met Asn Tyr Arg Asn Pro 145 150 155 160 Ile Thr Asn Val Arg Thr Tyr Gly Ser Asp Pro Ile Arg Val Ala Gln 165 170 175 Met Ser Lys Ala Phe Met Lys Gly Ile His Glu Ser Gly Leu Ala Ala 180 185 190 Ala Val Lys His Phe Pro Gly Asp Gly Val Asp Asp Arg Asp Gln His 195 200 205 Leu Leu Ser Ser Val Asn Thr Leu Ser Thr Glu Glu Trp Asp Gln Thr 210 215 220 Phe Gly Met Val Tyr Gln Glu Met Ile Asp Ser Gly Ala Lys Ser Ile 225 230 235 240 Met Ala Gly His Ile Met Leu Pro Glu Tyr Ser Arg Glu Leu Leu Pro 245 250 255 Gly Ile Glu Asp Glu Gln Ile Met Pro Ala Thr Leu Ala Pro Glu Leu 260 265 270 Leu Asn Gly Leu Leu Arg Glu Lys Leu Gly Phe Asn Gly Leu Ile Val 275 280 285 Thr Asp Ala Ser Pro Met Leu Gly Phe Thr Thr Ser Glu Arg Arg Glu 290 295 300 Ile Ala Val Pro Lys Ala Ile Ala Ser Gly Cys Asp Met Phe Leu Phe 305 310 315 320 Asn Arg Asn Ile Lys Glu Asp Tyr Glu Phe Met Leu Asn Gly Ile Glu 325 330 335 Thr Gly Ile Leu Thr Leu Glu Arg Val Asp Glu Ala Val Thr Arg Val 340 345 350 Leu Ala Leu Lys Ala Ser Leu Gly Leu Asn Val Gln Lys Glu Leu Gly 355 360 365 Ile Leu Val Pro Glu Glu Ala Glu Leu Ser Val Leu Gln Ser Glu Glu 370 375 380 His Leu Asp Trp Ala Arg Glu Cys Ala Asp Gln Ser Val Thr Leu Val 385 390 395 400 Lys Asp Thr Gln Lys Leu Leu Pro Ile Ser Ala Asp Gln Tyr Lys Arg 405 410 415 Val Arg Leu Tyr Val Leu Gly Asp Gln Glu Gly Gly Leu Lys Glu Gly 420 425 430 Gly Ser Val Thr Gln Pro Phe Ile Asp Ser Leu Lys Asn Ala Gly Phe 435 440 445 Glu Val Asp Leu Tyr Asn Asp Lys Gln Val Asn Phe Gln Glu Leu Phe 450 455 460 Met Ser Val Asn Glu Phe Lys Lys Asn Tyr Asp Leu Ile Ile Tyr Val 465 470 475 480 Ala Asn Leu Glu Thr Ala Ser Asn Gln Thr Thr Val Arg Ile Asn Trp 485 490 495 Gln Gln Pro Leu Asn Ala Asn Ala Pro Trp Phe Val Lys Asp Ile Pro 500 505 510 Thr Leu Phe Ile Ser Val Ala Asn Pro Tyr His Leu Gln Asp Val Pro 515 520 525 Met Val Lys Thr Tyr Ile Asn Ala Tyr Ser Ser Asn Glu Tyr Val Val 530 535 540 Glu Ala Ile Val Asp Lys Ile Leu Gly Lys Ser Glu Phe Lys Gly Lys 545 550 555 560 Asn Pro Val Asp Pro Phe Cys Gly Lys Trp Asp Thr Arg Leu 565 570 93546DNAUnknownObtained from environmental sample 93atgagaataa aaaatttaaa aacgaaccgt atcacaaacc cgctgggatt tgatatagga 60aaaccacgta tatcttttgt cacttatgac actacggcta aaaagcaaac agcagcgcaa 120atacaggttg cgctagatca agagtttacg aacctaacat ttgacagtgg gaaaagcacg 180gagatagata gtctagcata cgaactgcca tttcaattag agtcttacac tcgctactac 240tggcgtgtga ccgtttgggc ggataatggg gatgtggcca caagtgaaat tgcttggttt 300gaaacagcca aactaggcga ttcttgggag gccaagtgga ttacccccga ttttgataag 360gaaatccatc ccgtactatc aagggaattt gatttgtcaa aagaagtcgt ttctgcccgt 420gcctatgttt gcggtttggg attatatgaa atggagatta atggtctaaa ggctggggat

480gaatatctga cccctaattt caacgcctat gataaatggc tgcagtacca gacctatgat 540attaca 54694182PRTUnknownObtained from environmental sample 94Met Arg Ile Lys Asn Leu Lys Thr Asn Arg Ile Thr Asn Pro Leu Gly 1 5 10 15 Phe Asp Ile Gly Lys Pro Arg Ile Ser Phe Val Thr Tyr Asp Thr Thr 20 25 30 Ala Lys Lys Gln Thr Ala Ala Gln Ile Gln Val Ala Leu Asp Gln Glu 35 40 45 Phe Thr Asn Leu Thr Phe Asp Ser Gly Lys Ser Thr Glu Ile Asp Ser 50 55 60 Leu Ala Tyr Glu Leu Pro Phe Gln Leu Glu Ser Tyr Thr Arg Tyr Tyr 65 70 75 80 Trp Arg Val Thr Val Trp Ala Asp Asn Gly Asp Val Ala Thr Ser Glu 85 90 95 Ile Ala Trp Phe Glu Thr Ala Lys Leu Gly Asp Ser Trp Glu Ala Lys 100 105 110 Trp Ile Thr Pro Asp Phe Asp Lys Glu Ile His Pro Val Leu Ser Arg 115 120 125 Glu Phe Asp Leu Ser Lys Glu Val Val Ser Ala Arg Ala Tyr Val Cys 130 135 140 Gly Leu Gly Leu Tyr Glu Met Glu Ile Asn Gly Leu Lys Ala Gly Asp 145 150 155 160 Glu Tyr Leu Thr Pro Asn Phe Asn Ala Tyr Asp Lys Trp Leu Gln Tyr 165 170 175 Gln Thr Tyr Asp Ile Thr 180 952298DNAUnknownObtained from environmental sample 95atgatcaatc aagatataaa acaattaatc tcacaaatga ccttggaaga aaaagctggt 60ctttgttctg gattagattt ttggaattta aaaggtatcg aaagactggg aataccctcg 120ataatggtaa ccgatggtcc gcatggactc cgtaaacaaa aaatgggagc agatcattta 180gggctgtttg acagtattcc tgcgacatgt ttcccatctg cagccggttt agctagtact 240tggaataaag agttaatata tgaagttggg gttgcattag gaaaggaatg ccaggcagag 300gatgtggcaa tacttcttgg ccctggagca aacattaagc gctcacccct ttgtggcaga 360aactttgaat atttttcgga agatccattc ctttcatcag aaatggctgc gtcccatatc 420aagggtgttc aaagtgaggg ggttgggaca tcacttaagc acttcgctgc aaataatcaa 480gaacaccgaa gaatgtcgac agatgctatt gtggatgaaa ggacgttgcg agaaatatat 540ttggccagct ttgaaaacgc tgtaaagaaa gcgcagccat ggactgtgat gtgcgcctac 600aacaaggtca atggagactt tgcatcagaa aataaaacat tgttaactga catcctgcga 660gatgagtggg gctttgaagg aattgttgtt tctgactggg gggcggttaa tgaacctgtt 720gacggattaa atgccgggtt agacctggaa atgccttcaa gtagtgggat tggtgaaaag 780aaaatcatca atgctgtaag aaatggtcag cttttagaag ataaactaga tcaggcagtt 840gaaagaattc tacgtattat cttaatggca gtagaaaaca agaaagaaac cgctgactat 900gataaagaac aacatcataa gcttgcaaga aaagcagcaa gtgaaagtat ggttttatta 960aagaatgaag ataatatcct gccgttaaag aaagaaggaa ccatttcgat tattggttca 1020tttgccaaaa aaccaaggta tcaaggcggt ggaagctcac acattaaccc gacaaagctt 1080gaaaatatct atgaagaaat agagaaaaca gcgggccaaa atgtgaacgt tttatacgcg 1140gaaggatatc atcttgaaaa ggatttaatc gatgatcaat taattgaaga ggcaaaaaaa 1200acggcagcaa aatccgatgt aaccgtattg tttgtaggtc ttcctgaccg atatgaatct 1260gaaggatatg atagagagca cctgaatata ccggagaatc accgtctttt agtcgaagcg 1320gttgcggaag tacaaaagaa tatagttgtt gtactaagta atggggcacc gcttgttatg 1380ccatggcttg ataaggtgaa ggggctgctg gaaagttacc tgggaggtca ggcactagga 1440ggtgcgattg cagacatcct attcggagaa gttaatccaa gtggaaagct tgccgaaact 1500tttcccgtaa aattaggtga caatccttct tatctcaact ttccaggaga gagggataaa 1560gttgagtata aagaaggcat ctttgttggt tatcgttatt acgatacaaa acagattgag 1620ccgctgtttc catttggata tggtttaagc tatacaaact ttgaatataa aaaccttgta 1680attgataaaa aagaaataaa agatacagaa attgtcacag ttaccgtgaa tgtgaaaaat 1740acaggaaaag tgcctgggaa agaaatcatc cagttatatg taaaagatat aaaaagcagt 1800gtagttcgtc ctgaaaaaga gttaaaaggc tttggaaagg tttccttaca gcctggggaa 1860gacaaaacta tttcctttaa attggataaa cgcgcatttg catattacaa cacggaattg 1920aaggattggt atgtagaatc aggagaattt gaaattttgg tggggaaatc gtccagagaa 1980attgaactaa cagaaaaaat tatggttcac tctacttccc cagttttctt ggaggttcac 2040cgaaattcca cggtcggaga tcttttaact gatccaattc taggtgaaaa agctaatgct 2100ctaattagag agctaacaaa aggaagtcca ttatttgatg ctgggtcaga tcacggagag 2160ggtgcagaaa tgatggaagc gatgttaaaa tacatgcctt tgcgtgctct tatgaatttt 2220agtggtggag acattaccga agagaaacta actgaattta ttaaggaact taattcaact 2280aattttgtaa gcctttaa 229896765PRTUnknownObtained from environmental sample 96Met Ile Asn Gln Asp Ile Lys Gln Leu Ile Ser Gln Met Thr Leu Glu 1 5 10 15 Glu Lys Ala Gly Leu Cys Ser Gly Leu Asp Phe Trp Asn Leu Lys Gly 20 25 30 Ile Glu Arg Leu Gly Ile Pro Ser Ile Met Val Thr Asp Gly Pro His 35 40 45 Gly Leu Arg Lys Gln Lys Met Gly Ala Asp His Leu Gly Leu Phe Asp 50 55 60 Ser Ile Pro Ala Thr Cys Phe Pro Ser Ala Ala Gly Leu Ala Ser Thr 65 70 75 80 Trp Asn Lys Glu Leu Ile Tyr Glu Val Gly Val Ala Leu Gly Lys Glu 85 90 95 Cys Gln Ala Glu Asp Val Ala Ile Leu Leu Gly Pro Gly Ala Asn Ile 100 105 110 Lys Arg Ser Pro Leu Cys Gly Arg Asn Phe Glu Tyr Phe Ser Glu Asp 115 120 125 Pro Phe Leu Ser Ser Glu Met Ala Ala Ser His Ile Lys Gly Val Gln 130 135 140 Ser Glu Gly Val Gly Thr Ser Leu Lys His Phe Ala Ala Asn Asn Gln 145 150 155 160 Glu His Arg Arg Met Ser Thr Asp Ala Ile Val Asp Glu Arg Thr Leu 165 170 175 Arg Glu Ile Tyr Leu Ala Ser Phe Glu Asn Ala Val Lys Lys Ala Gln 180 185 190 Pro Trp Thr Val Met Cys Ala Tyr Asn Lys Val Asn Gly Asp Phe Ala 195 200 205 Ser Glu Asn Lys Thr Leu Leu Thr Asp Ile Leu Arg Asp Glu Trp Gly 210 215 220 Phe Glu Gly Ile Val Val Ser Asp Trp Gly Ala Val Asn Glu Pro Val 225 230 235 240 Asp Gly Leu Asn Ala Gly Leu Asp Leu Glu Met Pro Ser Ser Ser Gly 245 250 255 Ile Gly Glu Lys Lys Ile Ile Asn Ala Val Arg Asn Gly Gln Leu Leu 260 265 270 Glu Asp Lys Leu Asp Gln Ala Val Glu Arg Ile Leu Arg Ile Ile Leu 275 280 285 Met Ala Val Glu Asn Lys Lys Glu Thr Ala Asp Tyr Asp Lys Glu Gln 290 295 300 His His Lys Leu Ala Arg Lys Ala Ala Ser Glu Ser Met Val Leu Leu 305 310 315 320 Lys Asn Glu Asp Asn Ile Leu Pro Leu Lys Lys Glu Gly Thr Ile Ser 325 330 335 Ile Ile Gly Ser Phe Ala Lys Lys Pro Arg Tyr Gln Gly Gly Gly Ser 340 345 350 Ser His Ile Asn Pro Thr Lys Leu Glu Asn Ile Tyr Glu Glu Ile Glu 355 360 365 Lys Thr Ala Gly Gln Asn Val Asn Val Leu Tyr Ala Glu Gly Tyr His 370 375 380 Leu Glu Lys Asp Leu Ile Asp Asp Gln Leu Ile Glu Glu Ala Lys Lys 385 390 395 400 Thr Ala Ala Lys Ser Asp Val Thr Val Leu Phe Val Gly Leu Pro Asp 405 410 415 Arg Tyr Glu Ser Glu Gly Tyr Asp Arg Glu His Leu Asn Ile Pro Glu 420 425 430 Asn His Arg Leu Leu Val Glu Ala Val Ala Glu Val Gln Lys Asn Ile 435 440 445 Val Val Val Leu Ser Asn Gly Ala Pro Leu Val Met Pro Trp Leu Asp 450 455 460 Lys Val Lys Gly Leu Leu Glu Ser Tyr Leu Gly Gly Gln Ala Leu Gly 465 470 475 480 Gly Ala Ile Ala Asp Ile Leu Phe Gly Glu Val Asn Pro Ser Gly Lys 485 490 495 Leu Ala Glu Thr Phe Pro Val Lys Leu Gly Asp Asn Pro Ser Tyr Leu 500 505 510 Asn Phe Pro Gly Glu Arg Asp Lys Val Glu Tyr Lys Glu Gly Ile Phe 515 520 525 Val Gly Tyr Arg Tyr Tyr Asp Thr Lys Gln Ile Glu Pro Leu Phe Pro 530 535 540 Phe Gly Tyr Gly Leu Ser Tyr Thr Asn Phe Glu Tyr Lys Asn Leu Val 545 550 555 560 Ile Asp Lys Lys Glu Ile Lys Asp Thr Glu Ile Val Thr Val Thr Val 565 570 575 Asn Val Lys Asn Thr Gly Lys Val Pro Gly Lys Glu Ile Ile Gln Leu 580 585 590 Tyr Val Lys Asp Ile Lys Ser Ser Val Val Arg Pro Glu Lys Glu Leu 595 600 605 Lys Gly Phe Gly Lys Val Ser Leu Gln Pro Gly Glu Asp Lys Thr Ile 610 615 620 Ser Phe Lys Leu Asp Lys Arg Ala Phe Ala Tyr Tyr Asn Thr Glu Leu 625 630 635 640 Lys Asp Trp Tyr Val Glu Ser Gly Glu Phe Glu Ile Leu Val Gly Lys 645 650 655 Ser Ser Arg Glu Ile Glu Leu Thr Glu Lys Ile Met Val His Ser Thr 660 665 670 Ser Pro Val Phe Leu Glu Val His Arg Asn Ser Thr Val Gly Asp Leu 675 680 685 Leu Thr Asp Pro Ile Leu Gly Glu Lys Ala Asn Ala Leu Ile Arg Glu 690 695 700 Leu Thr Lys Gly Ser Pro Leu Phe Asp Ala Gly Ser Asp His Gly Glu 705 710 715 720 Gly Ala Glu Met Met Glu Ala Met Leu Lys Tyr Met Pro Leu Arg Ala 725 730 735 Leu Met Asn Phe Ser Gly Gly Asp Ile Thr Glu Glu Lys Leu Thr Glu 740 745 750 Phe Ile Lys Glu Leu Asn Ser Thr Asn Phe Val Ser Leu 755 760 765 97615DNAUnknownObtained from environmental sample 97atgttatacc caattataac tgaaactcgc agtatcatcg atttaaatgg tatctggaaa 60tttaaattag ataatggtga aggactgcag gaaaaatggt atgaaaacgg attaacagac 120acgatcagta tggctgtacc atcttccttt aatgatattg gagtaaatgc cagtatacgc 180gatcatgttg gctgggtatg gtatgagcgg gaattttctg tccccgccat ccttcaatct 240gagcgtgtgg ttttgcgatt cggttccgca acacatctag ctaaggtttt cgtaaatggt 300gaacttgttg ttgaacataa gggcggtttt ttaccgtttg aagcagaaat aaataagttt 360ttacaaaaag ggaaaaatcg aataacggtt gctgtcaaca atattcttga ttactcaact 420ttacccgttg gcacagtaat agaaaaggat attcctggag ttggcaaagt aatacgcaat 480cagccaaatt ttgacttctt caactacgct ggcttgcacc gtccagtgaa aatatatact 540acaccgacta cttatgtgaa ggatgtaacc attgtaacgg aaatagatgg acaggttcac 600tattcaattg attaa 61598204PRTUnknownObtained from environmental sample 98Met Leu Tyr Pro Ile Ile Thr Glu Thr Arg Ser Ile Ile Asp Leu Asn 1 5 10 15 Gly Ile Trp Lys Phe Lys Leu Asp Asn Gly Glu Gly Leu Gln Glu Lys 20 25 30 Trp Tyr Glu Asn Gly Leu Thr Asp Thr Ile Ser Met Ala Val Pro Ser 35 40 45 Ser Phe Asn Asp Ile Gly Val Asn Ala Ser Ile Arg Asp His Val Gly 50 55 60 Trp Val Trp Tyr Glu Arg Glu Phe Ser Val Pro Ala Ile Leu Gln Ser 65 70 75 80 Glu Arg Val Val Leu Arg Phe Gly Ser Ala Thr His Leu Ala Lys Val 85 90 95 Phe Val Asn Gly Glu Leu Val Val Glu His Lys Gly Gly Phe Leu Pro 100 105 110 Phe Glu Ala Glu Ile Asn Lys Phe Leu Gln Lys Gly Lys Asn Arg Ile 115 120 125 Thr Val Ala Val Asn Asn Ile Leu Asp Tyr Ser Thr Leu Pro Val Gly 130 135 140 Thr Val Ile Glu Lys Asp Ile Pro Gly Val Gly Lys Val Ile Arg Asn 145 150 155 160 Gln Pro Asn Phe Asp Phe Phe Asn Tyr Ala Gly Leu His Arg Pro Val 165 170 175 Lys Ile Tyr Thr Thr Pro Thr Thr Tyr Val Lys Asp Val Thr Ile Val 180 185 190 Thr Glu Ile Asp Gly Gln Val His Tyr Ser Ile Asp 195 200 991404DNAUnknownObtained from environmental sample 99atgaatcatt ccctttcatt tccgccatcc tttgtatggg gcgcggcaac cgcaagctac 60caactggaag gatcaaccca aggcgtggac ggctgcgccg agtccgtctg ggatatgcac 120tgccgaagat ccggcgcgat caaggacggc tcgaacggat tcgtcgcctg cgatcactac 180catcgctatc gcgaggatgt ggcgctcatg aacgagcttg gcttgaatgc ctatcgattc 240tcaatcatgt ggccccgcgt catgcccgaa ggcaccggcg cggtgaacga gaagggcatg 300gatttctacg atcggttggt tgatgaactg ctcgccgccg gcatcacacc ttgggttact 360ttgttccact gggactttcc cctagccttg ttccaacgcg gtggctggct gaatgcggat 420tccccgcaat ggtttgagga ttacactcgg gaagtggtta aacgcttgtc ggatcgtgtg 480catcactggc taacgctcaa cgaaccggcg tgcttcattg agtttggcca ccgtaccggc 540atgcatgcac ccggcttgca actggcggac aaggaagcct gccgggtctg gcaccatgcc 600atgctggccc acggtcgcgc cgttcgcgct attcgccagg aatccgtgca tccatcaccc 660caggtcggct acgcgccggt cttccgcact accatcccgg acactgaaga tcctgccgac 720atcgaagcgg cccggacctc gatgtttgct catcaggccg gcaacctgtt cgatacgcgg 780tggaacctcg acccctgctt tcggggcgcg tatccggaga tcatgatgca gtattggggc 840gatgccgcgc cgcgcatcca ggacggcgac atggagttga tccgtcagga actcgatttt 900ctcggcctga atatttacca gtccgagcgc attcgggccg gtgcggatgg cgcacccgag 960gtggtgccat accctgcgga ttatccgcgc aaccagctcg gttggcccat cacgccggag 1020gccctgcgct gggcgaccct ctttctcttt gaggagtacg ggaaacccct gatcatcaca 1080gaaaacggaa tcaccctcga cgacaagccc aatgcagacg gcgaggtgaa tgatgtccag 1140cggatcgctt ttctgaatga ctatcttagc ggtctccagc gcagcgtgga cgacggcatc 1200cctgtactgg gctatttcca ctggtcgctg tgcgacaact ttgagtgggc agaaggctat 1260gtccctcgct tcggcctgat ccatgtggac tatgccagtc aacgcagaac catcaaggcc 1320tcaggacggt tttaccgcga catcattcgg ggccagacag ccacgccctg catcgcccaa 1380tccagtcagc cggaaacaac ctaa 1404100467PRTUnknownObtained from environmental sample 100Met Asn His Ser Leu Ser Phe Pro Pro Ser Phe Val Trp Gly Ala Ala 1 5 10 15 Thr Ala Ser Tyr Gln Leu Glu Gly Ser Thr Gln Gly Val Asp Gly Cys 20 25 30 Ala Glu Ser Val Trp Asp Met His Cys Arg Arg Ser Gly Ala Ile Lys 35 40 45 Asp Gly Ser Asn Gly Phe Val Ala Cys Asp His Tyr His Arg Tyr Arg 50 55 60 Glu Asp Val Ala Leu Met Asn Glu Leu Gly Leu Asn Ala Tyr Arg Phe 65 70 75 80 Ser Ile Met Trp Pro Arg Val Met Pro Glu Gly Thr Gly Ala Val Asn 85 90 95 Glu Lys Gly Met Asp Phe Tyr Asp Arg Leu Val Asp Glu Leu Leu Ala 100 105 110 Ala Gly Ile Thr Pro Trp Val Thr Leu Phe His Trp Asp Phe Pro Leu 115 120 125 Ala Leu Phe Gln Arg Gly Gly Trp Leu Asn Ala Asp Ser Pro Gln Trp 130 135 140 Phe Glu Asp Tyr Thr Arg Glu Val Val Lys Arg Leu Ser Asp Arg Val 145 150 155 160 His His Trp Leu Thr Leu Asn Glu Pro Ala Cys Phe Ile Glu Phe Gly 165 170 175 His Arg Thr Gly Met His Ala Pro Gly Leu Gln Leu Ala Asp Lys Glu 180 185 190 Ala Cys Arg Val Trp His His Ala Met Leu Ala His Gly Arg Ala Val 195 200 205 Arg Ala Ile Arg Gln Glu Ser Val His Pro Ser Pro Gln Val Gly Tyr 210 215 220 Ala Pro Val Phe Arg Thr Thr Ile Pro Asp Thr Glu Asp Pro Ala Asp 225 230 235 240 Ile Glu Ala Ala Arg Thr Ser Met Phe Ala His Gln Ala Gly Asn Leu 245 250 255 Phe Asp Thr Arg Trp Asn Leu Asp Pro Cys Phe Arg Gly Ala Tyr Pro 260 265 270 Glu Ile Met Met Gln Tyr Trp Gly Asp Ala Ala Pro Arg Ile Gln Asp 275 280 285 Gly Asp Met Glu Leu Ile Arg Gln Glu Leu Asp Phe Leu Gly Leu Asn 290 295 300 Ile Tyr Gln Ser Glu Arg Ile Arg Ala Gly Ala Asp Gly Ala Pro Glu 305 310 315 320 Val Val Pro Tyr Pro Ala Asp Tyr Pro Arg Asn Gln Leu Gly Trp Pro 325 330 335 Ile Thr Pro Glu Ala Leu Arg Trp Ala Thr Leu Phe Leu Phe Glu Glu 340 345 350 Tyr Gly Lys Pro Leu Ile Ile Thr Glu Asn Gly Ile Thr Leu Asp Asp 355 360 365 Lys Pro Asn Ala Asp Gly Glu Val Asn Asp Val Gln Arg Ile Ala Phe 370 375 380 Leu Asn Asp Tyr Leu Ser Gly Leu Gln Arg Ser Val Asp Asp Gly Ile 385 390 395 400 Pro Val Leu Gly Tyr Phe His Trp Ser Leu Cys Asp

Asn Phe Glu Trp 405 410 415 Ala Glu Gly Tyr Val Pro Arg Phe Gly Leu Ile His Val Asp Tyr Ala 420 425 430 Ser Gln Arg Arg Thr Ile Lys Ala Ser Gly Arg Phe Tyr Arg Asp Ile 435 440 445 Ile Arg Gly Gln Thr Ala Thr Pro Cys Ile Ala Gln Ser Ser Gln Pro 450 455 460 Glu Thr Thr 465 1011101DNAUnknownObtained from environmental sample 101atgagaaatc atctgaatgt acccttttac tttatcttct tttttttaat agcgtcaata 60tttacagtct gttcatcatc aactgcttct gataacaatg agcatccacc gccagtggaa 120gtcgcggatc aggacgcttt tcgtgatgct tttgaagtga atgaattact tggacgcggt 180attaatctgg gtaatgccct tgaagcgccc aatgaaggcg aatggggaat ggtaatccag 240gaagagtttc ttgatctgat acttgcagca ggttttgagt ctgtacgaat tccgattcgc 300tggaatgccc atgccagtga aagtcaccct ttcaccattc aacgatcgtt ttttgatcgg 360gttgatgaag tcatccaatg gtcgctggat cgtggccttt ctgtaatgat caatattcat 420cactacaatg aactgatgca aaacccgcag cagcaccggc agcggttttt gcgactctgg 480aaccagattg ctacacacta taaagattat ccggataatc tggtttttga aatccttaat 540gaacctcatg ataatctgac tccttctatc tggaatagtt atttgaggga tgctattggc 600atgattcgcc agacaaaccc acgcagggtt atcgctatcg gaacagcaaa ctggggtggt 660ttcggagcat tatcacaact tgaaatcccc tcaaacgatc gccagatcat tgcaactgtt 720cattattatg aacccttcag gttcacccat cagggggctg aatgggcagg accggaaaca 780aacgattggc tggggacacg atgggatgga tcggatgagg aaaaatttga tattgaaagt 840ggttttgatg ccgtacagtc ctgggcagtg acaaataacc ggcctgttca tctcggagaa 900ttcggtgctt acagtactgc cgataatgaa tcacgcgaac gctggacaac ctttgttcgg 960gaatccgctg agcaacgcaa tttcagctgg gcatactggg aatttgcagc cggttttggg 1020atctatgacc gtaatcagtg gcaatggagg gattatctgt tgagggcttt gataccggat 1080agcccggtcc tgttggagta a 1101102366PRTUnknownObtained from environmental sample 102Met Arg Asn His Leu Asn Val Pro Phe Tyr Phe Ile Phe Phe Phe Leu 1 5 10 15 Ile Ala Ser Ile Phe Thr Val Cys Ser Ser Ser Thr Ala Ser Asp Asn 20 25 30 Asn Glu His Pro Pro Pro Val Glu Val Ala Asp Gln Asp Ala Phe Arg 35 40 45 Asp Ala Phe Glu Val Asn Glu Leu Leu Gly Arg Gly Ile Asn Leu Gly 50 55 60 Asn Ala Leu Glu Ala Pro Asn Glu Gly Glu Trp Gly Met Val Ile Gln 65 70 75 80 Glu Glu Phe Leu Asp Leu Ile Leu Ala Ala Gly Phe Glu Ser Val Arg 85 90 95 Ile Pro Ile Arg Trp Asn Ala His Ala Ser Glu Ser His Pro Phe Thr 100 105 110 Ile Gln Arg Ser Phe Phe Asp Arg Val Asp Glu Val Ile Gln Trp Ser 115 120 125 Leu Asp Arg Gly Leu Ser Val Met Ile Asn Ile His His Tyr Asn Glu 130 135 140 Leu Met Gln Asn Pro Gln Gln His Arg Gln Arg Phe Leu Arg Leu Trp 145 150 155 160 Asn Gln Ile Ala Thr His Tyr Lys Asp Tyr Pro Asp Asn Leu Val Phe 165 170 175 Glu Ile Leu Asn Glu Pro His Asp Asn Leu Thr Pro Ser Ile Trp Asn 180 185 190 Ser Tyr Leu Arg Asp Ala Ile Gly Met Ile Arg Gln Thr Asn Pro Arg 195 200 205 Arg Val Ile Ala Ile Gly Thr Ala Asn Trp Gly Gly Phe Gly Ala Leu 210 215 220 Ser Gln Leu Glu Ile Pro Ser Asn Asp Arg Gln Ile Ile Ala Thr Val 225 230 235 240 His Tyr Tyr Glu Pro Phe Arg Phe Thr His Gln Gly Ala Glu Trp Ala 245 250 255 Gly Pro Glu Thr Asn Asp Trp Leu Gly Thr Arg Trp Asp Gly Ser Asp 260 265 270 Glu Glu Lys Phe Asp Ile Glu Ser Gly Phe Asp Ala Val Gln Ser Trp 275 280 285 Ala Val Thr Asn Asn Arg Pro Val His Leu Gly Glu Phe Gly Ala Tyr 290 295 300 Ser Thr Ala Asp Asn Glu Ser Arg Glu Arg Trp Thr Thr Phe Val Arg 305 310 315 320 Glu Ser Ala Glu Gln Arg Asn Phe Ser Trp Ala Tyr Trp Glu Phe Ala 325 330 335 Ala Gly Phe Gly Ile Tyr Asp Arg Asn Gln Trp Gln Trp Arg Asp Tyr 340 345 350 Leu Leu Arg Ala Leu Ile Pro Asp Ser Pro Val Leu Leu Glu 355 360 365 1031101DNAUnknownObtained from environmental sample 103atgctgataa ttggaggcct tcttgtttta ctgggatttt cttcttgcgg gcggcaggca 60gaacctgctg ctgactcttt cagggggttt catgactttg acatcaggcg tggggtgaac 120atcagccact ggttgtcgca gagtggaagg cgtggtgctg atcgggaggc gttctttacc 180agggcggatg tggaggccat cgccggcttc ggttatgatc acattcgttt gcccattgat 240gaggagcaga tgtgggatga gtcgggcaac aaggaaccac gtgcctttga attgctgcat 300gaagccattg gctgggcttt ggacaatgag ctcagggtca ttgtcgacct gcacatcatc 360aggtcgcact attttaatgc gcctgagaac ccgctttgga ccgatcgtgc tgaacagttg 420aaatttgttg agatgtggcg acagttgtct gatgagctgc agggctatcc gctcgatagg 480gtggcctatg aattgatgaa tgaggccgtg gctgatgatc cggacgattg gaaccggctt 540gtggctgaga cgatggaggc gctacggatg ctggaaccgg agcgcaagat tgtcattggc 600tccaaccgct ggcagtctgt gcatacattt cctgacctgg tgatcccgga taatgacccg 660catatcatat tgagttttca cttctacgaa ccatttctgc tgacgcacca caaggcctcc 720tggacacaca tccgtgatta caccggtccg gtgaactatc cgggtttgac tgtagacccg 780acccacctgg aggggttgtc tgaagaactg gtgacccgga ttggccatca caatggggtg 840tatacaaaag aaacgatgga ggagatgatc atgatcccac tgcaatatgc caaagaccgg 900gggctccccc tttattgtgg agagtgggga tgtttcccga ccatgcccca ggagatgcgc 960ctgcaatggt acgccgatgt gcgtgcgatc ctggaaaagc atgagattgc ctgggcaaac 1020tgggattaca agggtggttt cggtgtggtt gaccgcaacg gcgaacccca ccatgattta 1080ttggaagtgc tcttaaaata a 1101104366PRTUnknownObtained from environmental sample 104Met Leu Ile Ile Gly Gly Leu Leu Val Leu Leu Gly Phe Ser Ser Cys 1 5 10 15 Gly Arg Gln Ala Glu Pro Ala Ala Asp Ser Phe Arg Gly Phe His Asp 20 25 30 Phe Asp Ile Arg Arg Gly Val Asn Ile Ser His Trp Leu Ser Gln Ser 35 40 45 Gly Arg Arg Gly Ala Asp Arg Glu Ala Phe Phe Thr Arg Ala Asp Val 50 55 60 Glu Ala Ile Ala Gly Phe Gly Tyr Asp His Ile Arg Leu Pro Ile Asp 65 70 75 80 Glu Glu Gln Met Trp Asp Glu Ser Gly Asn Lys Glu Pro Arg Ala Phe 85 90 95 Glu Leu Leu His Glu Ala Ile Gly Trp Ala Leu Asp Asn Glu Leu Arg 100 105 110 Val Ile Val Asp Leu His Ile Ile Arg Ser His Tyr Phe Asn Ala Pro 115 120 125 Glu Asn Pro Leu Trp Thr Asp Arg Ala Glu Gln Leu Lys Phe Val Glu 130 135 140 Met Trp Arg Gln Leu Ser Asp Glu Leu Gln Gly Tyr Pro Leu Asp Arg 145 150 155 160 Val Ala Tyr Glu Leu Met Asn Glu Ala Val Ala Asp Asp Pro Asp Asp 165 170 175 Trp Asn Arg Leu Val Ala Glu Thr Met Glu Ala Leu Arg Met Leu Glu 180 185 190 Pro Glu Arg Lys Ile Val Ile Gly Ser Asn Arg Trp Gln Ser Val His 195 200 205 Thr Phe Pro Asp Leu Val Ile Pro Asp Asn Asp Pro His Ile Ile Leu 210 215 220 Ser Phe His Phe Tyr Glu Pro Phe Leu Leu Thr His His Lys Ala Ser 225 230 235 240 Trp Thr His Ile Arg Asp Tyr Thr Gly Pro Val Asn Tyr Pro Gly Leu 245 250 255 Thr Val Asp Pro Thr His Leu Glu Gly Leu Ser Glu Glu Leu Val Thr 260 265 270 Arg Ile Gly His His Asn Gly Val Tyr Thr Lys Glu Thr Met Glu Glu 275 280 285 Met Ile Met Ile Pro Leu Gln Tyr Ala Lys Asp Arg Gly Leu Pro Leu 290 295 300 Tyr Cys Gly Glu Trp Gly Cys Phe Pro Thr Met Pro Gln Glu Met Arg 305 310 315 320 Leu Gln Trp Tyr Ala Asp Val Arg Ala Ile Leu Glu Lys His Glu Ile 325 330 335 Ala Trp Ala Asn Trp Asp Tyr Lys Gly Gly Phe Gly Val Val Asp Arg 340 345 350 Asn Gly Glu Pro His His Asp Leu Leu Glu Val Leu Leu Lys 355 360 365 1051047DNAUnknownObtained from environmental sample 105atgcaacact tcatcaacgg cgtcaacctg ggaggctggc tctcccaata ccagaaatac 60gaccatgagc acttccgcac cttcatcacc cggcgcgata tcgaacaaat cgcatcctgg 120ggcttcgacc acatccgcct gccggtcgat tatccggttc tcgaatcgga cgacgcgccc 180ggtatctatc atgaagatgg ctttgcctat cttgactctt gcctggaatg gtgccaggcc 240gctgggctgg cagtcgtctt cgacctgcat catgcccccg gctacagttt cacgaacacg 300ctcaagcctg aaaccctgca cctgaacgta ctcttcgagc aggaaatcgc ccaaaatcga 360tttatcgccc tctgggaaac cattgttcgg cgctaccagg ccgccggctt gcctatcatc 420tttgaactac tgaatgaaat ggtgctgcca gacagcggcc cctggaacgc cctggcccac 480aaaaccgtcg ccgccctgcg acagatttcg cccgattgca aaatcatgat tggcggcaat 540aactacaacg ccgcatccga actcaaaaac ataaccctgc acaacgaccc caacatccta 600tacaccttcc atttctacga accggccctg ttcacccacc agaaagcccc ctgggtgcag 660attgctgtcg aatacaacca ggaactcgaa taccctggct cgtacaccaa cctggccgcc 720tttctccggc gcaatcccca ctatcaagaa tcctatggat ggcaggtcaa ccgccgtatc 780gaccgcgacc tcctgctcga attcacccaa cccgccctgg actttgtcca gcagaccggg 840cgcgacctgt actgcggtga attcggcgtc attgaatacg tcgagcctgc cagccgccaa 900aactggcacg ccgacctgct ggacatcctg cgccagcaga agattggccg cgccgtctgg 960acttataaac aaatggattt tggcctggtg gacgcggacg gcaaggtggt cgaccccaaa 1020cttctcgaaa tcttgtgtca atcctga 1047106348PRTUnknownObtained from environmental sample 106Met Gln His Phe Ile Asn Gly Val Asn Leu Gly Gly Trp Leu Ser Gln 1 5 10 15 Tyr Gln Lys Tyr Asp His Glu His Phe Arg Thr Phe Ile Thr Arg Arg 20 25 30 Asp Ile Glu Gln Ile Ala Ser Trp Gly Phe Asp His Ile Arg Leu Pro 35 40 45 Val Asp Tyr Pro Val Leu Glu Ser Asp Asp Ala Pro Gly Ile Tyr His 50 55 60 Glu Asp Gly Phe Ala Tyr Leu Asp Ser Cys Leu Glu Trp Cys Gln Ala 65 70 75 80 Ala Gly Leu Ala Val Val Phe Asp Leu His His Ala Pro Gly Tyr Ser 85 90 95 Phe Thr Asn Thr Leu Lys Pro Glu Thr Leu His Leu Asn Val Leu Phe 100 105 110 Glu Gln Glu Ile Ala Gln Asn Arg Phe Ile Ala Leu Trp Glu Thr Ile 115 120 125 Val Arg Arg Tyr Gln Ala Ala Gly Leu Pro Ile Ile Phe Glu Leu Leu 130 135 140 Asn Glu Met Val Leu Pro Asp Ser Gly Pro Trp Asn Ala Leu Ala His 145 150 155 160 Lys Thr Val Ala Ala Leu Arg Gln Ile Ser Pro Asp Cys Lys Ile Met 165 170 175 Ile Gly Gly Asn Asn Tyr Asn Ala Ala Ser Glu Leu Lys Asn Ile Thr 180 185 190 Leu His Asn Asp Pro Asn Ile Leu Tyr Thr Phe His Phe Tyr Glu Pro 195 200 205 Ala Leu Phe Thr His Gln Lys Ala Pro Trp Val Gln Ile Ala Val Glu 210 215 220 Tyr Asn Gln Glu Leu Glu Tyr Pro Gly Ser Tyr Thr Asn Leu Ala Ala 225 230 235 240 Phe Leu Arg Arg Asn Pro His Tyr Gln Glu Ser Tyr Gly Trp Gln Val 245 250 255 Asn Arg Arg Ile Asp Arg Asp Leu Leu Leu Glu Phe Thr Gln Pro Ala 260 265 270 Leu Asp Phe Val Gln Gln Thr Gly Arg Asp Leu Tyr Cys Gly Glu Phe 275 280 285 Gly Val Ile Glu Tyr Val Glu Pro Ala Ser Arg Gln Asn Trp His Ala 290 295 300 Asp Leu Leu Asp Ile Leu Arg Gln Gln Lys Ile Gly Arg Ala Val Trp 305 310 315 320 Thr Tyr Lys Gln Met Asp Phe Gly Leu Val Asp Ala Asp Gly Lys Val 325 330 335 Val Asp Pro Lys Leu Leu Glu Ile Leu Cys Gln Ser 340 345 1071137DNAUnknownObtained from environmental sample 107atggaaaagc aaatctgttc aaatgttttc agtacgatgc tgataattgg aggccttctt 60gttttactgg gattttcttc ttgcgggcgg caggcagaac ctgctgctga ctctttcagg 120gggtttcacg actttgacat caggcgcggg gtgaacatca gccattggtt gtcgcagagt 180ggaaggcgtg gtgctgatcg ggaggcgttc tttaccaggg cggatgtgga ggccatcgcc 240ggcttcggtt atgatcacat tcgtttgccc atcgatgaag agcagatgtg ggatgagtcg 300ggcaacaagg agccacgtgc ctttgaattg ctgcatgagg ccattggctg ggctttggac 360aatgagctca gggtcattgt tgacctgcac atcatcaggt cgcactattt taatgcgcct 420gagaacccgc tttggaccga tcgtgctgaa cagttgaaat ttgttgagat gtggcgacag 480ttgtctgatg agctgcaggg ctatccgctc gatagggtgg cctatgaatt gatgaatgag 540gccgtggctg atgatccgga cgattggaac cggcttgtgg ctgagacgat ggaggcgcta 600cggatgctgg aaccggagcg caagattgtc attggctcca accgctggca gtctgtgcat 660acatttcctg acctggtgat cccggataat gacccgcata tcatattgag ttttcacttc 720tacgaaccat ttctgctgac gcaccacaag gcctcctgga cacacatccg tgattacacc 780ggtccggtga actatccggg tttgactgta gacccgaccc acctggaggg gttgtctgaa 840gaactggtga cccggattgg ccatcacaat ggggtgtata caaaagaaac gatggaggag 900atgatcatga tcccactgca atatgccaaa gaacgggggc tccccctgta ttgcggggag 960tggggatgtt tcccgaccat gccccaggag atgcgcctgc aatggtacgc cgatgtgcgt 1020gcgatcctgg aaaagcatga gattgcctgg gcaaactggg attacaaggg tggtttcggt 1080gtggttgacc gcaacggcga accccaccat gatttattgg aagtcttact aaaataa 1137108378PRTUnknownObtained from environmental sample 108Met Glu Lys Gln Ile Cys Ser Asn Val Phe Ser Thr Met Leu Ile Ile 1 5 10 15 Gly Gly Leu Leu Val Leu Leu Gly Phe Ser Ser Cys Gly Arg Gln Ala 20 25 30 Glu Pro Ala Ala Asp Ser Phe Arg Gly Phe His Asp Phe Asp Ile Arg 35 40 45 Arg Gly Val Asn Ile Ser His Trp Leu Ser Gln Ser Gly Arg Arg Gly 50 55 60 Ala Asp Arg Glu Ala Phe Phe Thr Arg Ala Asp Val Glu Ala Ile Ala 65 70 75 80 Gly Phe Gly Tyr Asp His Ile Arg Leu Pro Ile Asp Glu Glu Gln Met 85 90 95 Trp Asp Glu Ser Gly Asn Lys Glu Pro Arg Ala Phe Glu Leu Leu His 100 105 110 Glu Ala Ile Gly Trp Ala Leu Asp Asn Glu Leu Arg Val Ile Val Asp 115 120 125 Leu His Ile Ile Arg Ser His Tyr Phe Asn Ala Pro Glu Asn Pro Leu 130 135 140 Trp Thr Asp Arg Ala Glu Gln Leu Lys Phe Val Glu Met Trp Arg Gln 145 150 155 160 Leu Ser Asp Glu Leu Gln Gly Tyr Pro Leu Asp Arg Val Ala Tyr Glu 165 170 175 Leu Met Asn Glu Ala Val Ala Asp Asp Pro Asp Asp Trp Asn Arg Leu 180 185 190 Val Ala Glu Thr Met Glu Ala Leu Arg Met Leu Glu Pro Glu Arg Lys 195 200 205 Ile Val Ile Gly Ser Asn Arg Trp Gln Ser Val His Thr Phe Pro Asp 210 215 220 Leu Val Ile Pro Asp Asn Asp Pro His Ile Ile Leu Ser Phe His Phe 225 230 235 240 Tyr Glu Pro Phe Leu Leu Thr His His Lys Ala Ser Trp Thr His Ile 245 250 255 Arg Asp Tyr Thr Gly Pro Val Asn Tyr Pro Gly Leu Thr Val Asp Pro 260 265 270 Thr His Leu Glu Gly Leu Ser Glu Glu Leu Val Thr Arg Ile Gly His 275 280 285 His Asn Gly Val Tyr Thr Lys Glu Thr Met Glu Glu Met Ile Met Ile 290 295 300 Pro Leu Gln Tyr Ala Lys Glu Arg Gly Leu Pro Leu Tyr Cys Gly Glu 305 310 315 320 Trp Gly Cys Phe Pro Thr Met Pro Gln Glu Met Arg Leu Gln Trp Tyr 325 330 335 Ala Asp Val Arg Ala Ile Leu Glu Lys His Glu Ile Ala Trp Ala Asn 340 345 350 Trp Asp Tyr Lys Gly Gly Phe Gly Val Val Asp Arg Asn Gly Glu Pro 355 360 365 His His Asp Leu Leu Glu Val Leu Leu Lys 370 375 1091248DNAUnknownObtained from environmental sample 109atgaagacac atagcttcaa cctcagatca cggatcacct tgttgaccgc ggcactgctt 60ttcatcgggg caacggccgg ggccgccacg acacctatca ccctcaaaga cgcctacaaa 120gaccatttcc ttatgggtgt agccatcaac cgcctgattg caatgggcga tacgaatgtc 180cgggccgaca

acgccagccg gaccccggaa cagctcaagg gggacattgc cctggtcaag 240gcgcagttca acctgatcgt caatgagaac gatctgaaac cgattctcat tcacccgagg 300ccaggaccgg acgggtacga cttcgcccca gcggatgcct tcgtgaagtt cggcatggac 360aacaatatgt atatcgtggg ccacaccctc ctctggcaca gccaggtgcc caactggttc 420ttccaagggt ctgctccggc gactccggaa acgccacctg ctgccacgga cgcggcggtc 480gcaccccgcg gcggacgagg aggtcgcggc gggattaccg gccccctggc gacccgcgag 540gagttgatcg aacgcatgcg cgagcacatt cacaccgtcg tcggccgcta taagggaaag 600atcaaggtct gggacgtcgt caacgaagcc ctcgccgacg gcggcaccga gaccctgcga 660agcacgtact ggacccaaat catcgggccg gaattcatcg ccatggcctt tcgattcgcc 720cacgaagccg atccggatgc gatccttcgt tacaacgatt atggcctgga gaaccctgcc 780aagcgtgaga aactcaagaa gctgatcgcg tcgctccagg agcagaacgt tccggttcat 840gccatcggca cgcaaaccca tatcagcgtc tccacgacgt tcgaaagaat ggatgagacc 900ttgagggacc tggcatccat cgggcttccc gtccacatca ccgaactgga tgtcaacgcc 960gccgcggggg gccagagggg caccaatgcg gacattgccg gcactgccga gcgtacggcg 1020ggcggcgtgg tcagtgaagc cgacaagcgg ctggccgacg cctacgcgaa tctcttccgc 1080gcgatcatga agcacaagga ctcggtgaag atggtcacgt tctggggcgt caatgacgcg 1140gtttcgtggc tcgcacgcgg caccccgctg ctgttcgacg gcaacaatca gcccaagccg 1200gctttcgatg cggtcattcg cgtcgccacg gaggcggcac agaactga 1248110415PRTUnknownObtained from environmental sample 110Met Lys Thr His Ser Phe Asn Leu Arg Ser Arg Ile Thr Leu Leu Thr 1 5 10 15 Ala Ala Leu Leu Phe Ile Gly Ala Thr Ala Gly Ala Ala Thr Thr Pro 20 25 30 Ile Thr Leu Lys Asp Ala Tyr Lys Asp His Phe Leu Met Gly Val Ala 35 40 45 Ile Asn Arg Leu Ile Ala Met Gly Asp Thr Asn Val Arg Ala Asp Asn 50 55 60 Ala Ser Arg Thr Pro Glu Gln Leu Lys Gly Asp Ile Ala Leu Val Lys 65 70 75 80 Ala Gln Phe Asn Leu Ile Val Asn Glu Asn Asp Leu Lys Pro Ile Leu 85 90 95 Ile His Pro Arg Pro Gly Pro Asp Gly Tyr Asp Phe Ala Pro Ala Asp 100 105 110 Ala Phe Val Lys Phe Gly Met Asp Asn Asn Met Tyr Ile Val Gly His 115 120 125 Thr Leu Leu Trp His Ser Gln Val Pro Asn Trp Phe Phe Gln Gly Ser 130 135 140 Ala Pro Ala Thr Pro Glu Thr Pro Pro Ala Ala Thr Asp Ala Ala Val 145 150 155 160 Ala Pro Arg Gly Gly Arg Gly Gly Arg Gly Gly Ile Thr Gly Pro Leu 165 170 175 Ala Thr Arg Glu Glu Leu Ile Glu Arg Met Arg Glu His Ile His Thr 180 185 190 Val Val Gly Arg Tyr Lys Gly Lys Ile Lys Val Trp Asp Val Val Asn 195 200 205 Glu Ala Leu Ala Asp Gly Gly Thr Glu Thr Leu Arg Ser Thr Tyr Trp 210 215 220 Thr Gln Ile Ile Gly Pro Glu Phe Ile Ala Met Ala Phe Arg Phe Ala 225 230 235 240 His Glu Ala Asp Pro Asp Ala Ile Leu Arg Tyr Asn Asp Tyr Gly Leu 245 250 255 Glu Asn Pro Ala Lys Arg Glu Lys Leu Lys Lys Leu Ile Ala Ser Leu 260 265 270 Gln Glu Gln Asn Val Pro Val His Ala Ile Gly Thr Gln Thr His Ile 275 280 285 Ser Val Ser Thr Thr Phe Glu Arg Met Asp Glu Thr Leu Arg Asp Leu 290 295 300 Ala Ser Ile Gly Leu Pro Val His Ile Thr Glu Leu Asp Val Asn Ala 305 310 315 320 Ala Ala Gly Gly Gln Arg Gly Thr Asn Ala Asp Ile Ala Gly Thr Ala 325 330 335 Glu Arg Thr Ala Gly Gly Val Val Ser Glu Ala Asp Lys Arg Leu Ala 340 345 350 Asp Ala Tyr Ala Asn Leu Phe Arg Ala Ile Met Lys His Lys Asp Ser 355 360 365 Val Lys Met Val Thr Phe Trp Gly Val Asn Asp Ala Val Ser Trp Leu 370 375 380 Ala Arg Gly Thr Pro Leu Leu Phe Asp Gly Asn Asn Gln Pro Lys Pro 385 390 395 400 Ala Phe Asp Ala Val Ile Arg Val Ala Thr Glu Ala Ala Gln Asn 405 410 415 1111131DNAUnknownObtained from environmental sample 111atgcgaagac tgatcaccat catccttgcg acggctgtcg caatcttatc gaccacatca 60tgctccaaga ccgctgaacg agagggcttc ttgatcaagc gaggaaccaa cctcagccat 120tggctctccc agagcaagga aaggggagag gctcgcaggc tccatatcca ggaggatgac 180tttgctcgcc tcgacagcct cggtttcgac catgtgcgca tccctgtcga cgaggaacaa 240ctctgggacg aggatggcaa caagctcaca gaagcatggg aactgctcga tttcgccctc 300gacatggcgc gcaagtacaa cctgcgcgct atcgtggacc ttcacatcat ccgcgcccat 360tacttcaacg ccgtcaacga aggcgcgtcg aatactctct tcaccagcga ggaggcgcag 420cagggcctga tcaacctttg gtaccagctt tccgacttcc tcaaggaccg cagcgtcgac 480tgggttgcct acgagttcat gaacgagcca gtcgctcctg agcatgagca atggaacgcc 540ctcgtcgcaa aggtgcacaa ggcgcttcgt gagcgtgaac cggagcgtac cctcgtgatc 600ggttctaacc tgtggcaggg tcaccagacc ttcaagtacc tccgcgtacc tgagaatgac 660ccgaacatca tcctgagctt ccactactac aacccttcga tcctcaccca caacatggct 720ccgtggactc cggtgggcaa atataccggt tccatcaatt atccgggcgt catcgtctct 780gctgaggatt acgctgcgca gagccctgag gtgcaggccg aggtgaagca gtatacggag 840atggtctgga accgcgacac gatctacagc cagatgaagg atgcgatcga ggtggctgcc 900agctatggac tgcagctctt ctgcggcgaa tggggcgtgt atgaacctgt cgaccgtgag 960cttgcatacg catggaccaa ggatatgctg tcggtgttcg acgagttcga catcgcatgg 1020acgacctggt gttacgatgc cgacttcggc ttctgggacc aggcgaaaca tgatttcaag 1080gacaagcctc ttgtcgatct cctgatgggt tccaagggtc ttgaacaata g 1131112376PRTUnknownObtained from environmental sample 112Met Arg Arg Leu Ile Thr Ile Ile Leu Ala Thr Ala Val Ala Ile Leu 1 5 10 15 Ser Thr Thr Ser Cys Ser Lys Thr Ala Glu Arg Glu Gly Phe Leu Ile 20 25 30 Lys Arg Gly Thr Asn Leu Ser His Trp Leu Ser Gln Ser Lys Glu Arg 35 40 45 Gly Glu Ala Arg Arg Leu His Ile Gln Glu Asp Asp Phe Ala Arg Leu 50 55 60 Asp Ser Leu Gly Phe Asp His Val Arg Ile Pro Val Asp Glu Glu Gln 65 70 75 80 Leu Trp Asp Glu Asp Gly Asn Lys Leu Thr Glu Ala Trp Glu Leu Leu 85 90 95 Asp Phe Ala Leu Asp Met Ala Arg Lys Tyr Asn Leu Arg Ala Ile Val 100 105 110 Asp Leu His Ile Ile Arg Ala His Tyr Phe Asn Ala Val Asn Glu Gly 115 120 125 Ala Ser Asn Thr Leu Phe Thr Ser Glu Glu Ala Gln Gln Gly Leu Ile 130 135 140 Asn Leu Trp Tyr Gln Leu Ser Asp Phe Leu Lys Asp Arg Ser Val Asp 145 150 155 160 Trp Val Ala Tyr Glu Phe Met Asn Glu Pro Val Ala Pro Glu His Glu 165 170 175 Gln Trp Asn Ala Leu Val Ala Lys Val His Lys Ala Leu Arg Glu Arg 180 185 190 Glu Pro Glu Arg Thr Leu Val Ile Gly Ser Asn Leu Trp Gln Gly His 195 200 205 Gln Thr Phe Lys Tyr Leu Arg Val Pro Glu Asn Asp Pro Asn Ile Ile 210 215 220 Leu Ser Phe His Tyr Tyr Asn Pro Ser Ile Leu Thr His Asn Met Ala 225 230 235 240 Pro Trp Thr Pro Val Gly Lys Tyr Thr Gly Ser Ile Asn Tyr Pro Gly 245 250 255 Val Ile Val Ser Ala Glu Asp Tyr Ala Ala Gln Ser Pro Glu Val Gln 260 265 270 Ala Glu Val Lys Gln Tyr Thr Glu Met Val Trp Asn Arg Asp Thr Ile 275 280 285 Tyr Ser Gln Met Lys Asp Ala Ile Glu Val Ala Ala Ser Tyr Gly Leu 290 295 300 Gln Leu Phe Cys Gly Glu Trp Gly Val Tyr Glu Pro Val Asp Arg Glu 305 310 315 320 Leu Ala Tyr Ala Trp Thr Lys Asp Met Leu Ser Val Phe Asp Glu Phe 325 330 335 Asp Ile Ala Trp Thr Thr Trp Cys Tyr Asp Ala Asp Phe Gly Phe Trp 340 345 350 Asp Gln Ala Lys His Asp Phe Lys Asp Lys Pro Leu Val Asp Leu Leu 355 360 365 Met Gly Ser Lys Gly Leu Glu Gln 370 375 1131095DNAUnknownObtained from environmental sample 113atgaaggtga cccgaacagc tgtcgcgggc attgtcgccg cagcggtcct catcacgatc 60ggcacgtcga ccgcgtcggc tgaggatgaa ccaaccagcg agaacacgtc gacggatcag 120ccgttgcgcg tcctggcagc caaagccggg atcgcgttcg gcacggccgt cgacatgaac 180gcgtacaaca acgacgcgac ctaccgtgag ctcgtcggcc aggagttctc gagcgtcacg 240gccgagaacg tcatgaagtg gcagctcctc gagccgcagc gaggggtcta caactggggt 300ccggccgatc agctcgtgcg cgtagccaac gagaacggcc agaaggtgcg cgggcacacg 360ctcatctggc acaaccagct gcccacctgg cttaccagcg gagtcgcctc cggtgagatc 420acaccggacg agctccggca gctcctgagg aaccacatct tcacggtgat gcgccacttc 480aagggcgaga tccaccagtg ggatgtcgcc aacgaggtca tcgacgacag cggcaacctg 540cgcaacacga tctggctgca gaacctgggt ccgagctaca tcgcggacgc gttccggtgg 600gctcgcaagg ccgacccgga cgccgccctc tatctgaacg actacaacgt cgagggcccg 660aacgccaagg ccgatgcgta ctacgccctg gtcaagcagc tcctcgccga cgacgtgccg 720gtggacggct tcggaataca ggggcacctc ggtgtgcagt tcggcttctg gcccgcgagt 780gcggtggccg acaacatggg gcgcttcgag gcactcggcc tgcagacggc ggtcaccgag 840gcggatgtcc ggatgatcat gccgcccgac gaggacaagc tggccgcaca ggcacgtggc 900tacagcacgt tggtccaggg ctgcctgatg gccaagcgtt gcaggtcgtt caccgtctgg 960ggcttcaccg acaagtactc ctgggttccg ggcaccttcc ccggccaggg cgcggcgaac 1020ctcctggccg aggacttcca gcccaagccg gcttactacg ccgtccagga tgacctcgcg 1080cgcgccggac ggtag 1095114364PRTUnknownObtained from environmental sample 114Met Lys Val Thr Arg Thr Ala Val Ala Gly Ile Val Ala Ala Ala Val 1 5 10 15 Leu Ile Thr Ile Gly Thr Ser Thr Ala Ser Ala Glu Asp Glu Pro Thr 20 25 30 Ser Glu Asn Thr Ser Thr Asp Gln Pro Leu Arg Val Leu Ala Ala Lys 35 40 45 Ala Gly Ile Ala Phe Gly Thr Ala Val Asp Met Asn Ala Tyr Asn Asn 50 55 60 Asp Ala Thr Tyr Arg Glu Leu Val Gly Gln Glu Phe Ser Ser Val Thr 65 70 75 80 Ala Glu Asn Val Met Lys Trp Gln Leu Leu Glu Pro Gln Arg Gly Val 85 90 95 Tyr Asn Trp Gly Pro Ala Asp Gln Leu Val Arg Val Ala Asn Glu Asn 100 105 110 Gly Gln Lys Val Arg Gly His Thr Leu Ile Trp His Asn Gln Leu Pro 115 120 125 Thr Trp Leu Thr Ser Gly Val Ala Ser Gly Glu Ile Thr Pro Asp Glu 130 135 140 Leu Arg Gln Leu Leu Arg Asn His Ile Phe Thr Val Met Arg His Phe 145 150 155 160 Lys Gly Glu Ile His Gln Trp Asp Val Ala Asn Glu Val Ile Asp Asp 165 170 175 Ser Gly Asn Leu Arg Asn Thr Ile Trp Leu Gln Asn Leu Gly Pro Ser 180 185 190 Tyr Ile Ala Asp Ala Phe Arg Trp Ala Arg Lys Ala Asp Pro Asp Ala 195 200 205 Ala Leu Tyr Leu Asn Asp Tyr Asn Val Glu Gly Pro Asn Ala Lys Ala 210 215 220 Asp Ala Tyr Tyr Ala Leu Val Lys Gln Leu Leu Ala Asp Asp Val Pro 225 230 235 240 Val Asp Gly Phe Gly Ile Gln Gly His Leu Gly Val Gln Phe Gly Phe 245 250 255 Trp Pro Ala Ser Ala Val Ala Asp Asn Met Gly Arg Phe Glu Ala Leu 260 265 270 Gly Leu Gln Thr Ala Val Thr Glu Ala Asp Val Arg Met Ile Met Pro 275 280 285 Pro Asp Glu Asp Lys Leu Ala Ala Gln Ala Arg Gly Tyr Ser Thr Leu 290 295 300 Val Gln Gly Cys Leu Met Ala Lys Arg Cys Arg Ser Phe Thr Val Trp 305 310 315 320 Gly Phe Thr Asp Lys Tyr Ser Trp Val Pro Gly Thr Phe Pro Gly Gln 325 330 335 Gly Ala Ala Asn Leu Leu Ala Glu Asp Phe Gln Pro Lys Pro Ala Tyr 340 345 350 Tyr Ala Val Gln Asp Asp Leu Ala Arg Ala Gly Arg 355 360 115774DNAUnknownObtained from environmental sample 115atggacttgc agctaggcgg aaagcgcgtg ctgatcacgg gtgcgtccaa aggcatcggc 60ctggcctgcg ccgtcgcctt tgcgcgcgag ggtgccgacc cgattctggt ggcgcgcgat 120gatgcggcgt tgcatcacgc cacgtccgcc atccgcgaac aaagcggccg cgcggcacat 180gccatcacgc tggacctggc cctgcctggc gcggcggaaa agctggccaa ggaaaccggc 240cccatcgaca tactggtcaa caacgcgggc gcggtgcccg gcggcgcgct ggaccaggtg 300caagacgaac gctggcgcgc gggctgggaa ttgaaagtgc acggctacat cagcctggcg 360cgctgctact acccgcacat gcgcgaagcg ggcgcgggcg tcatcgccaa catcatcggc 420atggcgggcg cggcgccccg cgccgactac atctgcggcg cggcggccaa tgcctcactg 480attgccttta cccgcgcgct gggtggcgaa gcgccccgcc acggcgtgcg cgtctttggc 540gtcaacccct cgcgcacgcg gaccgaccgc gtgctgaccc tggcccggca acgcgcgcag 600gcgcgctggg gcgacgaaac ccgttggcag gaaacgctgt cggacctgcc cttcaaccgg 660ctgatggaac ccgccgaagt ggccgacatg attgtgttcg gcgcctcgcc gcgcgcgggt 720tacctgagcg gcacggtcat cgacctggac ggcggcgaac agtacgcgaa atag 774116257PRTUnknownObtained from environmental sample 116Met Asp Leu Gln Leu Gly Gly Lys Arg Val Leu Ile Thr Gly Ala Ser 1 5 10 15 Lys Gly Ile Gly Leu Ala Cys Ala Val Ala Phe Ala Arg Glu Gly Ala 20 25 30 Asp Pro Ile Leu Val Ala Arg Asp Asp Ala Ala Leu His His Ala Thr 35 40 45 Ser Ala Ile Arg Glu Gln Ser Gly Arg Ala Ala His Ala Ile Thr Leu 50 55 60 Asp Leu Ala Leu Pro Gly Ala Ala Glu Lys Leu Ala Lys Glu Thr Gly 65 70 75 80 Pro Ile Asp Ile Leu Val Asn Asn Ala Gly Ala Val Pro Gly Gly Ala 85 90 95 Leu Asp Gln Val Gln Asp Glu Arg Trp Arg Ala Gly Trp Glu Leu Lys 100 105 110 Val His Gly Tyr Ile Ser Leu Ala Arg Cys Tyr Tyr Pro His Met Arg 115 120 125 Glu Ala Gly Ala Gly Val Ile Ala Asn Ile Ile Gly Met Ala Gly Ala 130 135 140 Ala Pro Arg Ala Asp Tyr Ile Cys Gly Ala Ala Ala Asn Ala Ser Leu 145 150 155 160 Ile Ala Phe Thr Arg Ala Leu Gly Gly Glu Ala Pro Arg His Gly Val 165 170 175 Arg Val Phe Gly Val Asn Pro Ser Arg Thr Arg Thr Asp Arg Val Leu 180 185 190 Thr Leu Ala Arg Gln Arg Ala Gln Ala Arg Trp Gly Asp Glu Thr Arg 195 200 205 Trp Gln Glu Thr Leu Ser Asp Leu Pro Phe Asn Arg Leu Met Glu Pro 210 215 220 Ala Glu Val Ala Asp Met Ile Val Phe Gly Ala Ser Pro Arg Ala Gly 225 230 235 240 Tyr Leu Ser Gly Thr Val Ile Asp Leu Asp Gly Gly Glu Gln Tyr Ala 245 250 255 Lys 117747DNAUnknownObtained from environmental sample 117atgcccaaag tcatgctcgt taccggcggc agccgtggca tcggcgccgc cgtcgccaag 60ctggccgcgc gccgcggcta cgcggtcggc atcaactacc gcacccattc cgacgccgcc 120gacgccgtcg tggccgagat ccagcaggcg ggcggcaccg cgctggccat ccaggccgac 180gtgtcgcaag aagatgacgt gctgcacatg ttccgcacgc tggacgagcg cctgggccgc 240atcgacgcgc tggtcaataa cgccggcatc ctggaaacgc agatgcgcct ggaccagatg 300gaagcggacc gcctgctgcg cgtgctgtcc accaacgtca tcggcgcttt cctgtgtgcg 360cgcgaagcgg tgcgcaggat gtcgacgcgc catggcggcg tgggcggcgc catcgtcaac 420gtgtcttcgg cggcggcgcg cctgggctcg cccaatgaat acgtggatta cgcggcctcc 480aagggcgcgc tggacacgat gaccatcggc ctgtccaaag aggtagcgcc cgaaggtatc 540cgcgtgaatg gcgtgcgccc cggcaccatc tacaccgaca tgcacgcaag cggcggcgag 600ccgggccggg tggatcgcct gaaaagcgtg atcccgctgc ggcgcggcgg ctcggtggaa 660gaagtggcgg gcgccgtcat gtggctgttt tccgaagaag ccggctatac cagcggctcg 720ttcatcgacg tgtccggcgg tagttga 747118248PRTUnknownObtained from environmental sample 118Met Pro Lys Val Met Leu Val Thr Gly Gly Ser Arg Gly Ile Gly Ala 1 5 10 15 Ala Val Ala Lys Leu Ala Ala Arg Arg Gly Tyr Ala Val Gly Ile Asn 20 25 30 Tyr Arg Thr His Ser Asp Ala Ala Asp Ala Val Val Ala Glu Ile Gln 35 40 45 Gln Ala Gly Gly Thr Ala Leu Ala Ile Gln Ala Asp Val Ser Gln Glu 50 55 60 Asp Asp Val Leu His Met Phe Arg Thr Leu Asp Glu Arg Leu Gly Arg 65

70 75 80 Ile Asp Ala Leu Val Asn Asn Ala Gly Ile Leu Glu Thr Gln Met Arg 85 90 95 Leu Asp Gln Met Glu Ala Asp Arg Leu Leu Arg Val Leu Ser Thr Asn 100 105 110 Val Ile Gly Ala Phe Leu Cys Ala Arg Glu Ala Val Arg Arg Met Ser 115 120 125 Thr Arg His Gly Gly Val Gly Gly Ala Ile Val Asn Val Ser Ser Ala 130 135 140 Ala Ala Arg Leu Gly Ser Pro Asn Glu Tyr Val Asp Tyr Ala Ala Ser 145 150 155 160 Lys Gly Ala Leu Asp Thr Met Thr Ile Gly Leu Ser Lys Glu Val Ala 165 170 175 Pro Glu Gly Ile Arg Val Asn Gly Val Arg Pro Gly Thr Ile Tyr Thr 180 185 190 Asp Met His Ala Ser Gly Gly Glu Pro Gly Arg Val Asp Arg Leu Lys 195 200 205 Ser Val Ile Pro Leu Arg Arg Gly Gly Ser Val Glu Glu Val Ala Gly 210 215 220 Ala Val Met Trp Leu Phe Ser Glu Glu Ala Gly Tyr Thr Ser Gly Ser 225 230 235 240 Phe Ile Asp Val Ser Gly Gly Ser 245 1191611DNAUnknownObtained from environmental sample 119atgcaaaagc ggtatgacgt cattgtcgtg ggcagcggga tcgccggcct cagttttgcg 60ctaaaagtcg ccaaggcggg gcatcgcgta gggattttga ccaaaaaaga ccgtgctgaa 120agcaacacca attatgccca aggcggcatc gcggcagtca cttcgcagac agatgatttc 180gagctgcatg tgcaggacac attgaccgcg ggagatggac tctgcgacga ggcagtcgtc 240cgcacgatta tcggcgaggc tcccgcccga atccaggagc tgatcgattt gggggtggcc 300ttctcacatt tggaagatgg acgggtttcc ctccatcgcg aagggggtca ctcgaaaagg 360cgcattcttc acgttcagga tgtcaccggc aaagcgattg aagaagccct cctccatgcc 420atcgaacagt cgccgctgat cgacctgaat gagcacgtct ttgccatcga cttactgact 480gaacgcaagc tggcgctggc gggctttgag gtggaaggtg ctaaaaaccg ggtggtcgga 540ctctatgcgc tcgatgaagc cactcaggag gttcacgtat ttgaggctcc agtcgtcatg 600ctggcaacgg gaggcgtcgg gcaggtctac ctctacagca ccaacccaag gatcgcgacc 660ggtgatggat tggccatggc ttaccgggct ggcgccgaaa tccgcaacct cgagtgtatc 720caatttcatc ctacagcgct atacaccacc accaatgacc gctttctgat cagcgaagcc 780gtccggggtg aaggggccat cctccgcaat caggagggag aggctttcat ggctcgctac 840gatgaccgca aggacctcgc cccccgggat attgtggcca gagcaattga cagtgaaatg 900aagcagtccg gctcatccca tgtctggctc gacatcactc atcgggatga aaccgatctg 960cgggagcgtt tccccaacat tttcgaggcc tgcctgaagg tcggagtcaa catggcgcaa 1020tcctccatcc cggtggttcc ggcgatgcac tacctctgcg gaggcgtagc caccgacctc 1080aatgcggcca ccgacatcac tggactgttt gcctgtgggg aagttgcctg cacgggattg 1140catggtgcca accgtctcgc cagcaacagc ctgctggagg cagtggtcat ggcgcaccgg 1200gcctccgtcg cagtggatgc atacctcaac agcaaacctc accgctatgc acaattgccg 1260gaatggacgg atggcaacgt gcaggacagc gacgagcgtg tcgtgatcag ccacaactgg 1320gatgaactca aacgcacgat gtgggactac gtgggcatcg tccgcaccac caagcggctt 1380cagcgcgcgc aacgacgcat tcgtcacctc cagcaggaaa tcgaagagta ttactggaat 1440ttcaaggttg agtcctccct tctggagtta cggaatctgg ttgtggtggc ggatctggtt 1500atccactgtg ccctccaacg ccatgagagc cgtggcctgc attgcacccg ggattatccc 1560ggcaagttgc ccaccccgat caataccgcc gttcgcagaa gaaccggtta a 1611120536PRTUnknownObtained from environmental sample 120Met Gln Lys Arg Tyr Asp Val Ile Val Val Gly Ser Gly Ile Ala Gly 1 5 10 15 Leu Ser Phe Ala Leu Lys Val Ala Lys Ala Gly His Arg Val Gly Ile 20 25 30 Leu Thr Lys Lys Asp Arg Ala Glu Ser Asn Thr Asn Tyr Ala Gln Gly 35 40 45 Gly Ile Ala Ala Val Thr Ser Gln Thr Asp Asp Phe Glu Leu His Val 50 55 60 Gln Asp Thr Leu Thr Ala Gly Asp Gly Leu Cys Asp Glu Ala Val Val 65 70 75 80 Arg Thr Ile Ile Gly Glu Ala Pro Ala Arg Ile Gln Glu Leu Ile Asp 85 90 95 Leu Gly Val Ala Phe Ser His Leu Glu Asp Gly Arg Val Ser Leu His 100 105 110 Arg Glu Gly Gly His Ser Lys Arg Arg Ile Leu His Val Gln Asp Val 115 120 125 Thr Gly Lys Ala Ile Glu Glu Ala Leu Leu His Ala Ile Glu Gln Ser 130 135 140 Pro Leu Ile Asp Leu Asn Glu His Val Phe Ala Ile Asp Leu Leu Thr 145 150 155 160 Glu Arg Lys Leu Ala Leu Ala Gly Phe Glu Val Glu Gly Ala Lys Asn 165 170 175 Arg Val Val Gly Leu Tyr Ala Leu Asp Glu Ala Thr Gln Glu Val His 180 185 190 Val Phe Glu Ala Pro Val Val Met Leu Ala Thr Gly Gly Val Gly Gln 195 200 205 Val Tyr Leu Tyr Ser Thr Asn Pro Arg Ile Ala Thr Gly Asp Gly Leu 210 215 220 Ala Met Ala Tyr Arg Ala Gly Ala Glu Ile Arg Asn Leu Glu Cys Ile 225 230 235 240 Gln Phe His Pro Thr Ala Leu Tyr Thr Thr Thr Asn Asp Arg Phe Leu 245 250 255 Ile Ser Glu Ala Val Arg Gly Glu Gly Ala Ile Leu Arg Asn Gln Glu 260 265 270 Gly Glu Ala Phe Met Ala Arg Tyr Asp Asp Arg Lys Asp Leu Ala Pro 275 280 285 Arg Asp Ile Val Ala Arg Ala Ile Asp Ser Glu Met Lys Gln Ser Gly 290 295 300 Ser Ser His Val Trp Leu Asp Ile Thr His Arg Asp Glu Thr Asp Leu 305 310 315 320 Arg Glu Arg Phe Pro Asn Ile Phe Glu Ala Cys Leu Lys Val Gly Val 325 330 335 Asn Met Ala Gln Ser Ser Ile Pro Val Val Pro Ala Met His Tyr Leu 340 345 350 Cys Gly Gly Val Ala Thr Asp Leu Asn Ala Ala Thr Asp Ile Thr Gly 355 360 365 Leu Phe Ala Cys Gly Glu Val Ala Cys Thr Gly Leu His Gly Ala Asn 370 375 380 Arg Leu Ala Ser Asn Ser Leu Leu Glu Ala Val Val Met Ala His Arg 385 390 395 400 Ala Ser Val Ala Val Asp Ala Tyr Leu Asn Ser Lys Pro His Arg Tyr 405 410 415 Ala Gln Leu Pro Glu Trp Thr Asp Gly Asn Val Gln Asp Ser Asp Glu 420 425 430 Arg Val Val Ile Ser His Asn Trp Asp Glu Leu Lys Arg Thr Met Trp 435 440 445 Asp Tyr Val Gly Ile Val Arg Thr Thr Lys Arg Leu Gln Arg Ala Gln 450 455 460 Arg Arg Ile Arg His Leu Gln Gln Glu Ile Glu Glu Tyr Tyr Trp Asn 465 470 475 480 Phe Lys Val Glu Ser Ser Leu Leu Glu Leu Arg Asn Leu Val Val Val 485 490 495 Ala Asp Leu Val Ile His Cys Ala Leu Gln Arg His Glu Ser Arg Gly 500 505 510 Leu His Cys Thr Arg Asp Tyr Pro Gly Lys Leu Pro Thr Pro Ile Asn 515 520 525 Thr Ala Val Arg Arg Arg Thr Gly 530 535 121990DNAUnknownObtained from environmental sample 121atgccttttg atgccattgg agaaagcttc cgtgccagcc agcaactccc gctgatcaag 60gtcgacggca accgtttcgt gattgcggag accggtgagc cgatcgtctt ccggggcgtc 120tccgcctccg acccggctgc gctactggaa cgcggtcaat ggggtcgccg ttactttgaa 180gagatggcca agtggaatgc caacgttgtg cgcattcctg ttcacccggc agactggcgt 240aatctcggcg aagacatcta tctcgcccta ctcgaccagg cgattgaatg gtcggctgaa 300ctcggcatgc acgtcatcat cgactggcac actatcggca atattctgac cggtatttat 360caccgcgaca tttatgaaac cacccgtgat gagacttacc gtttttggta caccatcgcc 420attcgttatc agggtaaccc gacagtggcc ttttatgaac tctacaatga gcccaccaac 480cgaggcggtc gcatgggccc ccttccctgg gaagaatatg cccagttcat cgaagggctg 540atttccatgc tctacgccat cgacgacacc gttattccac tggtcgctgg cttcgactgg 600ggatatgatt tgagctatgt tgcggaacgc ccgatccgtt ttccaggagt cgcctatgtc 660acccaccctt acccgcagaa gcgccccgag ccttgggaac cgatctggca ggaggaatgg 720ggttttgtcg ccgacaccta tcccatgatc gccactgagt ttggcttcat gagtgaggac 780ggtcccggag cccacaaccc ggttatcggg gatgaacact atggcgaatc ggtcatccgc 840tttttcgagg aacgcggcat ttcctggacg gcctgggtgt ttgatcctct ctggtcaccc 900cagcttttcg aagactggga aacctatacc cccacccggc aaggccgatt ctttaaacag 960aaaatgatgg aactgaatcc cccgcgttga 990122329PRTUnknownObtained from environmental sample 122Met Pro Phe Asp Ala Ile Gly Glu Ser Phe Arg Ala Ser Gln Gln Leu 1 5 10 15 Pro Leu Ile Lys Val Asp Gly Asn Arg Phe Val Ile Ala Glu Thr Gly 20 25 30 Glu Pro Ile Val Phe Arg Gly Val Ser Ala Ser Asp Pro Ala Ala Leu 35 40 45 Leu Glu Arg Gly Gln Trp Gly Arg Arg Tyr Phe Glu Glu Met Ala Lys 50 55 60 Trp Asn Ala Asn Val Val Arg Ile Pro Val His Pro Ala Asp Trp Arg 65 70 75 80 Asn Leu Gly Glu Asp Ile Tyr Leu Ala Leu Leu Asp Gln Ala Ile Glu 85 90 95 Trp Ser Ala Glu Leu Gly Met His Val Ile Ile Asp Trp His Thr Ile 100 105 110 Gly Asn Ile Leu Thr Gly Ile Tyr His Arg Asp Ile Tyr Glu Thr Thr 115 120 125 Arg Asp Glu Thr Tyr Arg Phe Trp Tyr Thr Ile Ala Ile Arg Tyr Gln 130 135 140 Gly Asn Pro Thr Val Ala Phe Tyr Glu Leu Tyr Asn Glu Pro Thr Asn 145 150 155 160 Arg Gly Gly Arg Met Gly Pro Leu Pro Trp Glu Glu Tyr Ala Gln Phe 165 170 175 Ile Glu Gly Leu Ile Ser Met Leu Tyr Ala Ile Asp Asp Thr Val Ile 180 185 190 Pro Leu Val Ala Gly Phe Asp Trp Gly Tyr Asp Leu Ser Tyr Val Ala 195 200 205 Glu Arg Pro Ile Arg Phe Pro Gly Val Ala Tyr Val Thr His Pro Tyr 210 215 220 Pro Gln Lys Arg Pro Glu Pro Trp Glu Pro Ile Trp Gln Glu Glu Trp 225 230 235 240 Gly Phe Val Ala Asp Thr Tyr Pro Met Ile Ala Thr Glu Phe Gly Phe 245 250 255 Met Ser Glu Asp Gly Pro Gly Ala His Asn Pro Val Ile Gly Asp Glu 260 265 270 His Tyr Gly Glu Ser Val Ile Arg Phe Phe Glu Glu Arg Gly Ile Ser 275 280 285 Trp Thr Ala Trp Val Phe Asp Pro Leu Trp Ser Pro Gln Leu Phe Glu 290 295 300 Asp Trp Glu Thr Tyr Thr Pro Thr Arg Gln Gly Arg Phe Phe Lys Gln 305 310 315 320 Lys Met Met Glu Leu Asn Pro Pro Arg 325 1231398DNAUnknownObtained from environmental sample 123atgccgatga gcacagaaac gacttttcct tctgatttca cctggggcgc agcaacagcc 60gcctaccaga tcgaaggggg cgatcgcgct ggcgggcgcg gccgttccgt gtgggacatg 120ttttgcgaga aacgaggagc tatttgggag gggcatacgg ggcagcgagc gagtctgcat 180cttcagcgct ggcgtgagga cgtaatgttg atgcaacagc tcggactgcg gggctatcgt 240tttagcgtca gctggccgcg cgtcttcccg acaggagtcg gcaaagtcaa ccgtgaaggg 300ttggcctttt acgatcagct cgtagacgcc ttgctcgagg ccggcatcac cccctttata 360acgctatttc attgggactt cccgctcgat ttgtaccacc gaggcggctg gttgaatcgc 420gacagcgccg actggtttgc ctcctacgcc gagtgcctcg gcaaggcact gggcgacagg 480gtcaagcact gggtgaccct caacgagccg caggttttca taggcctcgg tcattacgaa 540gggcgtcatg ccccggggtt gaagctctcc atcgcggaaa tgctgcgctg cgggcaccac 600gccttgctcg cgcacgggaa ggccgtgcaa gccctgcgcg cttccgtcga cggcccctgc 660aagattggat ttgctccggt ggggattccc aagcttccgg cgagtgagag ctcagaggat 720atcgccgcgg cacgaaaggc ccagttcgcg gcgggagcgc cgccgtattg gacgctgagc 780tggtgggcgg atccggtgtt tcaggggaca tatcccgctg atgcctgcca ggctctcgga 840gcggacgcgc cgcaggtggc cgatcacgac atgagcatca tcagcgagcc gactgatttc 900ctgggcctca acctttatca aggggtggtg gtgcgtgccg atcacacggg tcaaccagaa 960acggtgccgt ttccgccggg attccccgtg actgcgctca actgggccgt aaccccagag 1020gcgctgtatt ggggcccgcg ctttgccttc gaacgctaca aaaagccgat tcacatcacg 1080gaaaacgggc tatcctgtcg tgactggccg tcgctcgacg ggcacgtcca cgacgccgac 1140cgcatcgact tcatggcccg gcacttgcgc gcagcgcatc gagccattcg cgatgggata 1200ccgatcgaag gctacttcca ctggtctgcg atcgacaact tcgagtgggc agaaggctac 1260aaggaacgct tcgggctcat ttacgtcgac tatacgagcg gcgagcgcat tccgaaggac 1320tcgtaccact ggtaccagaa ggtcattgcc tccgaggggc gggcagcgct cggcgcgccc 1380agtgctgctc gcccataa 1398124465PRTUnknownObtained from environmental sample 124Met Pro Met Ser Thr Glu Thr Thr Phe Pro Ser Asp Phe Thr Trp Gly 1 5 10 15 Ala Ala Thr Ala Ala Tyr Gln Ile Glu Gly Gly Asp Arg Ala Gly Gly 20 25 30 Arg Gly Arg Ser Val Trp Asp Met Phe Cys Glu Lys Arg Gly Ala Ile 35 40 45 Trp Glu Gly His Thr Gly Gln Arg Ala Ser Leu His Leu Gln Arg Trp 50 55 60 Arg Glu Asp Val Met Leu Met Gln Gln Leu Gly Leu Arg Gly Tyr Arg 65 70 75 80 Phe Ser Val Ser Trp Pro Arg Val Phe Pro Thr Gly Val Gly Lys Val 85 90 95 Asn Arg Glu Gly Leu Ala Phe Tyr Asp Gln Leu Val Asp Ala Leu Leu 100 105 110 Glu Ala Gly Ile Thr Pro Phe Ile Thr Leu Phe His Trp Asp Phe Pro 115 120 125 Leu Asp Leu Tyr His Arg Gly Gly Trp Leu Asn Arg Asp Ser Ala Asp 130 135 140 Trp Phe Ala Ser Tyr Ala Glu Cys Leu Gly Lys Ala Leu Gly Asp Arg 145 150 155 160 Val Lys His Trp Val Thr Leu Asn Glu Pro Gln Val Phe Ile Gly Leu 165 170 175 Gly His Tyr Glu Gly Arg His Ala Pro Gly Leu Lys Leu Ser Ile Ala 180 185 190 Glu Met Leu Arg Cys Gly His His Ala Leu Leu Ala His Gly Lys Ala 195 200 205 Val Gln Ala Leu Arg Ala Ser Val Asp Gly Pro Cys Lys Ile Gly Phe 210 215 220 Ala Pro Val Gly Ile Pro Lys Leu Pro Ala Ser Glu Ser Ser Glu Asp 225 230 235 240 Ile Ala Ala Ala Arg Lys Ala Gln Phe Ala Ala Gly Ala Pro Pro Tyr 245 250 255 Trp Thr Leu Ser Trp Trp Ala Asp Pro Val Phe Gln Gly Thr Tyr Pro 260 265 270 Ala Asp Ala Cys Gln Ala Leu Gly Ala Asp Ala Pro Gln Val Ala Asp 275 280 285 His Asp Met Ser Ile Ile Ser Glu Pro Thr Asp Phe Leu Gly Leu Asn 290 295 300 Leu Tyr Gln Gly Val Val Val Arg Ala Asp His Thr Gly Gln Pro Glu 305 310 315 320 Thr Val Pro Phe Pro Pro Gly Phe Pro Val Thr Ala Leu Asn Trp Ala 325 330 335 Val Thr Pro Glu Ala Leu Tyr Trp Gly Pro Arg Phe Ala Phe Glu Arg 340 345 350 Tyr Lys Lys Pro Ile His Ile Thr Glu Asn Gly Leu Ser Cys Arg Asp 355 360 365 Trp Pro Ser Leu Asp Gly His Val His Asp Ala Asp Arg Ile Asp Phe 370 375 380 Met Ala Arg His Leu Arg Ala Ala His Arg Ala Ile Arg Asp Gly Ile 385 390 395 400 Pro Ile Glu Gly Tyr Phe His Trp Ser Ala Ile Asp Asn Phe Glu Trp 405 410 415 Ala Glu Gly Tyr Lys Glu Arg Phe Gly Leu Ile Tyr Val Asp Tyr Thr 420 425 430 Ser Gly Glu Arg Ile Pro Lys Asp Ser Tyr His Trp Tyr Gln Lys Val 435 440 445 Ile Ala Ser Glu Gly Arg Ala Ala Leu Gly Ala Pro Ser Ala Ala Arg 450 455 460 Pro 465 1251350DNAUnknownObtained from environmental sample 125atgtcagatg ccgccccgac tgatccgaaa tccgcaatgc ccagacgctc ggacttcccc 60gagggttttg tcttcggcgc ggccaccgcg gcctatcaga tcgagggcca tgccttcggc 120ggcgcgggcc cctgccattg ggacagcttc gccgcaaccg ggcgtaacgt ggtcggcaat 180gaggatggcg cgcgcgcctg cgagcattac acccgctggc cgcaggatct ggacctgatc 240cgcgaggccg ggctcgacgc ctaccgcttc tcgacctcct gggcgcgggt gatgcccgat 300ggcgtgaccc tgaaccccga ggggctggat ttctacgacc gcctcgtcga tggcatgctc 360gagcgcgggc taaagcccta tctcaccctc taccattggg aattgccctc ggcgcttgcc 420gacaggggcg gctggaccaa tcgcgacacg gccgagcgct ttgccgattt cgcagcggtg 480gtgatggagc ggttgggcag ccgcgtcgcc cgcacggcca ccatcaacga gccatggtgc 540gtgagctggc tctcgcattt cgaaggccat cacgcgccgg gcctgcgcga catccgtgcc 600accgcacgcg ccatgcatca tgtgcaactg gcgcacggcc tcgcgctcgg gaagctgcgc 660gcgcaggggc atggcaatct cggcatcgtg ctgaatttct cggaaatcat tcccgccggg 720cgagagcacg cgaaggcggc tgatctcggc gacgcaatct cgaaccgctg gttcatcgag 780tcagtcgcgc

gtggcaccta tcccgatgtg gtcctcgagg gtctgggcaa gcacatgccc 840gagggctggc aggatgacat gaaaaccatc gcggccccgc tcgactggct gggtgtgaac 900tactacaccc gcggcatcgt cgcgcatgac ccggacgcgt cctggccctc gacccgagcg 960gaggaggggc ccctgcccaa gacgcagatg ggctgggaga tctaccccga gggcttgcgc 1020aacctgctgg tgcgcatggc gcgcgactat gtgggcgacc ttcccatggt cgtgaccgaa 1080aacgggatgg cctgggccga cgaggtcgcg gatggcgccg tcagagatac gatccgcacc 1140gaatatgtcg cagcccatct caacgcgacc cgcgaggcgc tggccggcgg ggcgaatatc 1200gaaggtttct tctattggtc gctgctcgac aattacgaat gggccttcgg ctatgccaag 1260cgcttcggcc tcgtccatgt cgatttcgac acgatggcac gcacgccgaa agcctcctac 1320cacgcgctga gggccgcgct gcagggttga 1350126449PRTUnknownObtained from environmental sample 126Met Ser Asp Ala Ala Pro Thr Asp Pro Lys Ser Ala Met Pro Arg Arg 1 5 10 15 Ser Asp Phe Pro Glu Gly Phe Val Phe Gly Ala Ala Thr Ala Ala Tyr 20 25 30 Gln Ile Glu Gly His Ala Phe Gly Gly Ala Gly Pro Cys His Trp Asp 35 40 45 Ser Phe Ala Ala Thr Gly Arg Asn Val Val Gly Asn Glu Asp Gly Ala 50 55 60 Arg Ala Cys Glu His Tyr Thr Arg Trp Pro Gln Asp Leu Asp Leu Ile 65 70 75 80 Arg Glu Ala Gly Leu Asp Ala Tyr Arg Phe Ser Thr Ser Trp Ala Arg 85 90 95 Val Met Pro Asp Gly Val Thr Leu Asn Pro Glu Gly Leu Asp Phe Tyr 100 105 110 Asp Arg Leu Val Asp Gly Met Leu Glu Arg Gly Leu Lys Pro Tyr Leu 115 120 125 Thr Leu Tyr His Trp Glu Leu Pro Ser Ala Leu Ala Asp Arg Gly Gly 130 135 140 Trp Thr Asn Arg Asp Thr Ala Glu Arg Phe Ala Asp Phe Ala Ala Val 145 150 155 160 Val Met Glu Arg Leu Gly Ser Arg Val Ala Arg Thr Ala Thr Ile Asn 165 170 175 Glu Pro Trp Cys Val Ser Trp Leu Ser His Phe Glu Gly His His Ala 180 185 190 Pro Gly Leu Arg Asp Ile Arg Ala Thr Ala Arg Ala Met His His Val 195 200 205 Gln Leu Ala His Gly Leu Ala Leu Gly Lys Leu Arg Ala Gln Gly His 210 215 220 Gly Asn Leu Gly Ile Val Leu Asn Phe Ser Glu Ile Ile Pro Ala Gly 225 230 235 240 Arg Glu His Ala Lys Ala Ala Asp Leu Gly Asp Ala Ile Ser Asn Arg 245 250 255 Trp Phe Ile Glu Ser Val Ala Arg Gly Thr Tyr Pro Asp Val Val Leu 260 265 270 Glu Gly Leu Gly Lys His Met Pro Glu Gly Trp Gln Asp Asp Met Lys 275 280 285 Thr Ile Ala Ala Pro Leu Asp Trp Leu Gly Val Asn Tyr Tyr Thr Arg 290 295 300 Gly Ile Val Ala His Asp Pro Asp Ala Ser Trp Pro Ser Thr Arg Ala 305 310 315 320 Glu Glu Gly Pro Leu Pro Lys Thr Gln Met Gly Trp Glu Ile Tyr Pro 325 330 335 Glu Gly Leu Arg Asn Leu Leu Val Arg Met Ala Arg Asp Tyr Val Gly 340 345 350 Asp Leu Pro Met Val Val Thr Glu Asn Gly Met Ala Trp Ala Asp Glu 355 360 365 Val Ala Asp Gly Ala Val Arg Asp Thr Ile Arg Thr Glu Tyr Val Ala 370 375 380 Ala His Leu Asn Ala Thr Arg Glu Ala Leu Ala Gly Gly Ala Asn Ile 385 390 395 400 Glu Gly Phe Phe Tyr Trp Ser Leu Leu Asp Asn Tyr Glu Trp Ala Phe 405 410 415 Gly Tyr Ala Lys Arg Phe Gly Leu Val His Val Asp Phe Asp Thr Met 420 425 430 Ala Arg Thr Pro Lys Ala Ser Tyr His Ala Leu Arg Ala Ala Leu Gln 435 440 445 Gly 127774DNAUnknownObtained from environmental sample 127atggacttgc agctaggcgg aaagcgcgtg ctgatcacgg gtgcgtccaa aggcatcggc 60ctggcctgcg ccgtcgcctt tgcgcgcgag ggtgccgacc cgattctggt ggcgcgcgat 120gatgcggcgt tgcatcacgc cacgtccgcc atccgcgaac aaagcggccg cgcggcacat 180gccatcacgc tggacctggc cctgcctggc gcggcggaaa agctggccaa ggaaaccggc 240cccatcgaca tactggtcaa caacgcgggc gcggtgcccg gcggcgcgct ggaccaggtg 300caagacgaac gctggcgcgc gggctgggaa ttgaaagtgc acggctacat cagcctggcg 360cgctgctact acccgcacat gcgcgaagcg ggcgcgggcg tcatcgccaa catcatcggc 420atggcgggcg cggcgccccg cgccgactac atctgcggcg cggcggccaa tgcctcactg 480attgccttta cccgcgcgct gggtggcgaa gcgccccgcc acggcgtgcg cgtctttggc 540gtcaacccct cgcgcacgcg gaccgaccgc gtgctgaccc tggcccggca acgcgcgcag 600gcgcgctggg gcgacgaaac gcgttggcag gaaacgctgt cggacctgcc cttcaaccgg 660ctgatggaac ccgccgaagt ggccgacatg attgtgttcg gcgcctcgcc acgcgcgggt 720tacctgagcg gcacggtcat cgacctggac ggcggcgaac agtacgcgaa atag 774128257PRTUnknownObtained from environmental sample 128Met Asp Leu Gln Leu Gly Gly Lys Arg Val Leu Ile Thr Gly Ala Ser 1 5 10 15 Lys Gly Ile Gly Leu Ala Cys Ala Val Ala Phe Ala Arg Glu Gly Ala 20 25 30 Asp Pro Ile Leu Val Ala Arg Asp Asp Ala Ala Leu His His Ala Thr 35 40 45 Ser Ala Ile Arg Glu Gln Ser Gly Arg Ala Ala His Ala Ile Thr Leu 50 55 60 Asp Leu Ala Leu Pro Gly Ala Ala Glu Lys Leu Ala Lys Glu Thr Gly 65 70 75 80 Pro Ile Asp Ile Leu Val Asn Asn Ala Gly Ala Val Pro Gly Gly Ala 85 90 95 Leu Asp Gln Val Gln Asp Glu Arg Trp Arg Ala Gly Trp Glu Leu Lys 100 105 110 Val His Gly Tyr Ile Ser Leu Ala Arg Cys Tyr Tyr Pro His Met Arg 115 120 125 Glu Ala Gly Ala Gly Val Ile Ala Asn Ile Ile Gly Met Ala Gly Ala 130 135 140 Ala Pro Arg Ala Asp Tyr Ile Cys Gly Ala Ala Ala Asn Ala Ser Leu 145 150 155 160 Ile Ala Phe Thr Arg Ala Leu Gly Gly Glu Ala Pro Arg His Gly Val 165 170 175 Arg Val Phe Gly Val Asn Pro Ser Arg Thr Arg Thr Asp Arg Val Leu 180 185 190 Thr Leu Ala Arg Gln Arg Ala Gln Ala Arg Trp Gly Asp Glu Thr Arg 195 200 205 Trp Gln Glu Thr Leu Ser Asp Leu Pro Phe Asn Arg Leu Met Glu Pro 210 215 220 Ala Glu Val Ala Asp Met Ile Val Phe Gly Ala Ser Pro Arg Ala Gly 225 230 235 240 Tyr Leu Ser Gly Thr Val Ile Asp Leu Asp Gly Gly Glu Gln Tyr Ala 245 250 255 Lys 129747DNAUnknownObtained from environmental sample 129atgcccaaag tcatgctcgt taccggcggc agccgtggca tcggcgccgc cgtcgccaag 60ctggccgcgc gccgcggcta cgcggtcggc atcaactacc gcacccattc cgacgccgcc 120gacgccgtcg tggccgaaat ccagcaggcg ggcggcaccg cgctggccat ccaggccgac 180gtgtcgcagg aagacgatgt gctgcacatg ttccgcacgc tggacgagcg cctgggccgc 240atcgacgcgc tggtcaataa cgccggcatc ctggaaacgc agatgcgcct ggaccagatg 300gaagccgacc gcctgctgcg cgtgctgtcc accaacgtca tcggcgcttt cctatgtgcg 360cgcgaagccg tgcgcaggat gtcgacgcgc catggcggcg tgggcggcgc catcgtcaac 420gtgtcttcgg cggcggcgcg cctgggctcg cccaatgaat acgtggatta cgcggcctcc 480aagggcgcgc tggacacgat gaccatcggc ctgtcgaaag aggtggcgcc cgaaggtatc 540cgcgtgaatg gcgtgcgccc cggcaccatc tacaccgaca tgcacgcaag cggcggcgag 600ccgggccggg tggatcgcct gaaaagcgtg atcccgctgc ggcgcggcgg ctcggtggaa 660gaagtggcgg gcgccgtcat gtggctgttt tccgaagaag ccggctatac cagcggttcg 720ttcatcgacg tgtccggcgg tagttga 747130248PRTUnknownObtained from environmental sample 130Met Pro Lys Val Met Leu Val Thr Gly Gly Ser Arg Gly Ile Gly Ala 1 5 10 15 Ala Val Ala Lys Leu Ala Ala Arg Arg Gly Tyr Ala Val Gly Ile Asn 20 25 30 Tyr Arg Thr His Ser Asp Ala Ala Asp Ala Val Val Ala Glu Ile Gln 35 40 45 Gln Ala Gly Gly Thr Ala Leu Ala Ile Gln Ala Asp Val Ser Gln Glu 50 55 60 Asp Asp Val Leu His Met Phe Arg Thr Leu Asp Glu Arg Leu Gly Arg 65 70 75 80 Ile Asp Ala Leu Val Asn Asn Ala Gly Ile Leu Glu Thr Gln Met Arg 85 90 95 Leu Asp Gln Met Glu Ala Asp Arg Leu Leu Arg Val Leu Ser Thr Asn 100 105 110 Val Ile Gly Ala Phe Leu Cys Ala Arg Glu Ala Val Arg Arg Met Ser 115 120 125 Thr Arg His Gly Gly Val Gly Gly Ala Ile Val Asn Val Ser Ser Ala 130 135 140 Ala Ala Arg Leu Gly Ser Pro Asn Glu Tyr Val Asp Tyr Ala Ala Ser 145 150 155 160 Lys Gly Ala Leu Asp Thr Met Thr Ile Gly Leu Ser Lys Glu Val Ala 165 170 175 Pro Glu Gly Ile Arg Val Asn Gly Val Arg Pro Gly Thr Ile Tyr Thr 180 185 190 Asp Met His Ala Ser Gly Gly Glu Pro Gly Arg Val Asp Arg Leu Lys 195 200 205 Ser Val Ile Pro Leu Arg Arg Gly Gly Ser Val Glu Glu Val Ala Gly 210 215 220 Ala Val Met Trp Leu Phe Ser Glu Glu Ala Gly Tyr Thr Ser Gly Ser 225 230 235 240 Phe Ile Asp Val Ser Gly Gly Ser 245 1311041DNAUnknownObtained from environmental sample 131gtggaaacct attttcccct gcaccgcggg atcaacatga gccactggct ttcgcaagtg 60aatgaaaaca ttcccgaccg ttccacctat gtgacggagc gggacctgca atttttgcgg 120gcagcgggct tcgaccatgt gcgtctgccg atcgatgaga tcgaactctg ggatgaggag 180ggccatcaga tcgaggaggc ctggcaatac atgcacaact ttatgcgctg gagccgaaag 240aatgacctcc gggttattct cgacctgcac acggtattgt cccaccactt caacgcgatc 300aacatgggag aggtcaacac cctctttaat gatcccaagg aacaggaaaa attcctcaat 360ctctgggagc aaatcatgga tgccgtaggg caccacccca acgagtttct cgcttatgaa 420atgctcaatg aggcggtcgc ggaagatgat gaagactgga acctgctcct caaccgtgcg 480attgaacgca tccgggaacg tgagccgcat cgcgttctga ttgccggggc caactggtgg 540cagcatgccg cccgcgttcc caacctgagg cttccccctg gtgatcccaa catcatcatc 600agttttcact tttactcacc ctttctcttc acgcactatc gcagcagctg gactgccatg 660cgggcatacc agggtttcgt ccaatacccc ggcattacca ttcccgccat ccatctcgaa 720ggaatgaact atccggagtc ctttgtccaa atgtgggaag agcacaatca gtattacgac 780atccattcaa tgtatgccga aatggtcccg gcggtgcgtt ttgccgaaaa gctgggcctt 840cggctctatt gcggcgaatt tggagccatg aagaccgttg atcgtgccca aatgctgcag 900tggtatcggg atgtggtcag agtctttgaa atgttggaca ttccctacac tgcctgggat 960tatcagggaa cctttggaat ccgcgatgag ctgaccggtg agcctgatca tgaactgatc 1020gacattctcc tcggccgcta a 1041132346PRTUnknownObtained from environmental sample 132Met Glu Thr Tyr Phe Pro Leu His Arg Gly Ile Asn Met Ser His Trp 1 5 10 15 Leu Ser Gln Val Asn Glu Asn Ile Pro Asp Arg Ser Thr Tyr Val Thr 20 25 30 Glu Arg Asp Leu Gln Phe Leu Arg Ala Ala Gly Phe Asp His Val Arg 35 40 45 Leu Pro Ile Asp Glu Ile Glu Leu Trp Asp Glu Glu Gly His Gln Ile 50 55 60 Glu Glu Ala Trp Gln Tyr Met His Asn Phe Met Arg Trp Ser Arg Lys 65 70 75 80 Asn Asp Leu Arg Val Ile Leu Asp Leu His Thr Val Leu Ser His His 85 90 95 Phe Asn Ala Ile Asn Met Gly Glu Val Asn Thr Leu Phe Asn Asp Pro 100 105 110 Lys Glu Gln Glu Lys Phe Leu Asn Leu Trp Glu Gln Ile Met Asp Ala 115 120 125 Val Gly His His Pro Asn Glu Phe Leu Ala Tyr Glu Met Leu Asn Glu 130 135 140 Ala Val Ala Glu Asp Asp Glu Asp Trp Asn Leu Leu Leu Asn Arg Ala 145 150 155 160 Ile Glu Arg Ile Arg Glu Arg Glu Pro His Arg Val Leu Ile Ala Gly 165 170 175 Ala Asn Trp Trp Gln His Ala Ala Arg Val Pro Asn Leu Arg Leu Pro 180 185 190 Pro Gly Asp Pro Asn Ile Ile Ile Ser Phe His Phe Tyr Ser Pro Phe 195 200 205 Leu Phe Thr His Tyr Arg Ser Ser Trp Thr Ala Met Arg Ala Tyr Gln 210 215 220 Gly Phe Val Gln Tyr Pro Gly Ile Thr Ile Pro Ala Ile His Leu Glu 225 230 235 240 Gly Met Asn Tyr Pro Glu Ser Phe Val Gln Met Trp Glu Glu His Asn 245 250 255 Gln Tyr Tyr Asp Ile His Ser Met Tyr Ala Glu Met Val Pro Ala Val 260 265 270 Arg Phe Ala Glu Lys Leu Gly Leu Arg Leu Tyr Cys Gly Glu Phe Gly 275 280 285 Ala Met Lys Thr Val Asp Arg Ala Gln Met Leu Gln Trp Tyr Arg Asp 290 295 300 Val Val Arg Val Phe Glu Met Leu Asp Ile Pro Tyr Thr Ala Trp Asp 305 310 315 320 Tyr Gln Gly Thr Phe Gly Ile Arg Asp Glu Leu Thr Gly Glu Pro Asp 325 330 335 His Glu Leu Ile Asp Ile Leu Leu Gly Arg 340 345 1331377DNAUnknownObtained from environmental sample 133atgacacaac tggcttttcc atctaacttc atctggggaa cagctacttc cgcttaccaa 60atcgaaggcg cctggaacgc agacggcaag ggcgaatcta tttgggatcg cttttcccat 120acgcagggga agatcattga cggcagcaac ggcgatgtgg cctgcgatca ctaccaccgc 180tggcgcgagg acgtggccct catgagagac ttgggtatgc aggcatatcg cttctccatc 240tcctggccac gcatcctgcc caccggtcat ggacagatca atcaggctgg gctggacttt 300tacaatcgcc tggtggacgg gttgctggaa gctggcatca agccctttgc caccctctac 360cactgggacc tgccgctggc gctacaggct gacggcggct ggccggagcg ctccacggcc 420aaggcctttg tcgaatacgc cgacgtggtc agccgcgcgc tgggcgatcg ggtgaagagc 480tggatcaccc ataacgaacc gtggtgcatc agcatgctga gccatcaaat tggggagcat 540gcgcccggct ggcgggactg gcaggctgcg ttggcggccg cgcaccacgt cctcctttcg 600catggttggg ccgtgccgga actgcgtcgc aacagccgcg atgcagaaat cggcatcacg 660ttgaacttta ccccggcgga gccagcttcg aacagcgcag ccgatttcaa ggcctatcgc 720cagttcgatg gctacttcaa ccgctggttc ctggacccgc tctatggccg ccactatccg 780gcagatatgg tgcacgatta catcgcgcaa ggctacctgc catcacaggg tttgactttc 840gtggaagctg gtgacctgga cgcgatcgcg acgcgcaccg atttcctggg tgtgaactat 900tacacgcgcg aagtggtccg tagccaggaa atcccagaga gtgagaacgc gccgcgcaca 960gtcttgcgcg cgccacagga agagtggaca gagatgggct gggaagtgta tcctgagggc 1020ctctacaggt tgctcaatcg gttgcacttt gaataccagc cgcgcaagct ctacgtgacc 1080gagagcggtt gcagctactc cgatggaccc ggccccaacg gtcggatacc ggaccaacgc 1140cgtatcaact acctgcgcga tcacttcgca gcggcgcatc aggcgataca atgcggcgtc 1200ccgctggccg gctacttcgt ctggtcgttc atggacaact tcgagtgggc caaagggtac 1260acccaacgtt ttggtatcgt atgggtggat tatcaatcgc aacgacggat accgaaagac 1320agcgcctact ggtatcgcga tgtcgtcgcc gccaacgcgg tgcaagttcc tgattag 1377134458PRTUnknownObtained from environmental sample 134Met Thr Gln Leu Ala Phe Pro Ser Asn Phe Ile Trp Gly Thr Ala Thr 1 5 10 15 Ser Ala Tyr Gln Ile Glu Gly Ala Trp Asn Ala Asp Gly Lys Gly Glu 20 25 30 Ser Ile Trp Asp Arg Phe Ser His Thr Gln Gly Lys Ile Ile Asp Gly 35 40 45 Ser Asn Gly Asp Val Ala Cys Asp His Tyr His Arg Trp Arg Glu Asp 50 55 60 Val Ala Leu Met Arg Asp Leu Gly Met Gln Ala Tyr Arg Phe Ser Ile 65 70 75 80 Ser Trp Pro Arg Ile Leu Pro Thr Gly His Gly Gln Ile Asn Gln Ala 85 90 95 Gly Leu Asp Phe Tyr Asn Arg Leu Val Asp Gly Leu Leu Glu Ala Gly 100 105 110 Ile Lys Pro Phe Ala Thr Leu Tyr His Trp Asp Leu Pro Leu Ala Leu 115 120 125 Gln Ala Asp Gly Gly Trp Pro Glu Arg Ser Thr Ala Lys Ala Phe Val 130 135 140 Glu Tyr Ala Asp Val Val Ser Arg Ala Leu Gly Asp Arg Val Lys Ser 145 150 155 160 Trp Ile Thr His Asn Glu Pro Trp Cys Ile Ser Met Leu Ser His Gln 165 170 175 Ile Gly Glu His Ala Pro Gly Trp Arg Asp Trp Gln Ala Ala Leu Ala 180 185 190 Ala Ala His His Val Leu Leu Ser His Gly Trp Ala Val Pro Glu Leu 195 200 205 Arg Arg Asn Ser Arg Asp Ala Glu Ile Gly Ile Thr Leu Asn Phe Thr 210 215 220 Pro Ala Glu Pro Ala Ser Asn Ser Ala Ala Asp Phe

Lys Ala Tyr Arg 225 230 235 240 Gln Phe Asp Gly Tyr Phe Asn Arg Trp Phe Leu Asp Pro Leu Tyr Gly 245 250 255 Arg His Tyr Pro Ala Asp Met Val His Asp Tyr Ile Ala Gln Gly Tyr 260 265 270 Leu Pro Ser Gln Gly Leu Thr Phe Val Glu Ala Gly Asp Leu Asp Ala 275 280 285 Ile Ala Thr Arg Thr Asp Phe Leu Gly Val Asn Tyr Tyr Thr Arg Glu 290 295 300 Val Val Arg Ser Gln Glu Ile Pro Glu Ser Glu Asn Ala Pro Arg Thr 305 310 315 320 Val Leu Arg Ala Pro Gln Glu Glu Trp Thr Glu Met Gly Trp Glu Val 325 330 335 Tyr Pro Glu Gly Leu Tyr Arg Leu Leu Asn Arg Leu His Phe Glu Tyr 340 345 350 Gln Pro Arg Lys Leu Tyr Val Thr Glu Ser Gly Cys Ser Tyr Ser Asp 355 360 365 Gly Pro Gly Pro Asn Gly Arg Ile Pro Asp Gln Arg Arg Ile Asn Tyr 370 375 380 Leu Arg Asp His Phe Ala Ala Ala His Gln Ala Ile Gln Cys Gly Val 385 390 395 400 Pro Leu Ala Gly Tyr Phe Val Trp Ser Phe Met Asp Asn Phe Glu Trp 405 410 415 Ala Lys Gly Tyr Thr Gln Arg Phe Gly Ile Val Trp Val Asp Tyr Gln 420 425 430 Ser Gln Arg Arg Ile Pro Lys Asp Ser Ala Tyr Trp Tyr Arg Asp Val 435 440 445 Val Ala Ala Asn Ala Val Gln Val Pro Asp 450 455 135987DNAUnknownObtained from environmental sample 135atggttgagc ctgccgatca gagtcatttt tcagatgctt ttcaggtaaa tcgcactctt 60ggaaaaggca tcaatcttgg taacacactg gaggctccaa atgaaggcga gtggggattg 120acaattcgcg aggagtattt tgatgaagtg aaacaagccg gatttgaatc cgtgcgtatt 180ccgatacgat ggaatgctca tgctctggaa ggttttccat atacgataga tgaatctttt 240tttgaccggg ttgatgaagt tattggctgg gcttttgatc gtgatcttgc agtcatgatt 300aacattcatc actacaacga attgatggag cagccacagg atcaccggga tcgctttttg 360aaactttggg agcaaattgc tgcgcactat aaagagtacc cggaagaact ggtattcgag 420attttaaacg aaccccacga taatctgacc ccggctatct ggaatagctt tttggctgat 480gctctcggta ttatacgcca aaccaatcca ggaagggtta ttgcagtcgg aacagctgaa 540tggggcggtt tcgggagttt gcaggatctt gagctgcctg ataatgaccg ccagataatc 600accaccgttc attactataa cccatttcat ttcacgcatc agggggcaga ttgggttgga 660gatgaagcgg atcagtggct tggaaccgaa tgggatggag cagatcatga aaaagctgaa 720gttgacagcg attttgactc tgtggaacag tgggcccgaa atcatgaccg gccaatacac 780gtgggagagt tcggagcttt cagcgccgca gatgatttgt cacgtgaaca gtggacggca 840tacgtacgtg agtcttcgga gaaccggcag tttagctggg cgtattggga gtttgggtca 900gggttcggtg cctatgatcc cggttccgga gaatggcgtg aatatttact ccgggcgtta 960atccccgaca gtccggtgat tgattaa 987136328PRTUnknownObtained from environmental sample 136Met Val Glu Pro Ala Asp Gln Ser His Phe Ser Asp Ala Phe Gln Val 1 5 10 15 Asn Arg Thr Leu Gly Lys Gly Ile Asn Leu Gly Asn Thr Leu Glu Ala 20 25 30 Pro Asn Glu Gly Glu Trp Gly Leu Thr Ile Arg Glu Glu Tyr Phe Asp 35 40 45 Glu Val Lys Gln Ala Gly Phe Glu Ser Val Arg Ile Pro Ile Arg Trp 50 55 60 Asn Ala His Ala Leu Glu Gly Phe Pro Tyr Thr Ile Asp Glu Ser Phe 65 70 75 80 Phe Asp Arg Val Asp Glu Val Ile Gly Trp Ala Phe Asp Arg Asp Leu 85 90 95 Ala Val Met Ile Asn Ile His His Tyr Asn Glu Leu Met Glu Gln Pro 100 105 110 Gln Asp His Arg Asp Arg Phe Leu Lys Leu Trp Glu Gln Ile Ala Ala 115 120 125 His Tyr Lys Glu Tyr Pro Glu Glu Leu Val Phe Glu Ile Leu Asn Glu 130 135 140 Pro His Asp Asn Leu Thr Pro Ala Ile Trp Asn Ser Phe Leu Ala Asp 145 150 155 160 Ala Leu Gly Ile Ile Arg Gln Thr Asn Pro Gly Arg Val Ile Ala Val 165 170 175 Gly Thr Ala Glu Trp Gly Gly Phe Gly Ser Leu Gln Asp Leu Glu Leu 180 185 190 Pro Asp Asn Asp Arg Gln Ile Ile Thr Thr Val His Tyr Tyr Asn Pro 195 200 205 Phe His Phe Thr His Gln Gly Ala Asp Trp Val Gly Asp Glu Ala Asp 210 215 220 Gln Trp Leu Gly Thr Glu Trp Asp Gly Ala Asp His Glu Lys Ala Glu 225 230 235 240 Val Asp Ser Asp Phe Asp Ser Val Glu Gln Trp Ala Arg Asn His Asp 245 250 255 Arg Pro Ile His Val Gly Glu Phe Gly Ala Phe Ser Ala Ala Asp Asp 260 265 270 Leu Ser Arg Glu Gln Trp Thr Ala Tyr Val Arg Glu Ser Ser Glu Asn 275 280 285 Arg Gln Phe Ser Trp Ala Tyr Trp Glu Phe Gly Ser Gly Phe Gly Ala 290 295 300 Tyr Asp Pro Gly Ser Gly Glu Trp Arg Glu Tyr Leu Leu Arg Ala Leu 305 310 315 320 Ile Pro Asp Ser Pro Val Ile Asp 325 137702DNAUnknownObtained from environmental sample 137atgagccacc gatcgcagga attcaacggc cagccactga tggtgtccga agacggccac 60ttcgtgctcg gattcgggcg cgacgacgag gccacccacc gactgcgcgt tcagctaccg 120gatgagcgag tctgggagaa gaatctgcgt ccggaatcgc gcgagttcga tattcagcgg 180atcgacggct tgccgcaaga ccaggtcacc ccaccccact ccgtgctggc gagaatccga 240gaggacgctt cgctgtcgcg ccgtgcccgc gaacgacgcg atccgcggac cgactggacc 300gatggctgga tctggccggc cgagggccgc atttccggcg tgtacggcag ccagcgcatc 360ctcaacggtg agcctcgcaa cccgcactgg gggctggata tcgccgcgcc aaccggcagc 420ccggtcgtgg cgcctgccgg cggcatcgtc agcctgactc atccggacat gtatttttcc 480ggcggcaccc tgttaatcga ccacggtcac ggcctggtgt ctgcgttcct ccacctgagt 540gaaatcctgg tcgaggaagg gcagcgggtc gagcaggggg atctgatcgc acgcattggc 600gccaccggtc gtgccaccgg gccgcacctg gactggcgga tcaatctcgg cgatgtacgc 660gtggacccac agctgctgct gccgccgatg gacgcgcagt ga 702138233PRTUnknownObtained from environmental sample 138Met Ser His Arg Ser Gln Glu Phe Asn Gly Gln Pro Leu Met Val Ser 1 5 10 15 Glu Asp Gly His Phe Val Leu Gly Phe Gly Arg Asp Asp Glu Ala Thr 20 25 30 His Arg Leu Arg Val Gln Leu Pro Asp Glu Arg Val Trp Glu Lys Asn 35 40 45 Leu Arg Pro Glu Ser Arg Glu Phe Asp Ile Gln Arg Ile Asp Gly Leu 50 55 60 Pro Gln Asp Gln Val Thr Pro Pro His Ser Val Leu Ala Arg Ile Arg 65 70 75 80 Glu Asp Ala Ser Leu Ser Arg Arg Ala Arg Glu Arg Arg Asp Pro Arg 85 90 95 Thr Asp Trp Thr Asp Gly Trp Ile Trp Pro Ala Glu Gly Arg Ile Ser 100 105 110 Gly Val Tyr Gly Ser Gln Arg Ile Leu Asn Gly Glu Pro Arg Asn Pro 115 120 125 His Trp Gly Leu Asp Ile Ala Ala Pro Thr Gly Ser Pro Val Val Ala 130 135 140 Pro Ala Gly Gly Ile Val Ser Leu Thr His Pro Asp Met Tyr Phe Ser 145 150 155 160 Gly Gly Thr Leu Leu Ile Asp His Gly His Gly Leu Val Ser Ala Phe 165 170 175 Leu His Leu Ser Glu Ile Leu Val Glu Glu Gly Gln Arg Val Glu Gln 180 185 190 Gly Asp Leu Ile Ala Arg Ile Gly Ala Thr Gly Arg Ala Thr Gly Pro 195 200 205 His Leu Asp Trp Arg Ile Asn Leu Gly Asp Val Arg Val Asp Pro Gln 210 215 220 Leu Leu Leu Pro Pro Met Asp Ala Gln 225 230 139351DNAUnknownObtained from environmental sample 139atggaaaaaa ttctcgttat cggatgcgcg ggccagatag gctcagagct tacgctcgaa 60cttcgtaaga tttatggtga tgacaatgtg gtggctactg acattaagcc ggccagcaag 120gaaattaccg agggcggccc ctttgaaatt cttgatgtgc tcgacaccca ccggcttttt 180ggcactgtaa gccgcaacaa gatcacccag atttatcacc ttgcagccat cctttcgggc 240aatgccgaga aaaaaccact tgcaagctgg cacattaaca tggagagttt gctcaacgtg 300cttgaactgg cccgtgaact gaagcttcat aaaattttct ggccaagctc a 351140117PRTUnknownObtained from environmental sample 140Met Glu Lys Ile Leu Val Ile Gly Cys Ala Gly Gln Ile Gly Ser Glu 1 5 10 15 Leu Thr Leu Glu Leu Arg Lys Ile Tyr Gly Asp Asp Asn Val Val Ala 20 25 30 Thr Asp Ile Lys Pro Ala Ser Lys Glu Ile Thr Glu Gly Gly Pro Phe 35 40 45 Glu Ile Leu Asp Val Leu Asp Thr His Arg Leu Phe Gly Thr Val Ser 50 55 60 Arg Asn Lys Ile Thr Gln Ile Tyr His Leu Ala Ala Ile Leu Ser Gly 65 70 75 80 Asn Ala Glu Lys Lys Pro Leu Ala Ser Trp His Ile Asn Met Glu Ser 85 90 95 Leu Leu Asn Val Leu Glu Leu Ala Arg Glu Leu Lys Leu His Lys Ile 100 105 110 Phe Trp Pro Ser Ser 115 1411350DNAUnknownObtained from environmental sample 141atgctgtcct atacgagtcc gttcccaaag aactttgtct ggggtgtggc gacggcggcg 60ccgcagatcg agggcgctgc gcgagaagac ggaaagggcg aatcgatatg ggatcgcttt 120tgccgcgtgc ccggaaaggt ccacaatggc gatactctcg atgttgcgtg cgaccactac 180caccggttcc gggaggattt cgcgctcatg cgagacttgg gcgtgcgcca ctaccggctt 240tcgcttgcct ggccccgcat attcccggac ggcgacggcg cattgaacca gcgcggagtg 300gatttctacc accggctctt tgaggccatg atcgagcacg ggattacgcc ttgggtgacg 360ctctttcact gggatttgcc gcaggcgctc gaggaccgcg gcggctggtg tgagcgtctc 420accgtcgatg cattcgggcg ctacgctgac accgtggtga aggcgtttgg cgatcgcgtg 480aagaattgga tcaccctgaa cgaaatccgc tgcttcacgt tgctcgctta cgatctctgc 540atcaaggccc cgggccgcaa ggtctcgcgg gcgcagctca accagaccta tcatcacgcg 600ctgatctgcc atgggcatgg cgtccgggcg gtccgcgaac acggcgggcg aggcgctcgc 660gtcgggctta ccgacaacag cgacgtatgc gtgcccgtca ccgagaccgc gcccgacatc 720attgcggcca gatcctggta tgcgtcgcga aatattcatc tgctcgatcc gatctatcgc 780ggcgagtatg cgccggaata cctcgaacgc tgcggtgcgg acgcgcccca ggtggccgag 840gacgatttcg cgctgatttc aatgccgacg gattttctcg ggctgaatgt atatacggcg 900acctttgtgc gtgccgacgc ggagggcagg ccggaggaga ttaaactgcc gcggaattac 960ccgcgcgcgg atagcgcgtg gttgaatatt gtgccccagt cgatgtactg ggccacacgg 1020ctggcgcggg aaacctacgg cgtgagatca atctacatca ccgaaaacgg ctgcggctac 1080gacgacgagc ccgtcgacgg cggcgaggtg ctcgacctgc atcgacgcga ttttctgcgc 1140aaccaccttc gggaattgca tcgcgccata ggcgacggcg tgcccgttga cgggtatttt 1200ctctggtcct tcatggacaa ctacgagtgg gaggacgggt atgcgcggcg gttcggcatc 1260gttcacgtcg acttcgaaag ccagaaacgg actccaaaac tctcggcgcg ctattacgcg 1320caggtaatga aagaaaaccg gatcctgtga 1350142449PRTUnknownObtained from environmental sample 142Met Leu Ser Tyr Thr Ser Pro Phe Pro Lys Asn Phe Val Trp Gly Val 1 5 10 15 Ala Thr Ala Ala Pro Gln Ile Glu Gly Ala Ala Arg Glu Asp Gly Lys 20 25 30 Gly Glu Ser Ile Trp Asp Arg Phe Cys Arg Val Pro Gly Lys Val His 35 40 45 Asn Gly Asp Thr Leu Asp Val Ala Cys Asp His Tyr His Arg Phe Arg 50 55 60 Glu Asp Phe Ala Leu Met Arg Asp Leu Gly Val Arg His Tyr Arg Leu 65 70 75 80 Ser Leu Ala Trp Pro Arg Ile Phe Pro Asp Gly Asp Gly Ala Leu Asn 85 90 95 Gln Arg Gly Val Asp Phe Tyr His Arg Leu Phe Glu Ala Met Ile Glu 100 105 110 His Gly Ile Thr Pro Trp Val Thr Leu Phe His Trp Asp Leu Pro Gln 115 120 125 Ala Leu Glu Asp Arg Gly Gly Trp Cys Glu Arg Leu Thr Val Asp Ala 130 135 140 Phe Gly Arg Tyr Ala Asp Thr Val Val Lys Ala Phe Gly Asp Arg Val 145 150 155 160 Lys Asn Trp Ile Thr Leu Asn Glu Ile Arg Cys Phe Thr Leu Leu Ala 165 170 175 Tyr Asp Leu Cys Ile Lys Ala Pro Gly Arg Lys Val Ser Arg Ala Gln 180 185 190 Leu Asn Gln Thr Tyr His His Ala Leu Ile Cys His Gly His Gly Val 195 200 205 Arg Ala Val Arg Glu His Gly Gly Arg Gly Ala Arg Val Gly Leu Thr 210 215 220 Asp Asn Ser Asp Val Cys Val Pro Val Thr Glu Thr Ala Pro Asp Ile 225 230 235 240 Ile Ala Ala Arg Ser Trp Tyr Ala Ser Arg Asn Ile His Leu Leu Asp 245 250 255 Pro Ile Tyr Arg Gly Glu Tyr Ala Pro Glu Tyr Leu Glu Arg Cys Gly 260 265 270 Ala Asp Ala Pro Gln Val Ala Glu Asp Asp Phe Ala Leu Ile Ser Met 275 280 285 Pro Thr Asp Phe Leu Gly Leu Asn Val Tyr Thr Ala Thr Phe Val Arg 290 295 300 Ala Asp Ala Glu Gly Arg Pro Glu Glu Ile Lys Leu Pro Arg Asn Tyr 305 310 315 320 Pro Arg Ala Asp Ser Ala Trp Leu Asn Ile Val Pro Gln Ser Met Tyr 325 330 335 Trp Ala Thr Arg Leu Ala Arg Glu Thr Tyr Gly Val Arg Ser Ile Tyr 340 345 350 Ile Thr Glu Asn Gly Cys Gly Tyr Asp Asp Glu Pro Val Asp Gly Gly 355 360 365 Glu Val Leu Asp Leu His Arg Arg Asp Phe Leu Arg Asn His Leu Arg 370 375 380 Glu Leu His Arg Ala Ile Gly Asp Gly Val Pro Val Asp Gly Tyr Phe 385 390 395 400 Leu Trp Ser Phe Met Asp Asn Tyr Glu Trp Glu Asp Gly Tyr Ala Arg 405 410 415 Arg Phe Gly Ile Val His Val Asp Phe Glu Ser Gln Lys Arg Thr Pro 420 425 430 Lys Leu Ser Ala Arg Tyr Tyr Ala Gln Val Met Lys Glu Asn Arg Ile 435 440 445 Leu 1431188DNAUnknownObtained from environmental sample 143atgaccatca ccttccccga cgggttctgg tgggggacgg cgacggccgc ccaccaggtg 60gagggcggca actggaacac cgactggtgg gcctacgagc acgccccggg cacccgctgc 120gcggagccgt ccggcgatgc gtgcgaccac tggcaccgct acccggagga catcgccctc 180ctcgccgcgc tcgggttcag tgcctaccgc ttctcggtgg aatgggctcg catcgagccc 240gaggaagggc atttctcccg cgccaccctc gaccactacc ggcgcatgat cgcctgctgc 300cgcgaccacg ggctggcccc ggtggtgacc ttccaccact tcaccacccc ccgctgggcc 360gcggccgggg gctgctggtc cgacccggtc accgccgagc gcttcgcccg ttactgcgag 420cgcaccgtgg ccgccctcgg cgacgagatc gcgatggcct gcacgatcaa cgagccgaac 480atcgtggcca ccctcgggta cttcctcggc gagttcccgc cggccgtcgc cgaccccgac 540cgctaccggc aggcgaacga cacgctgatc cgcgcccatc gcctcgccta cgaggcgctg 600aaggccgggc ccggcgagtt ccccgtcggc ctcaccctgt cgatggccga gttcgtcgcc 660gagcccggcg gcgaggccca cctcgcccag gtccggcaca cgatggagga catcttcctg 720gaggccgccc ggggcgacga cttcatcggg gtgcagacct acagccgcat gcgcttcggt 780cccgactcgc cgatcccgct cgggccggcc gagggcgtcg aggtcgtcca gatggggtac 840gagtactggc cgtgggcgct cgaggcgacg atccggcgcg ccgccgaggt caccggcacg 900gcggtccacg tcaccgagaa cggcatcggg accgccgacg acacgcagcg ggtcgcctac 960gtcaccgagg ccctccgggg gctgcggcgc tgcctcgacg acggcatcga cgtccgcagc 1020tacttctact ggacgctgct cgacaacttc gagtggacgc gcggctacgt gccgacgttc 1080gggctcgtcg ccgtcgaccg caccacccag cgccggtcgg tgaagccgag cgcggtgtgg 1140ctcggcgagg tcgcccgcac gaaccgcctc gagctcccgg accgctga 1188144395PRTUnknownObtained from environmental sample 144Met Thr Ile Thr Phe Pro Asp Gly Phe Trp Trp Gly Thr Ala Thr Ala 1 5 10 15 Ala His Gln Val Glu Gly Gly Asn Trp Asn Thr Asp Trp Trp Ala Tyr 20 25 30 Glu His Ala Pro Gly Thr Arg Cys Ala Glu Pro Ser Gly Asp Ala Cys 35 40 45 Asp His Trp His Arg Tyr Pro Glu Asp Ile Ala Leu Leu Ala Ala Leu 50 55 60 Gly Phe Ser Ala Tyr Arg Phe Ser Val Glu Trp Ala Arg Ile Glu Pro 65 70 75 80 Glu Glu Gly His Phe Ser Arg Ala Thr Leu Asp His Tyr Arg Arg Met 85 90 95 Ile Ala Cys Cys Arg Asp His Gly Leu Ala Pro Val Val Thr Phe His 100 105 110 His Phe Thr Thr Pro Arg Trp Ala Ala Ala Gly Gly Cys Trp Ser Asp 115 120 125 Pro Val Thr Ala Glu Arg Phe Ala Arg Tyr Cys Glu Arg Thr Val Ala 130 135 140 Ala Leu Gly Asp Glu Ile Ala Met Ala Cys Thr Ile Asn Glu Pro Asn 145 150

155 160 Ile Val Ala Thr Leu Gly Tyr Phe Leu Gly Glu Phe Pro Pro Ala Val 165 170 175 Ala Asp Pro Asp Arg Tyr Arg Gln Ala Asn Asp Thr Leu Ile Arg Ala 180 185 190 His Arg Leu Ala Tyr Glu Ala Leu Lys Ala Gly Pro Gly Glu Phe Pro 195 200 205 Val Gly Leu Thr Leu Ser Met Ala Glu Phe Val Ala Glu Pro Gly Gly 210 215 220 Glu Ala His Leu Ala Gln Val Arg His Thr Met Glu Asp Ile Phe Leu 225 230 235 240 Glu Ala Ala Arg Gly Asp Asp Phe Ile Gly Val Gln Thr Tyr Ser Arg 245 250 255 Met Arg Phe Gly Pro Asp Ser Pro Ile Pro Leu Gly Pro Ala Glu Gly 260 265 270 Val Glu Val Val Gln Met Gly Tyr Glu Tyr Trp Pro Trp Ala Leu Glu 275 280 285 Ala Thr Ile Arg Arg Ala Ala Glu Val Thr Gly Thr Ala Val His Val 290 295 300 Thr Glu Asn Gly Ile Gly Thr Ala Asp Asp Thr Gln Arg Val Ala Tyr 305 310 315 320 Val Thr Glu Ala Leu Arg Gly Leu Arg Arg Cys Leu Asp Asp Gly Ile 325 330 335 Asp Val Arg Ser Tyr Phe Tyr Trp Thr Leu Leu Asp Asn Phe Glu Trp 340 345 350 Thr Arg Gly Tyr Val Pro Thr Phe Gly Leu Val Ala Val Asp Arg Thr 355 360 365 Thr Gln Arg Arg Ser Val Lys Pro Ser Ala Val Trp Leu Gly Glu Val 370 375 380 Ala Arg Thr Asn Arg Leu Glu Leu Pro Asp Arg 385 390 395 1451386DNAUnknownObtained from environmental sample 145atgtcgtttc cgagaaattt cctgtgggga tcagccacct cctcctacca aatcgaaggc 60gcctggcaag aagacggcaa aggcccaaat atctgggacg tgttttcaca caccccgggg 120aaagtcgcca atggcgacac cggtgatatc gccatcgacc actaccaccg ataccgagac 180gacgttgccc tgatggctga gcttggactt caggcatacc gtttctcgtt ctcctgggcc 240agaataatgc cggaaggagc aggccccatc gagcaacggg gtctggactt ctacgaccgc 300ctcattgatg cactgctgga gaaaaacatc caacccatgg ccaccctcta ccactgggat 360ttaccagccg cactgcaaga cagagggggg tggactaacc gcgacagcgc gtcctggttt 420gctgactact cagccgttgt tcacgacgct ttttctgacc gggtgggaat gtgggcaacg 480ttgaacgagc cgtgggtgtc tgcatttttg ggccacggaa ctggcatcca cgcacctggc 540atcacaagcc cccacgcggc gttcgccgcg gggcatcacc tgcttctggg gcatggcaag 600gccatccaag cgatgcgcgc tcaatcgtct agcacccaac tgggaattgt tttgaacctc 660gcccccgtgt atctcgaagg tgacacccct gctgaccacc cggctcacac ctccgtggca 720ctacacgatg ccattttgaa tgggttgtgg acagagccgc ttctgcgctc cagatacccc 780gacctgcttc ttcaactagg cgacatggtg acaaaaaaca tccacgacgg tgacctcgcc 840atcatggccg agccgattga ctggatgggc atcaactact accaggacat tagatttgtg 900gccactgatg ttgcccccac ggctaacccg atggcccctc cgggtaacga cctgccgggc 960accgtcgggg tggagcctgc gccagcaatc ggaaacatca ccagctttgg ctggtccacc 1020acccccgacg gactgcgagt actgttggtg ggcctggatg aggaatacga caacctcccg 1080ccgatattca ttaccgaaaa cgggtgtgct tacgattacc ccgtcgagga cggtgtcgtc 1140aacgacaccc ttcgtgtcac atacatgcga gaacacctca ccgcgttgtc gcaggccatt 1200gaggcgggtg tgaatgtccg gggctatatg cactggtctc tgttcgacaa cttcgagtgg 1260gccgaagggt atcgccaacg ctttggcatg gtgcacgtcg actttgagac cttggagcgg 1320actcccaaag cctcagctca ctactattca cgtgtcatca caaataacgc cctctctgac 1380gactga 1386146461PRTUnknownObtained from environmental sample 146Met Ser Phe Pro Arg Asn Phe Leu Trp Gly Ser Ala Thr Ser Ser Tyr 1 5 10 15 Gln Ile Glu Gly Ala Trp Gln Glu Asp Gly Lys Gly Pro Asn Ile Trp 20 25 30 Asp Val Phe Ser His Thr Pro Gly Lys Val Ala Asn Gly Asp Thr Gly 35 40 45 Asp Ile Ala Ile Asp His Tyr His Arg Tyr Arg Asp Asp Val Ala Leu 50 55 60 Met Ala Glu Leu Gly Leu Gln Ala Tyr Arg Phe Ser Phe Ser Trp Ala 65 70 75 80 Arg Ile Met Pro Glu Gly Ala Gly Pro Ile Glu Gln Arg Gly Leu Asp 85 90 95 Phe Tyr Asp Arg Leu Ile Asp Ala Leu Leu Glu Lys Asn Ile Gln Pro 100 105 110 Met Ala Thr Leu Tyr His Trp Asp Leu Pro Ala Ala Leu Gln Asp Arg 115 120 125 Gly Gly Trp Thr Asn Arg Asp Ser Ala Ser Trp Phe Ala Asp Tyr Ser 130 135 140 Ala Val Val His Asp Ala Phe Ser Asp Arg Val Gly Met Trp Ala Thr 145 150 155 160 Leu Asn Glu Pro Trp Val Ser Ala Phe Leu Gly His Gly Thr Gly Ile 165 170 175 His Ala Pro Gly Ile Thr Ser Pro His Ala Ala Phe Ala Ala Gly His 180 185 190 His Leu Leu Leu Gly His Gly Lys Ala Ile Gln Ala Met Arg Ala Gln 195 200 205 Ser Ser Ser Thr Gln Leu Gly Ile Val Leu Asn Leu Ala Pro Val Tyr 210 215 220 Leu Glu Gly Asp Thr Pro Ala Asp His Pro Ala His Thr Ser Val Ala 225 230 235 240 Leu His Asp Ala Ile Leu Asn Gly Leu Trp Thr Glu Pro Leu Leu Arg 245 250 255 Ser Arg Tyr Pro Asp Leu Leu Leu Gln Leu Gly Asp Met Val Thr Lys 260 265 270 Asn Ile His Asp Gly Asp Leu Ala Ile Met Ala Glu Pro Ile Asp Trp 275 280 285 Met Gly Ile Asn Tyr Tyr Gln Asp Ile Arg Phe Val Ala Thr Asp Val 290 295 300 Ala Pro Thr Ala Asn Pro Met Ala Pro Pro Gly Asn Asp Leu Pro Gly 305 310 315 320 Thr Val Gly Val Glu Pro Ala Pro Ala Ile Gly Asn Ile Thr Ser Phe 325 330 335 Gly Trp Ser Thr Thr Pro Asp Gly Leu Arg Val Leu Leu Val Gly Leu 340 345 350 Asp Glu Glu Tyr Asp Asn Leu Pro Pro Ile Phe Ile Thr Glu Asn Gly 355 360 365 Cys Ala Tyr Asp Tyr Pro Val Glu Asp Gly Val Val Asn Asp Thr Leu 370 375 380 Arg Val Thr Tyr Met Arg Glu His Leu Thr Ala Leu Ser Gln Ala Ile 385 390 395 400 Glu Ala Gly Val Asn Val Arg Gly Tyr Met His Trp Ser Leu Phe Asp 405 410 415 Asn Phe Glu Trp Ala Glu Gly Tyr Arg Gln Arg Phe Gly Met Val His 420 425 430 Val Asp Phe Glu Thr Leu Glu Arg Thr Pro Lys Ala Ser Ala His Tyr 435 440 445 Tyr Ser Arg Val Ile Thr Asn Asn Ala Leu Ser Asp Asp 450 455 460 1471242DNAUnknownObtained from environmental sample 147atgctaaaag ttttacgtaa acctattatt tctggattag ctttagctct attattgccg 60gcaggggcag ctggtgccga aactaatatt tcaaagaagc caaatataag tggattaacc 120gcgccgcaat tagaccaaag atataaagat tctttcacca ttggtgctgc ggttgagccg 180tatcaattat tagatgcaaa agattcacaa atgctaaagc ggcattttaa tagtatcgta 240gcagagaatg tcatgaagcc tagtagttta cagccagtag aaggacaatt caactgggag 300ccggctgata aacttgttca gtttgcgaag gaaaatggaa tggacatgcg aggtcatacg 360cttgtctggc atagccaggt accggattgg ttctttgaag atgcggcagg aaatccaatg 420gttgtttggg aaaatggcag gcaagtggtt gccgatccat caaagcttca ggaaaacaaa 480gagctcttac ttagccgatt acaaaatcat attcaggcag tcgtaacgcg ttataaagat 540gatataaaat cttgggatgt tgtcaatgaa gtaatcgatg aatggggcgg acattctgaa 600gggctgcgtc aatctccatg gttcctcatc accggaacgg actatattaa agttgctttt 660gaaactgcaa gagaatatgc agctccagac gctaagctgt atatcaatga ttacaataca 720gaagtagaac caaaaaggac gcacctttat aacttagtaa aaagtttaaa agaagaacag 780aacgttccga ttgatggtgt tgggcatcag tctcacattc aaattggctg gccttcagaa 840aaagaaattg aagatactat taatatgttt gcagatcttg gtttagataa ccaaatcacc 900gagcttgatg ttagtatgta tggctggccg gtaaggtcgt atccaactta tgatgcgatc 960ccagaactta aattcatgga tcaagcagct cgttatgatc gtttatttaa gttatatgag 1020aaattaggag ataaaatcag taatgtgaca ttctggggta ttgcggataa ccatacatgg 1080ctgaatgacc gcgcagatgt ttactatgat gaaaatggaa atgttgtatt agatagagaa 1140acaccaagag tagaaagagg agcaggaaaa gatgcgccat ttgtatttga tcctgaatac 1200aatgtaaaac cagcttattg ggcaattatc gatcacaaat aa 1242148413PRTUnknownObtained from environmental sample 148Met Leu Lys Val Leu Arg Lys Pro Ile Ile Ser Gly Leu Ala Leu Ala 1 5 10 15 Leu Leu Leu Pro Ala Gly Ala Ala Gly Ala Glu Thr Asn Ile Ser Lys 20 25 30 Lys Pro Asn Ile Ser Gly Leu Thr Ala Pro Gln Leu Asp Gln Arg Tyr 35 40 45 Lys Asp Ser Phe Thr Ile Gly Ala Ala Val Glu Pro Tyr Gln Leu Leu 50 55 60 Asp Ala Lys Asp Ser Gln Met Leu Lys Arg His Phe Asn Ser Ile Val 65 70 75 80 Ala Glu Asn Val Met Lys Pro Ser Ser Leu Gln Pro Val Glu Gly Gln 85 90 95 Phe Asn Trp Glu Pro Ala Asp Lys Leu Val Gln Phe Ala Lys Glu Asn 100 105 110 Gly Met Asp Met Arg Gly His Thr Leu Val Trp His Ser Gln Val Pro 115 120 125 Asp Trp Phe Phe Glu Asp Ala Ala Gly Asn Pro Met Val Val Trp Glu 130 135 140 Asn Gly Arg Gln Val Val Ala Asp Pro Ser Lys Leu Gln Glu Asn Lys 145 150 155 160 Glu Leu Leu Leu Ser Arg Leu Gln Asn His Ile Gln Ala Val Val Thr 165 170 175 Arg Tyr Lys Asp Asp Ile Lys Ser Trp Asp Val Val Asn Glu Val Ile 180 185 190 Asp Glu Trp Gly Gly His Ser Glu Gly Leu Arg Gln Ser Pro Trp Phe 195 200 205 Leu Ile Thr Gly Thr Asp Tyr Ile Lys Val Ala Phe Glu Thr Ala Arg 210 215 220 Glu Tyr Ala Ala Pro Asp Ala Lys Leu Tyr Ile Asn Asp Tyr Asn Thr 225 230 235 240 Glu Val Glu Pro Lys Arg Thr His Leu Tyr Asn Leu Val Lys Ser Leu 245 250 255 Lys Glu Glu Gln Asn Val Pro Ile Asp Gly Val Gly His Gln Ser His 260 265 270 Ile Gln Ile Gly Trp Pro Ser Glu Lys Glu Ile Glu Asp Thr Ile Asn 275 280 285 Met Phe Ala Asp Leu Gly Leu Asp Asn Gln Ile Thr Glu Leu Asp Val 290 295 300 Ser Met Tyr Gly Trp Pro Val Arg Ser Tyr Pro Thr Tyr Asp Ala Ile 305 310 315 320 Pro Glu Leu Lys Phe Met Asp Gln Ala Ala Arg Tyr Asp Arg Leu Phe 325 330 335 Lys Leu Tyr Glu Lys Leu Gly Asp Lys Ile Ser Asn Val Thr Phe Trp 340 345 350 Gly Ile Ala Asp Asn His Thr Trp Leu Asn Asp Arg Ala Asp Val Tyr 355 360 365 Tyr Asp Glu Asn Gly Asn Val Val Leu Asp Arg Glu Thr Pro Arg Val 370 375 380 Glu Arg Gly Ala Gly Lys Asp Ala Pro Phe Val Phe Asp Pro Glu Tyr 385 390 395 400 Asn Val Lys Pro Ala Tyr Trp Ala Ile Ile Asp His Lys 405 410 1491068DNAUnknownObtained from environmental sample 149atgacccgaa tgcgcgggat aaacatgggc ggctggctca gccaaattga cgccatacag 60gaaaaagacc ctgatacatt tcccggaaca gacaaacata tggaaacttt tatccagcag 120aaggattttg ccaatgtcag gagatggggt ttcgatcatg tgcgaattcc aattgacgcg 180tatctgttct ttaccgaaaa aggagagccg attgaaaaca ggcttgccaa tcttgaccgc 240gccgtagagt atgcgctgcc cgccggcctc aacatgatat tggacctcca cgagtgtccg 300gggcacgatt tttcggaagc agtaaaaagc cctgtccaaa aacttttctc gggagatgac 360acctggataa ggaaaactga aaaaatatgg gcttgccttg ccgagcgtta ttctcaaaag 420ggccacgtcc tttttgagac gctcaatgag cctgtcgctc ccaccgcgga gatttggaac 480aatgttaagg acaggctctg ccgcgaaata cggctccacg ccccctggtc gactataatc 540accggctcca acatgtggaa ctcagcggca accttcgaca gcctcacgcc ctttgacgac 600gacaacatga tctacagcgt acatttttac gagccgctgc ttttcacgca ccagaacgca 660ttgtggatcg acaatccgga aatcaggatc gcaaggccgt atccgggcga ttacggtccc 720ggctttgtcc ccaaagacgg tttgacgctg tcggacggcg tctggaacag ggatcgtctc 780gccggcgcat tagcgcccgt gaacgcgttc aggaaaaagt acaatgcgaa gattatctgt 840aacgagttcg gcgtttacgc gcccgtagac cttcaatcgc agctgcgctg gtatgaagat 900ctgctctcaa tcctcaatga gacggggatc ggtttcacgt actggaacta taaaaatctc 960gacttcggga taatttccat aggggagaag ctgcacgaag cccttccgca gtacgacaat 1020agcgatcgaa taaataaatc ggttcttgaa gtgttaaaaa agtattag 1068150355PRTUnknownObtained from environmental sample 150Met Thr Arg Met Arg Gly Ile Asn Met Gly Gly Trp Leu Ser Gln Ile 1 5 10 15 Asp Ala Ile Gln Glu Lys Asp Pro Asp Thr Phe Pro Gly Thr Asp Lys 20 25 30 His Met Glu Thr Phe Ile Gln Gln Lys Asp Phe Ala Asn Val Arg Arg 35 40 45 Trp Gly Phe Asp His Val Arg Ile Pro Ile Asp Ala Tyr Leu Phe Phe 50 55 60 Thr Glu Lys Gly Glu Pro Ile Glu Asn Arg Leu Ala Asn Leu Asp Arg 65 70 75 80 Ala Val Glu Tyr Ala Leu Pro Ala Gly Leu Asn Met Ile Leu Asp Leu 85 90 95 His Glu Cys Pro Gly His Asp Phe Ser Glu Ala Val Lys Ser Pro Val 100 105 110 Gln Lys Leu Phe Ser Gly Asp Asp Thr Trp Ile Arg Lys Thr Glu Lys 115 120 125 Ile Trp Ala Cys Leu Ala Glu Arg Tyr Ser Gln Lys Gly His Val Leu 130 135 140 Phe Glu Thr Leu Asn Glu Pro Val Ala Pro Thr Ala Glu Ile Trp Asn 145 150 155 160 Asn Val Lys Asp Arg Leu Cys Arg Glu Ile Arg Leu His Ala Pro Trp 165 170 175 Ser Thr Ile Ile Thr Gly Ser Asn Met Trp Asn Ser Ala Ala Thr Phe 180 185 190 Asp Ser Leu Thr Pro Phe Asp Asp Asp Asn Met Ile Tyr Ser Val His 195 200 205 Phe Tyr Glu Pro Leu Leu Phe Thr His Gln Asn Ala Leu Trp Ile Asp 210 215 220 Asn Pro Glu Ile Arg Ile Ala Arg Pro Tyr Pro Gly Asp Tyr Gly Pro 225 230 235 240 Gly Phe Val Pro Lys Asp Gly Leu Thr Leu Ser Asp Gly Val Trp Asn 245 250 255 Arg Asp Arg Leu Ala Gly Ala Leu Ala Pro Val Asn Ala Phe Arg Lys 260 265 270 Lys Tyr Asn Ala Lys Ile Ile Cys Asn Glu Phe Gly Val Tyr Ala Pro 275 280 285 Val Asp Leu Gln Ser Gln Leu Arg Trp Tyr Glu Asp Leu Leu Ser Ile 290 295 300 Leu Asn Glu Thr Gly Ile Gly Phe Thr Tyr Trp Asn Tyr Lys Asn Leu 305 310 315 320 Asp Phe Gly Ile Ile Ser Ile Gly Glu Lys Leu His Glu Ala Leu Pro 325 330 335 Gln Tyr Asp Asn Ser Asp Arg Ile Asn Lys Ser Val Leu Glu Val Leu 340 345 350 Lys Lys Tyr 355 1511068DNAUnknownObtained from environmental sample 151atgaccagaa tgcgcggaat aaacatgggc ggctggctca gccagattga cgccatacag 60gaaaaagacc ccgataaatt tcccggaata gacaaacaca tggaaacatt tatcggttcc 120aatgattttt ccaatgtcag gaaatggggt ttcgatcatg tgcgaatccc gattgacgcg 180tacctttttt ttaccgatca ggaagccccg attgaaaaca ggcttgtcca tattgacaac 240gccgtaaaat acgcgcggag caacggcctc aaggtgatat tggacctcca cgagtgtccg 300gggcatgatt tttcggacgc ggcaaaaggc cctgtccaga aacttttctc cggagatgac 360acttatataa aaaagaccga aaaaatatgg gcatgtctgg ccgagcgtta ttcgaaaaac 420gacaacgtcc tctatgagac tctcaacgag cctgtcgccc ccacgcctga gatttggaac 480actgttaagg acaggctctg ccgggaaata cgcctgcacg ccccctgggc gacgataatc 540accggttcca atatgtggaa ttggccgagc acctttgaca gcctgacgcc ctttgacgac 600gacaacgtga tctacagcgt gcatttttac gagccgctgc tttttacgca ccagaacgcg 660ccctggatca acaattctga aatcaggatc acaaggccgt atccgggcga ttacggcccc 720ggctttgtcc gcaaatacgg cttaactctg tcagccggcg tctggaacag ggacaggctg 780gcgaaggaat tcgcgcccgt gaacgcgttc aggaaaaaat acaaggcgca ggttatatgc 840gacgaattcg gcgtttacgc gcctgtcgag attgaatcgc agcttcgatg gtatgaggat 900ttgctctcga tcctcaggga gatgggtata gggttttcgt actggaacta taaaaacctg 960gactttggga taatttccat aggggagaag ctgcacgaaa gccttctgca gtacggcaac 1020ggcgacagga taaatcatat ggttcttgac ttgctaaaga agtactaa 1068152355PRTUnknownObtained from environmental sample 152Met Thr Arg Met Arg Gly Ile Asn Met Gly Gly Trp Leu Ser Gln Ile 1 5 10 15 Asp Ala Ile Gln Glu Lys Asp Pro Asp Lys Phe Pro Gly Ile Asp Lys 20

25 30 His Met Glu Thr Phe Ile Gly Ser Asn Asp Phe Ser Asn Val Arg Lys 35 40 45 Trp Gly Phe Asp His Val Arg Ile Pro Ile Asp Ala Tyr Leu Phe Phe 50 55 60 Thr Asp Gln Glu Ala Pro Ile Glu Asn Arg Leu Val His Ile Asp Asn 65 70 75 80 Ala Val Lys Tyr Ala Arg Ser Asn Gly Leu Lys Val Ile Leu Asp Leu 85 90 95 His Glu Cys Pro Gly His Asp Phe Ser Asp Ala Ala Lys Gly Pro Val 100 105 110 Gln Lys Leu Phe Ser Gly Asp Asp Thr Tyr Ile Lys Lys Thr Glu Lys 115 120 125 Ile Trp Ala Cys Leu Ala Glu Arg Tyr Ser Lys Asn Asp Asn Val Leu 130 135 140 Tyr Glu Thr Leu Asn Glu Pro Val Ala Pro Thr Pro Glu Ile Trp Asn 145 150 155 160 Thr Val Lys Asp Arg Leu Cys Arg Glu Ile Arg Leu His Ala Pro Trp 165 170 175 Ala Thr Ile Ile Thr Gly Ser Asn Met Trp Asn Trp Pro Ser Thr Phe 180 185 190 Asp Ser Leu Thr Pro Phe Asp Asp Asp Asn Val Ile Tyr Ser Val His 195 200 205 Phe Tyr Glu Pro Leu Leu Phe Thr His Gln Asn Ala Pro Trp Ile Asn 210 215 220 Asn Ser Glu Ile Arg Ile Thr Arg Pro Tyr Pro Gly Asp Tyr Gly Pro 225 230 235 240 Gly Phe Val Arg Lys Tyr Gly Leu Thr Leu Ser Ala Gly Val Trp Asn 245 250 255 Arg Asp Arg Leu Ala Lys Glu Phe Ala Pro Val Asn Ala Phe Arg Lys 260 265 270 Lys Tyr Lys Ala Gln Val Ile Cys Asp Glu Phe Gly Val Tyr Ala Pro 275 280 285 Val Glu Ile Glu Ser Gln Leu Arg Trp Tyr Glu Asp Leu Leu Ser Ile 290 295 300 Leu Arg Glu Met Gly Ile Gly Phe Ser Tyr Trp Asn Tyr Lys Asn Leu 305 310 315 320 Asp Phe Gly Ile Ile Ser Ile Gly Glu Lys Leu His Glu Ser Leu Leu 325 330 335 Gln Tyr Gly Asn Gly Asp Arg Ile Asn His Met Val Leu Asp Leu Leu 340 345 350 Lys Lys Tyr 355 1531068DNAUnknownObtained from environmental sample 153atgcaaagaa tgcgaggctt aaatattggc ggctggctca gccagattga cgccatacag 60gaaaaggacc ctgagggctt tcccggaata gacaaacaca tggaaacatt cattgtttcc 120ggagattttt acaatatcag gaaatggggt ttcgaccatg tgcggcttcc cattgactcg 180tacctgttct ttacggaaga cgatgccccc attgagaaca ggtttgccca tcttgaccgc 240gccgtacaat tcgcgaagag caacagcctc aagctgatat tggacctcca cgagtgtccg 300ggacacgatt tttccgaagc cgcgaaagga cccgtccaga aacttttttc gggagatgac 360gtttacataa aaaaaaccga gaaaatctgg gcctgcctcg ccgagcgtta ttcgaaaaac 420gaccatgtac tctttgagac tctcaacgaa cctgtcgctc ccactgccga aatttggaac 480aaggttaagg acaggctctg cagagtaatc cgcatccacg cgccctggtc gaccataatc 540accggctcca atatgtggaa ctcgccgtcc gccttcgacg gtcttacgcc ctttgacgat 600ggcaacgtga tctacagcgt gcatttttac gagccgctgc tttttacgca tcagaacgcg 660ccgtggatcg acaatccgga gatcaggacg gcaaggccct atccgggcga ttacggcccc 720ggccttgtcc gcaaatacgg tatggcgcag tcggccggca tctggaacaa gaaacggctt 780gcaaaagaat ttgagcccgt ggacgcgttc aggaaaaaat acaaggcgcg cgttatctgt 840aacgagtttg gcgtgtacgc ccccgccgat ctggaatcgc agcttcgctg gtatgaggat 900ctgctctcaa tcctcaacgg gatgcagata ggttactcgt actggaacta caaaaatctg 960gatttcggaa taatttccat aggggagaaa ctgcacgaaa gactttcgca gtatgacaac 1020gacgagcgga taaaccaccc ggtgctgaat gtgctgaaga aatattaa 1068154355PRTUnknownObtained from environmental sample 154Met Gln Arg Met Arg Gly Leu Asn Ile Gly Gly Trp Leu Ser Gln Ile 1 5 10 15 Asp Ala Ile Gln Glu Lys Asp Pro Glu Gly Phe Pro Gly Ile Asp Lys 20 25 30 His Met Glu Thr Phe Ile Val Ser Gly Asp Phe Tyr Asn Ile Arg Lys 35 40 45 Trp Gly Phe Asp His Val Arg Leu Pro Ile Asp Ser Tyr Leu Phe Phe 50 55 60 Thr Glu Asp Asp Ala Pro Ile Glu Asn Arg Phe Ala His Leu Asp Arg 65 70 75 80 Ala Val Gln Phe Ala Lys Ser Asn Ser Leu Lys Leu Ile Leu Asp Leu 85 90 95 His Glu Cys Pro Gly His Asp Phe Ser Glu Ala Ala Lys Gly Pro Val 100 105 110 Gln Lys Leu Phe Ser Gly Asp Asp Val Tyr Ile Lys Lys Thr Glu Lys 115 120 125 Ile Trp Ala Cys Leu Ala Glu Arg Tyr Ser Lys Asn Asp His Val Leu 130 135 140 Phe Glu Thr Leu Asn Glu Pro Val Ala Pro Thr Ala Glu Ile Trp Asn 145 150 155 160 Lys Val Lys Asp Arg Leu Cys Arg Val Ile Arg Ile His Ala Pro Trp 165 170 175 Ser Thr Ile Ile Thr Gly Ser Asn Met Trp Asn Ser Pro Ser Ala Phe 180 185 190 Asp Gly Leu Thr Pro Phe Asp Asp Gly Asn Val Ile Tyr Ser Val His 195 200 205 Phe Tyr Glu Pro Leu Leu Phe Thr His Gln Asn Ala Pro Trp Ile Asp 210 215 220 Asn Pro Glu Ile Arg Thr Ala Arg Pro Tyr Pro Gly Asp Tyr Gly Pro 225 230 235 240 Gly Leu Val Arg Lys Tyr Gly Met Ala Gln Ser Ala Gly Ile Trp Asn 245 250 255 Lys Lys Arg Leu Ala Lys Glu Phe Glu Pro Val Asp Ala Phe Arg Lys 260 265 270 Lys Tyr Lys Ala Arg Val Ile Cys Asn Glu Phe Gly Val Tyr Ala Pro 275 280 285 Ala Asp Leu Glu Ser Gln Leu Arg Trp Tyr Glu Asp Leu Leu Ser Ile 290 295 300 Leu Asn Gly Met Gln Ile Gly Tyr Ser Tyr Trp Asn Tyr Lys Asn Leu 305 310 315 320 Asp Phe Gly Ile Ile Ser Ile Gly Glu Lys Leu His Glu Arg Leu Ser 325 330 335 Gln Tyr Asp Asn Asp Glu Arg Ile Asn His Pro Val Leu Asn Val Leu 340 345 350 Lys Lys Tyr 355 155954DNAUnknownObtained from environmental sample 155atgttaaagg attccggttt ttataagggc atcaatctcg gcggctggct gtcccagtgc 60gactacagcg aggagcgcct gaacagcttc atcaccgaaa aggactttga ggtgatcgcc 120tcctggggtt ttgaccacgt ccgcctcccg gtggactata atgtcatcca ggatgcggaa 180ggccgcatga tggagaaagg ccttgcacgc atcgacgccg cgcttcggtt ttgtgagaag 240accgggcttc acatggttct cgacctgcat aagacaccgg gcttttcctt cgacccgcag 300gagcaggaga tgggattctt ccggtcggcg cccgaccagc agctcttcta cacgatctgg 360gagagccttg ctgcccggta tgcagacaaa tcggagatac tcatgttcga tcttctgaac 420gagatcacgg agccggcgta tctggaggac tggaaccgga tttccgcgga atgcatccgc 480cgcatccggc gtacgatgcc ggacgtccga attctggtcg gaagctatca ccacaatgcc 540gtcagcgcgg taaaggacct gcctgcgccg gcagacgata aggtttttta cagctttcac 600tgttacgacc ctcacaccta tacccaccag ggcgcttact ggatgccgga tgactttgac 660atcgatgcaa gagtttcctt ccgcgacacc ggcgttaccc ccgtcttctt cgaaaagctg 720tttgcctccg ccgttgaaaa ggcgcaggcg gaagggacgg aactgtactg cggagaatac 780ggcgtcatcg acattgttcc gccggaggat gccgttctct ggttccggac cattcatgag 840gtctttgaag cattcgggat tgcaagaagc gtctggagct ataaggaaat ggatttcggt 900ctcgccgacc cccgcatgga tgcggtccgg gcagagctgc tgacctgtct ctga 954156317PRTUnknownObtained from environmental sample 156Met Leu Lys Asp Ser Gly Phe Tyr Lys Gly Ile Asn Leu Gly Gly Trp 1 5 10 15 Leu Ser Gln Cys Asp Tyr Ser Glu Glu Arg Leu Asn Ser Phe Ile Thr 20 25 30 Glu Lys Asp Phe Glu Val Ile Ala Ser Trp Gly Phe Asp His Val Arg 35 40 45 Leu Pro Val Asp Tyr Asn Val Ile Gln Asp Ala Glu Gly Arg Met Met 50 55 60 Glu Lys Gly Leu Ala Arg Ile Asp Ala Ala Leu Arg Phe Cys Glu Lys 65 70 75 80 Thr Gly Leu His Met Val Leu Asp Leu His Lys Thr Pro Gly Phe Ser 85 90 95 Phe Asp Pro Gln Glu Gln Glu Met Gly Phe Phe Arg Ser Ala Pro Asp 100 105 110 Gln Gln Leu Phe Tyr Thr Ile Trp Glu Ser Leu Ala Ala Arg Tyr Ala 115 120 125 Asp Lys Ser Glu Ile Leu Met Phe Asp Leu Leu Asn Glu Ile Thr Glu 130 135 140 Pro Ala Tyr Leu Glu Asp Trp Asn Arg Ile Ser Ala Glu Cys Ile Arg 145 150 155 160 Arg Ile Arg Arg Thr Met Pro Asp Val Arg Ile Leu Val Gly Ser Tyr 165 170 175 His His Asn Ala Val Ser Ala Val Lys Asp Leu Pro Ala Pro Ala Asp 180 185 190 Asp Lys Val Phe Tyr Ser Phe His Cys Tyr Asp Pro His Thr Tyr Thr 195 200 205 His Gln Gly Ala Tyr Trp Met Pro Asp Asp Phe Asp Ile Asp Ala Arg 210 215 220 Val Ser Phe Arg Asp Thr Gly Val Thr Pro Val Phe Phe Glu Lys Leu 225 230 235 240 Phe Ala Ser Ala Val Glu Lys Ala Gln Ala Glu Gly Thr Glu Leu Tyr 245 250 255 Cys Gly Glu Tyr Gly Val Ile Asp Ile Val Pro Pro Glu Asp Ala Val 260 265 270 Leu Trp Phe Arg Thr Ile His Glu Val Phe Glu Ala Phe Gly Ile Ala 275 280 285 Arg Ser Val Trp Ser Tyr Lys Glu Met Asp Phe Gly Leu Ala Asp Pro 290 295 300 Arg Met Asp Ala Val Arg Ala Glu Leu Leu Thr Cys Leu 305 310 315 157954DNAUnknownObtained from environmental sample 157atgttaaagg attccggttt ttataagggc atcaatctcg gcggctggct gtcccagtgc 60gactacagcg aggagcgcct gaacagcttc atcaccgaaa aagactttga ggtgatcgcc 120tcctggggtt ttgaccacgt ccgtctgccg gtggactata atgtcatcca ggatgcggaa 180ggccgcatga tggaggaagg cctcgcacgc atcgacgccg cgcttcggtt ttgtgaaaag 240accgggcttc acatggttct cgacctgcat aagacaccgg gcttttcctt cgacccgcag 300gagcaggaga tgggattctt ccggtcggcg cccgaccagc agcgcttcta cacgatctgg 360gagagccttg ctgcccggta tgcagacaaa tcggagatgc tcatgttcga tcttctgaac 420gagatcacgg agccggcgta tctgaaggac tggaaccgga tttccgcgga atgcatccgc 480cgcatccggc gtacgatgcc ggacgtccgg attctggtcg gaagctatca ccacaatgcc 540gtcagcgcgg taaaggacct gcctgcgccg gcggacgacc gggtttttta cagctttcac 600tgttacgacc ctcacaccta tacccaccag ggcgcttact ggatgccgga tgactttgac 660atcgatgcaa gagtttcctt ccgcgacatc ggcgtcaccc ccgccttctt cgaagagctg 720tttgcatctg ccgttgaaaa ggcgaaggtg gaagggacgg aactgtactg cggagaatac 780ggcgtcatcg acattgttcc gccggaggat gccgttctct ggttccggac cattcatgag 840gtctttgaga aatacgggat tgcaagaagc gtctggagct ataaggaaat ggatttcggt 900ctctccgacc cccgcatgga cgcggtccgg gcagagctgc tgacctgtct ctga 954158317PRTUnknownObtained from environmental sample 158Met Leu Lys Asp Ser Gly Phe Tyr Lys Gly Ile Asn Leu Gly Gly Trp 1 5 10 15 Leu Ser Gln Cys Asp Tyr Ser Glu Glu Arg Leu Asn Ser Phe Ile Thr 20 25 30 Glu Lys Asp Phe Glu Val Ile Ala Ser Trp Gly Phe Asp His Val Arg 35 40 45 Leu Pro Val Asp Tyr Asn Val Ile Gln Asp Ala Glu Gly Arg Met Met 50 55 60 Glu Glu Gly Leu Ala Arg Ile Asp Ala Ala Leu Arg Phe Cys Glu Lys 65 70 75 80 Thr Gly Leu His Met Val Leu Asp Leu His Lys Thr Pro Gly Phe Ser 85 90 95 Phe Asp Pro Gln Glu Gln Glu Met Gly Phe Phe Arg Ser Ala Pro Asp 100 105 110 Gln Gln Arg Phe Tyr Thr Ile Trp Glu Ser Leu Ala Ala Arg Tyr Ala 115 120 125 Asp Lys Ser Glu Met Leu Met Phe Asp Leu Leu Asn Glu Ile Thr Glu 130 135 140 Pro Ala Tyr Leu Lys Asp Trp Asn Arg Ile Ser Ala Glu Cys Ile Arg 145 150 155 160 Arg Ile Arg Arg Thr Met Pro Asp Val Arg Ile Leu Val Gly Ser Tyr 165 170 175 His His Asn Ala Val Ser Ala Val Lys Asp Leu Pro Ala Pro Ala Asp 180 185 190 Asp Arg Val Phe Tyr Ser Phe His Cys Tyr Asp Pro His Thr Tyr Thr 195 200 205 His Gln Gly Ala Tyr Trp Met Pro Asp Asp Phe Asp Ile Asp Ala Arg 210 215 220 Val Ser Phe Arg Asp Ile Gly Val Thr Pro Ala Phe Phe Glu Glu Leu 225 230 235 240 Phe Ala Ser Ala Val Glu Lys Ala Lys Val Glu Gly Thr Glu Leu Tyr 245 250 255 Cys Gly Glu Tyr Gly Val Ile Asp Ile Val Pro Pro Glu Asp Ala Val 260 265 270 Leu Trp Phe Arg Thr Ile His Glu Val Phe Glu Lys Tyr Gly Ile Ala 275 280 285 Arg Ser Val Trp Ser Tyr Lys Glu Met Asp Phe Gly Leu Ser Asp Pro 290 295 300 Arg Met Asp Ala Val Arg Ala Glu Leu Leu Thr Cys Leu 305 310 315 1591023DNAUnknownObtained from environmental sample 159atgaatccaa cattcagttc cgtaccggca ttaaaggagc tgtttgcggc ggacttcaac 60atcggggcgg cggtgaatcc gacgacgatc cggacgcagg aggcgttgct ggcttatcat 120tttaacagcc tgactgcgga gaacgagatg aagttcgtca gcgtgcatcc ggaggagcag 180acctatacct tcgaggcggc ggaccggctg gtcgaattcg cccgagagca cggcatggcc 240atgcggggac acacgctcgt atggcataac cagacgtccg attggctgtt ccaggatcgc 300caaggcggga gggtaagcaa ggaggtgctg ctcggaaggc tccgggagca tattcatacc 360atagtaggcc ggtacaagaa cgagatctac gcctgggacg tcgtcaacga ggtcatcgcg 420gacgaagggg aggcgctgct gcgcacttcc aaatggacgg aaatcgcggg acctgaattt 480atcgctaaag cgttcgagta tgcacatgag gcggatccac aggcgctgtt gttttataac 540gactacaacg aatcgaatcc tctgaaacgc gataaaattt acacactcgt tcattcgctg 600ctggagcaag gggtgccgat ccatggcatc ggattacaag cgcactggaa cctgtacgat 660ccatcgttgg atgagattaa ggcagcgatt gagaagtatg cttcgctggg tttgcagctg 720cagctgacgg agctggatct ctcgatgttc cgcttcgatg accggcgaac cgatttgacc 780gcgccagagc cggggatgct ggagcaacag gccgagcgtt atgaagccgt gttccggctg 840ttgctggagt atcgtgacgt catcagcggc gttaccttct ggggagcggc ggatgattat 900acctggctgg acaattttcc ggtgcgcggc cggaagaact ggccgtttct gttcgatgcc 960cagcaccagc cgaaggcagc ttatcaccgt gtggcggcat tggctgcgga gcaacgagca 1020taa 1023160340PRTUnknownObtained from environmental sample 160Met Asn Pro Thr Phe Ser Ser Val Pro Ala Leu Lys Glu Leu Phe Ala 1 5 10 15 Ala Asp Phe Asn Ile Gly Ala Ala Val Asn Pro Thr Thr Ile Arg Thr 20 25 30 Gln Glu Ala Leu Leu Ala Tyr His Phe Asn Ser Leu Thr Ala Glu Asn 35 40 45 Glu Met Lys Phe Val Ser Val His Pro Glu Glu Gln Thr Tyr Thr Phe 50 55 60 Glu Ala Ala Asp Arg Leu Val Glu Phe Ala Arg Glu His Gly Met Ala 65 70 75 80 Met Arg Gly His Thr Leu Val Trp His Asn Gln Thr Ser Asp Trp Leu 85 90 95 Phe Gln Asp Arg Gln Gly Gly Arg Val Ser Lys Glu Val Leu Leu Gly 100 105 110 Arg Leu Arg Glu His Ile His Thr Ile Val Gly Arg Tyr Lys Asn Glu 115 120 125 Ile Tyr Ala Trp Asp Val Val Asn Glu Val Ile Ala Asp Glu Gly Glu 130 135 140 Ala Leu Leu Arg Thr Ser Lys Trp Thr Glu Ile Ala Gly Pro Glu Phe 145 150 155 160 Ile Ala Lys Ala Phe Glu Tyr Ala His Glu Ala Asp Pro Gln Ala Leu 165 170 175 Leu Phe Tyr Asn Asp Tyr Asn Glu Ser Asn Pro Leu Lys Arg Asp Lys 180 185 190 Ile Tyr Thr Leu Val His Ser Leu Leu Glu Gln Gly Val Pro Ile His 195 200 205 Gly Ile Gly Leu Gln Ala His Trp Asn Leu Tyr Asp Pro Ser Leu Asp 210 215 220 Glu Ile Lys Ala Ala Ile Glu Lys Tyr Ala Ser Leu Gly Leu Gln Leu 225 230 235 240 Gln Leu Thr Glu Leu Asp Leu Ser Met Phe Arg Phe Asp Asp Arg Arg 245 250 255 Thr Asp Leu Thr Ala Pro Glu Pro Gly Met Leu Glu Gln Gln Ala Glu 260 265 270 Arg Tyr Glu Ala Val Phe Arg Leu Leu Leu Glu Tyr Arg Asp Val Ile 275 280 285 Ser Gly Val Thr Phe Trp Gly Ala Ala Asp Asp Tyr Thr Trp Leu Asp 290 295 300 Asn Phe Pro Val

Arg Gly Arg Lys Asn Trp Pro Phe Leu Phe Asp Ala 305 310 315 320 Gln His Gln Pro Lys Ala Ala Tyr His Arg Val Ala Ala Leu Ala Ala 325 330 335 Glu Gln Arg Ala 340 1612820DNAUnknownObtained from environmental sample 161atgtcctgcc gcaccctgat gagtaggcgt gtaggatggg gacttttatt gtggggaggt 60ttattcctca gaaccggttc ggttacagga caaacttaca attatgccga agtcctgcag 120aaatctatgt ttttctacga atgtcaggag tctaaaattg ccccgggcaa tcgggtgaca 180tggcgagcta atgcagccat gaacgatggg agcgatgttg gaaaagacct gacaggagga 240tggtttgatg caggtgacca tgtgaaattt aattttccca tggcgtttac cgctacggcg 300ctggcgtggg gagctattga ctttgctcag ggatacatta gttccgggca aatgcaatac 360ctgaaacgta atctgcgcta cgtcaatgac tatttcatta aatgtcacac agcccccaac 420gaattgtatg gtcaggtggg taatggaggc cttgaccatg ccttttgggg accacccgaa 480gtcatgcgca tggctaggcc tgcctataaa attgatgcgt caaaacccgg atcagatctg 540gctgccgaaa cagctgctgc aatggctgcc gccagcattg ttttcaaatc cgacgatcct 600acctatagcg ctactttgct gaatcatgca aaacagctgt tttcttttgc cgaaacctat 660aaaggaaaat attccgacgc tattaccgat gctgcaggat attataactc ctggagcggc 720tataacgatg aactggtatg gggagctata tggctttacc gggctaccgg cgatgcaacc 780tatctatcta aggcagaatc ctattacgac aatctgggta atcagggtca ggaacccgtt 840aaagcctaca aatggaccat tgcatgggat gacaaatcct atggctgtta tgccctactg 900gccaaattga caggtaagga aaaatacaaa attgacgccg aacgttttct cgactattgg 960accgatggtt ataatggttc ccggattact tataccccgg gaggactcgc tttcctcgat 1020atatggggat cgttgcgcta tgctatgaat actgcctttg ttgctgccta ctatgccgat 1080gcagccactt cagctgctaa aaccacaaaa tatctcaact ttgctaaaca acaactgcat 1140tatgctcttg gatccaatcc gagcaacaga agctatgtct gtggctttgg caataatcct 1200cccgttaatc ctcaccatag aggtgcacac ggagcatggt ctaataatgt tcaaggacct 1260cctaccgaaa cacgacatat cctctacggc gcattagtgg gtggaccagg cagtaatgac 1320tcctatactg acgaccgatc caattacacc aataacgaag tagcatgtga ctacaatgct 1380cttttctccg gactgcttgc aaagttcgtc attgattatg gaggcacacc gttagccaac 1440ttccctgttc gtgaaacccc aaaagatgaa tatttcgttg aagcaaaagc aaacgctaca 1500ggaaccaatt tctccgaatg gacggtatgg gtatacaacc acactgcatg gccagcccgt 1560gaaggttctg aatataaatt cagattatac gtaaatattt cggaaggact ggctgcaggc 1620tatactgcct caaattatgt tgtgcaaacc aataatgccg gtgtggtaaa ctttacccaa 1680cttttagctg ctgatgcagc taacggcatc tattataccg aagtaacctt taaacctggt 1740accgaaattt atcctggcgg gcaacagtat gacaagaagg aagctcagat gcgtattagt 1800ttgcccaatg ctccggcttc tgcatgggat ccgactaacg acccgtcatg ggcgggaatc 1860acctctacct tgaaacaaat gccgggtata cccatgtatg tagatggtgt aaaggtattt 1920ggtaatgagc ctgtcccagg tcagacagtt cccgtcaccg gagtaaccgt atcgcctacc 1980accctgagtc tgactgtagg acagaccagt acactcaccg ctaccgtatc gccggctaat 2040gctaccaaca aaaacgtcac ctggagcagc agcaatacca gcgtagccac ggtaagctca 2100acaggcgttg tcacagccgt agcagccggt tcggccacca tcaccgtaac cacagtcgat 2160ggcgctaaaa cagccacctg cgccgtaacg gtaacaggca gcaccaacgt tcccgtcacc 2220ggagtaaccg tatcgcccac cacgctgagt ctgaccgtag ggcagaccgc taccctcacc 2280gctaccgtat cgccggctaa tgctaccaac aagaacgtta cctggagcag cagcaatacc 2340agcgtagcca cggtaagttc aacaggcgta gttactgccg tagcggccgg ttcggccacc 2400atcaccgtaa ccaccgtcga tggagctaaa accgctacct gcaccgtaac ggtaacgggc 2460agcactaccg tacccgtcac cggcgtaact gtatcgccta ccaccctgag tctgaccgtt 2520ggacaaaccg ctaccctgac cgctaccgta tcgccagctg atgctaccaa caagaacgtc 2580acctggagca gcagcaatac cagcgtagcc acggtaagct caacaggcgt agtcactgcc 2640gtagcggccg gttcagctac catcaccgtg accacagtcg atggggctaa aactgctacc 2700tgtgccgtga ccgtaaccgc cggaggttcc accaccccct gcagtaatcc ggtaagcaaa 2760accctacctc tggtacagga tggtgccggc gaattcaggt tgagtaatag ttttaattaa 2820162939PRTUnknownObtained from environmental sample 162Met Ser Cys Arg Thr Leu Met Ser Arg Arg Val Gly Trp Gly Leu Leu1 5 10 15 Leu Trp Gly Gly Leu Phe Leu Arg Thr Gly Ser Val Thr Gly Gln Thr 20 25 30 Tyr Asn Tyr Ala Glu Val Leu Gln Lys Ser Met Phe Phe Tyr Glu Cys 35 40 45 Gln Glu Ser Lys Ile Ala Pro Gly Asn Arg Val Thr Trp Arg Ala Asn 50 55 60 Ala Ala Met Asn Asp Gly Ser Asp Val Gly Lys Asp Leu Thr Gly Gly65 70 75 80 Trp Phe Asp Ala Gly Asp His Val Lys Phe Asn Phe Pro Met Ala Phe 85 90 95 Thr Ala Thr Ala Leu Ala Trp Gly Ala Ile Asp Phe Ala Gln Gly Tyr 100 105 110 Ile Ser Ser Gly Gln Met Gln Tyr Leu Lys Arg Asn Leu Arg Tyr Val 115 120 125 Asn Asp Tyr Phe Ile Lys Cys His Thr Ala Pro Asn Glu Leu Tyr Gly 130 135 140 Gln Val Gly Asn Gly Gly Leu Asp His Ala Phe Trp Gly Pro Pro Glu145 150 155 160 Val Met Arg Met Ala Arg Pro Ala Tyr Lys Ile Asp Ala Ser Lys Pro 165 170 175 Gly Ser Asp Leu Ala Ala Glu Thr Ala Ala Ala Met Ala Ala Ala Ser 180 185 190 Ile Val Phe Lys Ser Asp Asp Pro Thr Tyr Ser Ala Thr Leu Leu Asn 195 200 205 His Ala Lys Gln Leu Phe Ser Phe Ala Glu Thr Tyr Lys Gly Lys Tyr 210 215 220 Ser Asp Ala Ile Thr Asp Ala Ala Gly Tyr Tyr Asn Ser Trp Ser Gly225 230 235 240 Tyr Asn Asp Glu Leu Val Trp Gly Ala Ile Trp Leu Tyr Arg Ala Thr 245 250 255 Gly Asp Ala Thr Tyr Leu Ser Lys Ala Glu Ser Tyr Tyr Asp Asn Leu 260 265 270 Gly Asn Gln Gly Gln Glu Pro Val Lys Ala Tyr Lys Trp Thr Ile Ala 275 280 285 Trp Asp Asp Lys Ser Tyr Gly Cys Tyr Ala Leu Leu Ala Lys Leu Thr 290 295 300 Gly Lys Glu Lys Tyr Lys Ile Asp Ala Glu Arg Phe Leu Asp Tyr Trp305 310 315 320 Thr Asp Gly Tyr Asn Gly Ser Arg Ile Thr Tyr Thr Pro Gly Gly Leu 325 330 335 Ala Phe Leu Asp Ile Trp Gly Ser Leu Arg Tyr Ala Met Asn Thr Ala 340 345 350 Phe Val Ala Ala Tyr Tyr Ala Asp Ala Ala Thr Ser Ala Ala Lys Thr 355 360 365 Thr Lys Tyr Leu Asn Phe Ala Lys Gln Gln Leu His Tyr Ala Leu Gly 370 375 380 Ser Asn Pro Ser Asn Arg Ser Tyr Val Cys Gly Phe Gly Asn Asn Pro385 390 395 400 Pro Val Asn Pro His His Arg Gly Ala His Gly Ala Trp Ser Asn Asn 405 410 415 Val Gln Gly Pro Pro Thr Glu Thr Arg His Ile Leu Tyr Gly Ala Leu 420 425 430 Val Gly Gly Pro Gly Ser Asn Asp Ser Tyr Thr Asp Asp Arg Ser Asn 435 440 445 Tyr Thr Asn Asn Glu Val Ala Cys Asp Tyr Asn Ala Leu Phe Ser Gly 450 455 460 Leu Leu Ala Lys Phe Val Ile Asp Tyr Gly Gly Thr Pro Leu Ala Asn465 470 475 480 Phe Pro Val Arg Glu Thr Pro Lys Asp Glu Tyr Phe Val Glu Ala Lys 485 490 495 Ala Asn Ala Thr Gly Thr Asn Phe Ser Glu Trp Thr Val Trp Val Tyr 500 505 510 Asn His Thr Ala Trp Pro Ala Arg Glu Gly Ser Glu Tyr Lys Phe Arg 515 520 525 Leu Tyr Val Asn Ile Ser Glu Gly Leu Ala Ala Gly Tyr Thr Ala Ser 530 535 540 Asn Tyr Val Val Gln Thr Asn Asn Ala Gly Val Val Asn Phe Thr Gln545 550 555 560 Leu Leu Ala Ala Asp Ala Ala Asn Gly Ile Tyr Tyr Thr Glu Val Thr 565 570 575 Phe Lys Pro Gly Thr Glu Ile Tyr Pro Gly Gly Gln Gln Tyr Asp Lys 580 585 590 Lys Glu Ala Gln Met Arg Ile Ser Leu Pro Asn Ala Pro Ala Ser Ala 595 600 605 Trp Asp Pro Thr Asn Asp Pro Ser Trp Ala Gly Ile Thr Ser Thr Leu 610 615 620 Lys Gln Met Pro Gly Ile Pro Met Tyr Val Asp Gly Val Lys Val Phe625 630 635 640 Gly Asn Glu Pro Val Pro Gly Gln Thr Val Pro Val Thr Gly Val Thr 645 650 655 Val Ser Pro Thr Thr Leu Ser Leu Thr Val Gly Gln Thr Ser Thr Leu 660 665 670 Thr Ala Thr Val Ser Pro Ala Asn Ala Thr Asn Lys Asn Val Thr Trp 675 680 685 Ser Ser Ser Asn Thr Ser Val Ala Thr Val Ser Ser Thr Gly Val Val 690 695 700 Thr Ala Val Ala Ala Gly Ser Ala Thr Ile Thr Val Thr Thr Val Asp705 710 715 720 Gly Ala Lys Thr Ala Thr Cys Ala Val Thr Val Thr Gly Ser Thr Asn 725 730 735 Val Pro Val Thr Gly Val Thr Val Ser Pro Thr Thr Leu Ser Leu Thr 740 745 750 Val Gly Gln Thr Ala Thr Leu Thr Ala Thr Val Ser Pro Ala Asn Ala 755 760 765 Thr Asn Lys Asn Val Thr Trp Ser Ser Ser Asn Thr Ser Val Ala Thr 770 775 780 Val Ser Ser Thr Gly Val Val Thr Ala Val Ala Ala Gly Ser Ala Thr785 790 795 800 Ile Thr Val Thr Thr Val Asp Gly Ala Lys Thr Ala Thr Cys Thr Val 805 810 815 Thr Val Thr Gly Ser Thr Thr Val Pro Val Thr Gly Val Thr Val Ser 820 825 830 Pro Thr Thr Leu Ser Leu Thr Val Gly Gln Thr Ala Thr Leu Thr Ala 835 840 845 Thr Val Ser Pro Ala Asp Ala Thr Asn Lys Asn Val Thr Trp Ser Ser 850 855 860 Ser Asn Thr Ser Val Ala Thr Val Ser Ser Thr Gly Val Val Thr Ala865 870 875 880 Val Ala Ala Gly Ser Ala Thr Ile Thr Val Thr Thr Val Asp Gly Ala 885 890 895 Lys Thr Ala Thr Cys Ala Val Thr Val Thr Ala Gly Gly Ser Thr Thr 900 905 910 Pro Cys Ser Asn Pro Val Ser Lys Thr Leu Pro Leu Val Gln Asp Gly 915 920 925 Ala Gly Glu Phe Arg Leu Ser Asn Ser Phe Asn 930 935 1632733DNAUnknownObtained from environmental sample 163atgcaaactt acaattatgc cgaagtcctg cagaaatcta tgtttttcta cgaatgtcag 60gagtctaaaa ttgccccggg caatcgggtg acatggcgag ctaatgcagc catgaacgat 120gggagcgatg ttggaaaaga cctgacagga ggatggtttg atgcaggtga ccatgtgaaa 180tttaattttc ccatggcgtt taccgctacg gcgctggcgt ggggagctat tgactttgct 240cagggataca ttagttccgg gcaaatgcaa tacctgaaac gtaatctgcg ctacgtcaat 300gactatttca ttaaatgtca cacagccccc aacgaattgt atggtcaggt gggtaatgga 360ggccttgacc atgccttttg gggaccaccc gaagtcatgc gcatggctag gcctgcctat 420aaaattgatg cgtcaaaacc cggatcagat ctggctgccg aaacagctgc tgcaatggct 480gccgccagca ttgttttcaa atccgacgat cctacctata gcgctacttt gctgaatcat 540gcaaaacagc tgttttcttt tgccgaaacc tataaaggaa aatattccga cgctattacc 600gatgctgcag gatattataa ctcctggagc ggctataacg atgaactggt atggggagct 660atatggcttt accgggctac cggcgatgca acctatctat ctaaggcaga atcctattac 720gacaatctgg gtaatcaggg tcaggaaccc gttaaagcct acaaatggac cattgcatgg 780gatgacaaat cctatggctg ttatgcccta ctggccaaat tgacaggtaa ggaaaaatac 840aaaattgacg ccgaacgttt tctcgactat tggaccgatg gttataatgg ttcccggatt 900acttataccc cgggaggact cgctttcctc gatatatggg gatcgttgcg ctatgctatg 960aatactgcct ttgttgctgc ctactatgcc gatgcagcca cttcagctgc taaaaccaca 1020aaatatctca actttgctaa acaacaactg cattatgctc ttggatccaa tccgagcaac 1080agaagctatg tctgtggctt tggcaataat cctcccgtta atcctcacca tagaggtgca 1140cacggagcat ggtctaataa tgttcaagga cctcctaccg aaacacgaca tatcctctac 1200ggcgcattag tgggtggacc aggcagtaat gactcctata ctgacgaccg atccaattac 1260accaataacg aagtagcatg tgactacaat gctcttttct ccggactgct tgcaaagttc 1320gtcattgatt atggaggcac accgttagcc aacttccctg ttcgtgaaac cccaaaagat 1380gaatatttcg ttgaagcaaa agcaaacgct acaggaacca atttctccga atggacggta 1440tgggtataca accacactgc atggccagcc cgtgaaggtt ctgaatataa attcagatta 1500tacgtaaata tttcggaagg actggctgca ggctatactg cctcaaatta tgttgtgcaa 1560accaataatg ccggtgtggt aaactttacc caacttttag ctgctgatgc agctaacggc 1620atctattata ccgaagtaac ctttaaacct ggtaccgaaa tttatcctgg cgggcaacag 1680tatgacaaga aggaagctca gatgcgtatt agtttgccca atgctccggc ttctgcatgg 1740gatccgacta acgacccgtc atgggcggga atcacctcta ccttgaaaca aatgccgggt 1800atacccatgt atgtagatgg tgtaaaggta tttggtaatg agcctgtccc aggtcagaca 1860gttcccgtca ccggagtaac cgtatcgcct accaccctga gtctgactgt aggacagacc 1920agtacactca ccgctaccgt atcgccggct aatgctacca acaaaaacgt cacctggagc 1980agcagcaata ccagcgtagc cacggtaagc tcaacaggcg ttgtcacagc cgtagcagcc 2040ggttcggcca ccatcaccgt aaccacagtc gatggcgcta aaacagccac ctgcgccgta 2100acggtaacag gcagcaccaa cgttcccgtc accggagtaa ccgtatcgcc caccacgctg 2160agtctgaccg tagggcagac cgctaccctc accgctaccg tatcgccggc taatgctacc 2220aacaagaacg ttacctggag cagcagcaat accagcgtag ccacggtaag ttcaacaggc 2280gtagttactg ccgtagcggc cggttcggcc accatcaccg taaccaccgt cgatggagct 2340aaaaccgcta cctgcaccgt aacggtaacg ggcagcacta ccgtacccgt caccggcgta 2400actgtatcgc ctaccaccct gagtctgacc gttggacaaa ccgctaccct gaccgctacc 2460gtatcgccag ctgatgctac caacaagaac gtcacctgga gcagcagcaa taccagcgta 2520gccacggtaa gctcaacagg cgtagtcact gccgtagcgg ccggttcagc taccatcacc 2580gtgaccacag tcgatggggc taaaactgct acctgtgccg tgaccgtaac cgccggaggt 2640tccaccaccc cctgcagtaa tccggtaagc aaaaccctac ctctggtaca ggatggtgcc 2700ggcgaattca ggttgagtaa tagttttaat taa 2733164910PRTUnknownObtained from environmental sample 164Met Gln Thr Tyr Asn Tyr Ala Glu Val Leu Gln Lys Ser Met Phe Phe1 5 10 15Tyr Glu Cys Gln Glu Ser Lys Ile Ala Pro Gly Asn Arg Val Thr Trp 20 25 30Arg Ala Asn Ala Ala Met Asn Asp Gly Ser Asp Val Gly Lys Asp Leu 35 40 45Thr Gly Gly Trp Phe Asp Ala Gly Asp His Val Lys Phe Asn Phe Pro 50 55 60Met Ala Phe Thr Ala Thr Ala Leu Ala Trp Gly Ala Ile Asp Phe Ala65 70 75 80Gln Gly Tyr Ile Ser Ser Gly Gln Met Gln Tyr Leu Lys Arg Asn Leu 85 90 95Arg Tyr Val Asn Asp Tyr Phe Ile Lys Cys His Thr Ala Pro Asn Glu 100 105 110Leu Tyr Gly Gln Val Gly Asn Gly Gly Leu Asp His Ala Phe Trp Gly 115 120 125Pro Pro Glu Val Met Arg Met Ala Arg Pro Ala Tyr Lys Ile Asp Ala 130 135 140Ser Lys Pro Gly Ser Asp Leu Ala Ala Glu Thr Ala Ala Ala Met Ala145 150 155 160Ala Ala Ser Ile Val Phe Lys Ser Asp Asp Pro Thr Tyr Ser Ala Thr 165 170 175Leu Leu Asn His Ala Lys Gln Leu Phe Ser Phe Ala Glu Thr Tyr Lys 180 185 190Gly Lys Tyr Ser Asp Ala Ile Thr Asp Ala Ala Gly Tyr Tyr Asn Ser 195 200 205Trp Ser Gly Tyr Asn Asp Glu Leu Val Trp Gly Ala Ile Trp Leu Tyr 210 215 220Arg Ala Thr Gly Asp Ala Thr Tyr Leu Ser Lys Ala Glu Ser Tyr Tyr225 230 235 240Asp Asn Leu Gly Asn Gln Gly Gln Glu Pro Val Lys Ala Tyr Lys Trp 245 250 255Thr Ile Ala Trp Asp Asp Lys Ser Tyr Gly Cys Tyr Ala Leu Leu Ala 260 265 270Lys Leu Thr Gly Lys Glu Lys Tyr Lys Ile Asp Ala Glu Arg Phe Leu 275 280 285Asp Tyr Trp Thr Asp Gly Tyr Asn Gly Ser Arg Ile Thr Tyr Thr Pro 290 295 300Gly Gly Leu Ala Phe Leu Asp Ile Trp Gly Ser Leu Arg Tyr Ala Met305 310 315 320Asn Thr Ala Phe Val Ala Ala Tyr Tyr Ala Asp Ala Ala Thr Ser Ala 325 330 335Ala Lys Thr Thr Lys Tyr Leu Asn Phe Ala Lys Gln Gln Leu His Tyr 340 345 350Ala Leu Gly Ser Asn Pro Ser Asn Arg Ser Tyr Val Cys Gly Phe Gly 355 360 365Asn Asn Pro Pro Val Asn Pro His His Arg Gly Ala His Gly Ala Trp 370 375 380Ser Asn Asn Val Gln Gly Pro Pro Thr Glu Thr Arg His Ile Leu Tyr385 390 395 400Gly Ala Leu Val Gly Gly Pro Gly Ser Asn Asp Ser Tyr Thr Asp Asp 405 410 415Arg Ser Asn Tyr Thr Asn Asn Glu Val Ala Cys Asp Tyr Asn Ala Leu 420 425 430Phe Ser Gly Leu Leu Ala Lys Phe Val Ile Asp Tyr Gly Gly Thr Pro 435 440 445Leu Ala Asn Phe Pro Val Arg Glu Thr Pro Lys Asp Glu Tyr Phe Val 450 455 460Glu Ala Lys Ala Asn Ala Thr Gly Thr Asn Phe Ser Glu Trp Thr Val465 470 475 480Trp Val

Tyr Asn His Thr Ala Trp Pro Ala Arg Glu Gly Ser Glu Tyr 485 490 495Lys Phe Arg Leu Tyr Val Asn Ile Ser Glu Gly Leu Ala Ala Gly Tyr 500 505 510Thr Ala Ser Asn Tyr Val Val Gln Thr Asn Asn Ala Gly Val Val Asn 515 520 525Phe Thr Gln Leu Leu Ala Ala Asp Ala Ala Asn Gly Ile Tyr Tyr Thr 530 535 540Glu Val Thr Phe Lys Pro Gly Thr Glu Ile Tyr Pro Gly Gly Gln Gln545 550 555 560Tyr Asp Lys Lys Glu Ala Gln Met Arg Ile Ser Leu Pro Asn Ala Pro 565 570 575Ala Ser Ala Trp Asp Pro Thr Asn Asp Pro Ser Trp Ala Gly Ile Thr 580 585 590Ser Thr Leu Lys Gln Met Pro Gly Ile Pro Met Tyr Val Asp Gly Val 595 600 605Lys Val Phe Gly Asn Glu Pro Val Pro Gly Gln Thr Val Pro Val Thr 610 615 620Gly Val Thr Val Ser Pro Thr Thr Leu Ser Leu Thr Val Gly Gln Thr625 630 635 640Ser Thr Leu Thr Ala Thr Val Ser Pro Ala Asn Ala Thr Asn Lys Asn 645 650 655Val Thr Trp Ser Ser Ser Asn Thr Ser Val Ala Thr Val Ser Ser Thr 660 665 670Gly Val Val Thr Ala Val Ala Ala Gly Ser Ala Thr Ile Thr Val Thr 675 680 685Thr Val Asp Gly Ala Lys Thr Ala Thr Cys Ala Val Thr Val Thr Gly 690 695 700Ser Thr Asn Val Pro Val Thr Gly Val Thr Val Ser Pro Thr Thr Leu705 710 715 720Ser Leu Thr Val Gly Gln Thr Ala Thr Leu Thr Ala Thr Val Ser Pro 725 730 735Ala Asn Ala Thr Asn Lys Asn Val Thr Trp Ser Ser Ser Asn Thr Ser 740 745 750Val Ala Thr Val Ser Ser Thr Gly Val Val Thr Ala Val Ala Ala Gly 755 760 765Ser Ala Thr Ile Thr Val Thr Thr Val Asp Gly Ala Lys Thr Ala Thr 770 775 780Cys Thr Val Thr Val Thr Gly Ser Thr Thr Val Pro Val Thr Gly Val785 790 795 800Thr Val Ser Pro Thr Thr Leu Ser Leu Thr Val Gly Gln Thr Ala Thr 805 810 815Leu Thr Ala Thr Val Ser Pro Ala Asp Ala Thr Asn Lys Asn Val Thr 820 825 830Trp Ser Ser Ser Asn Thr Ser Val Ala Thr Val Ser Ser Thr Gly Val 835 840 845Val Thr Ala Val Ala Ala Gly Ser Ala Thr Ile Thr Val Thr Thr Val 850 855 860Asp Gly Ala Lys Thr Ala Thr Cys Ala Val Thr Val Thr Ala Gly Gly865 870 875 880Ser Thr Thr Pro Cys Ser Asn Pro Val Ser Lys Thr Leu Pro Leu Val 885 890 895Gln Asp Gly Ala Gly Glu Phe Arg Leu Ser Asn Ser Phe Asn 900 905 9101651347DNAUnknownObtained from environmental sample 165atgacaatta acaacaaaac tacagcgagt cctagtattc ccagcaccca caattccctc 60ccgtcgcttc gcacactgtt taccaccagc ctgctcacgc tggccctgac cgcctgcggt 120ggttcttcca gcagcgacaa ggacccttca agctccagct ccagtgaatc atcaagttcc 180agcgaatcct cgagctcagc ttccagcgaa tcctcgagca gtgagtccag cagtagctct 240tccgcgggcc atttctccat cgagccggac ttccagctct acagcctggc caacttcccg 300gtgggcgtgg cggtctccgc cgccaacgag aacgacagca tcttcaacag tccggatgcc 360gccgaacgtc aggccgttat tattgagcac ttctctcagc tcaccgccgg caacatcatg 420aaaatgagct acctgcagcc gagtcaaggc aacttcacct tcgatgacgc cgacgagttg 480gttaacttcg cccaagccaa tggcatgacc gtacacggcc actccaccat ctggcacgcg 540gactaccaag taccgaactt catgagaaac tttgaaggtg accaggagga atgggcagaa 600attctgaccg atcacgtcac taccatcatc gagcacttcc ccgacgatgt ggtcatcagc 660tgggacgtgg tgaacgaggc tgtcgatcaa ggcacggcga acggctggcg ccattcggtg 720ttctacaatg cattcgacgc cccggaagaa ggcgacattc ccgaatacat caaagtcgct 780ttccgcgccg cgcgcgaggc tgacgccaac gtagacctct actacaacga ctacgacaat 840accgccaatg cccagcgcct ggccaaaaca ctgcaaattg ccgaggtact ggacgccgaa 900ggcaccattg acggcgtcgg tttccagatg cacgcctaca tggattaccc gagcctgacc 960cattttgaaa acgccttccg gcaagtcgtc gacctggggc tcaaagtgaa agttaccgag 1020ctggacgtat ccgtagtcaa cccctacggc ggcgaagcac ctccacaacc ggaatacgac 1080aaagaactgg ccggcgcgca aaaactgcgc ttctgccaaa tcgccgaagt ttacatgaac 1140actgtacccg aggagttacg cggtggcttc accgtctggg gcctgaccga tgatgaaagt 1200tggctgatgc aacagttcag aaacgccacc ggcgccgact acgacgacgt ctggccgtta 1260ctgttcaatg ccgacaaatc cgccaaaccg gcactgcaag gcgtggccga cgcctttacc 1320ggacaaacct gcacctccga gttctaa 1347166448PRTUnknownObtained from environmental sample 166Met Thr Ile Asn Asn Lys Thr Thr Ala Ser Pro Ser Ile Pro Ser Thr1 5 10 15His Asn Ser Leu Pro Ser Leu Arg Thr Leu Phe Thr Thr Ser Leu Leu 20 25 30Thr Leu Ala Leu Thr Ala Cys Gly Gly Ser Ser Ser Ser Asp Lys Asp 35 40 45Pro Ser Ser Ser Ser Ser Ser Glu Ser Ser Ser Ser Ser Glu Ser Ser 50 55 60Ser Ser Ala Ser Ser Glu Ser Ser Ser Ser Glu Ser Ser Ser Ser Ser65 70 75 80Ser Ala Gly His Phe Ser Ile Glu Pro Asp Phe Gln Leu Tyr Ser Leu 85 90 95Ala Asn Phe Pro Val Gly Val Ala Val Ser Ala Ala Asn Glu Asn Asp 100 105 110Ser Ile Phe Asn Ser Pro Asp Ala Ala Glu Arg Gln Ala Val Ile Ile 115 120 125Glu His Phe Ser Gln Leu Thr Ala Gly Asn Ile Met Lys Met Ser Tyr 130 135 140Leu Gln Pro Ser Gln Gly Asn Phe Thr Phe Asp Asp Ala Asp Glu Leu145 150 155 160Val Asn Phe Ala Gln Ala Asn Gly Met Thr Val His Gly His Ser Thr 165 170 175Ile Trp His Ala Asp Tyr Gln Val Pro Asn Phe Met Arg Asn Phe Glu 180 185 190Gly Asp Gln Glu Glu Trp Ala Glu Ile Leu Thr Asp His Val Thr Thr 195 200 205Ile Ile Glu His Phe Pro Asp Asp Val Val Ile Ser Trp Asp Val Val 210 215 220Asn Glu Ala Val Asp Gln Gly Thr Ala Asn Gly Trp Arg His Ser Val225 230 235 240Phe Tyr Asn Ala Phe Asp Ala Pro Glu Glu Gly Asp Ile Pro Glu Tyr 245 250 255Ile Lys Val Ala Phe Arg Ala Ala Arg Glu Ala Asp Ala Asn Val Asp 260 265 270Leu Tyr Tyr Asn Asp Tyr Asp Asn Thr Ala Asn Ala Gln Arg Leu Ala 275 280 285Lys Thr Leu Gln Ile Ala Glu Val Leu Asp Ala Glu Gly Thr Ile Asp 290 295 300Gly Val Gly Phe Gln Met His Ala Tyr Met Asp Tyr Pro Ser Leu Thr305 310 315 320His Phe Glu Asn Ala Phe Arg Gln Val Val Asp Leu Gly Leu Lys Val 325 330 335Lys Val Thr Glu Leu Asp Val Ser Val Val Asn Pro Tyr Gly Gly Glu 340 345 350Ala Pro Pro Gln Pro Glu Tyr Asp Lys Glu Leu Ala Gly Ala Gln Lys 355 360 365Leu Arg Phe Cys Gln Ile Ala Glu Val Tyr Met Asn Thr Val Pro Glu 370 375 380Glu Leu Arg Gly Gly Phe Thr Val Trp Gly Leu Thr Asp Asp Glu Ser385 390 395 400Trp Leu Met Gln Gln Phe Arg Asn Ala Thr Gly Ala Asp Tyr Asp Asp 405 410 415Val Trp Pro Leu Leu Phe Asn Ala Asp Lys Ser Ala Lys Pro Ala Leu 420 425 430Gln Gly Val Ala Asp Ala Phe Thr Gly Gln Thr Cys Thr Ser Glu Phe 435 440 445

Claims

1. An isolated or recombinant nucleic acid comprising (a) a nucleic acid sequence having at least 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more or complete sequence identity to 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 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 ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:71, SEQ ID NO:73, SEQ ID NO:75, SEQ ID NO:77, SEQ ID NO:79, SEQ ID NO:81, SEQ ID NO:83, SEQ ID NO:85, SEQ ID NO:87, SEQ ID NO:89, SEQ ID NO:91, SEQ ID NO:93, SEQ ID NO:95, SEQ ID NO:97, SEQ ID NO:99, SEQ ID NO:101, SEQ ID NO:103, SEQ ID NO:105, SEQ ID NO:107, SEQ ID NO:109, SEQ ID NO:111, SEQ ID NO:113, SEQ ID NO:115, SEQ ID NO:117, SEQ ID NO:119, SEQ ID NO:121, SEQ ID NO:123, SEQ ID NO:125, SEQ ID NO:127, SEQ ID NO:129, SEQ ID NO:131, SEQ ID NO:133, SEQ ID NO:135, SEQ ID NO:137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:143, SEQ ID NO:145, SEQ ID NO:147, SEQ ID NO:149, SEQ ID NO:151, SEQ ID NO:153, SEQ ID NO:155, SEQ ID NO:157, SEQ ID NO:159, SEQ ID NO:161, SEQ ID NO:163 or SEQ ID NO:165, over a region of at least about 20, 30, 40, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150 or more residues, wherein the nucleic acid encodes at least one polypeptide having a cellulase activity, and optionally the sequence identities are determined by analysis with a sequence comparison algorithm or by a visual inspection; or (b) a nucleic acid sequence that hybridizes under stringent conditions to a nucleic acid comprising 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 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 ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:71, SEQ ID NO:73, SEQ ID NO:75, SEQ ID NO:77, SEQ ID NO:79, SEQ ID NO:81, SEQ ID NO:83, SEQ ID NO:85, SEQ ID NO:87, SEQ ID NO:89, SEQ ID NO:91, SEQ ID NO:93, SEQ ID NO:95, SEQ ID NO:97, SEQ ID NO:99, SEQ ID NO:101, SEQ ID NO:103, SEQ ID NO:105, SEQ ID NO:107, SEQ ID NO:109, SEQ ID NO:111, SEQ ID NO:113, SEQ ID NO:115, SEQ ID NO:117, SEQ ID NO:119, SEQ ID NO:121, SEQ ID NO:123, SEQ ID NO:125, SEQ ID NO:127, SEQ ID NO:129, SEQ ID NO:131, SEQ ID NO:133, SEQ ID NO:135, SEQ ID NO:137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:143, SEQ ID NO:145, SEQ ID NO:147, SEQ ID NO:149, SEQ ID NO:151, SEQ ID NO:153, SEQ ID NO:155, SEQ ID NO:157, SEQ ID NO:159, SEQ ID NO:161, SEQ ID NO:163 or SEQ ID NO:165, wherein the nucleic acid encodes a polypeptide having a cellulase activity, and the stringent conditions include a wash step comprising a wash in 0.2.times.SSC at a temperature of about 65.degree. C. for about 15 minutes, and optionally the nucleic acid is at least about 20, 30, 40, 50, 60, 75, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000 or more residues in length or the full length of the gene or transcript; (c) a nucleic acid sequence encoding a polypeptide having a sequence as set forth 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 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:143, 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 or SEQ ID NO:166; or (d) a nucleic acid sequence complementary to (a), (b) or (c).

2. The isolated or recombinant nucleic acid of claim 1, wherein the nucleic acid sequence comprises a sequence as set forth in 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 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 ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:71, SEQ ID NO:73, SEQ ID NO:75, SEQ ID NO:77, SEQ ID NO:79, SEQ ID NO:81, SEQ ID NO:83, SEQ ID NO:85, SEQ ID NO:87, SEQ ID NO:89, SEQ ID NO:91, SEQ ID NO:93, SEQ ID NO:95, SEQ ID NO:97, SEQ ID NO:99, SEQ ID NO:101, SEQ ID NO:103, SEQ ID NO:105, SEQ ID NO:107, SEQ ID NO:109, SEQ ID NO:111, SEQ ID NO:113, SEQ ID NO:115, SEQ ID NO:117, SEQ ID NO:119, SEQ ID NO:121, SEQ ID NO:123, SEQ ID NO:125, SEQ ID NO:127, SEQ ID NO:129, SEQ ID NO:131, SEQ ID NO:133, SEQ ID NO:135, SEQ ID NO:137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:143, SEQ ID NO:145, SEQ ID NO:147, SEQ ID NO:149, SEQ ID NO:151, SEQ ID NO:153, SEQ ID NO:155, SEQ ID NO:157, SEQ ID NO:159, SEQ ID NO:161, SEQ ID NO:163 or SEQ ID NO:165.

3. The isolated or recombinant nucleic acid of claim 1, wherein the sequence comparison algorithm is a BLAST version 2.2.2 algorithm where a filtering setting is set to blastall-p blastp-d "nr pataa"-F F, and all other options are set to default.

4-21. (canceled)

22. The isolated or recombinant nucleic acid of claim 1, wherein the cellulase activity comprises hydrolyzing a cellulose, a cellulose derivative or a hemicellulose.

23. The isolated or recombinant nucleic acid of claim 22 wherein the cellulase activity comprises hydrolyzing a cellulose or a hemicellulose in a wood or paper pulp or a wood or paper product.

24-25. (canceled)

26. The isolated or recombinant nucleic acid of claim 1, wherein the cellulase activity comprises catalyzing hydrolysis of a glucan in a microbial cell, a fungal cell, a mammalian cell, a plant cell or any plant material comprising a cellulosic part.

27. The isolated or recombinant nucleic acid of claim 1, wherein the cellulase activity is thermostable.

28. The isolated or recombinant nucleic acid of claim 27, wherein the polypeptide retains a cellulase activity under conditions comprising a temperature range of between about 37.degree. C. to about 95.degree. C., or between about 55.degree. C. to about 85.degree. C., or between about 70.degree. C. to about 75.degree. C., or between about 70.degree. C. to about 95.degree. C., or between about 90.degree. C. to about 95.degree. C., or retains a cellulase activity in a temperature in the range between about 1.degree. C. to about 5.degree. C., between about 5.degree. C. to about 15.degree. C., between about 15.degree. C. to about 25.degree. C., between about 25.degree. C. to about 37.degree. C., or between about 37.degree. C. to about 95.degree. C., 96.degree. C., 97.degree. C., 98.degree. C. or 99.degree. C.

29. The isolated or recombinant nucleic acid of claim 1, wherein the cellulase activity is thermotolerant.

30. The isolated or recombinant nucleic acid of claim 29, wherein the polypeptide retains a cellulase activity after exposure to a temperature in the range from greater than 37.degree. C. to about 95.degree. C., from greater than 55.degree. C. to about 85.degree. C., or between about 70.degree. C. to about 75.degree. C., or from greater than 90.degree. C. to about 95.degree. C., or after exposure to a temperature in the range between about 1.degree. C. to about 5.degree. C., between about 5.degree. C. to about 15.degree. C., between about 15.degree. C. to about 25.degree. C., between about 25.degree. C. to about 37.degree. C., or between about 37.degree. C. to about 95.degree. C., 96.degree. C., 97.degree. C., 98.degree. C. or 99.degree. C.

31-36. (canceled)

37. An expression cassette comprising a nucleic acid comprising a sequence as set forth in claim 1.

38. A vector comprising a nucleic acid comprising a sequence as set forth in claim 1, wherein optionally the vehicle comprises an expression vector.

39. A cloning vehicle comprising a nucleic acid comprising a sequence as set forth in claim 1, wherein optionally the cloning vehicle comprises a viral vector, a plasmid, a phage, a phagemid, a cosmid, a fosmid, a bacteriophage or an artificial chromosome, and optionally the viral vector comprises an adenovirus vector, a retroviral vector or an adeno-associated viral vector, and optionally the cloning vehicle comprises a bacterial artificial chromosome (BAC), a plasmid, a bacteriophage P1-derived vector (PAC), a yeast artificial chromosome (YAC), or a mammalian artificial chromosome (MAC).

40. A transformed cell comprising a nucleic acid comprising a sequence as set forth in claim 1, or an expression cassette as set forth in claim 37, the vector of claim 38, or a cloning vehicle as set forth in claim 39, wherein optionally the cell is a bacterial cell, a mammalian cell, a fungal cell, a yeast cell, an insect cell or a plant cell.

41-47. (canceled)

48. An isolated or recombinant polypeptide (i) having an amino acid sequence having at least 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more, or 100% sequence identity to 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 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:143, 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 or SEQ ID NO:166, over a region of at least about 20, 25, 30, 35, 40, 45, 50, 55, 60, 75, 100, 150, 200, 250, 300 or more residues, wherein optionally the sequence identities are determined by analysis with a sequence comparison algorithm or by a visual inspection, and optionally the sequence comparison algorithm is a BLAST version 2.2.2 algorithm where a filtering setting is set to blastall-p blastp-d "nr pataa"-F F, and all other options are set to default; (ii) having an amino acid sequence encoded by a nucleic acid as set forth in claim 1, wherein the polypeptide has a cellulase activity or has immunogenic activity in that it is capable of generating an antibody that specifically binds to a polypeptide having a sequence as set forth 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 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:143, 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 or SEQ ID NO:166; or (iii) having an amino acid sequence as set forth in (i) or (ii), or a polypeptide encoded by a nucleic acid as set forth in claim 1, and comprising at least one amino acid residue conservative substitution, wherein optionally conservative substitution comprises replacement of an aliphatic amino acid with another aliphatic amino acid; replacement of a serine with a threonine or vice versa; replacement of an acidic residue with another acidic residue; replacement of a residue bearing an amide group with another residue bearing an amide group; exchange of a basic residue with another basic residue; or, replacement of an aromatic residue with another aromatic residue, or a combination thereof, and optionally the aliphatic residue comprises Alanine, Valine, Leucine, Isoleucine or a synthetic equivalent thereof the acidic residue comprises Aspartic acid, Glutamic acid or a synthetic equivalent thereof; the residue comprising an amide group comprises Aspartic acid, Glutamic acid or a synthetic equivalent thereof the basic residue comprises Lysine, Arginine or a synthetic equivalent thereof or, the aromatic residue comprises Phenylalanine, Tyrosine or a synthetic equivalent thereof.

49-127. (canceled)

128. A method for hydrolyzing, breaking up or disrupting a glucan- or cellulose-comprising composition comprising the following steps: (a) providing a polypeptide having a cellulase activity as set forth in claim 48, or a polypeptide encoded by a nucleic acid as set forth in claim 1; (b) providing a composition comprising a cellulose or a glucan; and (c) contacting the polypeptide of step (a) with the composition of step (b) under conditions wherein the cellulase hydrolyzes, breaks up or disrupts the glucan- or cellulose-comprising composition, wherein optionally the composition comprises a plant cell, a bacterial cell, a yeast cell, an insect cell, or an animal cell, and optionally the polypeptide has endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity.

129-143. (canceled)

144. A method for making a fuel comprising contacting a composition comprising a cellulose or a fermentable sugar with a polypeptide as set forth in claim 48, or a polypeptide encoded by a nucleic acid as set forth in claim 1, wherein optionally the composition comprising a cellulose or a fermentable sugar comprises a plant, plant product or plant derivative, and optionally the plant or plant product comprises cane sugar plants or plant products, beets or sugarbeets, wheat, corn, soybeans, potato, rice or barley, and optionally the polypeptide has activity comprising cellulase, endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity, and optionally the fuel comprises a bioethanol or a gasoline-ethanol mix.

145. A method for making bioethanol comprising contacting a composition comprising a cellulose or a fermentable sugar with a polypeptide as set forth in claim 48, or a polypeptide encoded by a nucleic acid as set forth in claim 1, wherein optionally the composition comprising a cellulose or a fermentable sugar comprises a plant, plant product or plant derivative, and optionally the plant or plant product comprises cane sugar plants or plant products, beets or sugarbeets, wheat, corn, soybeans, potato, rice or barley, and optionally the polypeptide has activity comprising cellulase, endoglucanase, cellobiohydrolase, mannanase and/or beta-glucosidase activity.

146-161. (canceled)

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