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(12) Patent Application Publication (10) Pub. No.: US 2012/0266329 A1 Mathur Et Al US 2012026.6329A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2012/0266329 A1 Mathur et al. (43) Pub. Date: Oct. 18, 2012 (54) NUCLEICACIDS AND PROTEINS AND CI2N 9/10 (2006.01) METHODS FOR MAKING AND USING THEMI CI2N 9/24 (2006.01) CI2N 9/02 (2006.01) (75) Inventors: Eric J. Mathur, Carlsbad, CA CI2N 9/06 (2006.01) (US); Cathy Chang, San Marcos, CI2P 2L/02 (2006.01) CA (US) CI2O I/04 (2006.01) CI2N 9/96 (2006.01) (73) Assignee: BP Corporation North America CI2N 5/82 (2006.01) Inc., Houston, TX (US) CI2N 15/53 (2006.01) CI2N IS/54 (2006.01) CI2N 15/57 2006.O1 (22) Filed: Feb. 20, 2012 CI2N IS/60 308: Related U.S. Application Data EN f :08: (62) Division of application No. 1 1/817,403, filed on May AOIH 5/00 (2006.01) 7, 2008, now Pat. No. 8,119,385, filed as application AOIH 5/10 (2006.01) No. PCT/US2006/007642 on Mar. 3, 2006. C07K I4/00 (2006.01) CI2N IS/II (2006.01) (60) Provisional application No. 60/658,984, filed on Mar. AOIH I/06 (2006.01) 4, 2005. CI2N 15/63 (2006.01) Publication Classification (52) U.S. Cl. ................... 800/293; 435/320.1; 435/252.3: 435/325; 435/254.11: 435/254.2:435/348; (51) Int. Cl. 435/419; 435/195; 435/196; 435/198: 435/233; CI2N 15/52 (2006.01) 435/201:435/232; 435/208; 435/227; 435/193; CI2N 15/85 (2006.01) 435/200; 435/189: 435/191: 435/69.1; 435/34; CI2N 5/86 (2006.01) 435/188:536/23.2; 435/468; 800/298; 800/320; CI2N 15/867 (2006.01) 800/317.2: 800/317.4: 800/320.3: 800/306; CI2N 5/864 (2006.01) 800/312 800/320.2: 800/317.3; 800/322; CI2N 5/8 (2006.01) 800/320.1; 530/350, 536/23.1: 800/278; 800/294 CI2N I/2 (2006.01) CI2N 5/10 (2006.01) (57) ABSTRACT CI2N L/15 (2006.01) CI2N I/19 (2006.01) The invention provides polypeptides, including enzymes, CI2N 9/14 (2006.01) structural proteins and binding proteins, polynucleotides CI2N 9/16 (2006.01) encoding these polypeptides, and methods of making and CI2N 9/20 (2006.01) using these polynucleotides and polypeptides. Polypeptides, CI2N 9/90 (2006.01) including enzymes and antibodies, and nucleic acids of the CI2N 9/26 (2006.01) invention can be used in industrial, experimental, food and CI2N 9/88 (2006.01) feed processing, nutritional and pharmaceutical applications, CI2N 9/40 (2006.01) e.g., for food and feed Supplements, colorants, neutraceuti CI2N 9/78 (2006.01) cals, cosmetic and pharmaceutical needs. Patent Application Publication Oct. 18, 2012 Sheet 1 of 4 US 2012/0266329 A1 | NTERNA. stoRAGE DATA , , , , , , , 120 RETRIEWING Estay Estre Patent Application Publication Oct. 18, 2012 Sheet 2 of 4 US 2012/0266329 A1 200 opeNDATABASE of sequENCEs - READ FIRST SEQUENCE IN DATABASE - viparison of NewsECUENCE AND SORED SEQUENCE | 252 go to next SELENCEtt DATABASE sAABASE IEEE Patent Application Publication Oct. 18, 2012 Sheet 3 of 4 US 2012/0266329 A1 250 252 READ FIRST CHARACTER OF FIRstseauence -- YES ARACTERS ros. - READ? r NO DISPLAY HOMOLOGYLEVEL BETWEEN THE FIRST if AND SECOND SEQUENCES FIGRE 3 Patent Application Publication Oct. 18, 2012 Sheet 4 of 4 US 2012/0266329 A1 3.02. 3. YN 3A stoREA First sequence roMEMORY ------------, 9 OPEN DATABASE OF SEQUENCE FEATURES 3xxxx-xx-xxxx::::: ::..........g. - ... 899 READ FIRST FEATURE FROM DATAEASE - coMPARE FEArurEarTributes witHTHE First 3:6 SEQUENCE YES 3a isixxxessDISPLAY Found FEATURE to the user READ NEXT FATRE DATABASE FIG RE, i. US 2012/0266329 A1 Oct. 18, 2012 NUCLECACDS AND PROTEINS AND SUMMARY METHODS FOR MAKING AND USING THEMI 0005. The invention provides isolated or recombinant CROSS-REFERENCE TO RELATED nucleic acids comprising a nucleic acid sequence having at APPLICATIONS least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 0001. This application is a divisional of U.S. patent appli 58%, 59%, 60%, 61%. 62%, 63%, 64%. 65%, 66%, 67%, cation Ser. No. 1 1/817,403, filed Aug. 29, 2007, now U.S. Pat. 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, No. 8,119,385; which is the U.S. national phase, pursuant to 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 35 U.S.C. S371, of international application number PCT/ 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, US2006/007642, filed Mar. 3, 2006, designating the United 98%, 99%, or more, or complete (100%) sequence identity to States and published on Sep. 14, 2006 as publication number an exemplary nucleic acid of the invention, e.g., including WO 2006/096527, which claims priority under 35 USC S 119 SEQID NO:1, SEQID NO:3, SEQID NO:5, SEQID NO:7, (e)(1) of prior U.S. provisional application No. 60/658,984, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID filed Mar. 4, 2005, all of which are hereby incorporated by NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, reference. SEQ ID NO:23, SEQ ID NO:25, and all nucleic acids dis FIELD OF THE INVENTION closed in the SEQID listing, which include all odd numbered SEQID NO:s from SEQ ID NO:1 through SEQ ID NO:26, 0002. This invention relates to molecular and cellular biol ogy and biochemistry. In one aspect, the invention provides 897, over a region of at least about 10, 15, 20, 25, 30, 35, 40, polypeptides, including enzymes, structural proteins and 45, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, binding proteins (e.g., ligands, receptors), polynucleotides 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, encoding these polypeptides, and methods of making and 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, using these polynucleotides and polypeptides. In one aspect, 1650, 1700, 1750, 1800, 1850, 1900, 1950, 2000, 2050,2100, the invention is directed to polypeptides, e.g., enzymes, struc 2200, 2250, 2300, 2350, 2400, 2450, 2500, or more residues, tural proteins and binding proteins, including thermostable encodes at least one polypeptide having an enzyme, structural and thermotolerant activity, and polynucleotides encoding orbinding activity, and the sequence identities are determined these enzymes, structural proteins and binding proteins and by analysis with a sequence comparison algorithm or by a making and using these polynucleotides and polypeptides. visual inspection. In one aspect, the enzymes and proteins of The polypeptides of the invention can be used in a variety of the invention include, e.g. aldolases, alpha-galactosidases, pharmaceutical, agricultural and industrial contexts, includ amidases, e.g. secondary amidases, amylases, catalases, caro ing the manufacture of cosmetics and nutraceuticals. tenoid pathway enzymes, dehalogenases, endoglucanases, 0003. Additionally, the polypeptides of the invention can epoxide hydrolases, esterases, hydrolases, glucosidases, gly be used in food processing, brewing, bath additives, alcohol cosidases, inteins, isomerases, laccases, lipases, monooxyge production, peptide synthesis, enantioselectivity, hide prepa nases, nitroreductases, nitrilases, P450 enzymes, pectate ration in the leather industry, waste management and animal lyases, phosphatases, phospholipases, phytases, polymerases degradation, silver recovery in the photographic industry, and Xylanases. In another aspect, the isolated and recombi medical treatment, silk degumming, biofilm degradation, nant polypeptides of the invention, including enzymes, struc biomass conversion to ethanol, biodefense, antimicrobial tural proteins and binding proteins, and polynucleotides agents and disinfectants, personal care and cosmetics, biotech encoding these polypeptides, of the invention have activity as reagents, in corn wet milling and pharmaceuticals such as digestive aids and anti-inflammatory (anti-phlogistic) agents. described in Table 1, Table 2 or Table 3, below. 0006. In one aspect, the invention also provides isolated or BACKGROUND recombinant nucleic acids with a common novelty in that they 0004. The invention provides isolated and recombinant are all derived from a common Source, e.g., an environmental polypeptides, including enzymes, structural proteins and Source, mixed environmental sources or mixed cultures. The binding proteins, polynucleotides encoding these polypep invention provides isolated or recombinant nucleic acids iso tides, and methods of making and using these polynucleotides lated from a common Source, e.g. an environmental source, and polypeptides. The polypeptides of the invention, and the mixed environmental sources or mixed cultures comprising a polynucleotides encoding the polypeptides of the invention, polynucleotide of the invention, e.g., an exemplary sequence encompass many classes of enzymes, structural proteins and of the invention, including SEQ ID NO:1, SEQ ID NO:3, binding proteins. In one aspect, the enzymes and proteins of SEQID NO:5, SEQID NO:7, SEQIDNO:9, SEQID NO:11, the invention include, e.g. aldolases, alpha-galactosidases, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID amidases, e.g. secondary amidases, amylases, catalases, caro NO:19, SEQID NO:21, SEQID NO:23, SEQID NO:25, and tenoid pathway enzymes, dehalogenases, endoglucanases, all nucleic acids disclosed in the SEQ ID listing, which epoxide hydrolases, esterases, hydrolases, glucosidases, gly include all odd numbered SEQID NO:s from SEQID NO:1 cosidases, inteins, isomerases, laccases, lipases, monooxyge through SEQID NO:26,897, over a region of at least about nases, nitroreductases, nitrilases, P450 enzymes, pectate 10, 15, 20, 25, 30, 35, 40, 45,50, 75, 100, 150, 200, 250,300, lyases, phosphatases, phospholipases, phytases, polymerases 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, and Xylanases. The invention also provides isolated and 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, recombinant polypeptides, including enzymes, structural 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850, 1900, proteins and binding proteins, polynucleotides encoding 1950, 2000, 2050,2100, 2200,2250,2300, 2350,2400, 2450, these polypeptides, having the activities described in Table 1, 2500, or more residues, encodes at least one polypeptide Table 2 or Table 3, below.
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