USOO854.1220B2

(12) United States Patent (10) Patent No.: US 8,541.220 B2 Weiner et al. (45) Date of Patent: Sep. 24, 2013

(54) ISOMERASES, NUCLEICACIDS ENCODING (56) References Cited THEMAND METHODS FOR MAKING AND USING THEM FOREIGN PATENT DOCUMENTS WO 2005063O37 7/2005 (75) Inventors: David P. Weiner, San Diego, CA (US); WO 2006096527 9, 2006 Ellen G. Burke, San Diego, CA (US); OTHER PUBLICATIONS Peter Luginbuhl, San Diego, CA (US); Broun et al., Catalytic plasticity of fatty acid modification enzymes Analia Bueno, San Diego, CA (US); underlying chemical diversity of plant lipids. Science, 1998, vol. 282: Joslin M. Cuenca, San Diego, CA (US); 1315-1317. Mervyn L. De Souza, Ft. Collins, CO Chica et al., Semi-rational approaches to engineering enzyme activ (US); Sherry Kollmann, Rogers, MN ity: combining the benefits of directed evolution and rational design. (US) Curr. Opi. Biotechnol., 2005, vol. 16: 378-384.* Devos et al., Practical limits of function prediction. Proteins: Struc (73) Assignee: Verenium Corporation, San Diego, CA ture, Function, and Genetics. 2000, vol. 41: 98-107. Seffernicket al., Melamine deaminase and Atrazine chlorohydrolase: (US) 98 percent identical but functionally different. J. Bacteriol., 2001, vol. 183 (8): 2405-2410.* (*) Notice: Subject to any disclaimer, the term of this Sen et al., Developments in directed evolution for improving enzyme patent is extended or adjusted under 35 functions. Appl. Biochem. Biotechnol., 2007, vol. 143: 212-223.* U.S.C. 154(b) by 231 days. Whisstock et al., Prediction of protein function from protein sequence. Q. Rev. Biophysics., 2003, vol. 36 (3): 307-340.* Wishart et al. A single mutation converts a novel phosphotyrosine (21) Appl. No.: 12/810,067 binding domain into a dual-specificity phosphatase. J. Biol. Chem. 1995, vol. 270(45): 267.82-26785.* (22) PCT Filed: Dec. 22, 2008 Witkowski et al., Conversion of b-ketoacyl synthase to a Malonyl Decarboxylase by replacement of the active cysteine with glutamine. (86). PCT No.: PCT/US2O08/088066 Biochemistry, 1999, vol. 38: 11643-1 1650.* EP08870439.0 Extended EP Search Report & Opinion (Jun. 17, S371 (c)(1), 2011). (2), (4) Date: Sep. 30, 2010 UNIPARC Accession No. UPIO0013DD11F (May 6, 2007). EM EST Accession No. EG550964—de los Reyes (Oct. 25, 2006). (87) PCT Pub. No.: WO2009/088753 PCT/US2008/088066 ISR & WO Mar. 17, 2009. PCT/US2008/088066 IPRP Jul 15, 2010. PCT Pub. Date: Jul. 16, 2009 GENPEPT Accession No. AAC06592 Deckert (1998). EP08870439.0–Articla 94(3) Communication Oct. 29, 2012. (65) Prior Publication Data US 2011 FOO53245A1 Mar. 3, 2011 * cited by examiner Primary Examiner — Ganapathirama Raghu (74) Attorney, Agent, or Firm — Brian W. Siddons; Related U.S. Application Data Verenium Corporation (60) Provisional application No. 61/018,880, filed on Jan. (57) ABSTRACT 3, 2008. This invention relates generally to enzymes, polynucleotides encoding the enzymes, the use of Such polynucleotides and (51) Int. Cl. polypeptides and more specifically to enzymes having CI2N 9/90 (2006.01) isomerase activity, e.g., racemase activity, e.g., amino acid CI2N 9/88 (2006.01) racemase activity, alanine racemase activity, and/or epime CI2N 9/48 (2006.01) rase activity, and/or catalyze the re-arrangement of atoms within a molecule, catalyze the conversion of one isomer into CI2N 9/42 (2006.01) another, catalyze the conversion of an optically active Sub CI2N 9/16 (2006.01) strate into a raceme, which is optically inactive, catalyze the CO2F 3/34 (2006.01) interconversion of Substrate enantiomers, catalyze the stere A62D 3/00 (2007.01) ochemical inversion around the asymmetric carbon atom in a C7H 2L/04 (2006.01) Substrate having only one center of asymmetry, catalyze the C07K L/00 (2006.01) Stereochemical inversion of the configuration around an A2ID 2/00 (2006.01) asymmetric carbonatom in a Substrate having more than one A2.3L I/O (2006.01) asymmetric center, and/or catalyze the racemization of amino D2C3/20 (2006.01) acids. Thus, the invention provides enzymes, compositions, (52) U.S. Cl. methods for production of pharmaceutical compositions, USPC ...... 435/233; 435/232; 435/212:435/209; pharmaceutical intermediates, antibiotics, Sweeteners, pep 435/200; 435/196; 435/193; 435/192:435/262: tide enzymes, peptide hormones, fuel and fuel additive com 435/262.5:536/23.2:530/350: 162/72 positions, foods and food additives, beverage and beverage (58) Field of Classification Search additives, feeds and feed additives, drugs and drug additives, USPC ...... 435/233,232, 212, 209, 200, 196, dietary Supplements, textiles, wood, paper, pulp, and deter 435/193, 192, 262, 262.5: 426/20, 29: gents comprising the polypeptides or polynucleotides in 536/23.2; 530/350; 162/72 accordance with the invention. See application file for complete search history. 7 Claims, 4 Drawing Sheets U.S. Patent Sep. 24, 2013 Sheet 1 of 4 US 8,541.220 B2

Figure 1

COMPUTER SYSTEM

PROCESSOR u/

115

10 INTERNAL STORAGE

118 120

DATA U RETREVING DISPLAY DEVICE

U.S. Patent Sep. 24, 2013 Sheet 2 of 4 US 8,541.220 B2

Figure 2

200 201 N\ START

202 STORE NEW SECRUENCE TO A MEMORY u 204 OPEN DATABASE OF SEGUENCES y 206 READ FIRST SECRUENCE IN DATABASE u?

210 PERFORM COMPARISON OF NEW SECQUENCE AND STORED SEOUENCE

212

YES 214 y u/ DISPLAY STORED SECRUENCE NAME TO USER 224 NO

GO TONEXT SEOUENCE IN DATABASE

MORE SEOUENCES IN DATABASE?

NO 220 END U.S. Patent Sep. 24, 2013 Sheet 3 of 4 US 8,541.220 B2

FIGURE 3

252 250 N

254 STORE A FIRST SECRUENCE TO A MEMORY

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

264

YESy 268 READ NEXT CHARACTER OF FIRST AND SECOND P YES SEGUENCES

CHARACTERS TO

NO 276 DISPLAY HOMOLOGY LEVEL BETWEEN THE FIRST AND SECOND SECRUENCES

278 END U.S. Patent Sep. 24, 2013 Sheet 4 of 4 US 8,541.220 B2

Figure 4

302 3OO NY 304 STORE A FIRST SEOUENCE TO MEMORY 306 OPEN DATABASE OF SECQUENCE FEATURES U-/ ! 3 08 READ FIRST FEATURE FROM DATABASE u?

3 O COMPARE FEATURE ATTRIBUTES WITH THE FIRST SECRUENCE

YES 38 y - DISPLAY FOUND FEATURE TO THE USER 326

READ NEXT FEATURE IN DATABASE

MORE FEATURES IN DATABASE2

NO 324 END US 8,541,220 B2 1. 2 ISOMERASES, NUCLEICACIDS ENCODING sion of one isomer into another, catalyze the conversion of an THEMAND METHODS FOR MAKING AND optically active Substrate into a raceme, which is optically USING THEMI inactive, catalyze the interconversion of Substrate enanti omers, catalyze the stereochemical inversion around the CROSS REFERENCE TO RELATED asymmetric carbonatomina Substrate having only one center APPLICATIONS of asymmetry, catalyze the stereochemical inversion of the configuration around an asymmetric carbon atom in a Sub This application is a national stage application claiming the strate having more than one asymmetric center, and/or cata benefit of priority under 35 U.S.C. S371 to Patent Coopera lyze the racemization of amino acids. Isomerases, e.g., race tion Treaty (PCT) Application No. PCT/US2008/088066 10 mases, e.g., amino acid racemases, alanine racemases, and/or epimerases are of considerable commercial value, being used having an international filing date of Dec. 22, 2008, and in the pharmaceutical industry, in the food, feed and beverage published as WO 2009/088753, on Jul. 16, 2009, which industries, e.g. for the production of Sweeteners, in the wood/ claims the benefit of priority under 35 U.S.C. S 119(e) to U.S. paper industry and in the fuel industry. Provisional Application No. 61/018,880 filed Jan. 3, 2008. 15 The contents of the above mentioned patent applications are SUMMARY OF THE INVENTION incorporated by reference herein in their entirety and for all purposes. This invention provides enzymes having isomerase activ ity, e.g., racemase activity, e.g., amino acid racemase activity, REFERENCE TO SEQUENCE LISTING alanine racemase activity, and/or epimerase activity, and/or SUBMITTED VIA EFS-WEB catalyze the re-arrangement of atoms within a molecule, cata lyze the conversion of one isomer into another, catalyze the The entire content of the following electronic submission conversion of an optically active Substrate into a raceme, of the sequence listing via the USPTO EFS-WEB server, as which is optically inactive, catalyze the interconversion of authorized and set forth in MPEP 502.05(IX), is incorporated 25 Substrate enantiomers, catalyze the stereochemical inversion herein by reference in its entirety for all purposes. The around the asymmetric carbonatomina Substrate having only sequence listing is identified on the electronically filed.txt file one center of asymmetry, catalyze the stereochemical inver as follows: sion of the configuration around an asymmetric carbon atom in a Substrate having more than one asymmetric center, and/or 30 catalyze the racemization of amino acids. The invention fur FileName Date of Creation Size ther provides enzymes having isomerase activity, e.g., race mase activity, e.g., amino acid racemase activity, alanine D2440 01N. SequenceListing..txt Sep. 28, 2010 1,298.432 bytes racemase activity, and/or epimerase activity and nucleic acids encoding them, Vectors and cells comprising them, probes for 35 amplifying and identifying these an isomerase-, e.g., a race FIELD OF THE INVENTION mase-, e.g., an amino acid racemase-, an alanine racemase-, and/or an epimerase-isomerase-, e.g., racemase-, e.g., amino This invention relates generally to enzymes, polynucle acid racemase-, alanine racemase-, and/or epimerase-encod otides encoding the enzymes, the use of such polynucleotides ing nucleic acids, and methods for making and using these and polypeptides and more specifically to enzymes having 40 polypeptides and peptides. isomerase activity, e.g., racemase activity, e.g., amino acid The invention provides enzymes, compositions, methods racemase activity, alanine racemase activity, and/or epime for production of pharmaceutical (drug) compositions, phar rase activity, and/or catalyze the re-arrangement of atoms maceutical (drug) precursors and intermediates, antibiotics, within a molecule, catalyze the conversion of one isomer into Sweeteners, peptide enzymes, peptide hormones, fuel and another, catalyze the conversion of an optically active Sub 45 fuel additive compositions, foods and food additives, bever strate into a raceme, which is optically inactive, catalyze the age and beverage additives, feeds and feed additives, drugs interconversion of Substrate enantiomers, catalyze the stere and drug additives, dietary Supplements, textiles, wood, ochemical inversion around the asymmetric carbon atom in a paper, pulp, and detergents comprising the polypeptides or Substrate having only one center of asymmetry, catalyze the polynucleotides in accordance with the invention. These Stereochemical inversion of the configuration around an 50 compositions can be formulated in a variety of forms, such as asymmetric carbonatom in a Substrate having more than one tablets, gels, pills, implants, liquids, sprays, films, micelles, asymmetric center, and/or catalyze the racemization of amino powders, food, feed pellets or as any type of encapsulated acids. Thus, the invention provides enzymes, compositions, form. methods for production of pharmaceutical (drug) composi In some embodiments, the isomerases, e.g., racemases, tions, pharmaceutical (drug) precursors and intermediates, 55 e.g., amino acid racemases, alanine racemases, and/or epime antibiotics, Sweeteners, peptide enzymes, peptide hormones, rases and/or compositions thereof may be useful in pharma fuel and fuel additive compositions, foods and food additives, ceutical, industrial, and/or agricultural contexts. beverage and beverage additives, feeds and feed additives, In some embodiments, the isomerases, e.g., racemases, drugs and drug additives, dietary Supplements, textiles, wood, e.g., amino acid racemases, alanine racemases, and/or epime paper, pulp, and detergents comprising the polypeptides or 60 rases and/or compositions thereof may be useful for cata polynucleotides in accordance with the invention. lyzing the inversion of Stereochemistry in biological mol ecules. In some embodiments, the isomerases, e.g., BACKGROUND racemases, e.g., amino acid racemases, alanine racemases, and/or epimerases and/or compositions thereofmay be useful Isomerases, e.g., racemases, e.g., amino acid racemases, 65 for catalyzing the interconversion of Substrate enantiomers. alanine racemases, and/or epimerases catalyze the re-ar In some embodiments, isomerases, e.g., racemases, e.g., rangement of atoms within a molecule, catalyze the conver amino acid racemases, and/or alanine racemases catalyze the US 8,541,220 B2 3 4 Stereochemical inversion around the asymmetric carbonatom acid racemase activity, analanine racemase activity, and/oran in a substrate having only one center of asymmetry. In some epimerase activity but lacking a signal sequence, a prepro embodiments, isomerases, e.g., epimerases catalyze the Ste domain and/or other domain. reochemical inversion of the configuration around an asym In alternative embodiments, the invention provides metric carbon atom in a Substrate having more than one polypeptides (and the nucleic acids that encode them) having asymmetric center. In some embodiments, isomerases, e.g., an isomerase activity, e.g., a racemase activity, e.g., an amino racemases, e.g., amino acid racemases, and/or alanine race acid racemase activity, analanine racemase activity, and/oran mases are provided that catalyze the racemization of amino epimerase activity further comprising a heterologous acids. In some embodiments, racemases are provided that sequence; and in one aspect, the heterologous sequence com catalyze the racemization of a specific amino acid. In some 10 prises, or consists of a sequence encoding: (i) a heterologous embodiments, isomerases, e.g., racemases, e.g., amino acid signal sequence, a heterologous domain, a heterologous racemases, and/or alanine racemases are provided that cata dockerin domain, a heterologous catalytic domain (CD), or a lyze the racemization of several amino acids. combination thereof; (ii) the sequence of (i), wherein the In some embodiments, the racemases, e.g., amino acid heterologous signal sequence, domain or catalytic domain racemases, alanine racemases, and/or epimerases and/or 15 (CD) is derived from a heterologous enzyme; or, (iii) a tag, an compositions thereofmay be useful in D-amino acid metabo epitope, a targeting peptide, a cleavable sequence, a detect lism. D-amino acids are necessary for bacterial growth and able moiety oran enzyme; and in one aspect, the heterologous for peptidoglycan assembly and cross linking. D-amino acids signal sequence targets the encoded protein to a vacuole, the are also present in the brains of newborn humans. Bacterial endoplasmic reticulum, a chloroplast or a starch granule. serine racemase plays and important role in Vancomycin In alternative embodiments, the invention provides resistance. Some amino acid racemases are PLP dependent; polypeptides (and the nucleic acids that encode them) having other amino acid racemases are PLP independent. (see, e.g., an isomerase activity, e.g., a racemase activity, e.g., an amino Yoshimura, T., N. Esaki, 2003, Journal of Bioscience and acid racemase activity, analanine racemase activity, and/oran Bioengineering. 96:103-109). In alternative embodiments, epimerase activity, wherein the polypeptides are cofactor the racemases, e.g., amino acid racemases, alanine race 25 dependent or cofactor independent. In one embodiment, a mases, and/or epimerases and/or combinations thereof are cofactor dependent polypeptide requires the presence of a components in pharmaceutical (drug) compositions, pharma non-protein component to be functional. In one embodiment, ceutical (drug) precursors and/or intermediates, e.g. as anti the cofactor comprises a metalion, a coenzyme, a pyridoxal biotics or for treatment of amino acid deficiencies. phosphate and or a phosphopantetheline. In alternative embodiments, the isomerases, e.g., race 30 The invention provides isolated, synthetic or recombinant mases, e.g., amino acid racemases, alanine racemases, and/or nucleic acids comprising (a) a nucleic acid (polynucleotide) epimerases of the invention and/or compositions thereof of encoding at least one polypeptide, wherein the nucleic acid may be useful as an antibiotic or in the preparation of antibi comprises a sequence having at least about 50%, 51%, 52%, otics (see, e.g., Strych, U. M. J. Benedik. 2002, Journal of 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, Bacteriology. 184:4321-4325). 35 63%, 64%. 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, In alternative embodiments, the isomerases, e.g., race 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, mases, e.g., amino acid racemases, alanine racemases, and/or 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, epimerases of the invention and/or compositions thereof of 93%, 94%, 95%, 96%,97%.98%, 99%, or more or complete may be useful as in mediation of mammal nervous transmis (100%) sequence identity to the nucleic acid (polynucleotide) sion and maintenance of bacterial cell wall rigidity and 40 sequence of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, strength (see, e.g. Liu, L., K. Iwata, M. Yohda, K. Miki. 2002, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID FEBS. 528: 114-118). NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, In alternative embodiments, the invention provides SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID enzymes and processes for the bioconversion of any biomass NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, into fuel, e.g. biofuel, e.g., ethanol, propanol, butanol, metha 45 SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID nol, and/or biodiesel or biofuels such as synthetic liquids or NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, gases, such as Syngas, and the production of other fermenta SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID tion products, e.g. Succinic acid, lactic acid, or acetic acid. NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, In alternative embodiments, the invention provides SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, SEQ ID polypeptides (and the nucleic acids that encode them) having 50 NO:69, SEQ ID NO:71, SEQ ID NO:73, SEQ ID NO:75, at least one conservative amino acid substitution and retain SEQ ID NO:77, SEQ ID NO:79, SEQ ID NO:81, SEQ ID ing its isomerase activity, e.g., racemase activity, e.g., amino NO:83, SEQ ID NO:85, SEQ ID NO:87, SEQ ID NO:89, acid racemase activity, alanine racemase activity, and/or epi SEQ ID NO:91, SEQ ID NO:93, SEQ ID NO:95, SEQ ID merase activity; or, wherein the at least one conservative NO:97, SEQID NO:99, SEQID NO:101, SEQID NO:103, amino acid substitution comprises Substituting an amino acid 55 SEQID NO:105, SEQID NO:107, SEQIDNO:109, SEQID with another amino acid of like characteristics; or, a conser NO:111, SEQ ID NO: 113, SEQ ID NO:115, SEQ ID Vative Substitution comprises: replacement of an aliphatic NO:117, SEQ ID NO:119, SEQ ID NO:121, SEQ ID amino acid with anotheraliphatic amino acid; replacement of NO:123, SEQ ID NO:125, SEQ ID NO.127, SEQ ID a Serine with a Threonine or vice versa; replacement of an NO:129, SEQ ID NO:131, SEQ ID NO:133, SEQ ID acidic residue with another acidic residue; replacement of a 60 NO:135, SEQ ID NO:137, SEQ ID NO:139, SEQ ID residue bearing an amide group with another residue bearing NO:141, SEQ ID NO:143, SEQ ID NO:145, SEQ ID an amide group; exchange of a basic residue with another NO:147, SEQ ID NO:149, SEQ ID NO:151, SEQ ID basic residue; or replacement of an aromatic residue with NO:153, SEQ ID NO:155, SEQ ID NO:157, SEQ ID another aromatic residue; NO:159, SEQ ID NO:161, SEQ ID NO:163, SEQ ID In alternative embodiments, the invention provides 65 NO:165, SEQ ID NO:167, SEQ ID NO:169, SEQ ID polypeptides (and the nucleic acids that encode them) having NO:171, SEQ ID NO:173, SEQ ID NO:175, SEQ ID an isomerase activity, e.g., a racemase activity, e.g., an amino NO:177, SEQ ID NO:179, SEQ ID NO:181, SEQ ID US 8,541,220 B2 5 6 NO:183, SEQ ID NO:185, SEQ ID NO:187, SEQ ID 800, 850, 900,950, 1000, 1050, 1100, 1150 or more residues, NO:189, SEQ ID NO:191, SEQ ID NO:193, SEQ ID or over the full length of a cDNA, transcript (mRNA) or gene: NO:195, SEQ ID NO:197, SEQ ID NO:199, SEQ ID (c) the nucleic acid (polynucleotide) of (a) or (b), wherein NO:201, SEQ ID NO:203, SEQ ID NO:205, SEQ ID the sequence comparison algorithm is a BLAST version 2.2.2 NO:207, SEQ ID NO:209, SEQ ID NO:211, SEQ ID algorithm where a filtering setting is set to blastall-p blastp-d NO:213, SEQ ID NO:215, SEQ ID NO:217, SEQ ID “nr pataa’-FF, and all other options are set to default; NO:219, SEQ ID NO:221, SEQ ID NO:223, SEQ ID (d) a nucleic acid (polynucleotide) encoding at least one NO:225, SEQ ID NO:227, SEQ ID NO:229, SEQ ID polypeptide or peptide, wherein the nucleic acid comprises a NO:231, SEQ ID NO:233, SEQ ID NO:235, SEQ ID sequence that hybridizes under Stringent conditions to a NO:237, SEQ ID NO:239, SEQ ID NO:241, SEQ ID 10 nucleic acid comprising the sequence of SEQID NO:1, SEQ ID ID ID ID NO:3, SEQID NO:5, SEQID NO:7, SEQID NO:9, SEQ NO:243, SEQ NO:245, SEQ NO:247, SEQ ID NO:11, SEQID NO:13, SEQID NO:15, SEQID NO:17, NO:249, SEQ ID NO:251, SEQ ID NO:253, SEQ ID SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:255, SEQ ID NO:257, SEQ ID NO:259, SEQ ID ID ID ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, NO:261, SEQ NO:263, SEQ NO:265, SEQ 15 SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:267, SEQ ID NO:269, SEQ ID NO:271, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, NO:273, SEQ ID NO:275, SEQ ID NO:277, SEQ ID SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:279, SEQ ID NO:281, SEQ ID NO:283, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, NO:285, SEQ ID NO:287, SEQ ID NO:289, SEQ ID SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:291, SEQ ID NO:293, SEQ ID NO:295, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:71, SEQ ID NO:73, NO:297, SEQ ID NO:299, SEQ ID NO:301, SEQ ID SEQ ID NO:75, SEQ ID NO:77, SEQ ID NO:79, SEQ ID NO:303, SEQ ID NO:305, SEQ ID NO:307, SEQ ID NO:81, SEQ ID NO:83, SEQ ID NO:85, SEQ ID NO:87, NO:309, SEQ ID NO:311, SEQ ID NO:313, SEQ ID SEQ ID NO:89, SEQ ID NO:91, SEQ ID NO:93, SEQ ID NO:315, SEQ ID NO:317, SEQ ID NO:319, SEQ ID NO:95, SEQ ID NO:97, SEQ ID NO:99, SEQ ID NO:101, NO:321, SEQ ID NO:323, SEQ ID NO:325, SEQ ID 25 SEQID NO:103, SEQID NO:105, SEQIDNO:107, SEQID NO:327, SEQ ID NO:329, SEQ ID NO:331, SEQ ID NO:109, SEQ ID NO:111, SEQ ID NO:113, SEQ ID NO:333, SEQ ID NO:335, SEQ ID NO:337, SEQ ID NO:115, SEQ ID NO:117, SEQ ID NO:119, SEQ ID NO:339, SEQ ID NO:341, SEQ ID NO:343, SEQ ID NO:121, SEQ ID NO:123, SEQ ID NO:125, SEQ ID NO:345, SEQ ID NO:347, SEQ ID NO:349, SEQ ID NO:127, SEQ ID NO.129, SEQ ID NO:131, SEQ ID NO:351, SEQ ID NO:353, SEQ ID NO:355, SEQ ID 30 NO:133, SEQ ID NO:135, SEQ ID NO:137, SEQ ID NO:357, SEQ ID NO:359, SEQ ID NO:361, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:143, SEQ ID NO:363, SEQ ID NO:365, SEQ ID NO:367, SEQ ID NO:145, SEQ ID NO:147, SEQ ID NO:149, SEQ ID NO:369, SEQ ID NO:371, SEQ ID NO:373, SEQ ID NO:151, SEQ ID NO:153, SEQ ID NO:155, SEQ ID NO:375, SEQ ID NO:377, SEQ ID NO:379, SEQ ID NO:157, SEQ ID NO:159, SEQ ID NO:161, SEQ ID NO:381, SEQ ID NO:383, SEQ ID NO:385, SEQ ID 35 NO:163, SEQ ID NO:165, SEQ ID NO:167, SEQ ID NO:387, SEQ ID NO:389, SEQ ID NO:391, SEQ ID NO:169, SEQ ID NO:171, SEQ ID NO:173, SEQ ID NO:393, SEQ ID NO:395, SEQ ID NO:397, SEQ ID NO:175, SEQ ID NO:177, SEQ ID NO:179, SEQ ID NO:399, SEQ ID NO:401, SEQ ID NO:403, SEQ ID NO:181, SEQ ID NO:183, SEQ ID NO:185, SEQ ID NO:405, SEQ ID NO:407, SEQ ID NO:409, SEQ ID NO:187, SEQ ID NO:189, SEQ ID NO.191, SEQ ID NO:411, SEQ ID NO:413, SEQ ID NO:415, SEQ ID 40 NO:193, SEQ ID NO.195, SEQ ID NO:197, SEQ ID NO:417, SEQ ID NO:419, SEQ ID NO:421, SEQ ID NO:199, SEQ ID NO:201, SEQ ID NO:203, SEQ ID NO:423, SEQ ID NO:425, SEQ ID NO:427, SEQ ID NO:205, SEQ ID NO:207, SEQ ID NO:209, SEQ ID NO:429, SEQ ID NO:431, SEQ ID NO:433, SEQ ID NO:211, SEQ ID NO:213, SEQ ID NO:215, SEQ ID NO:435, SEQ ID NO:437, SEQ ID NO:439, SEQ ID NO:217, SEQ ID NO:219, SEQ ID NO:221, SEQ ID NO:441, SEQ ID NO:443, SEQ ID NO:445, SEQ ID 45 NO:223, SEQ ID NO:225, SEQ ID NO:227, SEQ ID NO:447, SEQ ID NO:449, SEQ ID NO:451, SEQ ID NO:229, SEQ ID NO:231, SEQ ID NO:233, SEQ ID NO:453, SEQ ID NO:455, SEQ ID NO:457, SEQ ID NO:235, SEQ ID NO:237, SEQ ID NO:239, SEQ ID NO:459, SEQ ID NO:461, SEQ ID NO:463, SEQ ID NO:241, SEQ ID NO:243, SEQ ID NO:245, SEQ ID NO:465, SEQ ID NO:467, SEQ ID NO:469, SEQ ID NO:247, SEQ ID NO:249, SEQ ID NO:251, SEQ ID NO:471, SEQ ID NO:473, SEQ ID NO:475, SEQ ID 50 NO:253, SEQ ID NO:255, SEQ ID NO:257, SEQ ID NO:477, SEQ ID NO:479, SEQ ID NO:481, SEQ ID NO:259, SEQ ID NO:261, SEQ ID NO:263, SEQ ID NO:483, SEQ ID NO:485, SEQ ID NO:487, SEQ ID NO:265, SEQ ID NO:267, SEQ ID NO:269, SEQ ID NO:489, SEQIDNO:491, SEQID NO:493, SEQID NO:495 NO:271, SEQ ID NO:273, SEQ ID NO:275, SEQ ID or SEQID NO:497; wherein the nucleic acid encodes at least NO:277, SEQ ID NO:279, SEQ ID NO:281, SEQ ID one polypeptide having an isomerase activity, e.g., a race 55 NO:283, SEQ ID NO:285, SEQ ID NO:287, SEQ ID mase activity, e.g., an amino acid racemase activity, an ala NO:289, SEQ ID NO:291, SEQ ID NO:293, SEQ ID nine racemase activity, and/or an epimerase activity, or NO:295, SEQ ID NO:297, SEQ ID NO:299, SEQ ID encodes a polypeptide or peptide capable of generating an NO:301, SEQ ID NO:303, SEQ ID NO:305, SEQ ID isomerase specific antibody, e.g., a racemase specific anti NO:307, SEQ ID NO:309, SEQ ID NO:311, SEQ ID body, e.g., an amino acid racemase, an alanine racemase, 60 NO:313, SEQ ID NO:315, SEQ ID NO:317, SEQ ID and/or an epimerase specific antibody (a polypeptide or pep NO:319, SEQ ID NO:321, SEQ ID NO:323, SEQ ID tide that acts as an epitope or immunogen), NO:325, SEQ ID NO:327, SEQ ID NO:329, SEQ ID (b) the nucleic acid (polynucleotide) of (a), wherein the NO:331, SEQ ID NO:333, SEQ ID NO:335, SEQ ID sequence identities are determined: (A) by analysis with a NO:337, SEQ ID NO:339, SEQ ID NO:341, SEQ ID sequence comparison algorithm or by a visual inspection, or 65 NO:343, SEQ ID NO:345, SEQ ID NO:347, SEQ ID (B) over a region of at least about 20,30,40, 50, 75, 100, 150, NO:349, SEQ ID NO:351, SEQ ID NO:353, SEQ ID 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, NO:355, SEQ ID NO:357, SEQ ID NO:359, SEQ ID US 8,541,220 B2 7 8 NO:361, SEQ ID NO:363, SEQ ID NO:365, SEQ ID NO:206, SEQ ID NO:208, SEQ ID NO:210, SEQ ID NO:367, SEQ ID NO:369, SEQ ID NO:371, SEQ ID NO:212, SEQ ID NO:214, SEQ ID NO:216, SEQ ID NO:373, SEQ ID NO:375, SEQ ID NO:377, SEQ ID NO:218, SEQ ID NO:220, SEQ ID NO:222, SEQ ID NO:379, SEQ ID NO:381, SEQ ID NO:383, SEQ ID NO:224, SEQ ID NO:226, SEQ ID NO:228, SEQ ID NO:385, SEQ ID NO:387, SEQ ID NO:389, SEQ ID 5 NO:230, SEQ ID NO:232, SEQ ID NO:234, SEQ ID NO:391, SEQ ID NO:393, SEQ ID NO:395, SEQ ID NO:236, SEQ ID NO:238, SEQ ID NO:240, SEQ ID NO:397, SEQ ID NO:399, SEQ ID NO:401, SEQ ID NO:242, SEQ ID NO:244, SEQ ID NO:246, SEQ ID NO:403, SEQ ID NO:405, SEQ ID NO:407, SEQ ID NO:248, SEQ ID NO:250, SEQ ID NO:252, SEQ ID NO:409, SEQ ID NO:411, SEQ ID NO:413, SEQ ID NO:254, SEQ ID NO:256, SEQ ID NO:258, SEQ ID NO:415, SEQ ID NO:417, SEQ ID NO:419, SEQ ID 10 NO:260, SEQ ID NO:262, SEQ ID NO:264, SEQ ID NO:421, SEQ ID NO:423, SEQ ID NO:425, SEQ ID NO:266, SEQ ID NO:268, SEQ ID NO:270, SEQ ID NO:427, SEQ ID NO:429, SEQ ID NO:431, SEQ ID NO:272, SEQ ID NO:274, SEQ ID NO:276, SEQ ID NO:433, SEQ ID NO:435, SEQ ID NO:437, SEQ ID NO:278, SEQ ID NO:280, SEQ ID NO:282, SEQ ID NO:439, SEQ ID NO:441, SEQ ID NO:443, SEQ ID NO:284, SEQ ID NO:286, SEQ ID NO:288, SEQ ID NO:445, SEQ ID NO:447, SEQ ID NO:449, SEQ ID 15 NO:290, SEQ ID NO:292, SEQ ID NO:294, SEQ ID NO:451, SEQ ID NO:453, SEQ ID NO:455, SEQ ID NO:296, SEQ ID NO:298, SEQ ID NO:300, SEQ ID NO:457, SEQ ID NO:459, SEQ ID NO:461, SEQ ID NO:302, SEQ ID NO:304, SEQ ID NO:306, SEQ ID NO:463, SEQ ID NO:465, SEQ ID NO:467, SEQ ID NO:308, SEQ ID NO:310, SEQ ID NO:312, SEQ ID NO:469, SEQ ID NO:471, SEQ ID NO:473, SEQ ID NO:314, SEQ ID NO:316, SEQ ID NO:318, SEQ ID NO:475, SEQ ID NO:477, SEQ ID NO:479, SEQ ID NO:320, SEQ ID NO:322, SEQ ID NO:324, SEQ ID NO:481, SEQ ID NO:483, SEQ ID NO:485, SEQ ID NO:326, SEQ ID NO:328, SEQ ID NO:330, SEQ ID NO:487, SEQ ID NO:489, SEQ ID NO:491, SEQ ID NO:332, SEQ ID NO:334, SEQ ID NO:336, SEQ ID NO:493, SEQID NO:495 or SEQID NO:497, NO:338, SEQ ID NO:340, SEQ ID NO:342, SEQ ID and the stringent conditions comprise a wash step compris NO:344, SEQ ID NO:346, SEQ ID NO:348, SEQ ID ing a wash in 0.2xSSC at a temperature of about 65° C. for 25 NO:350, SEQ ID NO:352, SEQ ID NO:354, SEQ ID about 15 minutes; NO:356, SEQ ID NO:358, SEQ ID NO:360, SEQ ID (e) the nucleic acid (polynucleotide) of any of (a) to (d) NO:362, SEQ ID NO:364, SEQ ID NO:366, SEQ ID having a length of at least about 20, 25, 30, 50, 75, 100, 125, NO:368, SEQ ID NO:370, SEQ ID NO:372, SEQ ID 150, 175, 200, 225, 300, 350, 400, 450, 500, 550, 600, 650, NO:374, SEQ ID NO:376, SEQ ID NO:378, SEQ ID 700, 750, 800, 850,900,950, 1000, 1050, 1100, 1150 or more 30 NO:380, SEQ ID NO:382, SEQ ID NO:384, SEQ ID nucleotide residues, or the full length of a gene or a transcript; NO:386, SEQ ID NO:388, SEQ ID NO:390, SEQ ID (f) a nucleic acid (polynucleotide) encoding at least one NO:392, SEQ ID NO:394, SEQ ID NO:396, SEQ ID polypeptide having an isomerase activity, e.g., a racemase NO:398, SEQ ID NO:400, SEQ ID NO:402, SEQ ID activity, e.g., an amino acid racemase activity, an alanine NO:404, SEQ ID NO:406, SEQ ID NO:408, SEQ ID racemase activity, and/or an epimerase activity, wherein the 35 NO:410, SEQ ID NO:412, SEQ ID NO:414, SEQ ID polypeptide comprises the sequence of SEQID NO:2, SEQ NO:416, SEQ ID NO:418, SEQ ID NO:420, SEQ ID IDNO:4, SEQIDNO:6, SEQID NO:8, SEQID NO:10, SEQ NO:422, SEQ ID NO:424, SEQ ID NO:426, SEQ ID ID NO:12, SEQID NO:14, SEQID NO:16, SEQID NO:18, NO:428, SEQ ID NO:430, SEQ ID NO:432, SEQ ID SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:434, SEQ ID NO:436, SEQ ID NO:438, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, 40 NO:440, SEQ ID NO:442, SEQ ID NO:444, SEQ ID SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:446, SEQ ID NO:448, SEQ ID NO:450, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, NO:452, SEQ ID NO:454, SEQ ID NO:456, SEQ ID SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:458, SEQ ID NO:460, SEQ ID NO:462, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, NO:464, SEQ ID NO:466, SEQ ID NO:468, SEQ ID SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID 45 NO:470, SEQ ID NO:472, SEQ ID NO:474, SEQ ID NO:68, SEQ ID NO:70, SEQ ID NO:72, SEQ ID NO:74, NO:476, SEQ ID NO:478, SEQ ID NO:480, SEQ ID SEQ ID NO:76, SEQ ID NO:78, SEQ ID NO:80, SEQ ID NO:482, SEQ ID NO:484, SEQ ID NO:486, SEQ ID NO:82, SEQ ID NO:84, SEQ ID NO:86, SEQ ID NO:88, NO:488, SEQ ID NO:490, SEQ ID NO:492, SEQ ID SEQ ID NO:90, SEQ ID NO:92, SEQ ID NO:94, SEQ ID NO:494, SEQID NO:496 or SEQID NO:498, or enzymati NO:96, SEQID NO:98, SEQID NO:100, SEQID NO:102, 50 cally active fragments thereof; SEQID NO:104, SEQID NO: 106, SEQID NO:108, SEQID (g) the nucleic acid (polynucleotide) of any of (a) to (f) and NO:110, SEQ ID NO:112, SEQ ID NO:114, SEQ ID encoding a polypeptide having at least one conservative NO:116, SEQ ID NO:118, SEQ ID NO:120, SEQ ID amino acid Substitution and retaining its isomerase activity, NO: 122, SEQ ID NO:124, SEQ ID NO.126, SEQ ID e.g., racemase activity, e.g., amino acid racemase activity, NO:128, SEQ ID NO: 130, SEQ ID NO:132, SEQ ID 55 alanine racemase activity, and/or epimerase activity, wherein NO:134, SEQ ID NO:136, SEQ ID NO:138, SEQ ID the at least one conservative amino acid substitution com NO: 140, SEQ ID NO:142, SEQ ID NO:143, SEQ ID prises Substituting an amino acid with another amino acid of NO:146, SEQ ID NO:148, SEQ ID NO:150, SEQ ID like characteristics; or, a conservative Substitution comprises: NO:152, SEQ ID NO:154, SEQ ID NO:156, SEQ ID replacement of an aliphatic amino acid with anotheraliphatic NO:158, SEQ ID NO:160, SEQ ID NO:162, SEQ ID 60 amino acid; replacement of a Serine with a Threonine or vice NO: 164, SEQ ID NO:166, SEQ ID NO:168, SEQ ID Versa; replacement of an acidic residue with another acidic NO:170, SEQ ID NO:172, SEQ ID NO:174, SEQ ID residue; replacement of a residue bearing an amide group NO:176, SEQ ID NO:178, SEQ ID NO:180, SEQ ID with another residue bearing an amide group; exchange of a NO:182, SEQ ID NO:184, SEQ ID NO:186, SEQ ID basic residue with another basic residue, or replacement of an NO:188, SEQ ID NO.190, SEQ ID NO:192, SEQ ID 65 aromatic residue with another aromatic residue. NO:194, SEQ ID NO:196, SEQ ID NO.198, SEQ ID (h) the nucleic acid (polynucleotide) of any of (a) to (g) NO:200, SEQ ID NO:202, SEQ ID NO:204, SEQ ID encoding a polypeptide having an isomerase activity, e.g., a US 8,541,220 B2 10 racemase activity, e.g., an amino acid racemase activity, an NO:242, SEQ ID NO:244, SEQ ID NO:246, SEQ ID alanine racemase activity, and/or an epimerase activity but NO:248, SEQ ID NO:250, SEQ ID NO:252, SEQ ID lacking a signal sequence, a prepro domain, and/or other NO:254, SEQ ID NO:256, SEQ ID NO:258, SEQ ID domain; NO:260, SEQ ID NO:262, SEQ ID NO:264, SEQ ID (i) the nucleic acid (polynucleotide) of any of (a) to (h) 5 NO:266, SEQ ID NO:268, SEQ ID NO:270, SEQ ID encoding a polypeptide having an isomerase activity, e.g., a NO:272, SEQ ID NO:274, SEQ ID NO:276, SEQ ID racemase activity, e.g., an amino acid racemase activity, an NO:278, SEQ ID NO:280, SEQ ID NO:282, SEQ ID alanine racemase activity, and/or an epimerase activity fur NO:284, SEQ ID NO:286, SEQ ID NO:288, SEQ ID ther comprising a heterologous sequence; NO:290, SEQ ID NO:292, SEQ ID NO:294, SEQ ID (j) the nucleic acid (polynucleotide) of (i), wherein the 10 NO:296, SEQ ID NO:298, SEQ ID NO:300, SEQ ID heterologous sequence comprises, or consists of a sequence NO:302, SEQ ID NO:304, SEQ ID NO:306, SEQ ID encoding: (A) a heterologous signal sequence, a heterologous NO:308, SEQ ID NO:310, SEQ ID NO:312, SEQ ID domain, a heterologous dockerin domain, a heterologous NO:314, SEQ ID NO:316, SEQ ID NO:318, SEQ ID catalytic domain (CD), or a combination thereof; (B) the NO:320, SEQ ID NO:322, SEQ ID NO:324, SEQ ID sequence of (i), wherein the heterologous signal sequence, 15 NO:326, SEQ ID NO:328, SEQ ID NO:330, SEQ ID domain or catalytic domain (CD) is derived from a heterolo NO:332, SEQ ID NO:334, SEQ ID NO:336, SEQ ID gous enzyme; or, (C) a tag, an epitope, a targeting peptide, a NO:338, SEQ ID NO:340, SEQ ID NO:342, SEQ ID cleavable sequence, a detectable moiety or an enzyme; NO:344, SEQ ID NO:346, SEQ ID NO:348, SEQ ID (k) the nucleic acid (polynucleotide) of (), wherein the NO:350, SEQ ID NO:352, SEQ ID NO:354, SEQ ID heterologous signal sequence targets the encoded protein to a NO:356, SEQ ID NO:358, SEQ ID NO:360, SEQ ID vacuole, the endoplasmic reticulum, a chloroplast or a starch NO:362, SEQ ID NO:364, SEQ ID NO:366, SEQ ID granule; or NO:368, SEQ ID NO:370, SEQ ID NO:372, SEQ ID (1) a nucleic acid sequence (polynucleotide) fully (com NO:374, SEQ ID NO:376, SEQ ID NO:378, SEQ ID pletely) complementary to the sequence of any of (a) to (k). NO:380, SEQ ID NO:382, SEQ ID NO:384, SEQ ID The invention provides isolated, synthetic or recombinant 25 NO:386, SEQ ID NO:388, SEQ ID NO:390, SEQ ID nucleic acids comprising a nucleic acid encoding at least one NO:392, SEQ ID NO:394, SEQ ID NO:396, SEQ ID polypeptide having an isomerase activity, e.g., a racemase NO:398, SEQ ID NO:400, SEQ ID NO:402, SEQ ID activity, e.g., an amino acid racemase activity, an alanine NO:404, SEQ ID NO:406, SEQ ID NO:408, SEQ ID racemase activity, and/or an epimerase activity, wherein the NO:410, SEQ ID NO:412, SEQ ID NO:414, SEQ ID polypeptide has a sequence as set forth in SEQID NO:2, SEQ 30 NO:416, SEQ ID NO:418, SEQ ID NO:420, SEQ ID IDNO:4, SEQIDNO:6, SEQID NO:8, SEQID NO:10, SEQ NO:422, SEQ ID NO:424, SEQ ID NO:426, SEQ ID ID NO:12, SEQID NO:14, SEQID NO:16, SEQID NO:18, NO:428, SEQ ID NO:430, SEQ ID NO:432, SEQ ID SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:434, SEQ ID NO:436, SEQ ID NO:438, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, NO:440, SEQ ID NO:442, SEQ ID NO:444, SEQ ID SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID 35 NO:446, SEQ ID NO:448, SEQ ID NO:450, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, NO:452, SEQ ID NO:454, SEQ ID NO:456, SEQ ID SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:458, SEQ ID NO:460, SEQ ID NO:462, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, NO:464, SEQ ID NO:466, SEQ ID NO:468, SEQ ID SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:470, SEQ ID NO:472, SEQ ID NO:474, SEQ ID NO:68, SEQ ID NO:70, SEQ ID NO:72, SEQ ID NO:74, 40 NO:476, SEQ ID NO:478, SEQ ID NO:480, SEQ ID SEQ ID NO:76, SEQ ID NO:78, SEQ ID NO:80, SEQ ID NO:482, SEQ ID NO:484, SEQ ID NO:486, SEQ ID NO:82, SEQ ID NO:84, SEQ ID NO:86, SEQ ID NO:88, NO:488, SEQ ID NO:490, SEQ ID NO:492, SEQ ID SEQ ID NO:90, SEQ ID NO:92, SEQ ID NO:94, SEQ ID NO:494, SEQID NO:496 or SEQID NO:498, or enzymati NO:96, SEQID NO:98, SEQID NO:100, SEQID NO:102, cally active fragments thereof, including the sequences SEQID NO:104, SEQID NO: 106, SEQID NO:108, SEQID 45 described herein and in Tables 1, 2 and 3, and the Sequence NO:110, SEQ ID NO:112, SEQ ID NO:114, SEQ ID Listing (all of these sequences are “exemplary enzymes/ NO:116, SEQ ID NO:118, SEQ ID NO:120, SEQ ID polypeptides of the invention'), and enzymatically active NO: 122, SEQ ID NO:124, SEQ ID NO.126, SEQ ID Subsequences (fragments) thereof and/or immunologically NO:128, SEQ ID NO: 130, SEQ ID NO:132, SEQ ID active Subsequences thereof (Such as epitopes or immuno NO:134, SEQ ID NO:136, SEQ ID NO:138, SEQ ID 50 gens) (all "peptides of the invention') and variants thereof (all NO: 140, SEQ ID NO:142, SEQ ID NO:143, SEQ ID of these sequences encompassing polypeptide and peptide NO:146, SEQ ID NO:148, SEQ ID NO:150, SEQ ID sequences of the invention) (or, hereinafter referred to as the NO:152, SEQ ID NO:154, SEQ ID NO:156, SEQ ID exemplary polypeptide sequences of the inventions). NO:158, SEQ ID NO:160, SEQ ID NO:162, SEQ ID The invention provides isolated, synthetic or recombinant NO: 164, SEQ ID NO:166, SEQ ID NO:168, SEQ ID 55 nucleic acids comprising sequences completely complemen NO:170, SEQ ID NO:172, SEQ ID NO:174, SEQ ID tary to all of these nucleic acid sequences of the invention NO:176, SEQ ID NO:178, SEQ ID NO:180, SEQ ID (complementary (non-coding) and coding sequences also NO:182, SEQ ID NO:184, SEQ ID NO:186, SEQ ID hereinafter collectively referred to as nucleic acid sequences NO:188, SEQ ID NO.190, SEQ ID NO:192, SEQ ID of the invention). NO:194, SEQ ID NO:196, SEQ ID NO.198, SEQ ID 60 In one aspect, the sequence identity is at least about 51%, NO:200, SEQ ID NO:202, SEQ ID NO:204, SEQ ID 52%. 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, NO:206, SEQ ID NO:208, SEQ ID NO:210, SEQ ID 62%, 63%, 64%. 65%, 66%, 67%, 68%, 69%, 70%, 71%, NO:212, SEQ ID NO:214, SEQ ID NO:216, SEQ ID 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, NO:218, SEQ ID NO:220, SEQ ID NO:222, SEQ ID 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, NO:224, SEQ ID NO:226, SEQ ID NO:228, SEQ ID 65 92%.93%, 94%, 95%,96%.97%, 98%.99%, or 100% (com NO:230, SEQ ID NO:232, SEQ ID NO:234, SEQ ID plete) sequence identity (homology). In one aspect, the NO:236, SEQ ID NO:238, SEQ ID NO:240, SEQ ID sequence identity is over a region of at least about 150, 175, US 8,541,220 B2 11 12 200, 225, 250, 275,300, 350, 400, 450, 500, 550, 600, 650, NO:389, SEQ ID NO:391, SEQ ID NO:393, SEQ ID 700, 750, 800, 850,900,950, 1000, 1050, 1100, 1150 or more NO:395, SEQ ID NO:397, SEQ ID NO:399, SEQ ID residues, or the full length of a gene or a transcript. For NO:401, SEQ ID NO:403, SEQ ID NO:405, SEQ ID example, the invention provides isolated, synthetic or recom NO:407, SEQ ID NO:409, SEQ ID NO:411, SEQ ID binant nucleic acids comprising a nucleic acid sequence of 5 NO:413. SEQ ID NO:415, SEQ ID NO:417, SEQ ID S EQID NO:1, SEQID NO:3, SEQID NO:5, SEQID NO:7, NO:419, SEQ ID NO:421, SEQ ID NO:423, SEQ ID S EQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:425, SEQ ID NO:427, SEQ ID NO:429, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, NO:431, SEQ ID NO:433, SEQ ID NO:435, SEQ ID EQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:437, SEQ ID NO:439, SEQ ID NO:441, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:35, 10 NO:443, SEQ ID NO:445, SEQ ID NO:447, SEQ ID EQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:449, SEQ ID NO:451, SEQ ID NO:453, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, NO:455, SEQ ID NO:457, SEQ ID NO:459, SEQ ID EQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:461, SEQ ID NO:463, SEQ ID NO:465, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, NO:467, SEQ ID NO:469, SEQ ID NO:471, SEQ ID EQ ID NO:65, SEQ ID NO:67, SEQ ID NO:69, SEQ ID 15 NO:473, SEQ ID NO:475, SEQ ID NO:477, SEQ ID NO:71, SEQ ID NO:73, SEQ ID NO:75, SEQ ID NO:77, NO:479, SEQ ID NO:481, SEQ ID NO:483, SEQ ID EQ ID NO:79, SEQ ID NO:81, SEQ ID NO:83, SEQ ID NO:485, SEQ ID NO:487, SEQ ID NO:489, SEQ ID NO:85, SEQ ID NO:87, SEQ ID NO:89, SEQ ID NO:91, NO:491, SEQ ID NO:493, SEQ ID NO:495 or SEQ ID EQ ID NO:93, SEQ ID NO:95, SEQ ID NO:97, SEQ ID NO:497, e.g., as described in Tables 1, 2 and 3 and in the NO:99, SEQID NO:101, SEQID NO:103, SEQID NO:105, Sequence Listing (all of these sequences are “exemplary p of EQID NO:107, SEQID NO:109, SEQID NO:111, SEQID the invention'), and enzymatically active Subsequences (frag NO: 113, SEQ ID NO:115, SEQ ID NO:117, SEQ ID ments) thereof. NO:119, SEQ ID NO:121, SEQ ID NO:123, SEQ ID The invention provides isolated, synthetic or recombinant NO:125, SEQ ID NO:127, SEQ ID NO.129, SEQ ID nucleic acids encoding a polypeptide having an isomerase NO: 131, SEQ ID NO:133, SEQ ID NO:135, SEQ ID 25 activity, e.g., a racemase activity, e.g., an amino acid race NO:137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID mase activity, analanine racemase activity, and/or an epime NO:143, SEQ ID NO:145, SEQ ID NO:147, SEQ ID rase activity, wherein the nucleic acid has at least one NO:149, SEQ ID NO:151, SEQ ID NO:153, SEQ ID sequence modification of an exemplary sequence of the NO:155, SEQ ID NO:157, SEQ ID NO:159, SEQ ID invention, or, any sequence of the invention. NO:161, SEQ ID NO:163, SEQ ID NO:165, SEQ ID 30 In one aspect (optionally), the isolated, synthetic or recom NO:167, SEQ ID NO:169, SEQ ID NO:171, SEQ ID binant nucleic acids of the invention have an isomerase activ NO:173, SEQ ID NO:175, SEQ ID NO:177, SEQ ID ity, e.g., a racemase activity, e.g., an amino acid racemase NO:179, SEQ ID NO:181, SEQ ID NO:183, SEQ ID activity, an alanine racemase activity, and/or an epimerase NO:185, SEQ ID NO:187, SEQ ID NO:189, SEQ ID activity, e.g., wherein the activity comprises catalyzing the NO:191 SEQ ID NO.193, SEQ ID NO.195, SEQ ID 35 re-arrangement of atoms within a molecule, catalyzing the NO: 197, SEQ ID NO:199, SEQ ID NO:201, SEQ ID conversion of one isomer into another, catalyzing the conver NO:203, SEQ ID NO:205, SEQ ID NO:207, SEQ ID sion of an optically active substrate into a raceme, which is NO:209, SEQ ID NO:211, SEQ ID NO:213, SEQ ID optically inactive, catalyzing the interconversion of substrate NO:215, SEQ ID NO:217, SEQ ID NO:219, SEQ ID enantiomers, catalyzing the stereochemical inversion around NO:221, SEQ ID NO:223, SEQ ID NO:225, SEQ ID 40 the asymmetric carbon atom in a Substrate having only one NO:227, SEQ ID NO:229, SEQ ID NO:231, SEQ ID center of asymmetry, catalyzing the stereochemical inversion NO:233, SEQ ID NO:235, SEQ ID NO:237, SEQ ID of the configuration around an asymmetric carbon atom in a NO:239, SEQ ID NO:241, SEQ ID NO:243, SEQ ID Substrate having more than one asymmetric center, and/or NO:245, SEQ ID NO:247, SEQ ID NO:249, SEQ ID catalyzing the racemization of amino acids. NO:251, SEQ ID NO:253, SEQ ID NO:255, SEQ ID 45 In one aspect, the isomerase activity, e.g., racemase activ NO:257, SEQ ID NO:259, SEQ ID NO:261, SEQ ID ity, e.g., amino acid racemase activity, alanine racemase NO:263, SEQ ID NO:265, SEQ ID NO:267, SEQ ID activity, and/or epimerase activity is thermostable, e.g., NO:269, SEQ ID NO:271, SEQ ID NO:273, SEQ ID wherein the polypeptide retains an isomerase activity, e.g., a NO:275, SEQ ID NO:277, SEQ ID NO:279, SEQ ID racemase activity, e.g., an amino acid racemase activity, an NO:281, SEQ ID NO:283, SEQ ID NO:285, SEQ ID 50 alanine racemase activity, and/or an epimerase activity under NO:287, SEQ ID NO:289, SEQ ID NO:291, SEQ ID conditions comprising a temperature range from about -100° NO:293, SEQ ID NO:295, SEQ ID NO:297, SEQ ID C. to about -80° C., about -80° C. to about -40°C., about NO:299, SEQ ID NO:301, SEQ ID NO:303, SEQ ID -40°C. to about -20°C., about -20°C. to about 0°C., about NO:305, SEQ ID NO:307, SEQ ID NO:309, SEQ ID 0° C. to about 5°C., about 5°C. to about 15°C., about 15° C. NO:311, SEQ ID NO:313, SEQ ID NO:315, SEQ ID 55 to about 25°C., about 25°C. to about 37°C., about 37° C. to NO:317, SEQ ID NO:319, SEQ ID NO:321, SEQ ID about 45° C., about 45° C. to about 55° C., about 55° C. to NO:323, SEQ ID NO:325, SEQ ID NO:327, SEQ ID about 70° C., about 70° C. to about 75° C., about 75° C. to NO:329, SEQ ID NO:331, SEQ ID NO:333, SEQ ID about 85°C., about 85°C. to about 90° C., about 90° C. to NO:335, SEQ ID NO:337, SEQ ID NO:339, SEQ ID about 95°C., about 95°C. to about 100° C., about 100° C. to NO:341, SEQ ID NO:343, SEQ ID NO:345, SEQ ID 60 about 105°C., about 105° C. to about 110°C., about 110° C. NO:347, SEQ ID NO:349, SEQ ID NO:351, SEQ ID to about 120°C., or 95°C., 96° C., 97°C., 98°C.,99°C., 100° NO:353, SEQ ID NO:355, SEQ ID NO:357, SEQ ID C., 101° C., 102°C., 103°C., 104°C., 105° C., 106° C., 107 NO:359, SEQ ID NO:361, SEQ ID NO:363, SEQ ID C., 108°C., 109° C., 110°C., 111° C., 112°C., 113°C., 114° NO:365, SEQ ID NO:367, SEQ ID NO:369, SEQ ID C., 115° C. or more. In some embodiments, the thermostable NO:371, SEQ ID NO:373, SEQ ID NO:375, SEQ ID 65 polypeptides according to the invention retains activity, e.g., NO:377, SEQ ID NO:379, SEQ ID NO:381, SEQ ID an isomerase activity, e.g., a racemase activity, e.g., an amino NO:383, SEQ ID NO:385, SEQ ID NO:387, SEQ ID acid racemase activity, analanine racemase activity, and/oran US 8,541,220 B2 13 14 epimerase activity, at a temperature in the ranges described e.g., a racemase activity, e.g., an amino acid racemase activ above, at about pH 3.0, about pH 3.5, about pH 4.0, about pH ity, analanine racemase activity, and/or an epimerase activity 4.5, about pH 5.0, about pH 5.5, about pH 6.0, about pH 6.5, after exposure to basic conditions comprising about pH7, pH about pH 7.0, about pH 7.5, about pH 8.0, about pH 8.5, about 7.5 pH 8.0, pH 8.5, pH 9, pH 9.5, pH 10, pH 10.5, pH 11, pH pH 9.0, about pH 9.5, about pH 10.0, about pH 10.5, about pH 11.5, pH 12, pH 12.5 or more (more basic). In one aspect, 11.0, about pH 11.5, about pH 12.0 or more. isomerase activity, e.g., racemase activity, e.g., amino acid In one aspect, the isomerase activity, e.g., racemase activ racemase activity, alanine racemase activity, and/or epime ity, e.g., amino acid racemase activity, alanine racemase rase activity of polypeptides encoded by nucleic acids of the activity, and/or epimerase activity is thermotolerant, e.g., invention retain activity at a temperature of at least about 80° wherein the polypeptide retains an isomerase activity, e.g., a 10 C., 81° C., 82° C., 83° C., 840 C., 850 C., 86° C., 87° C. 880 racemase activity, e.g., an amino acid racemase activity, an C., 89° C., 90° C., 910 C., 920 C., 93° C., 94° C., 95°C., 960 alanine racemase activity, and/or an epimerase activity after C., 97° C., 98°C.,990 C., 100° C. 101° C. 102°C., 103°C., exposure to a temperature in the range from about -100° C. to 103.5° C., 104°C., 1050 C., 1070 C., 108°C., 109° C. or 1100 about -80°C., about -80°C. to about -40°C., about -40°C. C., or more, and a basic pH of at least about pH 7.5 pH 8.0, pH to about -20°C., about -20°C. to about 0°C., about 0°C. to 15 8.5, pH 9, pH 9.5, pH 10, pH 10.5, pH 11, pH 11.5, pH 12, pH about 5°C., about 5°C. to about 15°C., about 15° C. to about 12.5 or more (more basic). 25°C., about 25°C. to about 37° C., about 37° C. to about 45° The invention provides expression cassettes, cloning C., about 45° C. to about 55° C., about 55° C. to about 70° C., vehicles, or a vector (e.g., expression vectors) comprising a about 70° C. to about 75° C., about 75° C. to about 85°C., nucleic acid comprising a sequence of the invention. The about 85°C. to about 90° C., about 90° C. to about 95°C., cloning vehicle can comprise a viral vector, a plasmid, a about 95°C. to about 100°C., about 100° C. to about 105°C., phage, a phagemid, a cosmid, a fosmid, a bacteriophage oran about 105° C. to about 110°C., about 110° C. to about 120° artificial chromosome. The viral vector can comprise an C., or 95° C., 96° C., 97° C., 98°C.,990 C., 100° C. 101° C., adenovirus vector, a retroviral vector or an adeno-associated 102°C., 103°C., 104°C., 105°C., 106° C., 107 C., 108°C., viral vector. The cloning vehicle can comprise an artificial 109° C., 110° C., 111° C., 112°C., 113°C., 114° C., 115° C. 25 chromosome comprising a bacterial artificial chromosome or more. The thermotolerant polypeptides according to the (BAC), a bacteriophage P1-derived vector (PAC), a yeast invention can retain activity, e.g. an isomerase activity, e.g., a artificial chromosome (YAC), or a mammalian artificial chro racemase activity, e.g., an amino acid racemase activity, an mosome (MAC). alanine racemase activity, and/or an epimerase activity, after The invention provides nucleic acid probes for identifying exposure to a temperature in the range from about -100° C. to 30 a nucleic acid encoding a polypeptide with an isomerase about -80°C., about -80°C. to about -40°C., about -40°C. activity, e.g., a racemase activity, e.g., an amino acid race to about -20°C., about -20°C. to about 0°C., about 0°C. to mase activity, analanine racemase activity, and/or an epime about 5°C., about 5°C. to about 15°C., about 15° C. to about rase activity, wherein the probe comprises at least about 10, 25°C., about 25°C. to about 37° C., about 37° C. to about 45° 15, 20, 25, 30, 35,40, 45, 50,55, 60, 65,70, 75, 100,125, 150, C., about 45° C. to about 55° C., about 55° C. to about 70° C., 35 175, 200, 225, 250, 275,300 or more consecutive bases of a about 70° C. to about 75° C., about 75° C. to about 85°C., nucleic acid comprising an exemplary sequence of the inven about 85°C. to about 90° C., about 90° C. to about 95°C., tion, or, any sequence of the invention (as defined herein), about 95°C. to about 100°C., about 100° C. to about 105°C., wherein in one aspect (optionally) the probe comprises an about 105° C. to about 110°C., about 110° C. to about 120° oligonucleotide comprising between at least about 10 to 300, C., or 95° C., 96° C., 97° C., 98°C.,990 C., 100° C. 101° C., 40 about 25 to 250, about 10 to 50, about 20 to 60, about 30 to 70, 102°C., 103°C., 104°C., 105°C., 106° C., 107 C., 108°C., about 40 to 80, about 60 to 100, or about 50 to 150 or more 109° C., 110° C., 111° C., 112°C., 113°C., 114° C., 115° C. consecutive bases. or more. In some embodiments, the thermotolerant polypep The invention provides amplification primer pairs for tides according to the invention retains activity, e.g. an amplifying a nucleic acid encoding a polypeptide having an isomerase activity, e.g., a racemase activity, e.g., an amino 45 isomerase activity, e.g., a racemase activity, e.g., an amino acid racemase activity, analanine racemase activity, and/oran acid racemase activity, analanine racemase activity, and/oran epimerase activity, after exposure to a temperature in the epimerase activity, wherein the primer pair is capable of ranges described above, at about pH 3.0, about pH 3.5, about amplifying a nucleic acid comprising an exemplary sequence pH 4.0, about pH 4.5, about pH 5.0, about pH 5.5, about pH of the invention, or, any sequence of the invention (as defined 6.0, about pH 6.5, about pH 7.0, about pH 7.5, about pH 8.0, 50 herein), or a Subsequence thereof, wherein optionally a mem about pH 8.5, about pH 9.0, about pH 9.5, about pH 10.0, ber of the amplification primer sequence pair comprises an about pH 10.5, about pH 11.0, about pH 11.5, about pH 12.0 oligonucleotide comprising at least about 10 to 50 consecu O. O. tive bases of the sequence, or, about 10, 11, 12, 13, 14, 15, 16, In one aspect, the isomerase activity, e.g., racemase activ 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,33, ity, e.g., amino acid racemase activity, alanine racemase 55 34, 35 or more consecutive bases of the sequence. The inven activity, and/or epimerase activity of polypeptides encoded tion provides amplification primer pairs wherein the primer by nucleic acids of the invention retain activity under acidic pair comprises a first member having a sequence as set forth conditions comprising about pH 6.5, pH 6, pH 5.5, pH 5, pH by about the first (the 5') 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 4.5, pH 4.0, pH 3.5, pH 3.0 or less (more acidic) pH, or, retain 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 or an isomerase activity, e.g., a racemase activity, e.g., an amino 60 more residues of an exemplary sequence of the invention, or, acid racemase activity, analanine racemase activity, and/oran any sequence of the invention (as defined herein), and a sec epimerase activity after exposure to acidic conditions com ond member having a sequence as set forth by about the first prising about pH 6.5, pH 6, pH 5.5, pH 5, pH 4.5, pH 4.0, pH (the 5') 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 3.5, pH 3.0 or less (more acidic) pH; or, retain activity under 25, 26, 27, 28, 29, 30, 31, 32,33,34, 35 or more residues of the basic conditions comprising about pH 7, pH 7.5 pH 8.0, pH 65 complementary strand of the first member. 8.5, pH 9, pH 9.5, pH 10, pH 10.5, pH 11, pH 11.5, pH 12, pH The invention provides an isomerase-, e.g., a racemase-, 12.5 or more (more basic) or, retain an isomerase activity, e.g., an amino acid racemase-, an alanine racemase-, and/or US 8,541,220 B2 15 16 an epimerase-encoding nucleic acids generated by amplifica under Stringent conditions to a sequence of the invention tion of a polynucleotide using an amplification primer pair of (including, e.g., exemplary sequences of the invention). the invention, wherein optionally the amplification is by poly The invention provides double-stranded inhibitory RNA merase chain reaction (PCR). In one aspect, the nucleic acid (RNAi) molecules comprising a Subsequence of a sequence is generated by amplification of a gene library, wherein in one of the invention (including, e.g., exemplary sequences of the aspect (optionally) the gene library is an environmental invention). The double-stranded inhibitory RNA (RNAi) library. The invention provides isolated, synthetic or recom molecule can be about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, binant isomerases, e.g., racemases, e.g., amino acid race 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 or more duplex mases, alanine racemases, and/or epimerases encoded by an nucleotides in length. The invention provides methods of isomerase-, e.g., a racemase-, e.g., an amino acid racemase 10 inhibiting the expression of an isomerase, e.g., a racemase, an alanine racemase-, and/or an epimerase-encoding nucleic e.g., an amino acid racemase, an alanine racemase, and/or an acid generated by amplification of a polynucleotide using an epimerase in a cell comprising administering to the cell or amplification primer pair of the invention. The invention pro expressing in the cell a double-stranded inhibitory RNA vides methods of amplifying a nucleic acid encoding a (iRNA), wherein the RNA comprises a subsequence of a polypeptide having an isomerase activity, e.g., a racemase 15 sequence of the invention (including, e.g., exemplary activity, e.g., an amino acid racemase activity, an alanine sequences of the invention). racemase activity, and/or an epimerase activity, the methods The invention provides isolated, synthetic or recombinant comprising the step of amplification of a template nucleic polypeptides having an isomerase activity, e.g., a racemase acid with an amplification primer sequence pair capable of activity, e.g., an amino acid racemase activity, an alanine amplifying an exemplary sequence of the invention, or, any racemase activity, and/or an epimerase activity, or polypep sequence of the invention (as defined herein), or a Subse tides capable of generating an immune response specific for quence thereof. an isomerase, e.g., a racemase, e.g., an amino acid racemase, The invention provides expression cassette, a vector or a an alanine racemase, and/or an epimerase (e.g., an epitope); cloning vehicle comprising a nucleic acid comprising a and in alternative aspects peptide and polypeptide of the sequence of the invention, wherein optionally the cloning 25 invention comprise a sequence: vehicle comprises a viral vector, a plasmid, a phage, a (a) comprising an amino acid sequence having at least phagemid, a cosmid, a fosmid, a bacteriophage oran artificial about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, chromosome. The viral vector can comprise an adenovirus 59%, 60%, 61%, 62%, 63%, 64%. 65%, 66%, 67%, 68%, vector, a retroviral vector oran adeno-associated viral vector, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, or, the artificial chromosome comprises a bacterial artificial 30 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, chromosome (BAC), a bacteriophage P1-derived vector 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, (PAC), a yeast artificial chromosome (YAC), or a mammalian 99%, or more, or has 100% (complete) sequence identity to artificial chromosome (MAC). SEQID NO:2, SEQID NO:4, SEQID NO:6, SEQID NO:8, The invention provides transformed cells comprising a SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID nucleic acid or vector of the invention, or an expression cas 35 NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, sette or cloning vehicle of the invention. The transformed cell SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID can be a bacterial cell, a mammaliancell, a fungal cell, a yeast NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, cell, an insect cell or a plant cell. SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID The invention provides transgenic non-human animals NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, comprising a sequence of the invention. The transgenic non 40 SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID human animal can be a mouse, a rat, a rabbit, a sheep, a pig, NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, a chicken, a goat, a fish, a dog, or a cow. The invention SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70, SEQ ID provides transgenic plants comprising a sequence of the NO:72, SEQ ID NO:74, SEQ ID NO:76, SEQ ID NO:78, invention, e.g., wherein the plant is a corn plant, a Sorghum SEQ ID NO:80, SEQ ID NO:82, SEQ ID NO:84, SEQ ID plant, a potato plant, a tomato plant, a wheat plant, an oilseed 45 NO:86, SEQ ID NO:88, SEQ ID NO:90, SEQ ID NO:92, plant, a rapeseed plant, a Soybean plant, a rice plant, a barley SEQ ID NO:94, SEQ ID NO:96, SEQ ID NO:98, SEQ ID plant, a grass, or a tobacco plant. The invention provides NO:100, SEQ ID NO:102, SEQ ID NO:104, SEQ ID transgenic seeds comprising a sequence of the invention, e.g., NO:106, SEQ ID NO:108, SEQ ID NO:110, SEQ ID wherein the seed is a corn seed, a wheat kernel, an oilseed, a NO:112, SEQ ID NO:114, SEQ ID NO:116, SEQ ID rapeseed, a Soybean seed, a palm kernel, a Sunflower seed, a 50 NO:118, SEQ ID NO:120, SEQ ID NO:122, SEQ ID sesame seed, a rice, a barley, a peanut or a tobacco plant seed. NO:124, SEQ ID NO:126, SEQ ID NO:128, SEQ ID The invention provides antisense oligonucleotides com NO:130, SEQ ID NO:132, SEQ ID NO:134, SEQ ID prising a nucleic acid sequence complementary to or capable NO:136, SEQ ID NO: 138, SEQ ID NO:140, SEQ ID of hybridizing under stringent conditions to a sequence of the NO:142, SEQ ID NO:143, SEQ ID NO:146, SEQ ID invention (including, e.g., exemplary sequences of the inven 55 NO:148, SEQ ID NO:150, SEQ ID NO:152, SEQ ID NO: tion), or a Subsequence thereof, wherein optionally the anti 154, SEQ ID NO: 156, SEQ ID NO: 158, SEQ ID NO:160, sense oligonucleotide is between about 10 to 50, about 20 to SEQID NO:162, SEQID NO: 164, SEQID NO:166, SEQID 60, about 30 to 70, about 40 to 80, or about 60 to 100 bases in NO:168, SEQ ID NO: 170, SEQ ID NO:172, SEQ ID length, and in one aspect (optionally) the stringent conditions NO:174, SEQ ID NO:176, SEQ ID NO:178, SEQ ID comprise a wash step comprising a wash in 0.2xSSC at a 60 NO:180, SEQ ID NO:182, SEQ ID NO:184, SEQ ID temperature of about 65° C. for about 15 minutes. NO:186, SEQ ID NO:188, SEQ ID NO.190, SEQ ID The invention provides methods of inhibiting the transla NO:192, SEQ ID NO:194, SEQ ID NO:196, SEQ ID tion of an isomerase, e.g., a racemase, e.g., an amino acid NO:198, SEQ ID NO:200, SEQ ID NO:202, SEQ ID racemase, an alanine racemase, and/or an epimerase message NO:204, SEQ ID NO:206, SEQ ID NO:208, SEQ ID in a cell comprising administering to the cell or expressing in 65 NO:210, SEQ ID NO:212, SEQ ID NO:214, SEQ ID the cell an antisense oligonucleotide comprising a nucleic NO:216, SEQ ID NO:218, SEQ ID NO:220, SEQ ID acid sequence complementary to or capable of hybridizing NO:222, SEQ ID NO:224, SEQ ID NO:226, SEQ ID US 8,541,220 B2 17 18 NO:228, SEQ ID NO:230, SEQ ID NO:232, SEQ ID version 2.2.2 algorithm where a filtering setting is set to NO:234, SEQ ID NO:236, SEQ ID NO:238, SEQ ID blastall-p blastp-d'nr pataa’-FF, and all other options are set NO:240, SEQ ID NO:242, SEQ ID NO:244, SEQ ID to default; NO:246, SEQ ID NO:248, SEQ ID NO:250, SEQ ID (d) an amino acid sequence encoded by the nucleic acid of NO:252, SEQ ID NO:254, SEQ ID NO:256, SEQ ID claim 1, wherein the polypeptide has (i) an isomerase activity, NO:258, SEQ ID NO:260, SEQ ID NO:262, SEQ ID e.g., a racemase activity, e.g., an amino acid racemase activ NO:264, SEQ ID NO:266, SEQ ID NO:268, SEQ ID ity, analanine racemase activity, and/oran epimerase activity, NO:270, SEQ ID NO:272, SEQ ID NO:274, SEQ ID or, (ii) has immunogenic activity in that it is capable of gen NO:276, SEQ ID NO:278, SEQ ID NO:280, SEQ ID erating an antibody that specifically binds to a polypeptide 10 having a sequence of (a), and/or enzymatically active Subse NO:282, SEQ ID NO:284, SEQ ID NO:286, SEQ ID quences (fragments) thereof; NO:288, SEQ ID NO:290, SEQ ID NO:292, SEQ ID (e) the amino acid sequence of any of (a) to (d), and com NO:294, SEQ ID NO:296, SEQ ID NO:298, SEQ ID prising at least one amino acid residue conservative Substitu NO:300, SEQ ID NO:302, SEQ ID NO:304, SEQ ID tion, and the polypeptide or peptide retains isomerase activity, ID ID ID NO:306, SEQ NO:308, SEQ NO:310, SEQ 15 e.g., racemase activity, e.g., amino acid racemase activity, NO:312, SEQ ID NO:314, SEQ ID NO:316, SEQ ID alanine racemase activity, and/or epimerase activity; NO:318, SEQ ID NO:320, SEQ ID NO:322, SEQ ID (e) the amino acid sequence of (d), wherein the conserva NO:324, SEQ ID NO:326, SEQ ID NO:328, SEQ ID tive Substitution comprises replacement of an aliphatic amino NO:330, SEQ ID NO:332, SEQ ID NO:334, SEQ ID acid with another aliphatic amino acid; replacement of a NO:336, SEQ ID NO:338, SEQ ID NO:340, SEQ ID serine with a threonine or vice versa; replacement of an acidic NO:342, SEQ ID NO:344, SEQ ID NO:346, SEQ ID residue with another acidic residue; replacement of a residue NO:348, SEQ ID NO:350, SEQ ID NO:352, SEQ ID bearing an amide group with another residue bearing an NO:354, SEQ ID NO:356, SEQ ID NO:358, SEQ ID amide group; exchange of a basic residue with another basic NO:360, SEQ ID NO:362, SEQ ID NO:364, SEQ ID residue; or, replacement of an aromatic residue with another NO:366, SEQ ID NO:368, SEQ ID NO:370, SEQ ID 25 aromatic residue, or a combination thereof, NO:372, SEQ ID NO:374, SEQ ID NO:376, SEQ ID (f) the amino acid sequence of (e), wherein the aliphatic NO:378, SEQ ID NO:380, SEQ ID NO:382, SEQ ID residue comprises Alanine, Valine, Leucine, Isoleucine or a NO:384, SEQ ID NO:386, SEQ ID NO:388, SEQ ID synthetic equivalent thereof; the acidic residue comprises NO:390, SEQ ID NO:392, SEQ ID NO:394, SEQ ID Aspartic acid, Glutamic acidora synthetic equivalent thereof. 30 the residue comprising an amide group comprises Aspartic NO:396, SEQ ID NO:398, SEQ ID NO:400, SEQ ID acid, Glutamic acid or a synthetic equivalent thereof; the NO:402, SEQ ID NO:404, SEQ ID NO:406, SEQ ID basic residue comprises Lysine, Arginine or a synthetic NO:408, SEQ ID NO:410, SEQ ID NO:412, SEQ ID equivalent thereof; or, the aromatic residue comprises Phe NO:414, SEQ ID NO:416, SEQ ID NO:418, SEQ ID nylalanine, Tyrosine or a synthetic equivalent thereof; ID ID ID NO:420, SEQ NO:422, SEQ NO:424, SEQ 35 (g) the polypeptide of any of (a) to (0 having an isomerase NO:426, SEQ ID NO:428, SEQ ID NO:430, SEQ ID activity, e.g., a racemase activity, e.g., an amino acid race NO:432, SEQ ID NO:434, SEQ ID NO:436, SEQ ID mase activity, analanine racemase activity, and/or an epime NO:438, SEQ ID NO:440, SEQ ID NO:442, SEQ ID rase activity but lacking a signal sequence, a prepro domain, NO:444, SEQ ID NO:446, SEQ ID NO:448, SEQ ID and/or other domain, NO:450, SEQ ID NO:452, SEQ ID NO:454, SEQ ID 40 (h) the polypeptide of any of (a) to (g) having an isomerase NO:456, SEQ ID NO:458, SEQ ID NO:460, SEQ ID activity, e.g., a racemase activity, e.g., an amino acid race NO:462, SEQ ID NO:464, SEQ ID NO:466, SEQ ID mase activity, analanine racemase activity, and/or an epime NO:468, SEQ ID NO:470, SEQ ID NO:472, SEQ ID rase activity further comprising a heterologous sequence; NO:474, SEQ ID NO:476, SEQ ID NO:478, SEQ ID (i) the polypeptide of (h), wherein the heterologous NO:480, SEQ ID NO:482, SEQ ID NO:484, SEQ ID 45 sequence comprises, or consists of: (A) a heterologous signal NO:486, SEQ ID NO:488, SEQ ID NO:490, SEQ ID sequence, a heterologous domain, a heterologous dockerin NO:492, SEQ ID NO:494, SEQ ID NO:496 or SEQ ID domain, a heterologous catalytic domain (CD), or a combi NO:498, or enzymatically active fragments thereof, nation thereof; (B) the sequence of (A), wherein the heterolo wherein the polypeptide or peptide of (i) or (ii) has an gous signal sequence, domain or catalytic domain (CD) is isomerase activity, e.g., a racemase activity, e.g., an amino 50 derived from a heterologous enzyme; and/or, (C) a tag, an acid racemase activity, analanine racemase activity, and/oran epitope, a targeting peptide, a cleavable sequence, a detect epimerase activity, or the polypeptide or peptide is capable of able moiety or an enzyme; generating an isomerase specific antibody, e.g., a racemase () polypeptide of (i), wherein the heterologous signal specific antibody, e.g., an amino acid racemase, an alanine sequence targets the encoded protein to a vacuole, the endo racemase, and/or an epimerase specific antibody (a polypep 55 plasmic reticulum, a chloroplast or a starch granule; or tide or peptide that acts as an epitope or immunogen), (k) comprising an amino acid sequence encoded any (b) the polypeptide or peptide of (a), wherein the sequence nucleic acid sequence of this invention. identities are determined: (A) by analysis with a sequence In one aspect, the isomerase activity, e.g., racemase activ comparison algorithm or by a visual inspection, or (B) over a ity, e.g., amino acid racemase activity, alanine racemase region of at least about 20, 25, 30, 35, 40, 45, 50, 55, 60, 75, 60 activity, and/or epimerase activity comprises catalyzing the 100, 150, 200, 250, 300 or more amino acid residues, or over re-arrangement of atoms within a molecule, catalyzing the the full length of the polypeptide or peptide or enzyme, and/or conversion of one isomer into another, catalyzing the conver enzymatically active Subsequences (fragments) thereof, sion of an optically active substrate into a raceme, which is (c) the polypeptide or peptide of (a) of (b), wherein the optically inactive, catalyzing the interconversion of substrate sequence identities are determined by analysis with a 65 enantiomers, catalyzing the stereochemical inversion around sequence comparison algorithm or by a visual inspection, and the asymmetric carbon atom in a Substrate having only one optionally the sequence comparison algorithm is a BLAST center of asymmetry, catalyzing the stereochemical inversion US 8,541,220 B2 19 20 of the configuration around an asymmetric carbon atom in a nine racemases, and/or epimerases, and other hydrolytic Substrate having more than one asymmetric center, and/or enzymes such as cellulases, mannanases, proteases, lipases, catalyzing the racemization of amino acids. amylases, or redox enzymes such as laccases, peroxidases, The invention provides isolated, synthetic or recombinant catalases, oxidases, or reductases. They can be used formu polypeptides comprising a polypeptide of the invention and lated in a solid form Such as a powder, a lyophilized prepara lacking a signal sequence or a prepro sequence. The invention tion, a granule, a tablet, a bar, a crystal, a capsule, a pill, a provides isolated, synthetic or recombinant polypeptides pellet, or in a liquid form Such as in an aqueous solution, an comprising a polypeptide of the invention and having a het aerosol, a gel, a paste, a slurry, an aqueous/oil emulsion, a erologous signal sequence or a heterologous prepro cream, a capsule, or in a vesicular or micellar Suspension. The Sequence. 10 formulations of the invention can comprise any or a combi In one aspect, a polypeptide of the invention has isomerase nation of the following ingredients: polyols such as a poly activity, e.g., racemase activity, e.g., amino acid racemase ethylene glycol, a polyvinylalcohol, a glycerol, a Sugar Such activity, alanine racemase activity, and/or epimerase activity as a Sucrose, a Sorbitol, a trehalose, a glucose, a fructose, a comprising a specific activity at about 37° C. in the range maltose, a mannose, a gelling agent Such as a guar gum, a from about 100 to about 1000 units per milligram of protein, 15 carageenan, an alginate, a dextrans, a cellulosic derivative, a from about 500 to about 750 units per milligram of protein, pectin, a salt such as a sodium chloride, a sodium sulfate, an from about 500 to about 1200 units per milligram of protein, ammonium Sulfate, a calcium chloride, a magnesium chlo or from about 750 to about 1000 units per milligram of pro ride, a Zinc chloride, a Zinc sulfate, a salt of a fatty acid and a tein. In alternative aspects, polypeptides of the invention have fatty acid derivative, a metal chelator such as an EDTA, an isomerase activity, e.g., racemase activity, e.g., amino acid EGTA, a sodium citrate, an antimicrobial agent Such as a fatty racemase activity, alanine racemase activity, and/or epime acidora fatty acid derivative, a paraben, a Sorbate, a benzoate, rase activity in the range of between about 0.05 to 20 units per an additional modulating compound to block the impact of an gram, or 0.05, 0.10, 0.20, 0.30, 0.40, 0.50, 0.60, 0.70, 0.80, enzyme Such as a protease, a bulk proteins such as a BSA, a 0.90, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0, 4.5, 5.0, 5.5, 6.0, 6.5, 7, wheat hydrolysate, aborate compound, an amino acid or a 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 or more units 25 peptide, an appropriate pH or temperature modulating com per gram, where a unit equals one umol of product released pound, an emulsifier Such as a non-ionic and/or an ionic per minute per mg of enzyme. In one embodiment, for race detergent, a redox agent such as a cystine/cysteine, a glu mases, one unit of activity equals oneumol of an isomer with tathione, an oxidized glutathione, a reduced oran antioxidant inverted configuration (from the starting isomer) produced compound Such as an ascorbic acid, or a dispersant. Cross per minute per mg of enzyme (formed from the respective 30 linking and protein modification Such as pegylation, fatty acid alpha-amino acid or amine). In an alternative embodiment, modification, glycosylation can also be used to improve for amino acid racemases, one unit of activity equals one enzyme stability. umol of R-amino acid produced perminute per mg of enzyme The invention provides arrays comprising immobilized formed from the corresponding S-amino acid. In an alterna polypeptide(s) and/or nucleic acids of the invention, and tive embodiment, foramino acid racemases, one unit of activ 35 arrays comprising an immobilized oligonucleotide of the ity equals oneumol of S-amino acid produced perminute per invention. The enzymes, fragments thereof and nucleic acids mg of enzyme formed from the corresponding R-amino acid. which encode the enzymes, or probes of the invention, and In one aspect, the polypeptides of the invention comprise at fragments thereof, can be affixed to a solid Support; and these least one glycosylation site or further comprises a polysac embodiments can be economical and efficient in the use of charide. The glycosylation can be an N-linked glycosylation, 40 enzymes and nucleic acids of the invention in industrial, e.g., wherein the polypeptide is glycosylated after being medical, research, pharmaceutical, food and feed and food expressed in a P. pastoris or a S. pombe. and feed Supplement processing and other applications and The invention provides protein preparation comprising a processes. For example, a consortium or cocktail of enzymes polypeptide of the invention, wherein the protein preparation (or active fragments thereof), which are used in a specific comprises a liquid, a slurry, a solid or a gel. The invention 45 chemical reaction, can be attached to a solid Support and provides heterodimers comprising a polypeptide of the inven dunked into a process Vat. The enzymatic reaction can occur. tion and a second domain. The second domain can be a Then, the Solid Support can be taken out of the vat, along with polypeptide and the heterodimer is a fusion protein. the sec the enzymes affixed thereto, for repeated use. In one embodi ond domain can be an epitope or a tag. ment of the invention, the isolated nucleic acid is affixed to a The invention provides homodimers or heterodimers com 50 solid support. In another embodiment of the invention, the prising a polypeptide of the invention. The invention provides Solid Support is selected from the group of a gel, a resin, a immobilized polypeptides, wherein the polypeptide com polymer, a ceramic, a glass, a microelectrode and any com prises a sequence of the invention, or a Subsequence thereof, bination thereof. ora polypeptide encoded by a nucleic acid of the invention, or For example, Solid Supports useful in this invention include a polypeptide comprising a polypeptide of the invention and 55 gels. Some examples of gels include Sepharose, gelatin, glu a second domain, e.g., wherein the polypeptide is immobi taraldehyde, chitosan-treated glutaraldehyde, albumin-glut lized on or inside a cell, a vesicle, a liposome, a film, a araldehyde, chitosan-Xanthan, toyopearl gel (polymer gel), membrane, a metal, a resin, a polymer, a ceramic, a glass, a alginate, alginate-polylysine, carrageenan, agarose, glyoxyl microelectrode, a graphitic particle, a bead, a gel, a plate, an agarose, magnetic agarose, dextran-agarose, poly(Carbam array, a capillary tube, a crystal, a tablet, a pill, a capsule, a 60 oyl Sulfonate) hydrogel, BSA-PEG hydrogel, phosphory powder, an agglomerate, a surface, a porous structure, or lated polyvinyl alcohol (PVA), monoaminoethyl-N-aminoet materials such as wood chips, brownstock, pulp, paper, and hyl (MANA), amino, or any combination thereof. Another materials deriving therefrom. Solid Support useful in the present invention are resins or The isomerases, e.g., racemases, e.g., amino acid race polymers. Some examples of resins or polymers include cel mases, alanine racemases, and/or epimerases of the invention 65 lulose, acrylamide, nylon, rayon, polyester, anion-exchange can be used or formulated alone or as mixture (a “cocktail”) of resin, AMBERLITETM XAD-7, AMBERLITETM XAD-8, isomerases, e.g., racemases, e.g., amino acid racemases, ala AMBERLITETM IRA-94, AMBERLITETM IRC-50, polyvi US 8,541,220 B2 21 22 nyl, polyacrylic, polymethacrylate, or any combination followed by expressing the nucleic acid of step (a), thereby thereof. Another type of solid support useful in the present producing a recombinant polypeptide in a transformed cell. invention is ceramic. Some examples include non-porous The invention provides methods for identifying a polypep ceramic, porous ceramic, SiO2, Al2O. Another type of Solid tide having an isomerase activity, e.g., a racemase activity, Support useful in the present invention is glass. Some e.g., an amino acid racemase activity, an alanine racemase examples include non-porous glass, porous glass, aminopro activity, and/or an epimerase activity comprising: (a) provid pyl glass or any combination thereof. Another type of Solid ing a polypeptide of the invention; (b) providing an Support which can be used is a microelectrode. An example is isomerase, e.g., a racemase, e.g., an amino acid racemase, an a polyethyleneimine-coated magnetite. Graphitic particles alanine racemase, and/or an epimerase Substrate; and (c) con 10 tacting the polypeptide with the substrate of step (b) and can be used as a solid Support. Another example of a solid detecting a decrease in the amount of Substrate or an increase Support is a cell. Such as a red blood cell. in the amount of a reaction product, whereina decrease in the There are many methods which would be known to one of amount of the Substrate or an increase in the amount of the skill in the art for immobilizing enzymes or fragments reaction product detects a polypeptide having an isomerase thereof, or nucleic acids, onto a solid Support. Some examples 15 activity, e.g., a racemase activity, e.g., an amino acid race of Such methods include electrostatic droplet generation, mase activity, analanine racemase activity, and/or an epime electrochemical means, via adsorption, via covalent binding, rase activity. via cross-linking, via chemical reaction or process, via encap The invention provides methods for identifying an Sulation, via entrapment, via calcium alginate, or via poly isomerase, e.g., a racemase, e.g., an amino acid racemase, an (2-hydroxyethyl methacrylate). Like methods are described alanine racemase, and/or an epimerase Substrate comprising: in Methods in Enzymology, Immobilized Enzymes and Cells, (a) providing a polypeptide of the invention; (b) providing a Part C. 1987. Academic Press. Edited by S. P. Colowick and test Substrate; and (c) contacting the polypeptide of step (a) N. O. Kaplan. Volume 136; and Immobilization of Enzymes with the test substrate of step (b) and detecting a decrease in and Cells. 1997. Humana Press. Edited by G. F. Bickerstaff. the amount of Substrate or an increase in the amount of reac Series: Methods in Biotechnology, Edited by J. M. Walker. 25 tion product, wherein a decrease in the amount of the Sub The invention provides isolated, synthetic or recombinant strate or an increase in the amount of a reaction product antibodies that specifically binds to a polypeptide of the identifies the test Substrate as an isomerase, e.g., a racemase, invention. The antibody can be a monoclonal or a polyclonal e.g., an amino acid racemase, an alanine racemase, and/or an antibody, or is a single chained antibody. The invention pro epimerase Substrate. vides hybridomas comprising an antibody that specifically 30 The invention provides methods of determining whether a binds to a polypeptide of the invention. test compound specifically binds to a polypeptide compris The invention provides methods of isolating or identifying ing: (a) expressing a nucleic acid or a vector comprising the a polypeptide with an isomerase activity, e.g., a racemase nucleic acid under conditions permissive for translation of the activity, e.g., an amino acid racemase activity, an alanine nucleic acid to a polypeptide, wherein the nucleic acid has a racemase activity, and/or an epimerase activity comprising 35 sequence of the invention; (b) providing a test compound; (c) the steps of: (a) providing an antibody of the invention; (b) contacting the polypeptide with the test compound; and (d) providing a sample comprising polypeptides; and (c) contact determining whether the test compound of step (b) specifi ing the sample of step (b) with the antibody of step (a) under cally binds to the polypeptide. conditions wherein the antibody can specifically bind to the The invention provides methods of determining whether a polypeptide, thereby isolating or identifying a polypeptide 40 test compound specifically binds to a polypeptide compris having an isomerase activity, e.g., a racemase activity, e.g., an ing: (a) providing a polypeptide of the invention; (b) provid amino acid racemase activity, an alanine racemase activity, ing a test compound; (c) contacting the polypeptide with the and/or an epimerase activity. The invention provides methods test compound; and (d) determining whether the test com of making an anti-isomerase, e.g., anti-racemase, e.g., anti pound of step (b) specifically binds to the polypeptide. amino acid racemase, anti-alanine racemase, and/or anti-epi 45 The invention provides methods for identifying a modula merase antibody comprising administering to a non-human tor of an isomerase activity, e.g., a racemase activity, e.g., an animal a nucleic acid of the invention or a Subsequence amino acid racemase activity, an alanine racemase activity, thereofinan amount Sufficient to generate a humoral immune and/or an epimerase activity comprising: (a) providing a response, thereby making an anti-isomerase, e.g., anti-race polypeptide of the invention; (b) providing a test compound; mase, e.g., anti-amino acid racemase, anti-alanine racemase, 50 (c) contacting the polypeptide of step (a) with the test com and/or anti-epimerase antibody. The invention provides pound of step (b) and measuring an activity of the isomerase, methods of making an anti-isomerase, e.g., anti-racemase, e.g., racemase, e.g., amino acid racemase, alanine racemase, e.g., anti-amino acid racemase, anti-alanine racemase, and/or and/or epimerase, wherein a change in the isomerase activity, anti-epimerase antibody comprising administering to a non e.g., racemase activity, e.g., amino acid racemase activity, human animal a polypeptide of the invention or a Subse 55 alanine racemase activity, and/or epimerase activity mea quence thereof in an amount Sufficient to generate a humoral Sured in the presence of the test compound compared to the immune response, thereby making an anti-isomerase, e.g., activity in the absence of the test compound provides a deter anti-racemase, e.g., anti-amino acid racemase, anti-alanine mination that the test compound modulates the isomerase racemase, and/or anti-epimerase antibody. activity, e.g., racemase activity, e.g., amino acid racemase The invention provides methods of producing a recombi 60 activity, alanine racemase activity, and/or epimerase activity. nant polypeptide comprising the steps of: (a) providing a The isomerase activity, e.g., racemase activity, e.g., amino nucleic acid operably linked to a promoter, wherein the acid racemase activity, alanine racemase activity, and/or epi nucleic acid comprises a sequence of the invention; and (b) merase activity can be measured by providing an isomerase, expressing the nucleic acid of step (a) under conditions that e.g., a racemase, e.g., an amino acid racemase, an alanine allow expression of the polypeptide, thereby producing a 65 racemase, and/or an epimerase Substrate and detecting a recombinant polypeptide. The method can further comprise decrease in the amount of the Substrate or an increase in the transforming a host cell with the nucleic acid of step (a) amount of a reaction product, or, an increase in the amount of US 8,541,220 B2 23 24 the Substrate or a decrease in the amount of a reaction product. from the environmental sample, thereby isolating or recover In one aspect, a decrease in the amount of the Substrate or an ing a nucleic acid encoding a polypeptide having an increase in the amount of the reaction product with the test isomerase activity, e.g., a racemase activity, e.g., an amino compound as compared to the amount of Substrate or reaction acid racemase activity, analanine racemase activity, and/oran product without the test compound identifies the test com epimerase activity from an environmental sample. One or pound as an activator of an isomerase activity, e.g., a race each member of the amplification primer sequence pair can mase activity, e.g., an amino acid racemase activity, an ala comprise an oligonucleotide comprising at least about 10 to nine racemase activity, and/or an epimerase activity. In one 50 consecutive bases of a sequence of the invention. In one aspect, an increase in the amount of the Substrate or a decrease aspect, the amplification primer sequence pair is an amplifi in the amount of the reaction product with the test compound 10 as compared to the amount of Substrate or reaction product cation pair of the invention. without the test compound identifies the test compound as an The invention provides methods for isolating or recovering inhibitor of an isomerase activity, e.g., a racemase activity, a nucleic acid encoding a polypeptide having an isomerase e.g., an amino acid racemase activity, an alanine racemase activity, e.g., a racemase activity, e.g., an amino acid race activity, and/or an epimerase activity. 15 mase activity, analanine racemase activity, and/or an epime The invention provides computer systems comprising a rase activity from an environmental sample comprising the processor and a data storage device wherein said data storage steps of: (a) providing a polynucleotide probe comprising a device has stored thereon a polypeptide sequence or a nucleic nucleic acid of the invention or a Subsequence thereof; (b) acid sequence, wherein the polypeptide sequence comprises isolating a nucleic acid from the environmental sample or sequence of the invention, a polypeptide encoded by a nucleic treating the environmental sample Such that nucleic acid in acid of the invention. The computer systems can further com the sample is accessible for hybridization to a polynucleotide prise a sequence comparison algorithm and a data storage probe of step (a); (c) combining the isolated nucleic acid or device having at least one reference sequence stored thereon. the treated environmental sample of step (b) with the poly In another aspect, the sequence comparison algorithm com nucleotide probe of step (a); and (d) isolating a nucleic acid prises a computer program that indicates polymorphisms. In 25 that specifically hybridizes with the polynucleotide probe of one aspect, the computer system can further comprise an step (a), thereby isolating or recovering a nucleic acid encod identifier that identifies one or more features in said sequence. ing a polypeptide having an isomerase activity, e.g., a race The invention provides computer readable media having mase activity, e.g., an amino acid racemase activity, an ala stored thereon a polypeptide sequence or a nucleic acid nine racemase activity, and/or an epimerase activity from an sequence of the invention. The invention provides methods 30 environmental sample. The environmental sample can com for identifying a feature in a sequence comprising the steps of prise a water sample, a liquid sample, a soil sample, an air (a) reading the sequence using a computer program which sample or a biological sample. In one aspect, the biological identifies one or more features in a sequence, wherein the sample can be derived from a bacterial cell, a protozoan cell, sequence comprises a polypeptide sequence or a nucleic acid an insect cell, a yeast cell, a plant cell, a fungal cell or a sequence of the invention; and (b) identifying one or more 35 mammalian cell. features in the sequence with the computer program. The The invention provides methods of generating a variant of invention provides methods for comparing a first sequence to a nucleic acid encoding a polypeptide having an isomerase a second sequence comprising the steps of: (a) reading the activity, e.g., a racemase activity, e.g., an amino acid race first sequence and the second sequence through use of a mase activity, analanine racemase activity, and/or an epime computer program which compares sequences, wherein the 40 rase activity comprising the steps of: (a) providing a template first sequence comprises a polypeptide sequence or a nucleic nucleic acid comprising a nucleic acid of the invention; and acid sequence of the invention; and (b) determining differ (b) modifying, deleting or adding one or more nucleotides in ences between the first sequence and the second sequence the template sequence, or a combination thereof, to generate with the computer program. The step of determining differ a variant of the template nucleic acid. In one aspect, the ences between the first sequence and the second sequence can 45 method can further comprise expressing the variant nucleic further comprise the step of identifying polymorphisms. In acid to generate a variant isomerase, e.g., racemase, e.g., one aspect, the method can further comprise an identifier that amino acid racemase, alanine racemase, and/or epimerase identifies one or more features in a sequence. In another polypeptide. The modifications, additions or deletions can be aspect, the method can comprise reading the first sequence introduced by a method comprising error-prone PCR, shuf using a computer program and identifying one or more fea 50 fling, oligonucleotide-directed mutagenesis, assembly PCR, tures in the sequence. sexual PCR mutagenesis, in Vivo mutagenesis, cassette The invention provides methods for isolating or recovering mutagenesis, recursive ensemble mutagenesis, exponential a nucleic acid encoding a polypeptide having an isomerase ensemble mutagenesis, site-specific mutagenesis, gene reas activity, e.g., a racemase activity, e.g., an amino acid race sembly (e.g., GeneReassembly, see, e.g., U.S. Pat. No. 6,537, mase activity, analanine racemase activity, and/or an epime 55 776), Gene Site Saturation Mutagenesis (GSSM), synthetic rase activity from an environmental sample comprising the ligation reassembly (SLR) or a combination thereof. In steps of: (a) providing an amplification primer sequence pair another aspect, the modifications, additions or deletions are for amplifying a nucleic acid encoding a polypeptide having introduced by a method comprising recombination, recursive an isomerase activity, e.g., a racemase activity, e.g., an amino sequence recombination, phosphothioate-modified DNA acid racemase activity, analanine racemase activity, and/oran 60 mutagenesis, uracil-containing template mutagenesis, epimerase activity, wherein the primer pair is capable of gapped duplex mutagenesis, point mismatch repair mutagen amplifying a nucleic acid of the invention; (b) isolating a esis, repair-deficient host strain mutagenesis, chemical nucleic acid from the environmental sample or treating the mutagenesis, radiogenic mutagenesis, deletion mutagenesis, environmental sample Such that nucleic acid in the sample is restriction-selection mutagenesis, restriction-purification accessible for hybridization to the amplification primer pair; 65 mutagenesis, artificial gene synthesis, ensemble mutagen and, (c) combining the nucleic acid of step (b) with the ampli esis, chimeric nucleic acid multimer creation and a combina fication primer pair of step (a) and amplifying nucleic acid tion thereof. US 8,541,220 B2 25 26 In one aspect, the method can be iteratively repeated until The invention provides methods for modifying codons in a an isomerase, e.g., a racemase, e.g., an amino acid racemase, nucleic acid encoding a polypeptide having an isomerase analanine racemase, and/or an epimerase having an altered or activity, e.g., a racemase activity, e.g., an amino acid race different activity or an altered or different stability from that mase activity, analanine racemase activity, and/or an epime of a polypeptide encoded by the template nucleic acid is rase activity to increase its expression in a host cell, the produced. In one aspect, the variant isomerase, e.g., race method comprising: (a) providing a nucleic acid of the inven mase, e.g., amino acid racemase, alanine racemase, and/or tion encoding an isomerase, e.g., a racemase, e.g., an amino epimerase polypeptide is thermotolerant, and retains some acid racemase, an alanine racemase, and/or an epimerase activity after being exposed to an elevated temperature. In polypeptide; and, (b) identifying a non-preferred or a less 10 preferred codon in the nucleic acid of step (a) and replacing it another aspect, the variant isomerase, e.g., racemase, e.g., with a preferred or neutrally used codon encoding the same amino acid racemase, alanine racemase, and/or epimerase amino acid as the replaced codon, wherein a preferred codon polypeptide has increased glycosylation as compared to the is a codon over-represented in coding sequences in genes in isomerase, e.g., the racemase, e.g., the amino acid racemase, the host cell and a non-preferred or less preferred codon is a the alanine racemase, and/or the epimerase encoded by a 15 codon under-represented in coding sequences in genes in the template nucleic acid. Alternatively, the variant isomerase, host cell, thereby modifying the nucleic acid to increase its e.g., racemase, e.g., amino acid racemase, alanine racemase, expression in a host cell. and/or epimerase polypeptide has an isomerase activity, e.g., The invention provides methods for modifying a codon in a racemase activity, e.g., an amino acid racemase activity, an a nucleic acid encoding a polypeptide having an isomerase alanine racemase activity, and/or an epimerase activity under activity, e.g., a racemase activity, e.g., an amino acid race a high temperature, wherein the isomerase, e.g., the race mase activity, analanine racemase activity, and/or an epime mase, e.g., the amino acid racemase, the alanine racemase, rase activity to decrease its expression in a host cell, the and/or the epimerase encoded by the template nucleic acid is method comprising: (a) providing a nucleic acid of the inven not active under the high temperature. In one aspect, the tion; and (b) identifying at least one preferred codon in the method can be iteratively repeated until an isomerase, e.g., a 25 nucleic acid of step (a) and replacing it with a non-preferred racemase, e.g., an amino acid racemase, an alanine racemase, or less preferred codon encoding the same amino acid as the and/or an epimerase coding sequence having an altered codon replaced codon, wherein a preferred codon is a codon over usage from that of the template nucleic acid is produced. In represented in coding sequences in genes in a host cell and a another aspect, the method can be iteratively repeated until an non-preferred or less preferred codon is a codon under-rep isomerase, e.g., a racemase, e.g., an amino acid racemase, an 30 resented in coding sequences in genes in the host cell, thereby alanine racemase, and/or an epimerase gene having higher or modifying the nucleic acid to decrease its expression in a host lower level of message expression or stability from that of the cell. In one aspect, the host cell can be a bacterial cell, a fungal template nucleic acid is produced. In another aspect, formu cell, an insect cell, a yeast cell, a plant cell or a mammalian lation of the final isomerase, e.g., racemase, e.g., amino acid cell. racemase, alanine racemase, and/or epimerase product 35 The invention provides methods for producing a library of enables an increase or modulation of the performance of the nucleic acids encoding a plurality of modified isomerase, e.g., isomerase, e.g., the racemase, e.g., the amino acid racemase, racemase, e.g., amino acid racemase, alanine racemase, and/ the alanine racemase, and/or the epimerase in the product. or epimerase active sites or Substrate binding sites, wherein The invention provides methods for modifying codons in a the modified active sites or substrate binding sites are derived nucleic acid encoding a polypeptide having an isomerase 40 from a first nucleic acid comprising a sequence encoding a activity, e.g., a racemase activity, e.g., an amino acid race first active site or a first substrate binding site the method mase activity, analanine racemase activity, and/or an epime comprising: (a) providing a first nucleic acid encoding a first rase activity to increase its expression in a host cell, the active site or first substrate binding site, wherein the first method comprising: (a) providing a nucleic acid of the inven nucleic acid sequence comprises a sequence that hybridizes tion encoding a polypeptide having an isomerase activity, 45 understringent conditions to a sequence of the invention, or a e.g., a racemase activity, e.g., an amino acid racemase activ Subsequence thereof, and the nucleic acid encodes an ity, analanine racemase activity, and/oran epimerase activity; isomerase, e.g., a racemase, e.g., an amino acid racemase, an and, (b) identifying a non-preferred or a less preferred codon alanine racemase, and/or an epimerase active site or an in the nucleic acid of step (a) and replacing it with a preferred isomerase, e.g., a racemase, e.g., an amino acid racemase, an or neutrally used codon encoding the same amino acid as the 50 alanine racemase, and/or an epimerase Substrate binding site; replaced codon, wherein a preferred codon is a codon over (b) providing a set of mutagenic oligonucleotides that encode represented in coding sequences in genes in the host cell and naturally-occurring amino acid variants at a plurality of tar a non-preferred or less preferred codon is a codon under geted codons in the first nucleic acid; and, (c) using the set of represented in coding sequences in genes in the host cell, mutagenic oligonucleotides to generate a set of active site thereby modifying the nucleic acid to increase its expression 55 encoding or Substrate binding site-encoding variant nucleic in a host cell. acids encoding a range of amino acid variations at each amino The invention provides methods for modifying codons in a acid codon that was mutagenized, thereby producing a library nucleic acid encoding a polypeptide having an isomerase of nucleic acids encoding a plurality of modified isomerase, activity, e.g., a racemase activity, e.g., an amino acid race e.g., racemase, e.g., amino acid racemase, alanine racemase, mase activity, analanine racemase activity, and/or an epime 60 and/or epimerase active sites or Substrate binding sites. In one rase activity; the method comprising: (a) providing a nucleic aspect, the method comprises mutagenizing the first nucleic acid of the invention; and, (b) identifying a codon in the acid of step (a) by a method comprising an optimized directed nucleic acid of step (a) and replacing it with a different codon evolution system, Gene Site Saturation Mutagenesis encoding the same amino acid as the replaced codon, thereby (GSSM), or a synthetic ligation reassembly (SLR). In one modifying codons in a nucleic acid encoding an isomerase, 65 aspect, the method comprises mutagenizing the first nucleic e.g., a racemase, e.g., an amino acid racemase, an alanine acid of step (a) or variants by a method comprising error racemase, and/or an epimerase. prone PCR, shuffling, oligonucleotide-directed mutagenesis, US 8,541,220 B2 27 28 assembly PCR, sexual PCR mutagenesis, in vivo mutagen isomerase, e.g., a racemase, e.g., an amino acid racemase, an esis, cassette mutagenesis, recursive ensemble mutagenesis, alanine racemase, and/or an epimerase enzyme, wherein the exponential ensemble mutagenesis, site-specific mutagen enzyme comprises a polypeptide of the invention, or a esis, gene reassembly (GeneReassembly, U.S. Pat. No. 6,537, polypeptide encoded by a nucleic acid of the invention, or a 776), Gene Site Saturation Mutagenesis (GSSM), synthetic 5 Subsequence thereof, and (b) deleting a plurality of amino ligation reassembly (SLR) and a combination thereof. In one acid residues from the sequence of step (a) and testing the aspect, the method comprises mutagenizing the first nucleic remaining Subsequence for an isomerase activity, e.g., a race acid of step (a) or variants by a method comprising recombi mase activity, e.g., an amino acid racemase activity, an ala nation, recursive sequence recombination, phosphothioate nine racemase activity, and/or an epimerase activity, thereby modified DNA mutagenesis, uracil-containing template 10 determining a functional fragment of an isomerase, e.g., a mutagenesis, gapped duplex mutagenesis, point mismatch racemase, e.g., an amino acid racemase, an alanine racemase, repair mutagenesis, repair-deficient host strain mutagenesis, and/or an epimerase enzyme. In one aspect, the isomerase chemical mutagenesis, radiogenic mutagenesis, deletion activity, e.g., racemase activity, e.g., amino acid racemase mutagenesis, restriction-selection mutagenesis, restriction activity, alanine racemase activity, and/or epimerase activity purification mutagenesis, artificial gene synthesis, ensemble 15 is measured by providing an isomerase, e.g., a racemase, e.g., mutagenesis, chimeric nucleic acid multimer creation and a an amino acid racemase, an alanine racemase, and/or an epi combination thereof. merase Substrate and detecting a decrease in the amount of the The invention provides methods for making a small mol Substrate or an increase in the amount of a reaction product. ecule comprising: (a) providing a plurality of biosynthetic The invention provides methods for whole cell engineering enzymes capable of synthesizing or modifying a small mol- 20 of new or modified phenotypes by using real-time metabolic ecule, wherein one of the enzymes comprises an isomerase, flux analysis, the method comprising: (a) making a modified e.g., a racemase, e.g., an amino acid racemase, an alanine cell by modifying the genetic composition of a cell, wherein racemase, and/or an epimerase enzyme encoded by a nucleic the genetic composition is modified by addition to the cell of acid of the invention; (b) providing a Substrate for at least one a nucleic acid of the invention; (b) culturing the modified cell of the enzymes of step (a); and (c) reacting the Substrate of 25 to generate a plurality of modified cells; (c) measuring at least step (b) with the enzymes under conditions that facilitate a one metabolic parameter of the cell by monitoring the cell plurality of biocatalytic reactions to generate a small mol culture of step (b) in real time; and, (d) analyzing the data of ecule by a series of biocatalytic reactions. The invention step (c) to determine if the measured parameter differs from a provides methods for modifying a small molecule compris comparable measurement in an unmodified cell under similar ing: (a) providing an isomerase, e.g., a racemase, e.g., an 30 conditions, thereby identifying an engineered phenotype in amino acid racemase, an alanine racemase, and/or an epime the cell using real-time metabolic flux analysis. In one aspect, rase enzyme, wherein the enzyme comprises a polypeptide of the genetic composition of the cell can be modified by a the invention, or, a polypeptide encoded by a nucleic acid of method comprising deletion of a sequence or modification of the invention, or a Subsequence thereof; (b) providing a small a sequence in the cell, or, knocking out the expression of a molecule; and (c) reacting the enzyme of step (a) with the 35 gene. In one aspect, the method can further comprise select small molecule of step (b) under conditions that facilitate an ing a cell comprising a newly engineered phenotype. In enzymatic reaction catalyzed by the isomerase, e.g., the race another aspect, the method can comprise culturing the mase, e.g., the amino acid racemase, the alanine racemase, selected cell, thereby generating a new cell strain comprising and/or the epimerase enzyme, thereby modifying a small a newly engineered phenotype. molecule by an isomerase, e.g., a racemase, e.g., an amino 40 The invention provides isolated, synthetic or recombinant acid racemase, an alanine racemase, and/or an epimerase signal sequences consisting of, or comprising, a sequence as enzymatic reaction. In one aspect, the method can comprise a set forth in residues 1 to 12, 1 to 13, 1 to 14, 1 to 15, 1 to 16, plurality of small molecule substrates for the enzyme of step 1 to 17, 1 to 18, 1 to 19, 1 to 20, 1 to 21, 1 to 22, 1 to 23, 1 to (a), thereby generating a library of modified Small molecules 24, 1 to 25, 1 to 26, 1 to 27, 1 to 28, 1 to 28, 1 to 30, 1 to 31, produced by at least one enzymatic reaction catalyzed by the 45 1 to 32, 1 to 33, 1 to 34, 1 to 35, 1 to 36, 1 to 37, 1 to 38, 1 to isomerase, e.g., the racemase, e.g., the amino acid racemase, 40, 1 to 41, 1 to 42, 1 to 43 or 1 to 44, of a polypeptide of the the alanine racemase, and/or the epimerase enzyme. In one invention, including exemplary polypeptide sequences of the aspect, the method can comprise a plurality of additional invention. enzymes under conditions that facilitate a plurality of bio The invention provides chimeric polypeptides comprising catalytic reactions by the enzymes to form a library of modi- 50 at least a first domain comprising a signal peptide (SP) and at fied small molecules produced by the plurality of enzymatic least a second domain comprising a heterologous polypeptide reactions. In another aspect, the method can further comprise or peptide comprising a sequence of the invention, or a Sub the step of testing the library to determine if a particular sequence thereof, wherein the heterologous polypeptide or modified small molecule that exhibits a desired activity is peptide is not naturally associated with the signal peptide present within the library. The step of testing the library can 55 (SP). In one aspect, the signal peptide (SP) is not derived from further comprise the steps of systematically eliminating all an isomerase, e.g., a racemase, e.g., an amino acid racemase, but one of the biocatalytic reactions used to produce a portion an alanine racemase, and/or an epimerase. The heterologous of the plurality of the modified small molecules within the polypeptide or peptide can be amino terminal to, carboxy library by testing the portion of the modified small molecule terminal to or on both ends of the signal peptide (SP) or an for the presence or absence of the particular modified small 60 isomerase, e.g., a racemase, e.g., an amino acid racemase, an molecule with a desired activity, and identifying at least one alanine racemase, and/or an epimerase catalytic domain specific biocatalytic reaction that produces the particular (CD). The invention provides isolated, synthetic or recombi modified small molecule of desired activity. nant nucleic acids encoding a chimeric polypeptide, wherein The invention provides methods for determining a func the chimeric polypeptide comprises at least a first domain tional fragment of an isomerase, e.g., a racemase, e.g., an 65 comprising signal peptide (SP) and at least a second domain amino acid racemase, an alanine racemase, and/or an epime comprising a heterologous polypeptide or peptide compris rase enzyme comprising the steps of: (a) providing an ing a sequence of the invention, or a Subsequence thereof, US 8,541,220 B2 29 30 wherein the heterologous polypeptide or peptide is not natu nucleic acid of the invention, wherein the polypeptide has an rally associated with the signal peptide (SP). isomerase activity, e.g., a racemase activity, e.g., an amino The invention provides methods of increasing thermotol acid racemase activity, analanine racemase activity, and/oran erance or thermostability of an isomerase, e.g., a racemase, epimerase activity. The isomerase, e.g., racemase, e.g., amino e.g., an amino acid racemase, an alanine racemase, and/or an acid racemase, alanine racemase, and/or epimerase can be epimerase polypeptide, the method comprising glycosylating nonsurface-active or Surface-active. The isomerase, e.g., the an isomerase, e.g., a racemase, e.g., an amino acid racemase, racemase, e.g., the amino acid racemase, the alanine race an alanine racemase, and/or an epimerase polypeptide, mase, and/or the epimerase can be formulated in a non-aque wherein the polypeptide comprises at least thirty contiguous ous liquid composition, a cast Solid, a granular form, a par amino acids of a polypeptide of the invention; or a polypep 10 ticulate form, a compressed tablet, a gel form, a paste or a tide encoded by a nucleic acid sequence of the invention, slurry form. The invention provides methods for washing an thereby increasing the thermotolerance or thermostability of object comprising: (a) providing a composition comprising a the isomerase, e.g., the racemase, e.g., the amino acid race polypeptide of the invention having an isomerase activity, mase, the alanine racemase, and/or the epimerase polypep e.g., a racemase activity, e.g., an amino acid racemase activ tide. In one aspect, the isomerase, e.g., the racemase, e.g., the 15 ity, analanine racemase activity, and/oran epimerase activity, amino acid racemase, the alanine racemase, and/or the epi or a polypeptide encoded by a nucleic acid of the invention; merase-specific activity can be thermostable or thermotoler (b) providing an object; and (c) contacting the polypeptide of antata temperature in the range from greater than about 0°C. step (a) and the object of step (b) under conditions wherein the to about 20°C., about 20° C. to about 37°C., about 37° C. to composition can wash the object. about 50° C., about 50° C. to about 70° C., about 70° C. to The invention provides textiles or fabrics, including, e.g., about 75° C., about 75° C. to about 80° C., about 80° C. to threads, comprising a polypeptide of the invention, or a about 85°C., about 85°C. to about 90° C., about 90° C. to polypeptide encoded by a nucleic acid of the invention. The about 95°C., about 95°C. to about 100° C., about 100° C. to invention provides methods for treating a textile or fabric about 110°C., or higher. (e.g., removing a stain from a composition) comprising: (a) The invention provides methods for overexpressing a 25 providing a composition comprising a polypeptide of the recombinant isomerase, e.g., racemase, e.g., amino acid race invention having an isomerase activity, e.g., a racemase activ mase, alanine racemase, and/or epimerase polypeptide in a ity, e.g., an amino acid racemase activity, analanine racemase cell comprising expressing a vector comprising a nucleic acid activity, and/or an epimerase activity, or a polypeptide comprising a nucleic acid of the invention or a nucleic acid encoded by a nucleic acid of the invention; (b) providing a sequence of the invention, wherein the sequence identities are 30 textile or fabric; and (c) contacting the polypeptide of step (a) determined by analysis with a sequence comparison algo and the composition of step (b) under conditions wherein the rithm or by visual inspection, wherein overexpression is isomerase, e.g., the racemase, e.g., the amino acid racemase, effected by use of a high activity promoter, a dicistronic the alanine racemase, and/or the epimerase can treat the tex vector or by gene amplification of the vector. tile or fabric (e.g., remove the stain). The invention provides The invention provides methods of making a transgenic 35 methods for improving the finish of a fabric comprising: (a) plant and seeds comprising: (a) introducing a heterologous providing a composition comprising a polypeptide of the nucleic acid sequence into the cell, wherein the heterologous invention having an isomerase activity, e.g., a racemase activ nucleic sequence comprises a nucleic acid sequence of the ity, e.g., an amino acid racemase activity, analanine racemase invention, thereby producing a transformed plant or seed cell; activity, and/or an epimerase activity, or a polypeptide and (b) producing a transgenic plant from the transformed 40 encoded by a nucleic acid of the invention; (b) providing a cell or seed. In one aspect, the step (a) can further comprise fabric; and (c) contacting the polypeptide of step (a) and the introducing the heterologous nucleic acid sequence by elec fabric of step (b) under conditions wherein the polypeptide troporation or microinjection of plant cell protoplasts. In can treat the fabric thereby improving the finish of the fabric. another aspect, the step (a) can further comprise introducing In one aspect, the fabric is a wool or a silk. In another aspect, the heterologous nucleic acid sequence directly to plant tissue 45 the fabric is a cellulosic fiber or a blend of a natural fiber and by DNA particle bombardment. Alternatively, the step (a) can a synthetic fiber. further comprise introducing the heterologous nucleic acid The invention provides feeds, foods, feed supplements, sequence into the plant cell DNA using an Agrobacterium food Supplements, dietary compositions or dietary aids com tumefaciens host. In one aspect, the plant cell can be a potato, prising a polypeptide of the invention, or a polypeptide corn, rice, wheat, tobacco, or barley cell. 50 encoded by a nucleic acid of the invention. The food or the The invention provides methods of expressing a heterolo feed can be, e.g., a cereal, a grain, a corn and the like. gous nucleic acid sequence in a plant cell comprising: (a) The invention provides dough, bread or baked products transforming the plant cell with a heterologous nucleic acid and/or dough, bread or baked product precursors comprising sequence operably linked to a promoter, wherein the heter a polypeptide having an isomerase activity, e.g., a racemase ologous nucleic sequence comprises a nucleic acid of the 55 activity, e.g., an amino acid racemase activity, an alanine invention; (b) growing the plant under conditions wherein the racemase activity, and/or an epimerase activity, wherein the heterologous nucleic acids sequence is expressed in the plant polypeptide comprises a sequence of the invention, or the cell. The invention provides methods of expressing a heter polypeptide is encoded by a nucleic acid comprising a ologous nucleic acid sequence in a plant cell comprising: (a) sequence of the invention, or an enzymatically active frag transforming the plant cell with a heterologous nucleic acid 60 ment thereof. sequence operably linked to a promoter, wherein the heter The invention provides beverages and beverage precursors ologous nucleic sequence comprises a sequence of the inven comprising a polypeptide, or an enzymatically active frag tion; (b) growing the plant under conditions wherein the ment thereof, having an isomerase activity, e.g., a racemase heterologous nucleic acids sequence is expressed in the plant activity, e.g., an amino acid racemase activity, an alanine cell. 65 racemase activity, and/or an epimerase activity, wherein the The invention provides detergent compositions comprising polypeptide comprises a sequence of the invention, or the a polypeptide of the invention, or a polypeptide encoded by a polypeptide is encoded by a nucleic acid comprising a US 8,541,220 B2 31 32 sequence of the invention. The invention provides methods of application of steam. The pelletizing conditions can comprise beverage production comprising administration of at least application of a temperature in excess of about 80° C. for one polypeptide having an isomerase activity, e.g., a race about 5 minutes and the enzyme retains a specific activity of mase activity, e.g., an amino acid racemase activity, an ala at least 350 to about 900 units per milligram of enzyme. nine racemase activity, and/or an epimerase activity, wherein The invention provides methods for treating, e.g. improv the polypeptide comprises a sequence of the invention, or the ing texture and flavor of a dairy product comprising: (a) polypeptide is encoded by a nucleic acid comprising a providing a polypeptide of the invention having an isomerase sequence of the invention, or an enzymatically active frag activity, e.g., a racemase activity, e.g., an amino acid race ment thereof, to a beverage or a beverage precursor, wherein mase activity, analanine racemase activity, and/or an epime in one aspect (optionally) the beverage or beverage precursor 10 rase activity, or an isomerase, e.g., a racemase, e.g., an amino is a wort or a beer. acid racemase, an alanine racemase, and/or an epimerase The invention provides food, feed or nutritional supple encoded by a nucleic acid of the invention; (b) providing a ments, e.g. for a human or an animal comprising a polypep dairy product; and (c) contacting the polypeptide of step (a) tide of the invention, e.g., a polypeptide encoded by the and the dairy product of step (b) under conditions wherein the nucleic acid of the invention. In one aspect, the polypeptide in 15 isomerase, e.g., the racemase, e.g., the amino acid racemase, the food or nutritional Supplement can be glycosylated. The the alanine racemase, and/or the epimerase can treat, e.g. invention provides edible enzyme delivery matrices compris improve the texture or flavor of the dairy product. In one ing a polypeptide of the invention, e.g., a polypeptide aspect, the dairy product comprises a cheese orayoghurt. The encoded by the nucleic acid of the invention. In one aspect, invention provides dairy products comprising an isomerase, the delivery matrix comprises a pellet. In one aspect, the e.g., a racemase, e.g., an amino acid racemase, an alanine polypeptide can be glycosylated. In one aspect, the isomerase racemase, and/or an epimerase of the invention, or is encoded activity, e.g., racemase activity, e.g., amino acid racemase by a nucleic acid of the invention. activity, alanine racemase activity, and/or epimerase activity The invention provides methods for improving the extrac is thermotolerant. In another aspect, the isomerase activity, tion of oil from an oil-rich plant material comprising: (a) e.g., racemase activity, e.g., amino acid racemase activity, 25 providing a polypeptide of the invention having an isomerase alanine racemase activity, and/or epimerase activity is ther activity, e.g., a racemase activity, e.g., an amino acid race mostable. mase activity, analanine racemase activity, and/or an epime In one aspect, the isomerase, e.g., the racemase, e.g., the rase activity, or an isomerase, e.g., a racemase, e.g., an amino amino acid racemase, the alanine racemase, and/or the epi acid racemase, an alanine racemase, and/or an epimerase merase enzyme can be prepared by expression of a polynucle 30 encoded by a nucleic acid of the invention; (b) providing an otide encoding the isomerase, e.g., the racemase, e.g., the oil-rich plant material; and (c) contacting the polypeptide of amino acid racemase, the alanine racemase, and/or the epi step (a) and the oil-rich plant material. In one aspect, the merase in an organism selected from the group consisting of oil-rich plant material comprises an oil-rich seed. The oil can a bacterium, a yeast, a plant, an insect, a fungus and an animal. be a Soybean oil, an olive oil, a rapeseed (canola) oil or a The organism can be selected from the group consisting of an 35 sunflower oil. S. pombe, S. cerevisiae, Pichia pastoris, Pseudomonas sp., E. The invention provides methods for preparing a fruit or coli, Streptomyces sp., Bacillus sp. and Lactobacillus sp. Vegetable juice, syrup, puree or extract comprising: (a) pro The invention provides edible enzyme delivery matrix viding a polypeptide of the invention having an isomerase comprisingathermostable recombinant isomerase, e.g., race activity, e.g., a racemase activity, e.g., an amino acid race mase, e.g., amino acid racemase, alanine racemase, and/or 40 mase activity, analanine racemase activity, and/or an epime epimerase enzyme, e.g., a polypeptide of the invention. The rase activity, or an isomerase, e.g., a racemase, e.g., an amino invention provides methods for delivering an isomerase, e.g., acid racemase, an alanine racemase, and/or an epimerase a racemase, e.g., an amino acid racemase, an alanine race encoded by a nucleic acid of the invention; (b) providing a mase, and/or an epimerase Supplement to an animal, the composition or a liquid comprising a fruit or vegetable mate method comprising: preparing an edible enzyme delivery 45 rial; and (c) contacting the polypeptide of step (a) and the matrix in the form of pellets comprising a granulate edible composition, thereby preparing the fruit or vegetable juice, carrier and a thermostable recombinant isomerase, e.g., race syrup, puree or extract. mase, e.g., amino acid racemase, alanine racemase, and/or The invention provides methods for treating a wood, a epimerase enzyme, wherein the pellets readily disperse the wood product, a paper, a paper product, a pulp, a pulp prod isomerase, e.g., the racemase, e.g., the amino acid racemase, 50 uct, a paper waste or a paper recycling composition compris the alanine racemase, and/or the epimerase enzyme contained ing: (a) providing a polypeptide of the invention having an therein into aqueous media, and administering the edible isomerase activity, e.g., a racemase activity, e.g., an amino enzyme delivery matrix to the animal. The recombinant acid racemase activity, analanine racemase activity, and/oran isomerase, e.g., racemase, e.g., amino acid racemase, alanine epimerase activity, or an isomerase, e.g., a racemase, e.g., an racemase, and/or epimerase enzyme can comprise a polypep 55 amino acid racemase, an alanine racemase, and/or an epime tide of the invention. The granulate edible carrier can com rase encoded by a nucleic acid of the invention; (b) providing prise a carrier selected from the group consisting of a grain a composition comprising a wood, a wood product, a paper, a germ, a grain germ that is spent of oil, a hay, an alfalfa, a paper product, a pulp, a pulp product, a paper waste or a paper timothy, a soy hull, a Sunflower seed meal and a wheat midd. recycling composition; and (c) contacting the polypeptide of The edible carrier can comprise graingerm that is spent of oil. 60 step (a) and the composition, thereby treating the wood, wood The isomerase, e.g., the racemase, e.g., the amino acid race product, paper, paper product, pulp, pulp product, paper mase, the alanine racemase, and/or the epimerase enzyme can waste or paper recycling composition. In one aspect of the be glycosylated to provide thermostability at pelletizing con invention, the treatment comprises reducing or solubilizing ditions. The delivery matrix can be formed by pelletizing a lignin (delignification), bleaching or decoloring, and/or mixture comprising a grain germ and an isomerase, e.g., a 65 deinking. racemase, e.g., an amino acid racemase, an alanine racemase, The invention provides papers or paper products or paper and/or an epimerase. The pelletizing conditions can include pulp comprising an isomerase, e.g., a racemase, e.g., an US 8,541,220 B2 33 34 amino acid racemase, an alanine racemase, and/or an epime ity, e.g., an amino acid racemase activity, analanine racemase rase of the invention, or a polypeptide encoded by a nucleic activity, and/or an epimerase activity. acid of the invention. The invention provides methods for The invention provides pharmaceutical (drug) composi treating a paper or a paper or wood pulp comprising: (a) tions and pharmaceutical (drug) precursors and intermediates providing a polypeptide of the invention having an isomerase comprising a polypeptide having an isomerase activity, e.g., a activity, e.g., a racemase activity, e.g., an amino acid race racemase activity, e.g., an amino acid racemase activity, an mase activity, analanine racemase activity, and/or an epime alanine racemase activity, and/or an epimerase activity, rase activity, or an isomerase, e.g., a racemase, e.g., an amino wherein the polypeptide comprises a sequence of the inven acid racemase, an alanine racemase, and/or an epimerase tion, or the polypeptide is encoded by a nucleic acid compris 10 ing a sequence of the invention, or an enzymatically active encoded by a nucleic acid of the invention; (b) providing a fragment thereof. In one aspect, the pharmaceutical compo composition comprising a paperor a paper or wood pulp; and sition acts as a digestive aid, is an antibiotic or is useful for (c) contacting the polypeptide of step (a) and the composition treatment of amino acid deficiencies. In one aspect, the treat of step (b) under conditions wherein the isomerase, e.g., the ment is prophylactic. racemase, e.g., the amino acid racemase, the alanine race 15 In one aspect, the invention provides oral care products mase, and/or the epimerase can treat the paper or paper or comprising a polypeptide of the invention having an wood pulp. isomerase activity, e.g., a racemase activity, e.g., an amino The invention provides methods for bleaching a thread, acid racemase activity, analanine racemase activity, and/oran fabric, yarn, cloth or textile comprising contacting the fabric, epimerase activity, or an isomerase, e.g., a racemase, e.g., an yarn, cloth or textile with an isomerase, e.g., a racemase, e.g., amino acid racemase, an alanine racemase, and/or an epime an amino acid racemase, an alanine racemase, and/or an epi rase encoded by a nucleic acid of the invention. The oral care merase under conditions suitable to produce a whitening of product can comprise a toothpaste, a dental cream, a gel or a the textile, wherein the isomerase, e.g., the racemase, e.g., the tooth powder, an odontic, a mouth wash, a pre- or post brush amino acid racemase, the alanine racemase, and/or the epi ing rinse formulation, a chewing gum, a lozenge or a candy. merase comprises a polypeptide of the invention, or an enzy 25 The invention provides contact lens cleaning compositions matically active fragment thereof. The thread, fabric, yarn, comprising a polypeptide of the invention having an cloth or textile can comprise a non-cotton cellulosic thread, isomerase activity, e.g., a racemase activity, e.g., an amino fabric, yarn, cloth or textile. The invention provides fabrics, acid racemase activity, analanine racemase activity, and/oran yarns, cloths or textiles comprising a polypeptide having a epimerase activity, or an isomerase, e.g., a racemase, e.g., an sequence of the invention, or a polypeptide encoded by a 30 amino acid racemase, an alanine racemase, and/or an epime nucleic acid comprising a sequence of the invention, or an rase encoded by a nucleic acid of the invention. enzymatically active fragment thereof, wherein in one aspect The invention provides chimeric isomerases, e.g., race (optionally) the fabric, yarn, cloth or textile comprises a non mases, e.g., amino acid racemases, alanine racemases, and/or cotton cellulosic fabric, yarn, cloth or textile. epimerases comprising a polypeptide sequence of the inven The invention provides wood, wood chips, wood pulp, 35 tion and at least one heterologous domain, e.g. a binding wood products, paper pulps, paper products, newspapers or domain or a dockerin domain. The invention provides meth paper waste comprising a polypeptide of the invention, or an ods for designing a chimeric isomerase, e.g., racemase, e.g., enzymatically active fragment thereof. The invention pro amino acid racemase, alanine racemase, and/or epimerase vides thread, fabric, yarn, cloth or textile comprising a having a new specificity or an enhanced specificity, compris polypeptide of the invention, or an enzymatically active frag 40 ing inserting a heterologous or an additional endogenous ment thereof. domain, e.g. a binding domain or a dockerin domain, into an The invention provides methods for making ethanol com isomerase, e.g., a racemase, e.g., an amino acid racemase, an prising contacting an organic material, e.g. a biomass with a alanine racemase, and/oran epimerase, wherein the domain is polypeptide having an isomerase activity, e.g., a racemase inserted into an isomerase, e.g., a racemase, e.g., an amino activity, e.g., an amino acid racemase activity, an alanine 45 acid racemase, an alanine racemase, and/or an epimerase racemase activity, and/or an epimerase activity, wherein the sequence of the invention. polypeptide has a sequence of the invention, or the polypep The invention provides enzyme mixtures, or “cocktails' tide is encoded by a nucleic acid comprising a sequence of the comprising at least one enzyme of the invention and one or invention, or an enzymatically active fragment thereof. The more other enzyme(s), which can be another isomerase, e.g., invention provides compositions comprising an ethanol and a 50 racemase, e.g., amino acid racemase, alanine racemase, and/ polypeptide having an isomerase activity, e.g., a racemase or epimerase, or any other enzyme; for example, the "cock activity, e.g., an amino acid racemase activity, an alanine tails” of the invention, in addition to at least one enzyme of racemase activity, and/or an epimerase activity, wherein the this invention, can comprise any other enzyme, such as Xyla polypeptide has a sequence of the invention, or the polypep nase, cellulases, lipases, esterases, proteases, or endoglycosi tide is encoded by a nucleic acid comprising a sequence of the 55 dases, endo-beta.-1,4-glucanases, beta-glucanases, endo invention, or an enzymatically active fragment thereof. The beta-1,3(4)-glucanases, cutinases, peroxidases, catalases, invention provides methods for making ethanol comprising: laccases, amylases, glucoamylases, pectinases, transferases, (a) providing at least one polypeptide having an isomerase transaminases, amino transferases, dehydrogenases, oxi activity, e.g., a racemase activity, e.g., an amino acid race doreductases, reductases, oxidases, phenoloxidases, ligni mase activity, analanine racemase activity, and/or an epime 60 nases, pullulanases, arabinanases, hemicellulases, mannan rase activity, or an enzymatically active fragment thereof; (b) ases, Xyloglucanases, pectin acetyl esterases, providing an organic composition; and (c) contacting the rhamnogalacturonan acetyl esterases, polygalacturonases, composition of step (b) with the polypeptide of step (a). rhamnogalacturonases, galactanases, pectin lyases, pectin The invention provides methods of making a pharmaceu methylesterases, cellobiohydrolases and/or transglutami tical (drug) composition, a pharmaceutical (drug) precursor, 65 nases, to name just a few examples. In alternative embodi or a drug intermediate, comprising using a polypeptide of this ments, these enzyme mixtures, or "cocktails' comprising at invention having an isomerase activity, e.g., a racemase activ least one enzyme of the invention can be used in any process US 8,541,220 B2 35 36 or method of the invention, or composition of the invention, drugs and drug additives, dietary Supplements, textiles, wood, e.g., in foods or feeds, food or feed Supplements, textiles, paper, pulp, detergents and the like. papers, processed woods, etc. and methods for making them, In one aspect, an enzyme of the invention is thermotolerant and in compositions and methods for treating paper, pulp. and/or tolerant of high and/or low pH conditions. For wood, paper, pulp or wood waste or by-products, and the like, example, in one aspect, an isomerase, e.g., a racemase, e.g., and in the final products thereof. an amino acid racemase, an alanine racemase, and/or an epi The details of one or more embodiments of the invention merase of the invention retains activity under conditions com are set forth in the accompanying drawings and the descrip prising a temperature of at least about 80°C., 85°C., 86°C., tion below. Other features, objects, and advantages of the 87° C., 88° C., 89° C., 90° C., 910 C., 920 C., 93° C., 940 C., invention will be apparent from the description and drawings, 10 95° C., 96° C., 97° C., 98° C. 999 C., 100° C. 101° C. 1020 C., 103° C., 103.5° C., 104°C., 105° C., 107° C., 108°C., and from the claims. 109° C. or 110°C., or more, and a basic pH of at least about All publications, patents, patent applications, GenBank pH 11, or more. sequences and ATCC deposits, cited herein are hereby The invention provides isolated, synthetic or recombinant expressly incorporated by reference for all purposes. 15 nucleic acids comprising a nucleic acid encoding at least one polypeptide having an isomerase activity, e.g., a racemase BRIEF DESCRIPTION OF THE DRAWINGS activity, e.g., an amino acid racemase activity, an alanine racemase activity, and/or an epimerase activity, or other activ The following drawings are illustrative of aspects of the ity as described herein, wherein the nucleic acid comprises a invention and are not meant to limit the scope of the invention sequence having at least about 50%, 51%, 52%. 53%, 54%, as encompassed by the claims. 55%, 56%, 57%, 58%, 59%, 60%, 61%. 62%, 63%, 64%, The patent or application file contains at least one drawing 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, executed in color. Copies of this patent or patent application 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, publication with color drawing(s) will be provided by the 85%. 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, Office upon request and payment of the necessary fee. 25 95%, 96%, 97%, 98%, 99%, or more, or complete (100%) FIG. 1 is a block diagram of a computer system. sequence identity (homology) to SEQ ID NO:1, SEQ ID FIG. 2 is a flow diagram illustrating one aspect of a process NO:3, SEQID NO:5, SEQID NO:7, SEQID NO:9, SEQID for comparing a new nucleotide or protein sequence with a NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, database of sequences in order to determine the homology SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID levels between the new sequence and the sequences in the 30 NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, database. SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID FIG. 3 is a flow diagram illustrating one aspect of a process NO:39, SEQ ID NO:41, SEQID NO:43, SEQ ID NO:45, in a computer for determining whether two sequences are SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID homologous. NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, FIG. 4 is a flow diagram illustrating one aspect of an 35 SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID identifier process 300 for detecting the presence of a feature in NO:67, SEQ ID NO:69, SEQ ID NO:71, SEQ ID NO:73, a Sequence. SEQ ID NO:75, SEQ ID NO:77, SEQ ID NO:79, SEQ ID Like reference symbols in the various drawings indicate NO:81, SEQ ID NO:83, SEQ ID NO:85, SEQ ID NO:87, like elements. SEQ ID NO:89, SEQ ID NO:91, SEQ ID NO:93, SEQ ID 40 NO:95, SEQ ID NO:97, SEQ ID NO:99, SEQ ID NO:101, DETAILED DESCRIPTION OF THE INVENTION SEQID NO:103, SEQID NO:105, SEQIDNO:107, SEQID NO:109, SEQ ID NO:111, SEQ ID NO:113, SEQ ID The invention provides isomerases, e.g., racemases, e.g., NO:115, SEQ ID NO:117, SEQ ID NO:119, SEQ ID amino acid racemases, alanine racemases, and/or epimerases, NO:121, SEQ ID NO:123, SEQ ID NO:125, SEQ ID and polynucleotides encoding them and methods of making 45 NO:127, SEQ ID NO.129, SEQ ID NO:131, SEQ ID and using them. Isomerases, e.g., racemases, e.g., amino acid NO:133, SEQ ID NO:135, SEQ ID NO:137, SEQ ID racemases, alanine racemases, and/or epimerases, of the NO:139, SEQ ID NO:141, SEQ ID NO:143, SEQ ID polypeptides of the invention encompasses enzymes having NO:145, SEQ ID NO:147, SEQ ID NO:149, SEQ ID isomerase activity, e.g., racemase activity, e.g., amino acid NO:151, SEQ ID NO:153, SEQ ID NO:155, SEQ ID racemase activity, alanine racemase activity, and/or epime 50 NO:157, SEQ ID NO:159, SEQ ID NO:161, SEQ ID rase activity, and/or catalyze the re-arrangement of atoms NO:163, SEQ ID NO:165, SEQ ID NO:167, SEQ ID within a molecule, catalyze the conversion of one isomer into NO:169, SEQ ID NO:171, SEQ ID NO:173, SEQ ID another, catalyze the conversion of an optically active Sub NO:175, SEQ ID NO:177, SEQ ID NO:179, SEQ ID strate into a raceme, which is optically inactive, catalyze the NO:181, SEQ ID NO:183, SEQ ID NO:185, SEQ ID interconversion of Substrate enantiomers, catalyze the stere 55 NO:187, SEQ ID NO:189, SEQ ID NO.191, SEQ ID ochemical inversion around the asymmetric carbon atom in a NO:193, SEQ ID NO.195, SEQ ID NO:197, SEQ ID Substrate having only one center of asymmetry, catalyze the NO:199, SEQ ID NO:201, SEQ ID NO:203, SEQ ID Stereochemical inversion of the configuration around an NO:205, SEQ ID NO:207, SEQ ID NO:209, SEQ ID asymmetric carbonatom in a Substrate having more than one NO:211, SEQ ID NO:213, SEQ ID NO:215, SEQ ID asymmetric center, and/or catalyze the racemization of amino 60 NO:217, SEQ ID NO:219, SEQ ID NO:221, SEQ ID acids. The enzymes, e.g., racemases of the invention can be NO:223, SEQ ID NO:225, SEQ ID NO:227, SEQ ID used to make and/or process pharmaceutical (drug) compo NO:229, SEQ ID NO:231, SEQ ID NO:233, SEQ ID sitions, pharmaceutical (drug) precursors and intermediates, NO:235, SEQ ID NO:237, SEQ ID NO:239, SEQ ID Such as molecules comprising unnatural amino acids or anti NO:241, SEQ ID NO:243, SEQ ID NO:245, SEQ ID biotics, Sweeteners, peptide enzymes, peptide hormones, fuel 65 NO:247, SEQ ID NO:249, SEQ ID NO:251, SEQ ID and fuel additive compositions, foods and food additives, NO:253, SEQ ID NO:255, SEQ ID NO:257, SEQ ID beverage and beverage additives, feeds and feed additives, NO:259, SEQ ID NO:261, SEQ ID NO:263, SEQ ID

US 8,541,220 B2 39 40 and in Tables 1, 2 and 3, below, and in the Sequence Listing GENESEQTM database, which is available through Thomson (all of these sequences are “exemplary enzymes/polypeptides Derwent (Philadelphia, Pa.). All results from searches against of the invention'), and enzymatically active Subsequences this database are found in the columns entitled “GEN (fragments) thereof. ESEQTM Protein Description”, “GENESEQTM Protein Tables 1, 2 and 3, below, are charts describing selected 5 Accession Code”, “Evalue”, “GENESEQTM DNA Descrip characteristics of exemplary nucleic acids and polypeptides tion”, “GENESEQTM DNA Accession Code” or “Evalue”. of the invention, including sequence identity comparison of The information found in these columns is comparable to the the exemplary sequences to public databases. information found in the NR columns described above, Table 1, below, describes the assigned activity (as deter except that it was derived from BLAST searches against the mined by experimental data, see Examples 1-19, below) of 10 GENESEQTM database instead of the NCBI databases. In the exemplary polypeptides (encoded by the exemplary poly addition, this table includes the column “Predicted EC No.”. nucleotides) of the invention. Table 1 further indicates An EC number is the number assigned to a type of enzyme whether the polynucleotide (encoding a polypeptide) of the according to a scheme of standardized enzyme nomenclature invention is a clone (a genomic sequence isolated from the developed by the Enzyme Commission of the Nomenclature original Source, as described in Table 2) or is a subclone 15 Committee of the International Union of Biochemistry and (where the clone is manipulated by, e.g. removal of a native Molecular Biology (IUBMB). The results in the “Predicted signal sequence, addition of a start Methionine, addition of a EC No. column are determined by a BLAST search against tag, etc). Table 1 also indicates the clone and Subclone rela the Kegg (Kyoto Encyclopedia of Genes and Genomes) data tionship, e.g. which Subclone was derived from which clone. base. If the top BLAST match has an Evalue equal to or less For aid in reading Table 1, for example, Columns 1 and 4. thane-6, the EC number assigned to the top match is entered rows 1 and 2, indicate that SEQID NO:34 (encoded by SEQ into the table. The EC number of the top hit is used as a guide ID NO:33) is a clone with the corresponding subclone being to what the EC number of the sequence of the invention might SEQ ID NO:464 (encoded by SEQID NO:463), denoted as be. The columns “Query DNA Length” and “Query Protein “Clone/subclone pair 1. Length” refer to the number of nucleotides or the number Table 2, below, indicates the source from which the exem 25 amino acids, respectively, in the sequence of the invention plary nucleic acids and polypeptides of the invention were that was searched or queried against either the NCBI or GEN first derived. Table 2, below, also indicates the “Signalp ESEQTM databases. The columns “Subject DNA Length” and Cleavage Site” for the exemplary enzyme’s signal sequence “Subject Protein Length” refer to the number of nucleotides (or “signal peptide', or SP), as determined by the paradigm or the number amino acids, respectively, in the sequence of Signalp, as discussed below (see Nielsen (1997), infra); the 30 the top match from the BLAST searches. The results provided “Predicted Signal Sequence' is listed from the amino termi in these columns are from the search that returned the lower nal to the carboxy terminal, for example, for the polypeptide Evalue, either from the NCBI databases or the Geneseq data SEQIDNO:42, the signal peptide is “MPFCRTLLAVSLGL base. The columns “% ID Protein and “% ID DNA refer to LITGOAPLYA (amino acids 1-24 of SEQID NO:42). the percent sequence identity between the sequence of the Table 3, below describes selected characteristics of exem 35 plary nucleic acids and polypeptides of the invention, includ invention and the sequence of the top BLAST match. The ing sequence identity comparison of the exemplary results provided in these columns are from the search that sequences to public databases. To further aid in reading Table returned the lower Evalue, either from the NCBI databases or 3, for example, the first row, labeled “SEQ ID NO:”, the the GENESEQTM database. numbers “1, 2’ represent the exemplary polypeptide of the 40 invention having a sequence as set forth in SEQ ID NO:2. TABLE 1 encoded by, e.g., SEQID NO:1. All sequences described in Clone Table 2 (all the exemplary sequences of the invention) have Subclone Sequence type been subject to a BLAST search (as described in detail, pair SEQ ID NO: Activity (Clone or subclone) below) against two sets of databases. The first database set is 45 1 33, 34 Racemase Clone available through NCBI (National Center for Biotechnology 1 463,464 Racemase Subclone 2 131, 132 Racemase Clone Information). All results from searches against these data 2 457, 458 Racemase Subclone bases are found in the columns entitled “NR Description', 3 13, 14 Racemase Clone “NR Accession Code”, “NR Evalue” or “NR Organism”. 3 387,388 Racemase Subclone “NR’refers to the Non-Redundant nucleotide database main 50 4 25, 26 Racemase Clone 4 389, 390 Racemase Subclone tained by NCBI. This database is a composite of GenBank, 5 23, 24 Racemase Clone GenBank updates, and EMBL updates. The entries in the 5 391,392 Racemase Subclone column “NR Description” refer to the definition line in any 6 61, 62 Racemase Clone given NCBI record, which includes a description of the 6 411, 412 Racemase Subclone (leaderless) sequence. Such as the source organism, gene name/protein 55 6 489, 490 Racemase Subclone 7 297, 298 Racemase Clone name, or some description of the function of the sequence. 7 467, 468 Racemase Subclone The entries in the column “NRAccession Code' refer to the 8 11, 12 Racemase Clone unique identifier given to a sequence record. The entries in the 8 397, 398 Racemase Subclone 9 311, 312 Racemase Clone column “NR Evalue' refer to the Expect value (Evalue), 9 469,470 Racemase Subclone which represents the probability that an alignment score as 60 10 3, 4 Racemase Clone good as the one found between the query sequence (the 10 393, 394 Racemase Subclone sequences of the invention) and a database sequence would be 11 49, 50 Racemase Clone found in the same number of comparisons between random 11 423, 424 Racemase Subclone 12 367, 368 Racemase Clone sequences as was done in the present BLAST search. The 12 471,472 Racemase Subclone entries in the column “NR Organism' refer to the source 65 13 41, 42 Racemase Clone organism of the sequence identified as the closest BLAST hit. 13 399, 400 Racemase Subclone (leaderless) The second set of databases is collectively known as the US 8,541,220 B2 41 42 TABLE 1-continued TABLE 1-continued

Clone Clone Subclone Sequence type Subclone Sequence type pair SEQ ID NO: Activity (Clone or subclone) 5 pair SEQ ID NO: Activity (Clone or subclone) 3 491,492 Racemase Subclone 371,372 Epimerase Clone 4 43, 44 Racemase Clone 377,378 Epimerase Clone 4 431,432 Racemase Subclone 17, 18 Racemase Clone 5 45, 46 Racemase Clone 19, 20 Racemase Clone 5 409, 410 Racemase Subclone (leaderless) 15, 16 Racemase Clone 5 495, 496 Racemase Subclone 10 29, 30 Racemase Clone 6 47, 48 Racemase Clone 27, 28 Racemase Clone 6 407,408 Racemase Subclone (leaderless) 255, 256 Racemase Clone 6 493, 494 Racemase Subclone 321,322 Racemase Clone 7 287, 288 Racemase Clone 323,324 Racemase Clone 7 453,454 Racemase Subclone 327,328 Racemase Clone 8 35, 36 Racemase Clone 15 307, 308 Racemase Clone 8 385, 386 Racemase Subclone 303,304 Racemase Clone 9 51, 52 Racemase Clone 309,310 Racemase Clone 9 401, 402 Racemase Subclone (leaderless) 305,306 Racemase Clone 9 497, 498 Racemase Subclone 21, 22 Racemase Clone 2O 53, 54 Racemase Clone 479,480 Racemase Clone 2O 403, 404 Racemase Subclone (leaderless) 313,314 Racemase Clone 2O 427,428 Racemase Subclone 2O 315, 316 Racemase Clone 21 55, 56 Racemase Clone 1, 2 Racemase Clone 21 433,434 Racemase Subclone 85, 86 Racemase Clone 22 107, 108 Racemase Clone 87, 88 Racemase Clone 22 473,474 Racemase Subclone 89,90 Racemase Clone 23 57, 58 Racemase Clone 91, 92 Racemase Clone 23 405, 406 Racemase Subclone (leaderless) 25 93, 94 Racemase Clone 23 429, 430 Racemase Subclone 99, 100 Racemase Clone 24 O9, 110 Racemase Clone 77,78 Racemase Clone 24 415, 416 Racemase Subclone 331,332 Racemase Clone 25 21, 122 Racemase Clone 345,346 Racemase Clone 25 425,426 Racemase Subclone 347, 348 Racemase Clone 26 301,302 Racemase Clone 30 333,334 Racemase Clone 26 477,478 Racemase Subclone 325, 326 Racemase Clone 27 23, 124 Racemase Clone 319, 320 Racemase Clone 27 439, 440 Racemase Subclone 335,336 Racemase Clone 28 25, 126 Racemase Clone 349,350 Racemase Clone 28 461, 462 Racemase Subclone 339, 340 Racemase Clone 29 299, 300 Racemase Clone 35 341, 342 Racemase Clone 29 475,476 Racemase Subclone 343, 344 Racemase Clone 30 11, 112 Racemase Clone 355,356 Racemase Clone 30 4.17, 418 Racemase Subclone 353,354 Racemase Clone 31 19, 120 Racemase Clone 351,352 Racemase Clone 31 459, 460 Racemase Subclone 317,318 Racemase Clone 32 13, 114 Racemase Clone 329, 330 Racemase Clone 32 435,436 Racemase Subclone 40 167, 168 Racemase Clone 33 15, 116 Racemase Clone 213,214 Racemase Clone 33 419,420 Racemase Subclone 285,286 Racemase Clone 34 17, 118 Racemase Clone 289, 290 Racemase Clone 34 421, 422 Racemase Subclone 37, 38 Racemase Clone 35 223, 224 Racemase Clone 39, 40 Racemase Clone 35 441, 442 Racemase Subclone 45 483,484 Racemase Clone 36 217, 218 Racemase Clone 485,486 Racemase Clone 36 443, 444 Racemase Subclone 487,488 Racemase Clone 37 233,234 Racemase Clone 31, 32 Racemase Clone 37 445,446 Racemase Subclone 101, 102 Racemase Clone 38 243, 244 Racemase Clone 169, 170 Racemase Clone 38 447,448 Racemase Subclone 50 171, 172 Racemase Clone 39 247, 248 Racemase Clone 59, 60 Racemase Clone 39 449, 450 Racemase Subclone 135, 136 Racemase Clone 40 273, 274 Racemase Clone 173, 174 Racemase Clone 40 451,452 Racemase Subclone 137, 138 Racemase Clone 41 105,106 Racemase Clone 337,338 Racemase Clone 41 465,466 Racemase Subclone 55 357, 358 Racemase Clone 42 103, 104 Racemase Clone 359, 360 Racemase Clone 42 437,438 Racemase Subclone 361,362 Racemase Clone 43 7, 8 Racemase Clone 363,364 Racemase Clone 43 413, 414 Racemase Subclone 365,366 Racemase Clone 44 9, 10 Racemase Clone 175, 176 Racemase Clone 44 395,396 Racemase Subclone 177, 178 Racemase Clone 45 129, 130 Racemase Clone 60 179, 180 Racemase Clone 45 455,456 Racemase Subclone 181, 182 Racemase Clone 379,380 Epimerase Clone 143,144 Racemase Clone 381,382 Epimerase Clone 187, 188 Racemase Clone 369,370 Epimerase Clone 189, 190 Racemase Clone 375, 376 Epimerase Clone 133, 134 Racemase Clone 383,384 SO(8Se. Clone 65 145, 146 Racemase Clone 373,374 Epimerase Clone 481,482 Racemase Clone US 8,541,220 B2 43 44 TABLE 1-continued TABLE 1-continued

Clone Clone Subclone Sequence type Subclone Sequence type pair SEQ ID NO: Activity (Clone or subclone) pair SEQ ID NO: Activity (Clone or subclone) 63, 64 Racemase Clone 211, 212 Racemase Clone 193, 194 Racemase Clone 219, 220 Racemase Clone 153,154 Racemase Clone 221, 222 Racemase Clone 155, 156 Racemase Clone 225, 226 Racemase Clone 195, 196 Racemase Clone 227, 228 Racemase Clone 157, 158 Racemase Clone 10 229, 230 Racemase Clone 159, 160 Racemase Clone 231, 232 Racemase Clone 161, 162 Racemase Clone 235, 236 Racemase Clone 163, 164 Racemase Clone 237,238 Racemase Clone 165,166 Racemase Clone 239, 240 Racemase Clone 65, 66 Racemase Clone 241, 242 Racemase Clone 147,148 Racemase Clone 15 293,294 Racemase Clone 149, 150 Racemase Clone 245, 246 Racemase Clone 191, 192 Racemase Clone 295, 296 Racemase Clone 151, 152 Racemase Clone 249, 250 Racemase Clone 71, 72 Racemase Clone 251,252 Racemase Clone 69, 70 Racemase Clone 253,254 Racemase Clone 73, 74 Racemase Clone 257,258 Racemase Clone 75, 76 Racemase Clone 259,260 Racemase Clone 95, 96 Racemase Clone 261,262 Racemase Clone 97, 98 Racemase Clone 263,264 Racemase Clone 79, 80 Racemase Clone 265,266 Racemase Clone 81, 82 Racemase Clone 267,268 Racemase Clone 83, 84 Racemase Clone 269,270 Racemase Clone 67, 68 Racemase Clone 25 271, 272 Racemase Clone 183, 184 Racemase Clone 275,276 Racemase Clone 139, 140 Racemase Clone 141, 142 Racemase Clone 277,278 Racemase Clone 185, 186 Racemase Clone 279, 280 Racemase Clone 197, 198 Racemase Clone 281, 282 Racemase Clone 199, 200 Racemase Clone 30 283,284 Racemase Clone 201, 202 Racemase Clone 291, 292 Racemase Clone 203, 204 Racemase Clone 215, 216 Racemase Clone 205, 206 Racemase Clone 5, 6 Racemase Clone 207,208 Racemase Clone 127, 128 Racemase Clone 209, 210 Racemase Clone

TABLE 2

SEO ID NO: Source Signalp Cleavage Site Predicted Signal Sequence 1, 2 Aquifex aeolicus 3, 4 Aquifex aeolicus

5, 6 Bacteria

7, 8 Bacteria

9, 10 Bacteria

11, 12 Unknown

13, 14 Unknown

15, 16 Unknown

17, 18 Unknown

19, 2O Unknown

21, 22 Unknown

23, 24 Unknown

25, 26 Unknown 27, 28 Pelagibacter ubique

29, 30 Unknown

31, 32 Unknown US 8,541,220 B2 45 46 TABLE 2- Continued

SEO ID NO: Source Signalp Cleavage Site Predicted Signal Sequence 33, 34 Un

35, 36 Un

37, 38 Un

39, 40 Un

41, 42 Un Probabi ity: 999 RT (AWSIG LLITGOAPLYA 24 AA2 : 25

43, 44 Un Probabi ity: 999 (AWSIG LLITGOAPLYA 24 AA2 : 25

45, 46 Un Probabi ity: OOO (AWSIG LLITGOAPLYA 24 AA2 : 25

47, 48 Un Probabi ity: OOO RT (AWSIG LLITGOAPLYA 24 AA2 : 25

49, 50 Un Probabi ity: OOO AASL.A. LLITGOAPLYA 24 AA2 : 25

51, 52 Un Probabi ity: OOO RT ALSIG LWLWOGOWHA 23 AA2 : 24

53, 54 Un Probabi ity: OOO ALSIG LWLWOGQAHA 23 AA2 : 24

55, 56 Un Probabi ity: OOO RT ALSIG LWLWOGOWHA 23 AA2 : 24

57, 58 Un Probabi ity: OOO AASL.A. I PLYA 24 AA2 : 25

59, 6 O Un Probabi ity: OOO RT AASL.A. I PLYA 24 AA2 : 25

61, 62 Un Probabi ity: 999 FA IIL ITCLC 33 AA2 : 34

63, 64 Un Probabi ity: OOO AASL.A. I GLA PLYA 24 AA2 : 25

65, 66 Un Probabi ity: OOO AASL.A. I PLYA 24 AA2 : 25

67, 68 Un Probabi ity: OOO RT AASL.A. W AQA PLYA 24 AA2 : 25

69, 7 O Un Probabi ity: OOO AASL.A. PLYA 24 AA2 : 25

71, 72 Un Probabi ity: OOO AASL.A. PLYA 24 AA2 : 25

73, 74 Un Probabi ity: OOO RT AASL.A. PLYA 24 AA2 : 25

75, 76 Un Probabi ity: OOO AASL.A. PLYA 24 AA2 : 25

77, 78 Un Probabi ity: OOO RT AASL.A. PLYA 24 AA2 : 25

79, 8O Un Probabi ity: OOO AASL.A. PLYA 24 AA2 : 25

81, 82 Un Probabi ity: OOO RT AASL.A. PLYA 24 AA2 : 25

83, 84 Un Probabi ity: OOO AASL.A. PLYA 24 AA2 : 25

85, 86 Un Probabi ity: OOO RT AASL.A. PLFA 24 AA2 : 25 US 8,541,220 B2 47 48 TABLE 2- Continued

SEQ ID NO: Source Signalp Cleavage Site Predicted Signa Sequence 87, 88 Un Probabi ity: OOO AA PFCRT LAAS LA LITGOAP YA 24 AA2 : 25

89, 90 Un Probabi ity: OOO LA LITGOAP FA 24 AA2 : 25

91, 92 Un Probabi ity: OOO LA LITGOAP YA 24 AA2 : 25

93, 94 Un Probabi ity: OOO LA LITGOAP YA 24 AA2 : 25

95, 96 Un Probabi ity: OOO LA LITGOAP YA 24 AA2 : 25

97, 98 Un Probabi ity: OOO LA LITGOAP YA 24 AA2 : 25

99, O Un Probabi ity: OOO LA LITGOAP YA 24 AA2 : 25

O1, O2 Un

O3, O4 Un Probability: 826 AA1: MKNNKCIAILGGMGPOASS 19 AA2 :

O6 Un

O8 Un Probabi ity: OOO A. I LAGQAVA 22

10 Un ity: OOO A. I LAGQAVA 22

11, 12 Un ity: OOO A. I LAGQAVA 22

13, 14 Un ity: OOO A. W LAGQAVA 22

15, 16 Un ity: OOO A. W LAGQAVA 22

17, 18 Un Probabi ity: OOO A. W LAGQAVA 22

19, 2O Un Probabi ity: OOO A. W LAGQAVA 22

21, 22 Un

23, 24 Un

25, 26 Un

27, 28 Un

29, 3 O Un

31, 32 Un

33, 34 Un Probability: OOO AA1: MHKKTLLATLILGLLAGOAVA 21 AA2 : 22

35, 36 Un Probability: OOO AA1: MHKKTLLATLIFGLLAGOAVA 21 AA2 : 22

37, 38 Un Probability: OOO AA1: MHKKTLLATLIFGLLAGOAVA 21 AA2 : 22

39, 40 Un Probability: OOO AA1: MHKKTLLATLILGLLAGOAVA 21 AA2 : 22

41, 42 Un Probability: OOO AA1: MHKKTLLATLIFGLLAGOAVA 21 AA2 : 22 US 8,541,220 B2 49 TABLE 2 - continued

SEO ID NO: Source Signalp Cleavage Site Predicted Signal Sequence

43, 44. Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

45, 46 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

47, 48 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

49, 50 Unknown Probability: . OOO AA1: HKKTLLATLVFGLLAGOAVA 21 AA2: 22

51, 52 Unknown Probability: . OOO AA1: HKKTLLATLVFGLLAGOAVA 21 AA2: 22

53, 54. Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

55, 56 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

57, 58 Unknown Probability: . OOO AA1: HKKTLLATLVFGLLAGOAVA 21 AA2: 22

59, 60 Unknown Probability: . OOO AA1: HKKTLLATLVFGLLAGOAVA 21 AA2: 22

61, 62 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

63, 64. Unknown

65, 66 Unknown

67, 68 Unknown

69, 7O Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

71, 72 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

73, 74. Unknown Probability: . OOO AA1: HKKTLLATLIFGLLAGOAVA 21 AA2: 22

75, 76 Unknown Probability: . OOO AA1: HKKTLLATLVFGLLAGOAVA 21 AA2: 22

77, 78 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

79, 80 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

81, 82 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

83, 84 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

85, 86 Unknown Probability: . OOO AA1: HKKTLLATLIFGLLAGOAVA 21 AA2: 22

87, 188 Unknown Probability: 1. OOO AA1: MHKKTLLATLILGLLAGQAVA 21 AA2: 22

89, 90 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

91, 192 Unknown Probability: 1. OOO AA1: MHKKTLLATLVFGLLAGQAVA 21 AA2: 22

93, 194 Unknown Probability: 1. OOO AA1: MHKKTLLATLVFGLLAGQAVA 21 AA2: 22 US 8,541,220 B2 51 TABLE 2 - continued

SEO ID NO: Source Signalp Cleavage Site Predicted Signal Sequence

195, 196 Unknown Probability: . OOO AA1: HKKTLLATLVFGLLAGOAVA 21 AA2: 22

197, 198 Unknown Probability: . OOO AA1: HKKTLLATLVFGLLAGOAVA 21 AA2: 22

199, 2O0 Unknown Probability: . OOO AA1: HKKTLLATLIFGLLAGOAVA 21 AA2: 22

2O1, 202 Unknown Probability: . OOO AA1: HKKTLLATLIFGLLAGOAVA 21 AA2: 22

2O3, 204 Unknown Probability: . OOO AA1: HKKTLLATLIFGLLAGOAVA 21 AA2: 22

2O5, 206 Unknown Probability: . OOO AA1: HKKTLLATLIFGLLAGOAVA 21 AA2: 22

2O7, 208 Unknown Probability: . OOO AA1: HKKTLLATLVFGLLAGOAVA 21 AA2: 22

209, 210 Unknown Probability: . OOO AA1: HKKTLLATLVFGLLAGOAVA 21 AA2: 22

211, 212 Unknown Probability: . OOO AA1: HKKTLLATLVFGLLAGOAVA 21 AA2: 22

213, 214 Unknown Probability: . OOO AA1: HKKTLLATLVFGLLAGOAVA 21 AA2: 22

215, 216 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

217, 218 Unknown Probability: . OOO AA1: HKKTLLATLVFGLLAGOAVA 21 AA2: 22

219, 220 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

221, 222 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

223, 224. Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

225, 226 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

227, 228 Unknown Probability: . OOO AA1: HKKTLLATLVFGLLAGOAVA 21 AA2: 22

229, 23 OUnknown Probability: . OOO AA1: HKKTLLATLVFGLLAGOAVA 21 AA2: 22

231, 232 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

233, 234 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

235 236 Unknown Probability: . OOO AA1: HKKTLLATLIFGLLAGOAVA 21 AA2: 22

237, 238 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

239, 24 OUnknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

241, 242 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

243, 244. Unknown Probability: . OOO AA1: HKKTLLATLIFGLLAGOAVA 21 AA2: 22 US 8,541,220 B2 53 TABLE 2 - continued

SEO ID NO: Source Signalp Cleavage Site Predicted Signal Sequence

245, 246 Unknown Probability: 1. OOO AA1: MHKKTLLATLIFGLLAGQAVA 21 AA2: 22 247, 248 Unknown Probability: 1. OOO AA1: MHKKTLLATLIFGLLAGQAVA 21 AA2: 22 249 250 Unknown Probability: 1. OOO AA1: MHKKTLLATLIFGLLAGQAVA 21 AA2: 22 251, 252 Unknown Probability: 1. OOO AA1: MHKKTLLATLIFGLLAGQAVA 21 AA2: 22 253, 254 Unknown Probability: 1. OOO AA1: MHKKTLLATLIFGLLAGQAVA 21 AA2: 22

255, 256 Unknown

257, 258 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

259, 260 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

261, 262 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

263, 264 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

265, 266 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

267, 268 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

269, 270 Unknown Probability: . OOO AA1: HKKTLLATLVLGLLAGOAVA 21 AA2: 22

271, 272 Unknown Probability: . OOO AA1: HKKTLLATLVFGLLAGOAVA 21 AA2: 22

273, 274 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

275, 276 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

277 2 78 Unknown Probability: . OOO AA1: HKKTLLATLVFGLLAGOAVA 21 AA2: 22

279, 280 Unknown Probability: . OOO AA1: HKKTLLATLVFGLLAGOAVA 21 AA2: 22

281, 282 Unknown Probability: . OOO AA1: HKKTLLATLVFGLLAGOAVA 21 AA2: 22

283, 284 Unknown Probability: . OOO AA1: HKKTLLATLVFGLLAGOAVA 21 AA2: 22

285 286 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

287, 288 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

289, 290 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

291, 292 Unknown Probability: . OOO AA1: HKKTLLATLVFGLLAGOAVA 21 AA2: 22

293, 294 Unknown Probability: . OOO AA1: HKKTLLATLILGLLAGOAVA 21 AA2: 22

295, 296 Unknown Probability: . OOO AA1: HKKTLLATLIFGLLAGOAVA 21 AA2: 22 US 8,541,220 B2 55 TABLE 2 - continued

SEO ID NO: Source Signalp Cleavage Site Predicted Signal Sequence

297, 298 Unknown 299, 3 OO Unknown Probability: 1. OOO AA1: MPFTRTVLALSLGLVLLQSQVHA 23 AA2: 24

301, 3 O2 Unknown Probability: 1. OOO AA1: MKFTPTLLAVALAGCLSTQVQA 22 AA2: 23

3O3, 304 Unknown

3 O5, 306 Unknown

3 O7, 308 Unknown

309, 310 Unknown

311, 312 Unknown

313, 314 Unknown

315, 316 Unknown

317, 318 Unknown

319, 32O Unknown

321, 322 Unknown

323, 324 Unknown

325, 326 Unknown

327, 328 Unknown

329, 330 Unknown

331, 332 Unknown

333, 334 Unknown

335, 336 Unknown

337, 338 Unknown

339, 340 Unknown

341, 342 Unknown

343, 344 Unknown

345, 346 Unknown

347, 348 Unknown

349, 350 Unknown

351, 352 Unknown

353, 354 Unknown

355, 356 Unknown

357, 358 Unknown

359, 360 Unknown

361, 362 Unknown

363, 364 Unknown

365, 366 Unknown 367, 368 Pseudomonas straminea ATCC 33 6.36 US 8,541,220 B2 57 TABLE 2 - continued

SEO ID NO: Source Signalp Cleavage Site Predicted Signal Sequence 369, 370 Unknown

371, 372 Unknown

373, 374 Unknown

375, 376 Unknown

377, 378 Unknown

379, 380 Unknown

381, 382 Unknown

383, 384 Unknown

385, 386 Unknown

387, 388 Unknown

389, 390 Unknown

391, 392 Unknown

393, 394 Unknown

395, 396 Unknown

397, 398 Unknown

399, 4 OO Unknown

401, 4 O2 Unknown

4 O3, 404 Unknown

4 O5, 406 Unknown

4 O7, 408 Unknown

409, 410 Unknown

411, 412 Unknown

413, 414 Unknown

415, 416 Unknown

417 418 Unknown

419, 420 Unknown

421, 422 Unknown

423, 424 Unknown

425, 426 Unknown 427, 428 Unknown Probability: 1. OOO AA1: MPFCRTLLALSLGLVLWQGQAHA 23 AA2: 24 429, 430 Unknown Probability: 1. OOO AA1: MPFSRTLLAASLALLITGQAPLYA 24 AA2: 25

431, 432 Unknown

433, 434 Unknown

435, 436 Unknown 437, 438 Unknown Probability: 0.826 AA1: MKNNKCIAILGGMGPQASS 19 AA2: 2O

439, 440 Unknown

441, 442 Unknown US 8,541,220 B2 59 60 TABLE 2 - continued

SEO ID NO: Source Signalp Cleavage Site Predicted Signal Sequence 443, 444. Unknown

445, 446 Unknown

447, 448 Unknown

449, 450 Unknown

451, 452 Unknown

453, 454 Unknown

455, 456 Unknown 457, 458 Unknown Probability: 0.742 AA1: MARVVLRWARSAYIRITTGSHALF 3 O AA2: 31 ADATLA

459, 460 Unknown

461, 462 Unknown

463, 464 Unknown

465, 466 Unknown

467, 468 Unknown

469, 470 Unknown

471, 472 Unknown

473, 474 Unknown

475, 476 Unknown

477, 478 Unknown

479, 480 Unknown

481, 482 Unknown

483, 484 Unknown

485, 486 Unknown

487, 488 Unknown

TABLE 3 Genes eq NR Protein SEQ Acces- Genes eq Acces ID Sion NR Protein Sion NO: NR Description Code Evalue Organism Description Code Evalue

1, 2 hypothetical 156058141. OOE-128 Aquifex Prokaryotic ABU25 646 3. OOE-47 protein Aquifex aeolicus essential aeolicus. gene 3474. O.

3, 4 alanine racemase 156O 6873. O Aquifex Aquifex ABBO 62961. OOE-147 Aquifex aeolicus. aeolicus pyrophilus heat resistant alanine accelas 6 encoding DNA.

5, 6 hypothetical 298326681. OOE-101 Streptomyces Prokaryotic ABU194995. OOE-37 protein SAV6126 avermitilis essential Streptomyces MA- gene avermitilis MA- 468 O 3474. O. 468O US 8,541,220 B2 61 62 TABLE 3 - Continued

7, 8 hypothetical 2983 O835 O Streptomyces Propionibacterium ABM543582. OOE-53 protein SAV4292 avermitilis CeS Streptomyces MA predicted avermitilis MA 468 O ORF 468O encoded polypeptide

alanine racemase 21223.1241. OOE-166 Streptomyces Prokaryotic ABU34 223 6 OOE-9 O Streptomyces coelicolor essential coelicolor A3 (2) A3 (2) gene 3474. O.

alanine racemase 867 486271 OOE-106 Rhodopseudomonas Pseudomonas ABO84274. 4. OOE-50 Rhodopseudomonas palustris aeruginosa palustris HaA2 polypeptide HaA2 3.

alanine racemase 564774.261. OOE-128 Azoarcus Prokaryotic ABU413981. OOE-110 Azoarcus sp. sp. EbN1 essential EbN1) gene 3474. O.

Aspartate 1.49E-084. OOE-93 Marinobacter Klebsiella ABO 655O31 OOE-71 accelas 6 algicola pneumoniae Marinobacter DG893 polypeptide algicola DG893 seqid 7178.

glutamate 111E-O81. OOE-106 Cytophaga Prokaryotic ABU25.1742. OOE-44 accelas 6 hutchinsonii essential Cytophaga ATCC gene hutchinsonii ATCC 334 O6 3474. O. 33406

19, glutamate 39998O141. OOE-74 Geobacter M. Xanthus ABM9 O755 2. OOE-67 2O accelas 6 sulfurreducens protein Geobacter PCA sequence, sulfurreducens seq id PCA) 9726. 21, Putative 3.359 67.485. OOE-40 Bordeteila Thermococcus ADN4691. O 5 OOE-27 22 decarboxylase parapertus sis kodakaraensis Bordetella 12822 KOD1 parapertus sis protein 12822 sequence SeqID4.

23, alanine racemase Enterobacter Enterobacter 24 Enterobacter sp. so. cloacae 638) 638 protein amino acid sequence - SEO ID 5666.

25, alanine racemase Enterobacter Enterobacter 26 Enterobacter sp. so. cloacae 638) 638 protein amino acid sequence - SEO ID 5666.

27, hypothetical 71083 0671. OOE-121 Candidatus Prokaryotic ABU2429 O2 OOE-31 28 protein Pelagibacter essential SAR11 O3 61 ubique gene Candidatus HTCC1062 3474. O. Pelagibacter ubique HTCC1062) 29, putative proline 1.49E-081. OOE-13 O Brucella Pseudomonas ABO821341. OOE-127 3 O a Cease ovis aeruginos Brucella ovis ATCC polypeptide ATCC 2584 Ol 2584 O E3. 31, proline racemase, 1, 19E-081. OOE-109 Stappia Acinetobacter ADA352281. OOE-105 32 putative Stappia aggregata baumannii aggregata IAM IAM protein US 8,541,220 B2 63 64 TABLE 3 - continued 12614 1261.4 E19. gi 11843594 Ogb EAV42584.1 proline racemase, putative Stappia aggregata IAM 12614 33, alanine racemase 1.11E--O81. OOE-124 Mesorhizobium Prokaryotic ABU388293. OOE-46 34 Mesorhizobium sp. BNC1 essential sp. BNC1 gene 3474. O.

35, putative alanine 9 O4184396 OOE-49 Aurantimonas Achromobacter AEH192775. OOE-47 36 accelas 6 so. xylos oxidans Aurantimonas sp. SI85-9A1 DTA SI85-9A1 SEO ID NO gieO3381.11gb EAS51762. 1 6. putative alanine accelas 6 Aurantimonas sp. SI85-9A1 37, Alanine racemase 1.45E-081. OOE-38 Magnetospirillium Aquifex ABBO 629 62. OOE-2O 38 Magnetospirillium gryphis wall dense pyrophilus gryphis Waldense MSR-1 heat MSR-1 resistant alanine accelas 6 encoding DNA.

39, putative proline 91.77922.22 OOE-36 Burkholderia Prokaryotic ABU21813 5. OOE-37 4 O accelas 6 XeoWOS essential Burkholderia LB4 OO gene Xe(VOS 3474. O. LB4 OO

41, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED118O3 O 42 Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

43, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED118O3 O 44 Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

45, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED118O3 O 46 Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

47, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED118O3 O 48 Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

49, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED118O3 O SO Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

51, alanine racemase 1.26E-O8 O Pseudomonas T. maritima AED118O31 OOE-18O 52 Pseudomonas putida D-alanine putida GB-1 GB-1 D-alanine gi 126314851 gb EAZ66O19.1 ligase. alanine racemase Pseudomonas putida GB-1

53, alanine racemase 1.26E-O81. OOE-18O Pseudomonas T. maritima AED118O31 OOE-18O 54 Pseudomonas putida D-alanine putida GB-1 GB-1 D-alanine gi 126314851 gb EAZ66O19.1 ligase. alanine racemase Pseudomonas putida GB-1 US 8,541,220 B2 65 66 TABLE 3 - continued

55, alanine racemase 1.26E-O81. OOE-18 O Pseudomonas T. maritima AED118O31 OOE-179 56 Pseudomonas putida D-alanine putida GB-1 GB-1 D-alanine gi 126314851 gb EAZ66O19.1 ligase. alanine racemase Pseudomonas putida GB-1

57, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED11804 O 58 Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

59, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED11804 O 6 O Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

61, alanine racemase 1. 48E+087. OOE-19 Fusobacterium Aquifex ABBO 62961. OOE-12 62 Fusobacterium nucleatum pyrophilus nulceatum subsp. subsp. heat polymorphum polymorphum resistant ATCC 10953 ATCC alanine 10953 accelas 6 encoding DNA.

63, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED118O3 O 64 Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

65, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED118O3 O 66 Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

67, alanine racemase 1.26E-O8 O Pseudomonas T. maritima AED118O3 O 68 Pseudomonas putida D-alanine putida GB GB-1 D-alanine gi 126314851 gb EAZ66O19.1 ligase. alanine racemase Pseudomonas putida GB

69, alanine racemase 1.26E-O8 O Pseudomonas T. maritima AED118O3 O 70 Pseudomonas putida D-alanine putida GB GB-1 D-alanine gi 126314851 gb EAZ66O19.1 ligase. alanine racemase Pseudomonas utida GB

71, alanine racemase 1.26E-O8 O Pseudomonas T. maritima AED118O3 O 72 Pseudomonas putida D-alanine putida GB GB-1 D-alanine gi 126314851 gb EAZ66O19.1 ligase. alanine racemase Pseudomonas utida GB

73, alanine racemase 1.26E-O8 O Pseudomonas T. maritima AED118O3 O 74 Pseudomonas putida D-alanine putida GB GB-1 D-alanine gi 126314851 gb EAZ66O19.1 ligase. alanine racemase Pseudomonas putida GB

75, alanine racemase 1.26E-O8 O Pseudomonas T. maritima AED118O3 O 76 Pseudomonas putida D-alanine putida GB GB-1 D-alanine gi 126314851 gb EAZ66O19.1 ligase. alanine racemase Pseudomonas putida GB US 8 541,220 B2 67 68 TABLE 3 - continued

77, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED118O3 O 78 Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

79, alanine racemase 1.49E-08 O Pseudomonas AED11804 O 8O Pseudomonas putida F1 putida F1

81, alanine racemase 1.49E-08 O Pseudomonas AED11804 O 82 Pseudomonas putida F1 putida F1

83, alanine racemase 1.49E-08 O Pseudomonas AED11804 O 84 Pseudomonas putida F1 putida F1

85, alanine racemase 1.49E-08 O Pseudomonas AED118O3 O 86 Pseudomonas putida F1 putida F1

87, alanine racemase 1.49E-08 O Pseudomonas AED118O3 O 88 Pseudomonas putida F1 putida F1

89, alanine racemase 26990430 O Pseudomonas AED118O3 O 9 O Pseudomonas putida putida KT244 O KT244. O

91, alanine racemase 1.49E-08 O Pseudomonas AED118O3 O 92 Pseudomonas putida F1 putida F1

93, alanine racemase 1.49E-08 O Pseudomonas AED11804 O 94 Pseudomonas putida F1 putida F1

95, alanine racemase 1.26E-O8 O Pseudomonas AED118O3 O 96 Pseudomonas putida utida GB-1 GB-1 gi 126314851 gb EAZ66O19.1 a. anine racemase Pseudomonas utida GB-1 97, alanine racemase 1.26E-O8 O Pseudomonas T. maritima AED118O3 O 98 Pseudomonas putida D-alanine utida GB-1 GB-1 D-alanine gi 126314851 gb EAZ66O19.1 ligase. a. anine racemase Pseudomonas putida GB-1

99, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED118O3 O 1 OO Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

101, alanine racemase 158O 2. OOE-58 Escherichia Prokaryotic ABU45 O892. OOE-58 1 O2 2, catabolic 1412 coli essential Escherichia coli O157:H7 gene O157:H7 EDL933 3474. O. EDL933. 103, aspartate 1452 8. OOE-29 Pyrococcus Thermococcus ADN462O72. OOE-25 104 accelas 6 1575 abyssi kodakaraensis Pyrococcus KOD1 abyssi. protein sequence SeqID4. US 8,541,220 B2 69 70 TABLE 3 Continued 105, proline racemase 1.24E-O81. OOE-15 O Microscilla Bacterial ADS22995 1. OOE-128 106 Microscilla marina marina polypeptide ATCC 23134) ATCC E10001. gi 123984 O81 gb EAY24454.1 231.34 proline racemase Microscilla marina ATCC 23134)

107, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 108 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

109, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-129 11O Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

111, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 112 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

113, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 114 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

115, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 116 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

117, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 118 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

119, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 12O Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

121, alanine racemase 1.49E-081. OOE-13 6 Pseudomonas T. maritima AED118O31 OOE-137 122 Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

123, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-127 124 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide US 8,541,220 B2 71 72 TABLE 3 - continued 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

125, alanine racemase 1.26E-O81. OOE-155 Pseudomonas Empedobacter AED105811. OOE-159 126 Pseudomonas putida brevis putida GB-1 GB-1 mature gi 126314851 gb EAZ66O19.1 peptide alanine racemase synthesizing Pseudomonas enzyme putida GB-1 SEO ID NO: 3.

127, glutamate 2738 08133. OOE-26 Bradyrhizobium Photorhabdus ABM6863 ff. OOE-18 128 accelas 6 iaponicum luminescens Bradyrhizobium USDA protein iaponicum USDA 11O sequence 110 59. 129, proline racemase, 1, 19E-081. OOE-103 Stappia Prokaryotic ABU21813 1. OOE-101 13 O putative Stappia aggregata essential aggregata IAM IAM gene 12614 1261.4 3474. O. gi 11843594 Ogb EAV42584.1 proline racemase, putative Stappia aggregata IAM 12614 131, putative proline 1. O9E-085. OOE-75 Myxococcus M. Xanthus ABM96 6371. OOE-75 132 accelas 6 Xanthus protein Myxococcus DK 1622 sequence, Xanthus DK 1622 seq id 9726.

133, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 134 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

135, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-129 136 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

137, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-128 138 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

139, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 14 O Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

141, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 142 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3. US 8,541,220 B2 73 74 TABLE 3 - continued

143, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 144 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

145, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 146 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

147, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 148 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

149, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 150 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

151, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 152 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

153, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 154 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

155, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-133 156 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

157, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 158 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

159, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 16 O Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing US 8,541,220 B2 75 76 TABLE 3 - continued

7966 enzyme SEO ID NO: 3.

161, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 162 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

163, alanine racemase 1.49E-081. OOE-153 Pseudomonas Empedobacter AED10581. O 164 Pseudomonas putida F1 brevis putida F1 mature peptide synthesizing enzyme SEO ID NO: 3.

165, alanine racemase 1.49E-O81. OOE-153 Pseudomonas Empedobacter AED10581. O 166 Pseudomonas putida F1 brevis putida F1 mature peptide synthesizing enzyme SEO ID NO: 3.

167, proline racemase 887123941. OOE-69 Flavobacteriales Bacterial ADS22995 2. OOE-57 168 Flavobacteriales bacterium polypeptide bacterium HTCC2 17 O E10001. HTCC2170) gi 88708932 gb EARO1166. 1 proline racemase Flavobacteriales bacterium HTCC2170) 169, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 17O Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

171, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 172 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

173, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-129 174 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

175, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 176 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

177, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 178 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature US 8,541,220 B2 77 78 TABLE 3 - continued hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

179, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 18O Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

181, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 182 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

183, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 184 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

185, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-129 186 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

187, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 188 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

189, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 190 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

191, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 192 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

193, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 194 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3. US 8,541,220 B2 79 80 TABLE 3 - continued

195, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 196 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

197, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 198 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

199, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 2 OO Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

201, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-129 2O2 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

2O3, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 2O4. Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

2O5, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 2O6 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-133 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

209, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 210 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

211, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 212 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing US 8,541,220 B2 81 82 TABLE 3 - continued

7966 enzyme SEO ID NO: 3.

213, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-133 214 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

215, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 216 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

217, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 218 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

219, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-129 22O Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

221, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-128 222 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

223, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-133 224 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

225, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-130 226 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

227, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 228 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

229, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 23 O Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide US 8,541,220 B2 83 84 TABLE 3 - continued 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

231, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 232 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

233, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-128 234 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

235, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-128 236 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

237, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-128 238 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449) A449 synthesizing enzyme SEO ID NO: 3.

239, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-128 24 O Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

241, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-130 242 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

243, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-129 244 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

245, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-129 246 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

247, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 248 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature US 8,541,220 B2 85 86 TABLE 3 Continued hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

249, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-129 250 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

251, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 252 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

253, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-129 254 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila putida 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

255, hypothetical 13474743 1. OOE-170 Mesorhizobium Propionibacterium ABM37O681. OOE-77 256 protein loti CeS Mesorhizobium predicted loti. ORF encoded polypeptide H300.

257, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-129 258 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

259, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-130 26 O Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

261, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-130 262 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

263, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-128 264 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

265, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-129 266 Aeromonas salmonicida brevis salmonicida subsp. mature US 8,541,220 B2 87 88 TABLE 3 - continued subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

267, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-129 268 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

269, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 27 O Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

271, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 272 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

273, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 274 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

275, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-128 276 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

277, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-133 278 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

279, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 28O Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

281, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 282 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3. US 8,541,220 B2 89 90 TABLE 3 Continued

283, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 284 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

285, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-130 286 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

287, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-129 288 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

289, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-129 290 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

291, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 292 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

293, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-127 294 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

295, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-129 296 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

297, proline racemase 1, 18E-O81. OOE-104 Burkholderia Acinetobacter ADA352281. OOE-105 298 Burkholderia phymatum baumannii phymatum STM815 protein STM815) E19. gi 117982269 gb EAU96656.1 proline racemase Burkholderia phymatum STM815)

299, alanine racemase 1.26E-O81. OOE-17 O Pseudomonas T. maritima AED118O31 OOE-169 3 OO Pseudomonas putida D-alanine putida GB-1 GB-1 D-alanine gi 126314851 gb EAZ66O19.1 ligase. US 8,541,220 B2 91 92 TABLE 3 - continued alanine racemase Pseudomonas putida GB-1

301, alanine racemase 2699 O43 O1. OOE-143 Pseudomonas T. maritima AED118O31 OOE-144 3 O2 Pseudomonas putida D-alanine putida KT244 O KT244. O D-alanine ligase.

hypothetical 94.4142354. OOE-33 Pseudomonas Pseudomonas ABO821.55 4 OOE-33 protein aeruginosa aeruginosa PaerP 010O3.954 PAf polypeptide Pseudomonas E3. aeruginosa PA 7

AGR L 3 O51p 158916.411. OOE-128 Agrobacterium L. pneumophila AEB415963 OOE-39 Agrobacterium tumefaciens protein tumefaciens. SEO ID NO 3.367.

proline racemase 1.24E--O83. OOE-59 Microscilla Bacterial ADS229.953. OOE-47 Microscilla marina marina polypeptide ATCC 23134) ATCC E10001. gi 123984 O81 gb EAY24454.1 231.34 proline racemase Microscilla marina ATCC 23134)

309, alanine racemase 1.2E-O8 2. OOE-57 Stenotrophomonas Prokaryotic ABU413988. OOE-52 310 Stenotrophomonas maltophilia essential maltophilia R551-3 gene R551-3 3474. O. gi 11982 0021 gb EAX22642. 1 alanine racemase Stenotrophomonas maltophilia R551-3 311, mandellate 839533261. OOE-143 Sulfitobacter Klebsiella ABO 613. Of 2 OOE-71 312 racemase/muconate so. pneumonia lactonizing NAS polypeptide enzyme family 14.1 seqid 7178. protein Sulfitobacter sp. NAS-14. 1 gi 83842294 gb EAP81462.1 mandellate racemase/muconate lactonizing enzyme family protein Sulfitobacter sp. NAS-14. 1 313, proline racemase 134733941. OOE-120 Mesorhizobium Bacterial ADS22995 1. OOE-120 314 Mesorhizobium loti polypeptide loti. E10001.

315, proline racemase 887123941. OOE-106 Flavobacteriales Bacterial ADS22995 1. OOE-72 316 Flavobacteriales bacterium polypeptide bacterium HTCC2 17 O E10001. HTCC2170) gi 88708932 gb EARO1166. 1 proline racemase Flavobacteriales bacterium HTCC2170) 317, Mandellate 887125961. OOE-110 Flavobacteriales Bacteroides AEX286 OO 5 OOE-34 3.18 racemase/muconate bacterium fragilis lactonizing HTCC2 17 O strain enzyme 14 O 62 Flavobacteriales protein, bacterium SEQ: 5227. HTCC2170) gi 88 709134 gb EARO1368. 1 Mandellate racemase/muconate lactonizing enzyme US 8,541,220 B2 93 94 TABLE 3 - Continued Flavobacteriales bacterium HTCC2170) 319, COG3938 : Proline 8432.19521. OOE-60 Pseudomonas Pseudomonas ABO821.55 4. OOE-61 32O accelas 6 aeruginosa aeruginosa Pseudomonas C3719 polypeptide aeruginosa E3. C3719) gi843282O4 ref ZP OO976211.1 COG3938: Proline accelas 6 Pseudomonas aeruginosa 2.192 gi 1071 OO 719 ref ZP O1364.637.1 hypothetical protein PaerPA 01001746 Pseudomonas aeruginosa PACS2 gi 12616632 321, aspartate 1452.15752. OOE-28 Pyrococcus Thermococcus ADN462O77. OOE-25 322 accelas 6 abyssi kodakaraensis Pyrococcus KOD1 abyssi. protein sequence SeqID4.

323, proline racemase, 912.173611. OOE-152 Psychroflexus Bacterial ADS22995 1. OOE-110 324 putative torquis polypeptide Psychiroflexus ATCC E10001. torquis ATCC 7 OOfss 700755) gie 11844 69gb EAS 70852.1 proline racemase, putative Psychiroflexus torquis ATCC 700755)

325, proline racemase 1.24E-O81. OOE-145 Microscilla Bacterial ADS22995 1. OOE-126 326 Microscilla marina marina polypeptide ATCC 23134) ATCC E10001. gi 123984 O81 gb EAY24454.1 231.34 proline racemase Microscilla marina ATCC 23134)

327, proline racemase 1.24E-O81. OOE-147 Microscilla Bacterial ADS22995 1. OOE-132 328 Microscilla marina marina polypeptide ATCC 23134) ATCC E10001. gi 123984 O81 gb EAY24454.1 231.34 proline racemase Microscilla marina ATCC 23134) 329, putative proline 1. O9E-081. OOE-101 Myxococcus M. Xanthus ABM96 6371. OOE-101 330 accelas 6 Xanthus protein Myxococcus DK 1622 sequence, Xanthus DK 1622 seq id 9726.

331, AGR L 3 O51p 15891.6417. OOE-44 Agrobacterium Bacterial ADFOf 948 S. OOE-21 332 Agrobacterium tumefaciens polypeptide tumefaciens. E19.

333, putative alanine 1.16E-O89. OOE-97 Rhizobium Bacterial ADFOf 948 6. OOE-29 334 accelas 6 leguminosarum polypeptide Rhizobium bv. viciae E19. leguminosarum 3841 bv. viciae 3841 335, alanine racemase 8359 O9905. OOE-78 Moorella Prokaryotic ABU24721 1. 336 Moorella thermoacetica essential thermoacetica ATCC gene ATCC 39073) 39073 3474. O. US 8,541,220 B2 95 96 TABLE 3 Continued

337, alanine racemase 835909 903. OOE-77 Moorella Prokaryotic ABU24721 1 OOE-60 338 Moorella thermoacetica essential thermoacetica ATCC gene ATCC 39073) 39073 3474. O.

339, Alanine racemase 671554691. OOE-115 Azotobacter Prokaryotic ABU3979 5 1. OOE-115 34 O Azotobacter vinelandii essential vinelandii AvOP) AWOP gene gi 6708727 Ogb|EAMO6737.1 3474. O. Alanine racemase Azotobacter vinelandii AvOP) 341, mandellate 1. O3E-O82. OOE-99 Sphingopyxis Klebsiella ABO 613. Of 1 OOE-45 342 racemase/muconate alaskens is pneumoniae lactonizing RB2256 polypeptide enzyme seqid 7178. Sphingopyxis alaskensis RB2256 343, putative alanine 1.16E-O81. OOE-127 Rhizobium Pseudomonas ABO84274 8. OOE-42 344 accelas 6 leguminosarum aeruginosa Rhizobium bv. viciae polypeptide leguminosarum 3841 E3. bv. viciae 3841 345, AGR L 3 O51p 158916 412 OOE-79 Agrobacterium Photorhabdus ABM691141. OOE-27 346 Agrobacterium tumefaciens luminescens tumefaciens. protein sequence 59.

347, putative alanine 1.16E-O81. OOE-114 Rhizobium Prokaryotic ABU413981. OOE-36 348 accelas 6 leguminosarum essential Rhizobium by. viciae gene leguminosarum 3841 3474. O. bv. viciae 3841

349, Mandellate 1.49E-082. OOE-87 Methyliobacterium Klebsiella ABO 613. Of 1 OOE-63 350 racemase/muconate sp. 4- 46 pneumoniae lactonizing polypeptide enzyme; C seqid 7178. terminal domain protein Methyliobacterium sp. 4- 4 6

351, Mandellate 1.49E-083. OOE-93 Sphingomonas Klebsiella ABO 613. Of 3 OOE-48 352 racemase/muconate Wittichii pneumoniae lactonizing RW1 polypeptide enzyme; C seqid 7178. terminal domain protein Sphingomonas wittichii RW1

353, putative proline 91.77922.21 OOE-38 Burkholderia Prokaryotic ABU21813 3 OOE-39 3.54 accelas 6 XeoWOS essential Burkholderia LB4 OO gene Xe(VOS 3474. O. LB4 OO

355 alanine racemase 1.49E-082. OOE-67 Lentisphaera Prokaryotic ABU23921 1 OOE-56 356, Lentisphaera ae OS essential ae OS HTCC2 155 gene HTCC2155) 3474. O.

357, alanine racemase 1, 18E-O81. OOE-107 Roseiflexus Prokaryotic ABU2392.1 5 OOE-75 358 Roseiflexus castenholzii essential castenholzii DSM DSM gene 13941 13941 3474. O. gi 1180.10932 gb EAV2.4951. 1 alanine racemase Roseiflexus castenholzii DSM 13941 US 8,541,220 B2 97 98 TABLE 3 Continued

359, alanine racemase 1, 18E-O81. OOE-107 Roseiflexus Prokaryotic ABU23921.1. OOE-75 360 Roseiflexus castenholzii essential castenholzii DSM DSM gene 13941 13941 3474. O. gi 1180.10932 gb EAV2.4951. 1 alanine racemase Roseiflexus castenholzii DSM 13941 361, alanine racemase 1, 18E-O81. OOE-107 Roseiflexus Prokaryotic ABU23921. 5. OOE-75 362 Roseiflexus castenholzii essential castenholzii DSM DSM gene 13941 13941 3474. O. gi 1180.10932 gb EAV2.4951. 1 alanine racemase Roseiflexus castenholzii DSM 13941

363, alanine racemase 1, 18E-O81. OOE-107 Roseiflexus Prokaryotic ABU2392.13. OOE-75 364 Roseiflexus castenholzii essential castenholzii DSM DSM gene 13941 13941 3474. O. gi 1180.10932 gb EAV2.4951. 1 alanine racemase Roseiflexus castenholzii DSM 13941

365, alanine racemase 1, 18E-O81. OOE-107 Roseiflexus Prokaryotic ABU2392.13. OOE-76 366 Roseiflexus castenholzii essential castenholzii DSM DSM gene 13941 13941 3474. O. gi 1180.10932 gb EAV2.4951. 1 alanine racemase Roseiflexus castenholzii DSM 13941 367, alanine racemase 1. 46E--O81. OOE-168 Pseudomonas Prokaryotic ABU413981. OOE-160 3.68 Pseudomonas mendocina essential mendocina ymp ymp gene 3474. O.

369, diaminopimelate 172323333. OOE-78 NoStoc Bacterial ADS298489. OOE-79 37O epimerase Nostoc sp. PCC polypeptide sp. PCC 712O). 712 O E10001.

371, diaminopimelate 8585F916.2 OOE-76 Syntrophus Bacterial ADN174895. OOE-60 372 epimerase aciditrophicus polypeptide Syntrophus SB E10001. aciditrophicus SB

373, diaminopimelate 172323332. OOE-71 NoStoc Bacterial ADS29848 7. OOE-72 374 epimerase Nostoc sp. PCC polypeptide sp. PCC 712O). 712 O E10001.

375, Diaminopimelate 1.26E-O85. OOE-33 Clostridium Bacterial ADN271692. OOE-31 376 epimerase thermocellum polypeptide Clostridium ATCC E10001. thermocellum 274 OS ATCC 27405 377, 1, 18E-O82. OOE-97 Chloroflexus Prokaryotic ABU24769. 6. 378 acetylglucosamine aggregains essential 2-epimerase DSM gene Chloroflexus 94.85 3474. O. aggregains DSM 9.485) gi 117997 29 Ogb EAV11478.1

acetylglucosamine 2-epimerase Chloroflexus aggregains DSM 9.485) US 8,541,220 B2 99 100 TABLE 3 - Continued

379, NimrA family 1.34E-O82. OOE-88 Burkholderia Bacterial ADS227792. OOE-84 38O protein vietnamiensis polypeptide Burkholderia G4 E10001. vietnamiensis G4

381, hypothetical 1.16E-O82. OOE-87 Rhizobium Bacterial ADS227791. OOE-83 382 protein RL1205 leguminosarum polypeptide Rhizobium by. viciae E10001. leguminosarum 3841 by. viciae 3841

383, similar to 375226681. OOE-93 Gloeobacter L. pneumophila AEB372824. OOE-48 384 chloromuconate violaceus protein cycloisomerase PCC SEO ID NO Gloeobacter 7421 3.367. violaceus PCC 7421 Genesed SEQ Genes eq DNA Predicted Query Query Subject Subject 3. 3. ID DNA Accession EC DNA Protein DNA Protein ID ID NO: Description Code Evalue Number Length Length Length Length Protein DNA

Drosophila ABLO3829 O. 48 2.73. 687 228 687 228 1 OO 1OO melanogaster polypeptide SEQ ID NO 124465.

Aquifex ABL1496O7 2. OOE-OF 5.1.1.1 101.7 338 O 338 1 OO pyrophilus heat resistant alanine accease encoding DNA.

Human AAK8 O65O O. O32 2.73. 72 O 239 O 239 8O immune/haematopoietic antigen genomic sequence SEQ ID NO: 41436.

EST clone AAW88076 O. O48 1032 343 O 343 89 EP219.

Pseudomonas ABDO 87.32 1. OOE-Os 51.1.1 1149 382 O 391 78 aeruginosa polypeptide E3.

Pseudomonas ABDO 63 78 O. O.13 5.1.1.1 1122 373 O 388 58 aeruginosa polypeptide E3.

Pseudomonas ABDO 87.32 1. OOE-08 5.1.1.1 1065 3.54 O 353 64 aeruginosa polypeptide E3.

Klebsiella ACHS 9054 OOO2 5.1.1.13 7 O2 233 O 231 74 pneumoniae polypeptide seqid 7178.

17, Human AEB85185 OOO9 5.1.1.3 8. Of 268 O 269 72 18 phosphodiesterase 4D amino acid sequence N1 SEQ ID NO : 7. US 8,541,220 B2 101 102 TABLE 3 - continued

19, M. Xanthus ACL64794. O. O37 5.1.1.3 822 273 O 272 53 2O protein sequence, seq id 9726.

21, Bacterial ADS61806 1. OOE-04 5.2.1.1 768 255 O 265 41 22 polypeptide E10 OO1.

23, Enterobacter AEH55.699 O 5.1.1.1 108 O 359 O 359 95 24 cloacae protein amino acid sequence - SEQ ID 5666.

25, Enterobacter AEH55.699 O 5.1.1.1 108 O 359 O 359 95 26 cloacae protein amino acid sequence - SEQ ID 5666.

27, Prokaryotic ACA27845 OOO2 2.73. 651 216 O 216 1 OO 28 essential gene 3474. O.

29, Pseudomonas ABD15676 1. OOE-08 s 11.4 1032 343 O 342 64 3 O aeruginosa polypeptide E3.

31, Pseudomonas ABD15666 9. OOE-16 s 11.4 1011 336 O 31 O 58 32 aeruginosa polypeptide E3.

33, Human AEHS 853 O O. O.13 5.1.1.1 1116 3.71 O 385 61 34 CaCe associated cDNA SEQ ID NO 9.

35, N. meningitidis AAA81486 3.2 5.1.1. 1101 366 O 368 33 36 partial DNA sequence gnm 64 O SEQ ID NO: 64 O.

37, Pseudomonas ABD12586 O. 32 5.1.1.1. 489 162 O 369 51 38 aeruginosa polypeptide E3.

39, Prokaryotic ACA26332 8 OOE-23 5.1.1. 4 372 123 96.O 3.18 4 O essential gene 3474. O.

41, Pseudomonas ADB99538 O 5.1.1.1 123 O 4O9 O 4O9 97 42 putida accease peptide, SEQ ID 5.

43, Pseudomonas ADB99538 O 5.1.1.1 123 O 4O9 O 4O9 96 44 putida accease peptide, SEQ ID 5. US 8,541,220 B2 103 104 TABLE 3 - continued

45, Pseudomonas ADB99538 5.1.1.1 123 O 97 46 putida accease peptide, SEQ ID 5.

47, Pseudomonas ADB99538 123 O 97 48 putida accease peptide, SEQ ID 5.

49, Pseudomonas ADB99538 123 O 96 SO putida accease peptide, SEQ ID 5.

51, Pseudomonas ADB995.37 1. OOE-120 5.1.1.1 123 O 77 52 putida accease peptide, SEQ ID 5.

53, Pseudomonas ADB995.37 1. OOE-124 5.1.1.1 123 O 77 54 putida accease peptide, SEQ ID 5.

55, Pseudomonas ADB995.37 1. OOE-124 5.1.1.1 123 O 77 56 putida accease peptide, SEQ ID 5.

57, Pseudomonas ADB99538 123 O 96 58 putida accease peptide, SEQ ID 5.

59, Pseudomonas ADB99538 123 O 95 6 O putida accease peptide, SEQ ID 5.

61, Human 1614 s37 3.54 19 62 prostate expression marker cDNA

63, Pseudomonas ADB995.37 123 O 98 64 putida accease peptide, SEQ ID 5.

65, Pseudomonas ADB995.37 123 O 97 66 putida accease peptide, SEQ ID 5.

67, Pseudomonas ADB99538 123 O 90 68 putida accease peptide, SEQ ID 5.

69, Pseudomonas ADB995.37 123 O 95 70 putida accease peptide, SEQ ID 5. US 8,541,220 B2 105 106 TABLE 3 - continued

71, Pseudomonas ADB995.37 5.1.1.1 123 O 96 72 putida accease peptide, SEQ ID 5.

73, Pseudomonas ADB995.37 123 O 95 74 putida accease peptide, SEQ ID 5.

75, Pseudomonas ADB995.37 123 O 95 76 putida accease peptide, SEQ ID 5.

77, Pseudomonas ADB99538 123 O 95 78 putida accease peptide, SEQ ID 5.

79, Pseudomonas ADB99538 123 O 95 8O putida accease peptide, SEQ ID 5.

81, Pseudomonas ADB99538 123 O 96 82 putida accease peptide, SEQ ID 5.

83, Pseudomonas ADB99538 1230 409 409 94 84 putida accease peptide, SEQ ID 5.

85, Pseudomonas ADB995.37 123 O 96 86 putida accease peptide, SEQ ID 5.

87, Pseudomonas ADB99538 123 O 96 88 putida accease peptide, SEQ ID 5.

89, Pseudomonas ADB995.37 123 O 96 9 O putida accease peptide, SEQ ID 5.

91, Pseudomonas ADB99538 123 O 96 92 putida accease peptide, SEQ ID 5.

93, Pseudomonas ADB99538 123 O 96 94 putida accease peptide, SEQ ID 5.

95, Pseudomonas ADB995.37 123 O 95 96 putida accease peptide, SEQ ID 5. US 8,541,220 B2 107 108 TABLE 3 - continued

97, Pseudomonas ADB995.37 O 5.1.1.1 123 O 4O9 O 4O9 98 putida accease peptide, SEQ ID 5.

99, Pseudomonas ADB995.37 O 5.1.1.1 123 O 4O9 O 4O9 1 OO putida accease peptide, SEQ ID 5.

101, Enterobacter AEH531 O3 5. OOE-27 5.1.1.1 384 127 1071 356 1 O2 cloacae protein amino acid sequence - SEQ ID 5666.

103, Prokaryotic ACA27539 O. 13 5.1.1.13 714. 237 687 228 104 essential gene 3474. O.

105, Bovine AEN69487 2.9 5.1.1 .. 4 1OO2 333 O 333 106 ABCG2 related PCR primer E31.

107, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 108 putida accease peptide, SEQ ID 5.

109, Pseudomonas ADB99538 6. OOE-Os 51.1.1 1227 408 O 408 11O putida accease peptide, SEQ ID 5.

111, Pseudomonas ADB99538 2. OOE-11. 5.1.1.1 1227 408 O 408 112 putida accease peptide, SEQ ID 5.

113, Pseudomonas ADB99538 2. OOE-14 5.1.1.1 1224 4. Of O 408 114 putida accease peptide, SEQ ID 5.

115, Pseudomonas ADB99538 2. OOE-08 5.1.1.1 1227 408 O 408 116 putida accease peptide, SEQ ID 5.

117, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 118 putida accease peptide, SEQ ID 5.

119, Pseudomonas ADB99538 1. OOE-12 s.1.1.1 1227 408 O 408 12O putida accease peptide, SEQ ID 5. US 8,541,220 B2 109 110 TABLE 3 - continued

121, Pseudomonas ADB99538 2. OOE-26 5.1.1.1 1086 361 1227 4O9 122 putida accease peptide, SEQ ID 5.

123, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1086 361 O 408 88 124 putida accease peptide, SEQ ID 5.

125, Pseudomonas ADB99538 4 OOE-95 5.1.1.1 1086 361 1227 386 126 putida accease peptide, SEQ ID 5.

27, Prokaryotic ACA37866 2.2 5.1.1.3 261 86 O 265 63 28 essential gene 3474. O.

29, Prokaryotic ACA26332 5. OOE-11. 5.1.1. 4 95.7 3.18 O 31 O 56 3O essential gene 3474. O.

31, Prokaryotic ACA26332 1. OOE-18, 5.1.1. 4 1074 357 96.O 311 32 essential gene 3474. O.

33, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 99 34 putida accease peptide, SEQ ID 5.

135, Pseudomonas ADB99538 6. OOE-Os 51.1.1 1227 408 O 408 95 136 putida accease peptide, SEQ ID 5.

137, Pseudomonas ADB99538 OOO4 5.1.1.1 1221 4O6 O 408 95 138 putida accease peptide, SEQ ID 5.

139, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1224 4. Of O 408 99 14 O putida accease peptide, SEQ ID 5.

141, Pseudomonas ADB99538 1. OOE-15 5.1.1.1 1227 408 O 408 89 142 putida accease peptide, SEQ ID 5.

143, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 1 OO 144 putida accease peptide, SEQ ID 5.

145, Pseudomonas ADB99538 2. OOE-11. 5.1.1.1 1224 4. Of O 408 99 146 putida accease peptide, SEQ ID 5. US 8,541,220 B2 111 112 TABLE 3 - continued

147, Pseudomonas ADB99538 3 OOE-19 5.1.1.1 1224 4. Of O 408 148 putida accease peptide, SEQ ID 5.

149, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 150 putida accease peptide, SEQ ID 5.

151, Pseudomonas ADB99538 3 OOE-19 5.1.1.1 1227 408 O 408 152 putida accease peptide, SEQ ID 5.

153, Pseudomonas ADB99538 3 OOE-19 5.1.1.1 1224 4. Of O 408 154 putida accease peptide, SEQ ID 5.

155, Pseudomonas ADB99538 2. OOE-14 5.1.1.1 1227 408 O 408 156 putida accease peptide, SEQ ID 5.

157, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 158 putida accease peptide, SEQ ID 5.

159, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 16 O putida accease peptide, SEQ ID 5.

161, Pseudomonas ADB99538 3 OOE-19 5.1.1.1 1227 408 O 408 162 putida accease peptide, SEQ ID 5.

163, Pseudomonas ADB99538 1. OOE-64 5.1.1.1 1086 361 1227 386 164 putida accease peptide, SEQ ID 5.

165, Pseudomonas ADB99538 2. OOE-91 5.1.1.1 1083 360 1227 386 166 putida accease peptide, SEQ ID 5.

167, Bacterial ADS6 OO 41 O. O. Of 5.1.1 .. 4 657 218 O 335 168 polypeptide E10 OO1.

169, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 17O putida accease peptide, SEQ ID 5.

171, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 172 putida accease peptide, SEQ ID 5.

173, Pseudomonas ADB99538 6. OOE-Os 51.1.1 1224 4. Of O 408 174 putida accease US 8,541,220 B2 113 114 TABLE 3 - continued peptide, SEQ ID 5.

175, Pseudomonas ADB99538 2. OOE-14 5.1.1.1 1227 408 O 408 89 176 putida accease peptide, SEQ ID 5.

177, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 99 178 putida accease peptide, SEQ ID 5.

179, Pseudomonas ADB99538 3 OOE-10 5.1.1.1 1227 408 O 408 99 18O putida accease peptide, SEQ ID 5.

181, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 99 182 putida accease peptide, SEQ ID 5.

183, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 1 OO 184 putida accease peptide, SEQ ID 5.

185, Pseudomonas ADB99538 1. OOE-15 5.1.1.1 1227 408 O 408 89 186 putida accease peptide, SEQ ID 5.

187, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 99 188 putida accease peptide, SEQ ID 5.

189, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 99 190 putida accease peptide, SEQ ID 5.

191, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 91 192 putida accease peptide, SEQ ID 5.

193, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 92 194 putida accease peptide, SEQ ID 5.

195, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 92 196 putida accease peptide, SEQ ID 5.

197, Pseudomonas ADB99538 2. OOE-14 5.1.1.1 1227 408 O 408 91 198 putida accease peptide, SEQ ID 5.

199, Pseudomonas ADB99538 1. OOE-15 5.1.1.1 1227 408 O 408 90 2 OO putida accease peptide, SEQ ID 5. US 8,541,220 B2 115 116 TABLE 3 - continued

201, Pseudomonas ADB99538 1. OOE-15 5.1.1.1 1227 408 O 408 2O2 putida accease peptide, SEQ ID 5.

2O3, Pseudomonas ADB99538 4 OOE-18, 5.1.1.1 1227 408 O 408 2O4. putida accease peptide, SEQ ID 5.

2O5, Pseudomonas ADB99538 1. OOE-15 5.1.1.1 1227 408 O 408 2O6 putida accease peptide, SEQ ID 5.

2O7 Pseudomonas ADB99538 3 OOE-16 5.1.1.1 1224 4. Of O 408 2O8 putida accease peptide, SEQ ID 5.

209, Pseudomonas ADB99538 1. OOE-12 s.1.1.1 1227 408 O 408 210 putida accease peptide, SEQ ID 5.

211, Pseudomonas ADB99538 2. OOE-14 5.1.1.1 1224 4. Of O 408 212 putida accease peptide, SEQ ID 5.

213, Pseudomonas ADB99538 1. OOE-15 5.1.1.1 1224 4. Of O 408 214 putida accease peptide, SEQ ID 5.

215, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 216 putida accease peptide, SEQ ID 5.

217, Pseudomonas ADB99538 7. OOE-14 5.1.1.1 1224 4. Of O 408 218 putida accease peptide, SEQ ID 5.

219, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 22O putida accease peptide, SEQ ID 5.

221, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1224 4. Of O 408 222 putida accease peptide, SEQ ID 5.

223, Pseudomonas ADB99538 2. OOE-14 5.1.1.1 1224 4. Of O 408 224 putida accease peptide, SEQ ID 5.

225, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 226 putida accease peptide, SEQ ID 5. US 8,541,220 B2 117 118 TABLE 3 - continued

227, Pseudomonas ADB99538 2. OOE-14 5.1.1.1 1227 408 O 408 228 putida accease peptide, SEQ ID 5.

229, Pseudomonas ADB99538 3 OOE-13 5.1.1.1 1227 408 O 408 23 O putida accease peptide, SEQ ID 5.

231, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 232 putida accease peptide, SEQ ID 5.

233, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 234 putida accease peptide, SEQ ID 5.

235, Pseudomonas ADB99538 6. OOE-Os 51.1.1 1224 4. Of O 408 236 putida accease peptide, SEQ ID 5.

237, Pseudomonas ADB99538 6. OOE-Os 51.1.1 1227 408 O 408 238 putida accease peptide, SEQ ID 5.

239, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1224 4. Of O 408 24 O putida accease peptide, SEQ ID 5.

241, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 242 putida accease peptide, SEQ ID 5.

243, Pseudomonas ADB99538 4 OOE-06 5.1.1.1 1227 408 O 408 244 putida accease peptide, SEQ ID 5.

245, Pseudomonas ADB99538 4 OOE-06 5.1.1.1 1227 408 O 408 246 putida accease peptide, SEQ ID 5.

247, Pseudomonas ADB99538 4 OOE-06 5.1.1.1 1227 408 O 408 248 putida accease peptide, SEQ ID 5.

249, Pseudomonas ADB99538 4 OOE-06 5.1.1.1 1227 408 O 408 250 putida accease peptide, SEQ ID 5.

251, Pseudomonas ADB99538 4 OOE-06 5.1.1.1 1227 408 O 408 252 putida accease peptide, SEQ ID 5. US 8,541,220 B2 119 120 TABLE 3 - continued

253, Pseudomonas ADB99538 4 OOE-06 5.1.1.1 1224 4. Of O 408 254 putida accease peptide, SEQ ID 5.

255, Plant ADT17374 O2 5.1.1.1 1086 361 1827 608 256 polypeptide, SEQ ID 5546.

257, Pseudomonas ADB99538 2. OOE-08 5.1.1.1 1227 408 O 408 258 putida accease peptide, SEQ ID 5.

259, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 26 O putida accease peptide, SEQ ID 5.

261, Pseudomonas ADB99538 2. OOE-08 5.1.1.1 1227 408 O 408 262 putida accease peptide, SEQ ID 5.

263, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 264 putida accease peptide, SEQ ID 5.

265, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 266 putida accease peptide, SEQ ID 5.

267, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 268 putida accease peptide, SEQ ID 5.

269, Pseudomonas ADB99538 1. OOE-12 s.1.1.1 1227 408 O 408 27 O putida accease peptide, SEQ ID 5.

271, Pseudomonas ADB99538 3 OOE-13 5.1.1.1 123 O 4O9 O 408 272 putida accease peptide, SEQ ID 5.

273, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 274 putida accease peptide, SEQ ID 5.

275, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 276 putida accease peptide, SEQ ID 5.

277, Pseudomonas ADB99538 2. OOE-14 5.1.1.1 1227 408 O 408 278 putida accease peptide, SEQ ID 5. US 8,541,220 B2 121 122 TABLE 3 - continued

279, Pseudomonas ADB99538 1. OOE-15 5.1.1.1 1227 408 O 408 28O putida accease peptide, SEQ ID 5.

281, Pseudomonas ADB99538 1. OOE-18, 5.1.1.1 1227 408 O 408 282 putida accease peptide, SEQ ID 5.

283, Pseudomonas ADB99538 1. OOE-18, 5.1.1.1 1227 408 O 408 284 putida accease peptide, SEQ ID 5.

285, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 286 putida accease peptide, SEQ ID 5.

287, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 288 putida accease peptide, SEQ ID 5.

289, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 290 putida accease peptide, SEO ID 5.

291, Pseudomonas ADB99538 2. OOE-14 5.1.1.1 1227 408 O 408 292 putida accease peptide, SEQ ID 5.

293, Pseudomonas ADB99538 6. OOE-11. 5.1.1.1 1227 408 O 408 294 putida accease peptide, SEQ ID 5.

295, Pseudomonas ADB99538 4 OOE-06 5.1.1.1 1227 408 O 408 296 putida accease peptide, SEQ ID 5.

297, Prokaryotic ACA1965O 9 OOE-22 s.11 4 96.O 319 945 331 298 essential gene 3474. O.

299, Pseudomonas ADB99538 5 OOE-95 5.1.1.1 123 O 4O9 O 4O9 3 OO putida accease peptide, SEQ ID 5.

301, Pseudomonas ADB99538 5 OOE-27 5.1.1.1 1239 412 1227 4O9 3 O2 putida accease peptide, SEQ ID 5.

3O3, Prokaryotic ACA44058 7. OOE-14 5.1.1. 4 375 124 O 314 3O4. essential gene 3474. O. US 8,541,220 B2 123 124 TABLE 3 - continued

3 O5, Prokaryotic ACA27267 O 21 5.1.1.1 1125 374 1167 388 3 O6 essential gene 3474. O.

3 O7, Bacterial ADS6 OO 41 2 OOE-Os 51.1 .. 4 429 142 O 333 3O8 polypeptide E10 OO1.

309, Prokaryotic ACA436 65 3. OOE-13 5.1.1.1 408 135 O 355 310 essential gene 3474. O.

311, Nowel mar AAS46252 O. 67 5.1.2.2 939 312 O 321 312 regulated protein (NIMR) E29.

313, C. botulinum AEF996. Of O. 65 5.1.1 .. 4 909 3O2 1OO2 333 314 active BoNT/A modified open reading frame, SEQ ID No : 7.

315, Haemophilus ADTO5504 O. O3 5.1.1 .. 4 684 227 O 335 316 influenzae (NTHii) protein - SEQ ID 618.

317, Prokaryotic ACA234 65 2.9 5.5.1.1 1032 343 O 348 3.18 essential gene 3474. O.

319, Pseudomonas ABD15666 3. OOE-Os 51.1 .. 4 636 211 486 339 32O aeruginosa polypeptide E3.

321, Breast ACN8936O O. 49 5.1.1.13 699 232 687 228 322 CaCe related marker, seq id 2.

323, Bacterial ADS6 OO 41 O. 16 5.1.1 .. 4 885 294 O 336 324 polypeptide E10 OO1.

325, Bacterial ADS6 OO 41 5. OOE-08 s 11.4 1005 334 O 333 326 polypeptide E10 OO1.

327, Bacterial ADS6 OO 41 O. O.12 5.1.1 .. 4 1OO2 333 O 333 328 polypeptide E10 OO1.

329, Prokaryotic ACA23259 1 OOE-17 5.1.1. 4 95.7 3.18 O 311 330 essential gene 3474. O.

331, Mycobacterium AAI996.82 11 5.1.1.1 42O 139 1167 388 332 tuberculosis strain

genome SEQ ID NO 2. US 8,541,220 B2 125 126 TABLE 3 - continued

333, Plant full ADX51636 67 5.1.1.1 939 312 377 58 334 length insert polynucleotide seqid 498 O.

335, Enterobacter AEH5426 O 5.1.1.1 1143 373 41 336 cloacae protein amino acid sequence - SEQ ID 5666.

337, Bacillus AAD29866 8. OOE-04 5.1.1.1 11. Of 368 373 44 338 licheniformis ara.A. gene fragment amplifying PCR primer 1.

339, Prokaryotic ACA23293 OOE-05 106.8 355 418 60 34 O essential gene 3474. O.

341, Geranylgeranyl ADMS 8687 990 329 335 st 342 pyrophosphate synthase polypeptide 7.

343, Streptomyces ADO51695 83 1134 377 377 62 344 cattleya NRRL 805.7 or fy protein.

345, Prokaryotic ACA25617 777 258 1167 388 st 346 essential gene 3474. O.

347, Plant full ADX51636 ... 81 1113 37 O 377 58 348 length insert polynucleotide seqid 498 O.

349, Prokaryotic ACA426 41 72 993 33 O 326 51 350 essential gene 3474. O.

351, Klebsiella ACHS 4858 OOE-05 1005 334 3.54 52 352 pneumoniae polypeptide seqid 7178.

353, Prokaryotic ACA1965O OOE-22 381 126 945 3.18 3.54 essential gene 3474. O.

355 Prokaryotic ACA38093 OOE-04 1155 384 360 39 356, essential gene 3474. O.

357, Prokaryotic ACA4 O224 88 12O3 4 OO 849 52 358 essential gene 3474. O. US 8,541,220 B2 127 128 TABLE 3 - continued

359, T versicolor AAF2 64 41 O. 88 5.1.1.1 12O3 4 OO O 849 360 pyrF PCR primer SEQ ID 5.

361, T versicolor AAF2 64 41 O. 88 5.1.1.1 12O3 4 OO O 849 362 pyrF PCR primer SEQ ID 5.

363, T versicolor AAF2 64 41 O. 88 5.1.1.1 12O3 4 OO O 849 364 pyrF PCR primer SEQ ID 5.

365, T versicolor AAF2 64 41 O. 88 5.1.1.1 12O3 4 OO O 849 366 pyrF PCR primer SEQ ID 5.

367, Prokaryotic ACA436 65 7. OOE-32 5.1.1.1 1074 357 O 362 3.68 essential gene 3474. O.

369, S. lavendulae ADE1 O236 O. 16 5.1.1.7 861 286 1413 285 37O cit gene mutagenic PCR primer #2.

371, Bacterial ADT4 61.87 2. OOE-06 s. 1.17 813 27 O O 277 372 polypeptide E10 OO1.

373, Enviromental AEH474 13 O. 16 5.1.1.7 873 29 O 9 OO 285 374 isolate hydrolase, SEQ ID NO: 44.

375, Bacterial ADT4224.5 9.2 5.1.1.7 828 27s O 28O 376 polypeptide 1OOO1.

377, Prokaryotic ACA27O 41 6 OOE-08 s. 1.3.14 12 OO 399 O 386 378 essential gene 3474. O.

379, Bacterial ADS59825 3. OOE-06 1. 65.3 879 292 O 287 38O polypeptide 1OOO1

381, Bacterial ADS59825 1. OOE-08 16.53 879 292 O 289 382 polypeptide 1OOO1

383, Nowel ADQ53782 3.1 5.1.2.2 1071 356 O 356 384 canine microarray related DNA sequence SeqID10O21. US 8,541,220 B2 129 130 TABLE 3 - continued Genesed Genesed NR Genes eq Protein Geneseq Gene seq. DNA SEO ID Accession NR NR Protein Accession Protein DNA Accession NO. NR Description Code Evalue Organism Description Code Evalue Description Code 1, hypothetical 15605814 1. OOE-128 Aquifex Prokaryotic ABU25646 3. OOE-47 Drosophila ABLO3829 protein Aquifex aeolicus essential melanogaster aeolicus. gene polypeptide 3474. O. SEO ID NO 1244 65. Genes eq/ Genes eq/ Geneseq/ Geneseq/ Genes eq Predicted Query Query NR NR NR NR SEQ ID DNA EC DNA Protein DNA Protein & ID & ID NO. Evalue Number Length Length Length Length Protein DNA

1, 2 O. 48 2.73 687 228 687 228 1OO 1 OO

Genes eq NR Protein SEQ Acces- Genes eq Acces ID Sion NR Protein Sion NO: NR Description Code Evalue Organism Description Code Evalue

3, alanine racemase 156O 6873. O Aquifex Aquifex ABBO 62961. OOE-147 Aquifex aeolicus. aeolicus pyrophilus heat resistant alanine accelas 6 encoding DNA.

5, hypothetical 298326681. OOE-101 Streptomyces Prokaryotic ABU194995. OOE-37 protein SAV6126 avermitilis essential Streptomyces MA- gene avermitilis MA- 468 O 3474. O. 468O 7, hypothetical 2983 O835 O Streptomyces Propionibacterium ABM543582. OOE-53 protein SAV4292 avermitilis CeS Streptomyces MA- predicted avermitilis MA- 468 O ORF 468O encoded polypeptide 3OO

9, alanine racemase 212231241. OOE-166 Streptomyces Prokaryotic ABU34 223 6 OOE-9 O O Streptomyces coelicolor essential coelicolor A3 (2) A3 (2) gene 3474. O.

1, alanine racemase 867.486271. OOE-106 Rhodopseudomonas Pseudomonas ABO84274. 4. OOE-50 2 Rhodopseudomonas palustris aeruginosa palustris HaA2 polypeptide HaA2 3.

3, alanine racemase 564774.261. OOE-128 Azoarcus Prokaryotic ABU413981. OOE-110 4. Azoarcus sp. sp. EbN1 essential EbN1) gene 3474. O.

5, Aspartate 1.49E-- 084. OOE-93 Marinobacter Klebsiella ABO 655O31 OOE-71 6 accelas 6 algicola pneumoniae Marinobacter DG893 polypeptide algicola DG893 seqid 7178. 7, glutamate 1.11E-- 081. OOE-106 Cytophaga Prokaryotic ABU25.1742. OOE-44 8 accelas 6 hutchinsonii essential Cytophaga ATCC gene hutchinsonii ATCC 334 O6 3474. O. 33406

19, glutamate 39998O141. OOE-74 Geobacter M. Xanthus ABM9 O755 2. OOE-67 2O accelas 6 sulfurreducens protein Geobacter PCA sequence, sulfurreducens seq id PCA) 9726. US 8,541,220 B2 131 132 TABLE 3 Continued

21, Putative 3.359 67.485. OOE-40 Bordeteila Thermococcus ADN4691. O 5 OOE-27 22 decarboxylase parapertus sis kodakaraensis Bordetella 12822 KOD1 parapertus sis protein 12822 sequence SeqID4.

23, alanine racemase Enterobacter Enterobacter 24 Enterobacter sp. so. cloacae 638) 638 protein amino acid sequence - SEO ID 5666.

25, alanine racemase Enterobacter Enterobacter 26 Enterobacter sp. so. cloacae 638) 638 protein amino acid sequence - SEO ID 5666.

27, hypothetical 71083 0671. OOE-121 Candidatus Prokaryotic ABU2429 O2 OOE-31 28 protein Pelagibacter essential SAR11 O3 61 ubique gene Candidatus HTCC1062 3474. O. Pelagibacter ubique HTCC1062)

29, putative proline 1.49E-081. OOE-13 O Brucellaovis Pseudomonas ABO821341. OOE-127 3 O accelas 6 ATCC aeruginosa Brucella ovis 2584 O polypeptide ATCC 2584 Ol E3. 31, proline racemase, 1, 19E-081. OOE-109 Stappia Acinetobacter ADA352281. OOE-105 32 putative Stappia aggregata baumannii aggregata IAM IAM protein 12614 1261.4 E19. gi 11843594 Ogb EAV42584.1 proline racemase, putative Stappia aggregata IAM 12614 33, alanine racemase 1.11E--O81. OOE-124 Mesorhizobium Prokaryotic ABU388293. OOE-46 34 Mesorhizobium sp. BNC1 essential sp. BNC1 gene 3474. O.

35, putative alanine 9 O4184396 OOE-49 Aurantimonas Achromobacter AEH192775. OOE-47 36 accelas 6 so. xylos oxidans Aurantimonas sp. SI85-9A1 DTA SI85-9A1 SEO ID NO gieO3381.11gb EAS51762. 1 6. putative alanine accelas 6 Aurantimonas sp. S185-9A1 37, Alanine racemase 1.45E-081. OOE-38 Magnetospirillium Aquifex ABBO 629 62. OOE-2O 38 Magnetospirillium gryphis wall dense pyrophilus gryphis Waldense MSR-1 heat MSR-1 resistant alanine accelas 6 encoding DNA.

39, putative proline 91.77922.22 OOE-36 Burkholderia Prokaryotic ABU21813 5. OOE-37 4 O accelas 6 XeoWOS essential Burkholderia LB4 OO gene LB4 OO 3474. O.

41, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED118O3 O 42 Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase. US 8,541,220 B2 133 134 TABLE 3 - continued

43, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED118O3 O 44 Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

45, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED118O3 O 46 Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase

47, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED118O3 O 48 Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase

49, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED118O3 O SO Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase

51, alanine racemase 1.26E-O8 O Pseudomonas T. maritima AED118O31 OOE-18O 52 Pseudomonas putida D-alanine putida GB- GB-1 D-alanine gi 126314851 gb EAZ66O19.1 ligase alanine racemase Pseudomonas putida GB

53, alanine racemase 1.26E-O81. OOE-18 O Pseudomonas T. maritima AED118O31 OOE-18O 54 Pseudomonas putida D-alanine putida GB- GB-1 D-alanine gi 126314851 gb EAZ66O19.1 ligase. alanine racemase Pseudomonas putida GB

55, alanine racemase 1.26E-O81. OOE-18 O Pseudomonas T. maritima AED118O31 OOE-179 56 Pseudomonas putida D-alanine putida GB- GB-1 D-alanine gi 126314851 gb EAZ66O19.1 ligase. alanine racemase Pseudomonas putida GB

57, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED11804 O 58 Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

59, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED11804 O 6 O Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

61, alanine racemase 1. 48E+087. OOE-19 Fusobacterium Aquifex ABBO 62961. OOE-12 62 Fusobacterium nucleatum pyrophilus nucleatum subsp. subsp. heat polymorphum polymorphum resistant ATCC 10953 ATCC alanine 10953 accelas 6 encoding DNA.

63, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED118O3 O 64 Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

65, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED118O3 O 66 Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

67, alanine racemase 1.26E-O8 O Pseudomonas T. maritima AED118O3 O 68 Pseudomonas putida D-alanine putida GB-1 GB-1 D-alanine gi 126314851 gb EAZ66O19.1 ligase. alanine racemase Pseudomonas putida GB-1 US 8,541,220 B2 135 136 TABLE 3 - continued

69, alanine racemase 1.26E-O8 O Pseudomonas T. maritima AED118O3 O 70 Pseudomonas putida D-alanine putida GB- GB-1 D-alanine gi 126314851 gb EAZ66O19.1 ligase. alanine racemase Pseudomonas putida GB

71, alanine racemase 1.26E-O8 O Pseudomonas T. maritima AED118O3 O 72 Pseudomonas putida D-alanine putida GB- GB-1 D-alanine gi 126314851 gb EAZ66O19.1 ligase a Lale accela. See Pseudomonas putida GB

73, alanine racemase 1.26E-O8 O Pseudomonas T. maritima AED118O3 O 74 Pseudomonas putida D-alanine putida GB- GB-1 D-alanine gi 126314851 gb EAZ66O19.1 ligase a Lale accela. See Pseudomonas putida GB

75, alanine racemase 1.26E-O8 O Pseudomonas T. maritima AED118O3 O 76 Pseudomonas putida D-alanine putida GB- GB-1 D-alanine gi 126314851 gb EAZ66O19.1 ligase. alanine racemase Pseudomonas putida GB

77, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED118O3 O 78 Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

79, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED11804 O 8O Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

81, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED11804 O 82 Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

83, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED11804 O 84 Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

85, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED118O3 O 86 Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

87, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED118O3 O 88 Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

89, alanine racemase 26990430 O Pseudomonas T. maritima AED118O3 O 9 O Pseudomonas putida D-alanine putida KT244 O KT244. O D-alanine ligase.

91, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED118O3 O 92 Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

93, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED11804 O 94 Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase. US 8,541,220 B2 137 138 TABLE 3 - continued

95, alanine racemase 1.26E-O8 O Pseudomonas T. maritima AED118O3 O 96 Pseudomonas putida D-alanine utida GB-1 GB-1 D-alanine gi 126314851 gb EAZ66O19.1 ligase. a. anine racemase Pseudomonas utida GB-1

97, alanine racemase 1.26E-O8 O Pseudomonas T. maritima AED118O3 O 98 Pseudomonas putida D-alanine utida GB-1 GB-1 D-alanine gi 126314851 gb EAZ66O19.1 ligase. a. anine racemase Pseudomonas putida GB-1

99, alanine racemase 1.49E-08 O Pseudomonas T. maritima AED118O3 O 1 OO Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

101, alanine racemase 158O14122. OOE-58 Escherichia Prokaryotic ABU45 O892. OOE-58 1 O2 2, catabolic coli essential Escherichia coli O157:H7 gene O157:H7 EDL933 3474. O. EDL933.

103, aspartate 1452.15758. OOE-29 Pyrococcus Thermococcus ADN462O72. OOE-25 104 accelas 6 abyssi kodakaraensis Pyrococcus KOD1 abyssi. protein sequence SEO ID 4.

105, proline racemase 1.24E-O81. OOE-15 O Microscilla Bacterial ADS22995 1. OOE-128 106 Microscilla marina marina polypeptide ATCC 23134) ATCC E10 OOO1. gi 123984 O81 gb EAY24454.1 231.34 proline racemase Microscilla marina ATCC 23134)

107, alanine recemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 108 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

109, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-129 11O Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3

111, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 112 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

113, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 114 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3. US 8,541,220 B2 139 140 TABLE 3 - Continued

115, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 116 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

117, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 118 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

119, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 12O Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

121, alanine racemase 1.49E-081. OOE-13 6 Pseudomonas T. maritima AED118O31 OOE-137 122 Pseudomonas putida F1 D-alanine putida F1 D-alanine ligase.

123, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-127 124 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

125, alanine racemase 1.26E-O81. OOE-155 Pseudomonas Empedobacter AED105811. OOE-159 126 Pseudomonas putida brevis putida GB-1 GB-1 mature gi 126314851 gb EAZ66O19.1 peptide alanine racemase synthesizing Pseudomonas enzyme putida GB-1 SEO ID NO: 3.

127, glutamate 2738 08133. OOE-26 Bradyrhizobium Photorhabdus ABM6863 ff. OOE-18 128 accelas 6 iaponicum luminescens Bradyrhizobium USDA protein iaponicum USDA 11O sequence 110 59.

129, proline racemase, 1, 19E-081. OOE-103 Stappia Prokaryotic ABU21813 1. OOE-101 13 O putative Stappia aggregate essential aggregata IAM IAM gene 12614 1261.4 3474. O. gi 11843594 Ogb EAV42584.1 proline racemase, putative Stappia aggregate IAM 12614

131, putative proline 1. O9E-085. OOE-75 Myxococcus M. Xanthus ABM96 6371. OOE-75 132 accelas 6 Xanthus protein Myxococcus DK 1622 sequence, Xanthus DK 1622 seq id 9726.

133, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 134 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing US 8,541,220 B2 141 142 TABLE 3 - continued

7966 enzyme SEO ID NO: 3.

135, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-129 136 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

137, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-128 138 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

139, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 14 O Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

141, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 142 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

143, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 144 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

145, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 146 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

147, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 148 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

149, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 150 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

151, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 152 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide US 8,541,220 B2 143 144 TABLE 3 - continued 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

153, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 154 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

155, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-133 156 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

157, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 158 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

159, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 16 O Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966 ATCC synthesizing 7966 enzyme SEO ID NO: 3.

161, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 162 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

163, alanine racemase 1.49E-O81. OOE-153 Pseudomonas Empedobacter AED10581. O 164 Pseudomonas putida F1 brevis putida F1 mature peptide synthesizing enzyme SEO ID NO: 3.

165, alanine racemase 1.49E-O81. OOE-153 Pseudomonas Empedobacter AED10581. O 166 Pseudomonas putida F1 brevis putida F1 mature peptide synthesizing enzyme SEO ID NO: 3.

167, proline racemase 887123941. OOE-69 Flavobacteriales Bacterial ADS22995 2. OOE-57 168 Flavobacteriales bacterium polypeptide bacterium HTCC2 17 O E10001. HTCC2170) gi 88708932 gb EARO1166. 1 proline racemase Flavobacteriales bacterium HTCC2170) US 8,541,220 B2 145 146 TABLE 3 - continued

169, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 17O Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

171, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 172 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

173, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-129 174 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

175, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 176 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

177, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 178 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

179, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 18O Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

181, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 182 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

183, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 184 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

185, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-129 186 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing US 8,541,220 B2 147 148 TABLE 3 - continued

7966 enzyme SEO ID NO: 3.

187, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 188 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

189, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 190 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

191, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 192 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

193, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 194 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

195, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 196 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

197, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 198 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

199, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 2 OO Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

201, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-129 2O2 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

2O3, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 2O4. Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide US 8,541,220 B2 149 150 TABLE 3 - continued 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

2O5, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 2O6 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-133 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

209, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 210 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

211, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 212 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966 ATCC synthesizing 7966 enzyme SEO ID NO: 3.

213, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-133 214 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

215, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 216 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

217, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 218 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

219, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-129 22O Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

221, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-128 222 Aeromonas salmonicida brevis salmonicida subsp. mature US 8,541,220 B2 151 152 TABL E 3 - continued subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

223, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-133 224 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

225, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-130 226 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

227, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 228 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

229, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 23 O Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

231, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 232 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

233, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-128 234 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

235, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-128 236 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

237, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-128 238 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3. US 8,541,220 B2 153 154 TABLE 3 - continued

239, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-128 240 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

241, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-130 242 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

243, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-129 244 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

245, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-129 246 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

247, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 248 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

249, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-129 250 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

251, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 252 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

253, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-129 254 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3. 255, hypothetical 134.74743 1. OOE-17O Mesorhizobium Propionibacterium ABM37O681. OOE-77 256 protein loti CeS Mesorhizobium predicted loti. ORF encoded polypeptide H300. US 8,541,220 B2 155 156 TABLE 3 - continued

257, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-129 258 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

259, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-130 26 O Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

261, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-130 262 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

263, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-128 264 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

265, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-129 266 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

267, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-129 268 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

269, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 27 O Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

271, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 272 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

273, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-130 274 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing US 8,541,220 B2 157 158 TABLE 3 - continued

7966 enzyme SEO ID NO: 3.

275, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-128 276 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

277, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-133 278 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

279, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 28O Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

281, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 282 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

283, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-132 284 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

285, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-130 286 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

287, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-129 288 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

289, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-129 290 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

291, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-131 292 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide US 8,541,220 B2 159 160 TABLE 3 - continued 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

293, alanine racemase 1.45E-08 O Aeromonas Empedobacter AED105811. OOE-127 294 Aeromonas salmonicida brevis salmonicida subsp. mature subsp. salmonicida peptide salmonicida A449 A449 synthesizing enzyme SEO ID NO: 3.

295, alanine racemase 1, 18E-O8 O Aeromonas Empedobacter AED105811. OOE-129 296 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

297, proline racemase 1.18E+081. OOE-104 Burkholderia Acinetobacter ADA352281. OOE-105 298 Burkholderia phymatum baumannii phymatum STM815 protein STM815) E19. gi 117982269 gb EAU96656.1 proline racemase Burkholderia phymatum STM815) 299, alanine racemase 1.26E-O81. OOE-17 O Pseudomonas T. maritima AED118O31 OOE-169 3 OO Pseudomonas putida D-alanine putida GB-1 GB-1 D-alanine gi 126314851 gb EAZ66O19.1 ligase. alanine racemase Pseudomonas putida GB-1

301, alanine racemase 2699 O43 O1. OOE-143 Pseudomonas T. maritima AED118O31 OOE-144 3 O2 Pseudomonas putida D-alanine putida KT244 O KT244. O D-alanine ligase.

hypothetical 94.4142354. OOE-33 Pseudomonas Pseudomonas ABO821.55 4 OOE-33 protein aeruginosa aeruginosa Paer PO1 OO3954 PAf polypeptide Pseudomonas E3. aeruginosa PA 7

AGR L 3 O51p 158916411. OOE-128 Agrobacterium L. pneumophila AEB415963 OOE-39 Agrobacterium tumefaciens protein tumefaciens. SEO ID NO 3.367.

proline racemase 1.24E-- 083. OOE-59 Microscilla Bacterial ADS229.953. OOE-47 Microscilla marina marina polypeptide ATCC 23134) ATCC E10001. gi 123984 O81 gb EAY24454.1 231.34 proline racemase Microscilla marina ATCC 23134) 309, alanine racemase 1.2E+08 2. OOE-57 Stenotrophomonas Prokaryotic ABU413988. OOE-52 310 Stenotrophomonas maltophilia essential maltophilia R551-3 gene R551-3 3474. O. gi 11982 0021 gb EAX22642. 1 alanine racemase Stenotrophomonas maltophilia R551-3

311, mandellate 839533261. OOE-143 Sulfitobacter Klebsiella ABO 613. Of 2 OOE-71 312 racemase/muconate so. pneumonia lactonizing NAS- polypeptide enzyme family 14.1 seqid 7178. protein US 8,541,220 B2 161 162 TABLE 3 - Continued Sulfitobacter sp. NAS-14. 1 gi 83842294 gb EAP81462.1 mandellate racemase/muconate lactonizing enzyme family protein Sulfitobacter sp. NAS-14. 1 313, proline racemase 134733941. OOE-120 Mesorhizobium Bacterial ADS22995 1. OOE-120 314 Mesorhizobium loti polypeptide loti. E10001. 315, proline racemase 887123941. OOE-106 Flavobacteriales Bacterial ADS22995 1. OOE-72 316 Flavobacteriales bacterium polypeptide bacterium HTCC2 17 O E10001. HTCC2170) gi 88708932 gb EARO1166. 1 proline racemase Flavobacteriales bacterium HTCC2170)

317, Mandellate 887125961. OOE-110 Flavobacteriales Bacteroides AEX286 OO 5 OOE-34 3.18 racemase/muconate bacterium fragilis lactonizing HTCC2 17 O strain enzyme 14 O 62 Flavobacteriales protein, bacterium SEQ: 5227. HTCC2170) gi 88 709134 gb EARO1368. 1 Mandellate racemase/muconate lactonizing enzyme Flavobacteriales bacterium HTCC2170) 319, COG3938: Proline 8432.19521. OOE-60 Pseudomonas Pseudomonas ABO821.55 4 OOE-61 32O accelas 6 aeruginosa aeruginosa Pseudomonas C3719 polypeptide aeruginosa E3. C3719) gi843282O4 ref ZP OO976211.1 COG3938: Proline accelas 6 Pseudomonas aeruginosa 2.192 gi 1071 OO 719 ref ZP O1364.637.1 hypothetical protein Paer PAO1 OO1746 Pseudomonas aeruginosa PACS2 gi 12616632 321, aspartate 1452.15752. OOE-28 Pyrococcus Thermococcus ADN462O77. OOE-25 322 accelas 6 abyssi kodakaraensis Pyrococcus KOD1 abyssi. protein sequence SeqID4.

323, proline racemase, 912.173611. OOE-152 Psychroflexus Bacterial ADS22995 1. OOE-110 324 putative torquis polypeptide Psychiroflexus ATCC E10001. torquis ATCC 7 OOfss 700755) gie 11844 69gb EAS 70852.1 proline racemase, putative Psychiroflexus torquis ATCC 700755) US 8,541,220 B2 163 164 TABLE 3 Continued

325, proline racemase 1.24E--O81. OOE-145 Microscilla Bacterial ADS22995 1. OOE-126 326 Microscilla marina marina polypeptide ATCC 23134) ATCC E10001. gi 123984 O81 gb EAY24454.1 231.34 proline racemase Microscilla marina ATCC 23134) 327, proline racemase 1.24E--O81. OOE-147 Microscilla Bacterial ADS22995 1. OOE-132 328 Microscilla marina marina polypeptide ATCC 23134) ATCC E10001. gi 123984 O81 gb EAY24454.1 231.34 proline racemase Microscilla marina ATCC 23134)

329, putative proline 1. O9E-081. OOE-101 Myxococcus M. Xanthus ABM96 6371. OOE-101 330 accelas 6 Xanthus protein Myxococcus DK 1622 sequence, Xanthus DK 1622 seq id 9726.

331, AGR L 3 O51p 15891.6417. OOE-44 Agrobacterium Bacterial ADFOf 948 S. OOE-21 332 Agrobacterium tumefaciens polypeptide tumefaciens. 19. 333, putative alanine 1.16E-O89. OOE-97 Rhizobium ADFOf 948 6. OOE-29 334 accelas 6 leguminosarum Rhizobium bv. viciae leguminosarum 3841 bv. viciae 3841 335, alanine racemase 8359 O9905. OOE-78 Moorella Prokaryotic ABU24721 1. OOE-63 336 Moorella thermoacetica essential thermoacetica ATCC gene ATCC 39073) 39073 3474. O. 337, alanine racemase 835909 903. OOE-77 Moorella Prokaryotic ABU24721 1. OOE-60 338 Moorella thermoacetica essential thermoacetica ATCC gene ATCC 39073) 39073 3474. O.

339, Alanine racemase 671554691. OOE-115 Azotobacter Prokaryotic ABU397951. OOE-115 34 O Azotobacter vinelandii essential vinelandii AvOP) AWOP gene gi 6708727 Ogb|EAMO6737.1 3474. O. Alanine racemase Azotobacter vinelandii AvOP)

341, mandellate OOE-99 Sphingopyxis Klebsiella ABO 613. Of 1. OOE-45 342 racemase/muconate alaskens is pneumoniae lactonizing RB2256 polypeptide enzyme seqid 7178. Sphingopyxis alaskensis RB2256

343, putative alanine 1.16E--O81. OOE-127 Rhizobium Pseudomonas ABO84274 8. OOE-42 344 accelas 6 leguminosarum aeruginosa Rhizobium bv. viciae polypeptide leguminosarum 3841 E3. bv. viciae 3841 345, AGR L 3 O51p 158916 412. OOE-79 Agrobacterium Photorhabdus ABM69114 1. OOE-27 346 Agrobacterium tumefaciens luminescens tumefaciens. protein sequence 59.

347, putative alanine 1.16E--O81. OOE-114 Rhizobium Prokaryotic ABU413981. OOE-36 348 accelas 6 leguminosarum essential Rhizobium by. viciae gene leguminosarum 3841 3474. O. bv. viciae 3841 349, Mandellate 1.49E-082. OOE-87 Methyliobacterium Klebsiella ABO 613. Of 1. 350 racemase/muconate sp. 4- 46 pneumoniae lactonizing polypeptide US 8,541,220 B2 165 166 TABLE 3 Continued enzyme; C seqid 7178. terminal domain protein Methyliobacterium sp. 4- 4 6

351, Mandellate 1.49E-083. OOE-93 Sphingomonas Klebsiella ABO 613. Of 3 OOE-48 352 racemase/muconate Wittichii pneumoniae lactonizing RW1 polypeptide enzyme; C seqid 7178. terminal domain protein Sphingomonas wittichii RW1 353, putative proline 91.77922.21 OOE-38 Burkholderia Prokaryotic ABU21813 3 OOE-39 3.54 accelas 6 XeoWOS essential Burkholderia LB4 OO gene Xe(VOS 3474. O. LB4 OO

355, alanine racemase 1.49E-082. OOE-67 Lentisphaera Prokaryotic ABU23921 1 OOE-56 356 Lentisphaera ae OS essential ae OS HTCC2 155 gene HTCC2155 3474. O. 357, alanine racemase 1, 18E-O81. OOE-107 Roseiflexus Prokaryotic ABU2392.1 5 OOE-75 358 Roseiflexus castenholzii essential castenholzii DSM DSM gene 13941 13941 3474. O. gi 1180.10932 gb EAV2.4951. 1 alanine racemase Roseiflexus castenholzii DSM 13941

359, alanine racemase 1, 18E-O81. OOE-107 Roseiflexus Prokaryotic ABU23921 1 OOE-75 360 Roseiflexus castenholzii essential castenholzii DSM DSM gene 13941 13941 3474. O. gi 1180.10932 gb EAV2.4951. 1 alanine racemase Roseiflexus castenholzii DSM 13941 361, alanine racemase 1, 18E-O81. OOE-107 Roseiflexus Prokaryotic ABU2392.1 5 OOE-75 362 Roseiflexus castenholzii essential castenholzii DSM DSM gene 13941 13941 3474. O. gi 1180.10932 gb EAV2.4951. 1 alanine racemase Roseiflexus castenholzii DSM 13941

363, alanine racemase 1, 18E-O81. OOE-107 Roseiflexus Prokaryotic ABU2392.13. OOE-75 364 Roseiflexus castenholzii essential castenholzii DSM DSM gene 13941 13941 3474. O. gi 1180.10932 gb EAV2.4951. 1 alanine racemase Roseiflexus castenholzii DSM 13941

365, alanine racemase 1, 18E-O81. OOE-107 Roseiflexus Prokaryotic ABU2392.13. OOE-76 366 Roseiflexus castenholzii essential castenholzii DSM DSM gene 13941 13941 3474. O. gi 1180.10932 gb EAV2.4951. 1 alanine racemase Roseiflexus castenholzii DSM 13941 367, alanine racemase 1.46E-O81. OOE-168 Pseudomonas Prokaryotic ABU413981. OOE-160 3.68 Pseudomonas mendocina essential mendocina ymp ymp gene 3474. O. US 8,541,220 B2 167 168 TABLE 3 - continued

369, diaminopimelate 172323333. OOE-78 NoStoc Bacterial ADS298489. OOE-79 37O epimerase Nostoc sp. PCC polypeptide sp. PCC 712O). 712 O E10001.

371, diaminopimelate 8585F916.2. OOE-76 Syntrophus Bacterial ADN174895. OOE-60 372 epimerase aciditrophicus polypeptide Syntrophus SB E10001. aciditrophicus SB

373, diaminopimelate 172323332. OOE-71 NoStoc Bacterial ADS29848 7 OOE-72 374 epimerase Nostoc sp. PCC polypeptide sp. PCC 712O). 712 O E10001.

375, Diaminopimelate 1.26E-O85. OOE-33 Clostridium Bacterial ADN271692. OOE-31 376 epimerase thermocellum polypeptide Clostridium ATCC E10001. thermocellum 274 OS ATCC 27405

377, UDP-N- 1, 18E-O82. OOE-97 Chloroflexus Prokaryotic ABU24769 6 OOE-8O 378 acetylglucosamine aggregains essential 2-epimerase DSM gene Chloroflexus 94.85 3474. O. aggregains DSM 9.485) gi 117997 29 Ogb EAV11478.1

N acetylglucosamine 2-epimerase Chloroflexus aggregains DSM 9.485)

379, NimrA family 1.34E-O82. OOE-88 Burkholderia Bacterial ADS227792. OOE-84 38O protein vietnamiensis polypeptide Burkholderia G4 E10001. vietnamiensis G4

381, hypothetical 1.16E-O82. OOE-87 Rhizobium Bacterial ADS227791. OOE-83 382 protein RL1205 leguminosarum polypeptide Rhizobium bv. viciae E10001. leguminosarum 3841 bv. viciae 3841 383, similar to 375226681. OOE-93 Gloeobacter L. pneumophila AEB372824. OOE-48 384 chloromuconate violaceus protein cycloisomerase PCC SEO ID NO Gloeobacter 7421 3.367. violaceus PCC 7421 385, Aurantimonas AEH192775. OOE-47 386 so. SI85-9A1

387, Azoarcus ABU413981. OOE-110 388 sp. EbN1

389, Enterobacter 390 so. 638

391, Enterobacter 392 so. 638

393, Aquifex ABBO 62961. OOE-147 394 aeolicus WF's

395, Streptomyces ABU34 223 6 OOE-9 O 396 coelicolor A3 (2)

397, Rhodopseudomonas ABO84274. 4. OOE-50 398 palustris HaA2 US 8,541,220 B2 169 170 TABL E 3 - continued

399, Pseudomonas AED118O3 O 4 OO putida F1

401, Pseudomonas AED118031 OOE-174 4 O2 putida GB-1

403, Pseudomonas AED11804. 1 OOE-175 4O4. putida GB-1

Pseudomonas AED11804 O putida F1

4O7. Pseudomonas AED118O3 O 408 putida F1

409, Pseudomonas AED118O3 O 410 putida F1

411, alpha ABBO 62969. OOE-13 412 proteobacterium HTCC2255

413, Streptomyces ABM5435.82. OOE-53 414 avermitilis MA 468 O

415, Aeromonas AED105811. OOE-129 416 hydrophila subsp. hydrophila ATCC 7966

417 Aeromonas AED105811. OOE-131 418 hydrophila subsp. hydrophila ATCC 7966

419, Aeromonas AED105811. OOE-132 42O hydrophila subsp. hydrophila ATCC 7966

421, Aeromonas AED105811. OOE-131 422 hydrophila subsp. hydrophila ATCC 7966

423, Pseudomonas AED118O3 O 424 putida F1

425, Pseudomonas AED118031 OOE-137 426 putida F1

427, Pseudomonas AED118031 OOE-179 428 putida GB-1

429, Pseudomonas AED11804 O 43 O putida F1

431, Pseudomonas AED118O3 O 432 putida F1

433, Pseudomonas AED11804. 1 OOE-174 434 putida GB-1

435, Aeromonas AED105811 OOE-131 436 hydrophila subsp. US 8,541,220 B2 171 172 TABL E 3 - continued hydrophila ATCC 7966

437, Pyrococcus ADN462O72. OOE-25 4.38 abyssi GE5

439, Aeromonas AED105811. OOE-127 4 4 O hydrophila subsp. hydrophila ATCC 7966

441, Aeromonas AED105811. OOE-133 442 hydrophila subsp. hydrophila ATCC 7966

443, Aeromonas AED105811. OOE-132 444 hydrophila subsp. hydrophila ATCC 7966

445, Aeromonas AED105811. OOE-128 446 salmonicida subsp. salmonicida A449

447, Aeromonas AED105811. OOE-129 4 48 hydrophila subsp. hydrophila ATCC 7966

449, Aeromonas AED105811. OOE-130 450 hydrophila subsp. hydrophila ATCC 7966

451, Aeromonas AED105811. OOE-130 452 hydrophila subsp. hydrophila ATCC 7966

453, Aeromonas AED105811. OOE-129 454 salmonicida subsp. salmonicida A449

455, Stappia ABU21813 1. OOE-101 456 aggregata IAM 1261.4

457, Myxococcus ABM96 6371. OOE-75 458 Xanthus DK 1622

459, Aeromonas AED105811. OOE-130 460 hydrophila subsp. hydrophila ATCC 7966 US 8,541,220 B2 173 174 TABLE 3 - Continued

461, Pseudomonas AED105811. OOE-159 462 putida GB-1

463, Mesorhizobium ABU388293. OOE-46 464 sp. BNC1

465, Microscilla ADS22995 1. OOE-128 466 marina ATCC 231.34

467, Burkholderia ADA352281. OOE-105 468 phymatum STM815

469, Sulfitobacter ABO 613. Of 2. OOE-71 470 so. NAS 14.1

471, Pseudomonas ABU413981. OOE-160 472 mendocina ymp

473, Aeromonas AED105811. OOE-131 474 hydrophila subsp. hydrophila ATCC 7966

475, Pseudomonas AED105811. OOE-167 476 putida GB-1

477, Pseudomonas AED118O31. OOE-141 478 putida KT244. O

479, protein of 872OO8311. OOE-137 Novosphingobium Klebsiella ABO 641821. OOE-113 48O unknown function aromaticivorans pneumoniae DUF453 DSM polypeptide Novosphingobium 12444 seqid 7178. aromaticivorans DSM 12444

481, alanine racemase 1, 18E-O81. OOE-177 Aeromonas Empedobacter AED105811. OOE-129 482 Aeromonas hydrophila brevis hydrophila subsp. subsp. mature hydrophila ATCC hydrophila peptide 7966) ATCC synthesizing 7966 enzyme SEO ID NO: 3.

483, threonine aldolase 161273.36 O Caulobacter 484 family protein Crescents Caulobacter CB15 crescentus CB15 gi 13424764 gbAAK25068.1 threonine aldolase family protein Caulobacter crescentus CB15

485, hypothetical 15891O36 O Agrobacterium 486 protein tumefaciens AGR L 1837 Str. Agrobacterium tumefaciens str. C58) gi 1793.7630 ref NP 534419.1 hypothetical protein Atu3927 Agrobacterium tumefaciens str. C58) US 8,541,220 B2 175 176 TABLE 3 - continued gi 151593 65gbAAK894.93. 1 AGR L 1837p Agrobacterium tumefaciens str. C58) gi 1774.2368 gbAAL44735.1 conserved hypothetical protein Agrobacterium tumefaciens str. C58) 487, hypothetical 15891O21 O Agrobacterium 488 protein tumefaciens AGR L 1808 Str. Agrobacterium C58 tumefaciens str. C58) gi 15159347 IgbAAK89478.1 AGR L 1808p Agrobacterium tumefaciens str. C58) Genesed SEQ Gene seq. DNA Predicted Query Query Subject Subject 3. 3. ID DNA Accession EC DNA Protein DNA Protein ID ID NO: Description Code Evalue Number Length Length Length Length Protein DNA

3, 4 Aquifex ABL1496O7 2. OOE-OF 5.1.1.1 101.7 338 O 338 1 OO pyrophilus heat resistant alanine a cease encoding DNA.

5, 6 Human AAK8 O65O O. O32 2.73. 72 O 239 O 239 8O immune/haematopoietic antigen genomic sequence SEQ ID NO: 41436.

7, 8 EST clone AAW88076 O. O48 1032 343 O 343 89 EP219.

9, Pseudomonas ABDO 87.32 1. OOE-Os 51.1.1 1149 382 O 391 78 O aeruginosa polypeptide E3.

1, Pseudomonas ABDO 63 78 O. O.13 5.1.1.1 1122 373 O 388 58 2 aeruginosa polypeptide E3.

3, Pseudomonas ABDO 87.32 1. OOE-08 5.1.1.1 1065 3.54 O 353 64 4. aeruginosa polypeptide E3.

5, Klebsiella ACHS 9054 O. OO2 5.1.1.13 7 O2 233 O 231 74 6 pneumoniae polypeptide seqid 7178.

17, Human AEB85185 OOO9 5.1.1.3 8. Of 268 O 269 72 18 phosphodiesterase 4D amino acid sequence N1 SEQ ID NO : 7. US 8,541,220 B2 177 178 TABLE 3 - continued

19, M. Xanthus ACL64794 O. O37 5.1.1.3 822 273 272 53 2O protein sequence, seq id 9726.

21, Bacterial ADS61806 1. OOE-04 5.2.1.1 768 255 265 41 22 polypeptide E10001.

23, Enterobacter AEH55.699 O 5.1.1.1 108 O 359 359 95 24 cloacae protein amino acid sequence - SEQ ID 5666.

25, Enterobacter AEH55.699 O 5.1.1.1 108 O 359 359 95 26 cloacae protein amino acid sequence - SEQ ID 5666.

27, Prokaryotic ACA27845 O. OO2 651 216 216 1 OO 28 essential gene 3474O.

29, Pseudomonas ABD15676 1. OOE-08 1032 343 342 64 3 O aeruginosa polypeptide E3.

31, Pseudomonas ABD15666 9. OOE-16 1011 336 31 O 58 32 aeruginosa polypeptide E3.

33, Human AEHS 853 O O. O.13 1116 3.71 385 61 34 Calice associated cDNA SEQ ID NO 9.

35, N. meningitidis AAA81486 11 O1 366 368 33 36 partial DNA sequence gnm 64 O SEQ ID NO: 64 O.

37, Pseudomonas ABD12586 489 162 369 51 38 aeruginosa polypeptide E3.

39, Prokaryotic ACA26332 8. OOE-23 372 123 96.O 3.18 4 O essential gene 3474O.

41, Pseudomonas ADB99538 123 O 97 42 putida a cease peptide, SEQ ID 5.

43, Pseudomonas ADB99538 123 O 96 44 putida a cease peptide, SEQ ID 5. US 8,541,220 B2 179 180 TABLE 3 - continued

45, Pseudomonas ADB99538 5.1.1.1 123 O 97 46 putida a cease peptide, SEQ ID 5.

47, Pseudomonas ADB99538 123 O 97 48 putida a cease peptide, SEQ ID 5.

49, Pseudomonas ADB99538 123 O 96 SO putida a cease peptide, SEQ ID 5.

51, Pseudomonas ADB995.37 1. OOE-120 5.1.1.1 123 O 77 52 putida a cease peptide, SEQ ID 5.

53, Pseudomonas ADB995.37 1. OOE-124 5.1.1.1 123 O 77 54 putida a cease peptide, SEQ ID 5.

55, Pseudomonas ADB995.37 1. OOE-124 5.1.1.1 123 O 77 56 putida a cease peptide, SEQ ID 5.

57, Pseudomonas ADB99538 123 O 96 58 putida a cease peptide, SEQ ID 5.

59, Pseudomonas ADB99538 123 O 95 6 O putida a cease peptide, SEQ ID 5.

61, Human 1614 s37 3.54 19 62 prostate expression marker cDNA

63, Pseudomonas ADB995.37 123 O 98 64 putida a cease peptide, SEQ ID 5.

65, Pseudomonas ADB995.37 123 O 97 66 putida a cease peptide, SEQ ID 5.

67, Pseudomonas ADB99538 123 O 9 O 68 putida a cease peptide, SEQ ID 5.

69, Pseudomonas ADB995.37 123 O 95 70 putida a cease peptide, SEQ ID 5. US 8,541,220 B2 181 182 TABLE 3 - continued

71, Pseudomonas ADB995.37 5.1.1.1 123 O 96 72 putida a cease peptide SEQ ID 5.

73, Pseudomonas ADB995.37 123 O 95 74 putida a cease peptide, SEQ ID 5.

75, Pseudomonas ADB995.37 123 O 95 76 putida a cease peptide, SEQ ID 5.

77, Pseudomonas ADB99538 123 O 95 78 putida a cease peptida, SEQ ID 5.

79, Pseudomonas ADB99538 123 O 95 8O putida a cease peptide, SEQ ID 5.

81, Pseudomonas ADB99538 123 O 96 82 putida a cease peptide, SEQ ID 5.

83, Pseudomonas ADB99538 1230 409 409 94 84 putida a cease peptide, SEQ ID 5.

85, Pseudomonas ADB995.37 123 O 96 86 putida a cease peptide, SEQ ID 5.

87, Pseudomonas ADB99538 123 O 96 88 putida a cease peptide, SEQ ID 5.

89, Pseudomonas ADB995.37 123 O 96 9 O putida a cease peptide, SEQ ID 5.

91, Pseudomonas ADB99538 123 O 96 92 putida a cease peptide, SEQ ID 5.

93, Pseudomonas ADB99538 123 O 96 94 putida a cease peptide, SEQ ID 5.

95, Pseudomonas ADB995.37 123 O 95 96 putida a cease peptide, SEQ ID 5. US 8,541,220 B2 183 184 TABLE 3 - continued

97, Pseudomonas ADB995.37 O 5.1.1.1 123 O 96 98 putida a cease peptide, SEQ ID 5.

99, Pseudomonas ADB995.37 O 5.1.1.1 123 O 97 1 OO putida a cease peptide, SEQ ID 5.

101, Enterobacter 5. OOE-27 5.1.1.1 384 127 1071 356 86 76 1 O2 cloacae protein amino acid sequence SEQ ID 5666.

103, Prokaryotic ACA27539 714. 237 687 228 32 48 104 essential gene 3474O.

105, Bovine AEN69487 1 OO2 333 333 106 ABCG2 related PCR primer E31.

107, Pseudomonas ADB99538 6. OOE-11 1227 408 408 96 108 putida a cease peptide, SEQ ID 5.

109, Pseudomonas ADB99538 6. OOE-05 1227 408 408 95 11O putida a cease peptide, SEQ ID 5.

111, Pseudomonas ADB99538 2. OOE-11 1227 408 408 99 112 putida a cease peptide, SEQ ID 5.

113, Pseudomonas ADB99538 2. OOE-14 1224 4. Of 408 92 114 putida a cease peptide, SEQ ID 5.

115, Pseudomonas ADB99538 2. OOE-08 1227 408 408 92 116 putida a cease peptide, SEQ ID 5.

117, Pseudomonas ADB99538 6. OOE-11 1227 408 408 92 118 putida a cease peptide, SEQ ID 5.

119, Pseudomonas ADB99538 1. OOE-12 1227 408 408 95 12O putida a cease peptide, SEQ ID 5. US 8,541,220 B2 185 186 TABLE 3 - continued

121, Pseudomonas ADB99538 2. OOE-26 5.1.1.1 1086 361 1227 122 putida a cease peptide, SEQ ID 5.

123, Pseudomonas ADB99538 6. OOE-11 5. 1086 361 408 88 124 putida a cease peptide, SEQ ID 5.

125, Pseudomonas ADB99538 4. OOE-95 5. 1086 361 1227 386 126 putida a cease peptide, SEQ ID 5.

27, Prokaryotic ACA378.66 261 86 265 63 28 essential gene 3474O.

29, Prokaryotic ACA26332 5. OOE-11 95.7 3.18 31 O 56 3O essential gene 3474O.

31, Prokaryotic ACA26332 1. OOE-18 1074 357 96.O 311 32 essential gene 3474O.

33, Pseudomonas ADB99538 6. OOE-11 1227 408 408 99 34 putida a cease peptide, SEQ ID 5.

135, Pseudomonas ADB99538 6. OOE-05 1227 408 408 95 136 putida a cease peptide, SEQ ID 5.

137, Pseudomonas ADB99538 1221 408 95 138 putida a cease peptide, SEQ ID 5.

139, Pseudomonas ADB99538 6. OOE-11 1224 4. Of 408 99 14 O putida a cease peptide, SEQ ID 5.

141, Pseudomonas ADB99538 1. OOE-15 1227 408 408 89 142 putida a cease peptide, SEQ ID 5.

143, Pseudomonas ADB99538 6. OOE-11 1227 408 408 1 OO 144 putida a cease peptide, SEQ ID 5.

145, Pseudomonas ADB99538 2. OOE-11 1224 4. Of 408 99 146 putida a cease peptide, SEQ ID 5. US 8,541,220 B2 187 188 TABLE 3 - continued

147, Pseudomonas ADB99538 3. OOE-19 5.1.1.1 1224 4. Of 408 97 148 putida a cease peptide, SEQ ID 5.

149, Pseudomonas ADB99538 6. OOE-19 1227 408 408 93 150 putida a cease peptide, SEQ ID 5.

151, Pseudomonas ADB99538 3. OOE-19 1227 408 408 92 152 putida a cease peptide, SEQ ID 5.

153, Pseudomonas ADB99538 3. OOE-19 1224 4. Of 408 97 154 putida a cease peptide, SEQ ID 5.

155, Pseudomonas ADB99538 2. OOE-14 1227 408 408 96 156 putida a cease peptide, SEQ ID 5.

157, Pseudomonas ADB99538 6. OOE-11 1227 408 408 92 158 putida a cease peptide, SEO ID 5.

159, Pseudomonas ADB99538 6. OOE-11 1227 408 408 92 16 O putida a cease peptide, SEQ ID 5.

161, Pseudomonas ADB99538 3. OOE-19 1227 408 408 97 162 putida a cease peptide, SEQ ID 5.

163, Pseudomonas ADB99538 1. OOE-64 1086 361 1227 386 164 putida a cease peptide, SEQ ID 5.

165, Pseudomonas ADB99538 2. OOE-91 1083 360 1227 386 166 putida a cease peptide, SEQ ID 5.

167, Bacterial ADS6 OO 41 O. OOf 657 218 335 58 168 polypeptide E10001.

169, Pseudomonas ADB99538 6. OOE-11 5.1.1.1 1227 408 408 97 17O putida a cease peptide, SEQ ID 5.

171, Pseudomonas ADB99538 6. OOE-11 5.1.1.1 1227 408 408 96 172 putida a cease peptide, SEQ ID 5. US 8,541,220 B2 189 190 TABLE 3 - continued

173, Pseudomonas ADB99538 6. OOE-05 5.1.1.1 1224 4. Of 408 95 174 putida a cease peptide, SEQ ID 5.

175, Pseudomonas ADB99538 2. OOE-14 1227 408 408 89 176 putida a cease peptide, SEQ ID 5.

177, Pseudomonas ADB99538 6. OOE-11 1227 408 408 99 178 putida a cease peptide, SEQ ID 5.

179, Pseudomonas ADB99538 3. OOE-10 1227 408 408 99 18O putida a cease peptide, SEQ ID 5.

181, Pseudomonas ADB99538 6. OOE-11 1227 408 408 99 182 putida a cease peptide, SEQ ID 5.

183, Pseudomonas ADB99538 6. OOE-11 1227 408 408 1 OO 184 putida a cease peptide, SEQ ID 5.

185, Pseudomonas ADB99538 1. OOE-15 1227 408 408 89 186 putida a cease peptide, SEQ ID 5.

187, Pseudomonas ADB99538 6. OOE-11 1227 408 408 99 188 putida a cease peptide, SEQ ID 5.

189, Pseudomonas ADB99538 6. OOE-11 1227 408 408 99 190 putida a cease peptide, SEQ ID 5.

191, Pseudomonas ADB99538 6. OOE-11 1227 408 408 91 192 putida a cease peptide, SEQ ID 5.

193, Pseudomonas ADB99538 6. OOE-11 1227 408 408 92 194 putida a cease peptide, SEQ ID 5.

195, Pseudomonas ADB995.37 6. OOE-11 1227 408 408 92 196 putida a cease peptide, SEQ ID 5.

197, Pseudomonas ADB99538 2. OOE-14 1227 408 408 91 198 putida a cease peptide, SEQ ID 5.