ENZYMES HAVING GLYCOSIDASE ACTIVITY AND METHODS OF USE THEREOF

Abstract

a polypeptide having glycosidase activity. In addition methods of designing new glycosidases and method of use thereof are also provided. The glycosidases have increased activity and stability at increased pH and Temperature.

Description

CROSS REFERENCE TO RELATED APPLICATIONS

[0001]This application is a divisional of U.S. application Ser. No. 10/093,037, filed Mar. 6, 2002, currently pending; which is a continuation of U.S. application Ser. No. 09/910,579, filed Jul. 20, 2001, now abandoned; which is a continuation-in-part of U.S. application Ser. No. 09/134,078, filed Aug. 13, 1998, now U.S. Pat. No. 6,368,844, issued Apr. 9, 2002; which is a continuation of U.S. application Ser. No. 08/949,026, filed Oct. 10, 1997, now abandoned; which claims the benefit of U.S. Provisional Application No. 60/056,916, filed Dec. 6, 1996. The application is also related to U.S. application Ser. No. 08/583,787, filed Jan. 11, 1996, now abandoned.

[0002]All above applications are hereby incorporated in their entity and for all purposes.

REFERENCE TO SEQUENCE LISTING SUBMITTED VIA EFS-WEB

[0003]This application is being filed electronically via the USPTO EFS-WEB server, as authorized and set forth in the MPEP § 1730 II.B.2(a)(A), and this electronic filing includes an electronically submitted sequence (SEQ ID) listing. The entire content of this sequence listing is herein incorporated by reference for all purposes. The Sequence listing is identified on the electronically filed .txt file as follows:

TABLE-US-00001 File Name Date of Creation Size (bytes) D1320_6D1_seqlist Aug. 6, 2007 135,168 bytes

FIELD OF THE INVENTION

[0004]This invention relates generally to enzymes, polynucleotides encoding the enzymes, the use of such polynucleotides and polypeptides, and more specifically to enzymes having glycosidase activity.

BACKGROUND

[0005]The glycosidic bond of β-galactosides can be cleaved by different classes of enzymes: (i) phospho-β-galactosidases (EC3.2.1.85) are specific for a phosphorylated substrate generated via phosphoenolpyruvate phosphotransferase system (PTS)-dependent uptake; (ii) typical beta.-galactosidases (EC3.2.1.23), represented by the Escherichia coli LacZ enzyme, which are relatively specific for β-galactosides; and (iii)β-glucosidases (EC 3.2.1.21) such as the enzymes of Agrobacterium faecalis, Clostridium thermocellum, Pyrococcus furiosus or Sulfolobus solfataricus (Day, A. G. and Withers, S. G., (1986) Purification and characterization of a β-glucosidase from Alcaligenes faecalis. Can. J. Biochem. Cell. Biol. 64, 914-922; Kengen, S. W. M., et al. (1993) Eur. J. Biochem., 213, 305-312; Ait, N., Cruezet, N. and Cattaneo, J. (1982) Properties of β-glucosidase purified from Clostridium thermocellum. J. Gen. Microbiol. 128, 569-577; Grogan, D. W. (1991) Evidence that β-galactosidase of Sulfolobus solfataricus is only one of several activities of a thermostable beta.-glycodiase. Appl. Environ. Microbiol. 57, 1644-1649). Members of the latter group, although highly specific with respect to the β-anomeric configuration of the glycosidic linkage, often display a rather relaxed substrate specificity and hydrolyse beta.-glucosides as well as beta.-fucosides and β-galactosides.

[0006]Generally, beta.-galactosidases are enzymes that catalyze the hydrolysis of galactose groups on a polysaccharide backbone or hydrolyze the cleavage of di- or oligosaccharides comprising galactose.

[0007]Generally, β-mannanases are enzymes that catalyze the hydrolysis of mannose groups internally on a polysaccharide backbone or hydrolyze the cleavage of di- or oligosaccharides comprising mannose groupsβ-mannosidases hydrolyze non-reducing, terminal mannose residues on a mannose-containing polysaccharide and the cleavage of di- or oligosaccaharides comprising mannose groups.

[0008]Guar gum is a branched galactomannan polysaccharide composed of β-1,4 linked mannose backbone with a-1,6 linked galactose sidechains. The enzymes required for the degradation of guar are β-mannanase, β-mannosidase and alpha.-galactosidaseβ-mannanase hydrolyses the mannose backbone internally and alpha.-mannosidase hydrolyses non-reducing, terminal mannose residues. alpha.-galactosidase hydrolyses alpha.-linked galactose groups.

[0009]Galactomannan polysaccharides and the enzymes that degrade them have a variety of applications. Guar is commonly used as a thickening agent in food and is utilized in hydraulic fracturing in oil and gas recovery. Consequently, galactomannanases are industrially relevant for the degradation and modification of guar. Furthermore, a need exists for thermostable galactomannases that are active in extreme conditions associated with drilling and well stimulation.

[0010]There are other applications for these enzymes in various industries, such as in the beet sugar industry. 20-30% of the domestic U.S. sucrose consumption is sucrose from sugar beets. Raw beet sugar can contain a small amount of raffinose when the sugar beets are stored before processing and rotting begins to set in. Raffinose inhibits the crystallization of sucrose and also constitutes a hidden quantity of sucrose. Thus, there is merit to eliminating raffinose from raw beet sugar. alpha.-Galactosidase has also been used as a digestive aid to break down raffinose, stachyose, and verbascose in such foods as beans and other gassy foods.

[0011]beta.-Galactosidases which are active and stable at high temperatures appear to be superior enzymes for the production of lactose-free dietary milk products (Chaplin, M. F. and Bucke, C. (1990) In: Enzyme Technology, pp. 159-160, Cambridge University Press, Cambridge, UK). Also, several studies have demonstrated the applicability of beta.-galactosidases to the enzymatic synthesis of oligosaccharides via transglycosylation reactions (Nilsson, K. G. I. (1998) Enzymatic synthesis of oligosaccharides. Trends Biotechnol. 6, 156-264; Cote, G. L. and Tao, B. Y. (1990) Oligosaccharide synthesis by enzymatic transglycosylation. Glycoconjugate J. 7, 145-162). Despite the commercial potential, only a few β-galactosidases of thermophiles have been characterized so far. Two genes reported are β-galactoside-cleaving enzymes of the hyperthermophilic bacterium Thermotoga maritima, one of the most themiophilic organotrophic eubacteria described to date (Huber, R., Langworthy, T. A., Konig, H., Thomm, M., Woese, C. R., Sleytr, U. B. and Stetter, K. O. (1986) T. martima sp. nov. represents a new genus of unique extremely thermophilic eubacteria growing up to 90° C., Arch. Microbiol. 144, 324-333) one of the most thermophilic organotrophic eubacteria described to date. The gene products have been identified as a beta.-galactosidase and a β-glucosidase.

[0012]Pullulanase is well known as a debranching enzyme of pullulan and starch. The enzyme hydrolyzes α-1,6-glucosidic linkages on these polymers. Starch degradation for the production or sweeteners (glucose or maltose) is a very important industrial application of this enzyme. The degradation of starch is developed in two stages. The first stage involves the liquefaction of the substrate with α-amylase, and the second stage, or saccharification stage, is performed by beta.-amylase with pullalanase added as a debranching enzyme, to obtain better yields.

[0013]Endoglucanases can be used in a variety of industrial applications. For instance, the endoglucanases of the present invention can hydrolyze the internal β-1,4-glycosidic bonds in cellulose, which may be used for the conversion of plant biomass into fuels and chemicals. Endoglucanases also have applications in detergent formulations, the textile industry, in animal feed, in waste treatment, and in the fruit juice and brewing industry for the clarification and extraction of juices.

[0014]The polynucleotides and polypeptides of the present invention have been identified as glucosidases, alpha.-galactosidases, β-galactosidases, β-mannosidases, β-mannanases, endoglucanases, and pullalanases as a result of their enzymatic activity.

[0015]The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention.

SUMMARY OF THE INVENTION

[0016]The invention provides an isolated nucleic acid having a sequence as set forth in SEQ ID Nos.: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 57, 58, 59, 60, and variants thereof having at least 50% sequence identity to SEQ ID Nos.: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 57, 58, 59 and 60, and encoding polypeptides having glycosidase activity.

[0017]One aspect of the invention is an isolated nucleic acid having a sequence as set forth in SEQ ID Nos.: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 57, 58, 59, 60 (hereinafter referred to as "Group A nucleic acid sequences"), sequences substantially identical thereto, and sequences complementary thereto.

[0018]Another aspect of the invention is an isolated nucleic acid including at least 10 consecutive bases of a sequence as set forth in Group A nucleic acid sequences, sequences substantially identical thereto, and the sequences complementary thereto.

[0019]In yet another aspect, the invention provides an isolated nucleic acid encoding a polypeptide having a sequence as set forth in SEQ ID Nos.: 9, 10, 11, 12, 13, 14, 15, 16, 39, 40, 41, 42, 43, 44, 61, 62, 63, 64, and variants thereof encoding a polypeptide having glycosidase activity and having at least 50% sequence identity to such sequences.

[0020]Another aspect of the invention is an isolated nucleic acid encoding a polypeptide or a functional fragment thereof having a sequence as set forth in SEQ ID Nos.: 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 61, 62, 63, 64 (hereinafter referred to as "Group B amino acid sequences"), and sequences substantially identical thereto.

[0021]Another aspect of the invention is an isolated nucleic acid encoding a polypeptide having at least 10 consecutive amino acids of a sequence as set forth in Group B amino acid sequences, and sequences substantially identical thereto.

[0022]In yet another aspect, the invention provides a purified polypeptide having a sequence as set forth in Group B amino acid sequences, and sequences substantially identical thereto.

[0023]Another aspect of the invention is an isolated or purified antibody that specifically binds to a polypeptide having a sequence as set forth in Group B amino acid sequences, and sequences substantially identical thereto.

[0024]Another aspect of the invention is an isolated or purified antibody or binding fragment thereof, which specifically binds to a polypeptide having at least 10 consecutive amino acids of one of the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto.

[0025]Another aspect of the invention is a method of making a polypeptide having a sequence as set forth in Group B amino acid sequences, and sequences substantially identical thereto. The method includes introducing a nucleic acid encoding the polypeptide into a host cell, wherein the nucleic acid is operably linked to a promoter, and culturing the host cell under conditions that allow expression of the nucleic acid.

[0026]Another aspect of the invention is a method of making a polypeptide having at least 10 amino acids of a sequence as set forth in Group B amino acid sequences, and sequences substantially identical thereto. The method includes introducing a nucleic acid encoding the polypeptide into a host cell, wherein the nucleic acid is operably linked to a promoter, and culturing the host cell under conditions that allow expression of the nucleic acid, thereby producing the polypeptide.

[0027]Another aspect of the invention is a method of generating a variant including obtaining a nucleic acid having a sequence as set forth in Group A nucleic acid sequences, sequences substantially identical thereto, sequences complementary to the sequences of Group A nucleic acid sequences, fragments comprising at least 30 consecutive nucleotides of the foregoing sequences, and changing one or more nucleotides in the sequence to another nucleotide, deleting one or more nucleotides in the sequence, or adding one or more nucleotides to the sequence.

[0028]Another aspect of the invention is a computer readable medium having stored thereon a sequence as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto, or a polypeptide sequence as set forth in Group B amino acid sequences, and sequences substantially identical thereto.

[0029]Another aspect of the invention is a computer system including a processor and a data storage device wherein the data storage device has stored thereon a sequence as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto, or a polypeptide having a sequence as set forth in Group B amino acid sequences, and sequences substantially identical thereto.

[0030]Another aspect of the invention is a method for comparing a first sequence to a reference sequence wherein the first sequence is a nucleic acid having a sequence as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto, or a polypeptide code of Group B amino acid sequences, and sequences substantially identical thereto. The method includes reading the first sequence and the reference sequence through use of a computer program which compares sequences; and determining differences between the first sequence and the reference sequence with the computer program.

[0031]Another aspect of the invention is a method for identifying a feature in a sequence as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto, or a polypeptide having a sequence as set forth in Group B amino acid sequences, and sequences substantially identical thereto, including reading the sequence through the use of a computer program which identifies features in sequences; and identifying features in the sequence with the computer program.

[0032]Another aspect of the invention is an assay for identifying fragments or variants of Group B amino acid sequences, and sequences substantially identical thereto, which retain the enzymatic function of the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto. The assay includes contacting the polypeptide of Group B amino acid sequences, sequences substantially identical thereto, or polypeptide fragment or variant with a substrate molecule under conditions which allow the polypeptide fragment or variant to function, and detecting either a decrease in the level of substrate or an increase in the level of the specific reaction product of the reaction between the polypeptide and substrate thereby identifying a fragment or variant of such sequences.

BRIEF DESCRIPTION OF THE DRAWINGS

[0033]The following drawings are illustrative of embodiments of the invention and are not meant to limit the scope of the invention as encompassed by the claims.

[0034]FIG. 1 is a block diagram of a computer system.

[0035]FIG. 2 is a flow diagram illustrating one embodiment of a process for comparing a new nucleotide or protein sequence with a database of sequences in order to determine the homology levels between the new sequence and the sequences in the database.

[0036]FIG. 3 is a flow diagram illustrating one embodiment of a process in a computer for determining whether two sequences are homologous.

[0037]FIG. 4 is a flow diagram illustrating one embodiment of an identifier process 300 for detecting the presence of a feature in a sequence.

[0038]FIG. 5 is an illustration of the full length DNA sequence (SEQ ID NO: 1) and the corresponding deduced amino acid sequence (SEQ ID NO: 15) of M11 TL glycosidase (29G).

[0039]FIG. 6 is an illustration of the full length DNA sequence (SEQ ID NO: 2) and the corresponding deduced amino acid sequence (SEQ ID NO: 16) of OC1/4 glycosidase-33B/G.

[0040]FIG. 7 is an illustration of the full length DNA sequence (SEQ ID NO: 3) and the corresponding deduced amino acid sequence (SEQ ID NO: 17) of Staphylothermus marinus glycosidase-12G.

[0041]FIG. 8 is an illustration of the full length DNA sequence (SEQ ID NO: 4) and the corresponding deduced amino acid sequence (SEQ ID NO: 18) of Thermococcus 9N2 glycosidase-31 B/G.

[0042]FIG. 9 is an illustration of the full length DNA sequence (SEQ ID NO: 5) and the corresponding deduced amino acid sequence (SEQ ID NO: 19) of MSB8-6G.

[0043]FIG. 10 is an illustration of the full length DNA sequence (SEQ ID NO: 6) and the corresponding deduced amino acid sequence (SEQ ID NO: 20) of Thermococcus AEDII12RA glycosidase-18B/G.

[0044]FIG. 11 is an illustration of the full length DNA sequence (SEQ ID NO: 7) and the corresponding deduced amino acid sequence (SEQ ID NO: 21) of Thermococcus chitonophagus glycosidase-22G.

[0045]FIG. 12 is an illustration of the full length DNA sequence (SEQ ID NO: 8) and the corresponding deduced amino acid sequence (SEQ ID NO: 22) of Pyrococcus furiosus glycosidase-7G1.

[0046]FIG. 13 is an illustration of the full length DNA sequence (SEQ ID NO: 9) and the corresponding deduced amino acid sequence (SEQ ID NO: 23) of Bankis gouldi endoglucanase-37GPI.

[0047]FIG. 14 is an illustration of the full length DNA sequence (SEQ ID NO: 10) and the corresponding deduced amino acid sequence (SEQ ID NO: 24) of Thermotoga maritima alpha-galactosidase-6GC2.

[0048]FIG. 15 is an illustration of the full length DNA sequence (SEQ ID NO: 11) and the corresponding deduced amino acid sequence (SEQ ID NO: 25) of Thermotoga maritima beta-mannase-6GP2.

[0049]FIG. 16 is an illustration of the full length DNA sequence (SEQ ID NO: 12) and the corresponding deduced amino acid sequence (SEQ ID NO: 26) of AEPII 1 a beta-manosidase-63 GB 1.

[0050]FIG. 17 is an illustration of the full length DNA sequence (SEQ ID NO: 13) and the corresponding deduced amino acid sequence (SEQ ID NO: 27) of OC1/4V endoglucanase-33GP1.

[0051]FIG. 18 is an illustration of the full length DNA sequence (SEQ ID NO: 14) and the corresponding deduced amino acid sequence (SEQ ID NO: 28) of Thermotoga maritima pullulanase--6GP3. (plasmid 6GP3 deposited with the American Type Culture Collection (ATCC) 10801 University Blvd., Manassas, Va., on Jan. 20, 2004, and having patent deposit designation PTA-5788).

[0052]FIG. 19 is an illustration of the full-length DNA sequence (SEQ ID NO: 57) and the corresponding deduced amino acid sequence (SEQ ID NO: 61) of Thermotoga maritima MSB8-6GP2.

[0053]FIG. 20 is an illustration of the full-length DNA sequence (SEQ ID NO: 58) and the corresponding amino acid sequence (SEQ ID NO: 62) of Thermotoga maritima MSB8-6GP4.

[0054]FIG. 21 is an illustration of the full-length DNA sequence (SEQ ID NO: 59) and the corresponding deduced amino acid sequence (SEQ ID NO: 63) of Bankis gouldi 37GP4.

[0055]FIG. 22 is an illustration of the full-length DNA sequence (SEQ ID NO: 60) and the corresponding deduced amino acid sequence (SEQ ID NO: 64) of Pyrococcus furiosus VC1-7EG 1.

DETAILED DESCRIPTION OF THE INVENTION

[0056]The present invention relates to glycosidases and polynucleotides encoding them. As used herein, the term "glycosidase" encompasses enzymes having hydrolase activity, for example, enzymes capable of hydrolyzing glycosidic linkages present in starch.

[0057]The polynucleotides of the invention have been identified as encoding polypeptides having glycosidase activity.

DEFINITIONS

[0058]The phrases "nucleic acid" or "nucleic acid sequence" as used herein refer to an oligonucleotide, nucleotide, polynucleotide, or to a fragment of any of these, to DNA or RNA of genomic or synthetic origin which may be single-stranded or double-stranded and may represent a sense or antisense strand, to peptide nucleic acid (PNA), or to any DNA-like or RNA-like material, natural or synthetic in origin.

[0059]A "coding sequence of" or a "nucleotide sequence encoding" a particular polypeptide or protein, is a nucleic acid sequence which is transcribed and translated into a polypeptide or protein when placed under the control of appropriate regulatory sequences.

[0060]The term "gene" means the segment of DNA involved in producing a polypeptide chain; it includes regions preceding and following the coding region (leader and trailer) as well as, where applicable, intervening sequences (introns) between individual coding segments (exons).

[0061]Amino acid" or "amino acid sequence" as used herein refer to an oligopeptide, peptide, polypeptide, or protein sequence, or to a fragment, portion, or subunit of any of these, and to naturally occurring or synthetic molecules.

[0062]The term "polypeptide" as used herein, refers to amino acids joined to each other by peptide bonds or modified peptide bonds, i.e., peptide isosteres, and may contain modified amino acids other than the 20 gene-encoded amino acids. The polypeptides may be modified by either natural processes, such as post-translational processing, or by chemical modification techniques which are well known in the art. Modifications can occur anywhere in the polypeptide, including the peptide backbone, the amino acid side-chains and the amino or carboxyl termini. It will be appreciated that the same type of modification may be present in the same or varying degrees at several sites in a given polypeptide. Also a given polypeptide may have many types of modifications. Modifications include acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of a phosphytidylinositol, cross-linking cyclization, disulfide bond formation, demethylation, formation of covalent cross-links, formation of cysteine, formation of pyroglutamate, formylation, gamma-carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristolyation, oxidation, pergylation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, and transfer-RNA mediated addition of amino acids to protein such as arginylation. (See Creighton, T. E., Proteins--Structure and Molecular Properties 2nd Ed., W.H. Freeman and Company, New York (1993); Posttranslational Covalent Modification of Proteins, B. C. Johnson, Ed., Academic Press, New York, pp. 1-12 (1983)).

[0063]As used herein, the term "isolated" means that the material is removed from its original environment (e.g., the natural environment if it is naturally occurring). For example, a naturally-occurring polynucleotide or polypeptide present in a living animal is not isolated, but the same polynucleotide or polypeptide, separated from some or all of the coexisting materials in the natural system, is isolated. Such polynucleotides could be part of a vector and/or such polynucleotides or polypeptides could be part of a composition, and still be isolated in that such vector or composition is not part of its natural environment.

[0064]As used herein, the term "purified" does not require absolute purity; rather, it is intended as a relative definition. Individual nucleic acids obtained from a library have been conventionally purified to electrophoretic homogeneity. The sequences obtained from these clones could not be obtained directly either from the library or from total human DNA. The purified nucleic acids of the invention have been purified from the remainder of the genomic DNA in the organism by at least 104-106 fold. However, the term "purified" also includes nucleic acids which have been purified from the remainder of the genomic DNA or from other sequences in a library or other environment by at least one order of magnitude, typically two or three orders, and more typically four or five orders of magnitude.

[0065]As used herein, the term "recombinant" means that the nucleic acid is adjacent to a "backbone" nucleic acid to which it is not adjacent in its natural environment. Additionally, to be "enriched" the nucleic acids will represent 5% or more of the number of nucleic acid inserts in a population of nucleic acid backbone molecules. Backbone molecules according to the invention include nucleic acids such as expression vectors, self-replicating nucleic acids, viruses, integrating nucleic acids, and other vectors or nucleic acids used to maintain or manipulate a nucleic acid insert of interest. Typically, the enriched nucleic acids represent 15% or more of the number of nucleic acid inserts in the population of recombinant backbone molecules. More typically, the enriched nucleic acids represent 50% or more of the number of nucleic acid inserts in the population of recombinant backbone molecules. In a one embodiment, the enriched nucleic acids represent 90% or more of the number of nucleic acid inserts in the population of recombinant backbone molecules.

[0066]Recombinant" polypeptides or proteins refer to polypeptides or proteins produced by recombinant DNA techniques; i.e., produced from cells transformed by an exogenous DNA construct encoding the desired polypeptide or protein. "Synthetic" polypeptides or protein are those prepared by chemical synthesis. Solid-phase chemical peptide synthesis methods can also be used to synthesize the polypeptide or fragments of the invention. Such method have been known in the art since the early 1960's (Merrifield, R. B., J. Am. Chem. Soc., 85:2149-2154, 1963) (See also Stewart, J. M. and Young, J. D., Solid Phase Peptide Synthesis, 2nd Ed., Pierce Chemical Co., Rockford, III., pp. 11-12)) and have recently been employed in commercially available laboratory peptide design and synthesis kits (Cambridge Research Biochemicals). Such commercially available laboratory kits have generally utilized the teachings of H. M. Geysen et al, Proc. Natl. Acad. Sci., USA, 81:3998 (1984) and provide for synthesizing peptides upon the tips of a multitude of "rods" or "pins" all of which are connected to a single plate. When such a system is utilized, a plate of rods or pins is inverted and inserted into a second plate of corresponding wells or reservoirs, which contain solutions for attaching or anchoring an appropriate amino acid to the pin's or rod's tips. By repeating such a process step, i.e., inverting and inserting the rod's and pin's tips into appropriate solutions, amino acids are built into desired peptides. In addition, a number of available FMOC peptide synthesis systems are available. For example, assembly of a polypeptide or fragment can be carried out on a solid support using an Applied Biosystems, Inc. Model 431 A automated peptide synthesizer. Such equipment provides ready access to the peptides of the invention, either by direct synthesis or by synthesis of a series of fragments that can be coupled using other known techniques.

[0067]A promoter sequence is "operably linked to" a coding sequence when RNA polymerase which initiates transcription at the promoter will transcribe the coding sequence into mRNA.

[0068]Plasmids" are designated by a lower case "p" preceded and/or followed by capital letters and/or numbers. The starting plasmids herein are either commercially available, publicly available on an unrestricted basis, or can be constructed from available plasmids in accord with published procedures. In addition, equivalent plasmids to those described herein are known in the art and will be apparent to the ordinarily skilled artisan.

[0069]Digestion" of DNA refers to catalytic cleavage of the DNA with a restriction enzyme that acts only at certain sequences in the DNA. The various restriction enzymes used herein are commercially available and their reaction conditions, cofactors and other requirements were used as would be known to the ordinarily skilled artisan. For analytical purposes, typically 1 μg of plasmid or DNA fragment is used with about 2 units of enzyme in about 20 μl of buffer solution. For the purpose of isolating DNA fragments for plasmid construction, typically 5 to 50 μg of DNA are digested with 20 to 250 units of enzyme in a larger volume. Appropriate buffers and substrate amounts for particular restriction enzymes are specified by the manufacturer. Incubation times of about 1 hour at 37° C. are ordinarily used, but may vary in accordance with the supplier's instructions. After digestion, gel electrophoresis may be performed to isolate the desired fragment.

[0070]Oligonucleotide" refers to either a single stranded polydeoxynucleotide or two complementary polydeoxynucleotide strands which may be chemically synthesized. Such synthetic oligonucleotides have no 5' phosphate and thus will not ligate to another oligonucleotide without adding a phosphate with an ATP in the presence of a kinase. A synthetic oligonucleotide will ligate to a fragment that has not been dephosphorylated.

[0071]The phrase "substantially identical" in the context of two nucleic acids or polypeptides, refers to two or more sequences that have at least 50%, 60%, 70%, 80%, and in some aspects 90-95% nucleotide or amino acid residue identity, when compared and aligned for maximum correspondence, as measured using one of the known sequence comparison algorithms or by visual inspection. Typically, the substantial identity exists over a region of at least about 100 residues, and most commonly the sequences are substantially identical over at least about 150-200 residues. In some embodiments, the sequences are substantially identical over the entire length of the coding regions.

[0072]Additionally a "substantially identical" amino acid sequence is a sequence that differs from a reference sequence by one or more conservative or non-conservative amino acid substitutions, deletions, or insertions, particularly when such a substitution occurs at a site that is not the active site of the molecule, and provided that the polypeptide essentially retains its functional properties. A conservative amino acid substitution, for example, substitutes one amino acid for another of the same class (e.g., substitution of one hydrophobic amino acid, such as isoleucin, valine, leucine, or methionine, for another, or substitution of one polar amino acid for another, such as substitution of arginine for lysine, glutamic acid for aspartic acid or glutamine for asparagine). One or more amino acids can be deleted, for example, from a glycosidase polypeptide, resulting in modification of the structure of the polypeptide, without significantly altering its biological activity. For example, amino- or carboxyl-terminal amino acids that are not required for glycosidase biological activity can be removed. Modified polypeptide sequences of the invention can be assayed for glycosidase biological activity by any number of methods, including contacting the modified polypeptide sequence with an glycosidase substrate and determining whether the modified polypeptide decreases the amount of specific substrate in the assay or increases the bioproducts of the enzymatic reaction of a functional glycosidase polypeptide with the substrate.

[0073]Fragments" as used herein are a portion of a naturally occurring protein which can exist in at least two different conformations. Fragments can have the same or substantially the same amino acid sequence as the naturally occurring protein. "Substantially the same" means that an amino acid sequence is largely, but not entirely, the same, but retains at least one functional activity of the sequence to which it is related. In general two amino acid sequences are "substantially the same" or "substantially homologous" if they are at least about 85% identical. Fragments which have different three dimensional structures as the naturally occurring protein are also included. An example of this, is a "pro-form" molecule, such as a low activity proprotein that can be modified by cleavage to produce a mature enzyme with significantly higher activity.

[0074]Hybridization" refers to the process by which a nucleic acid strand joins with a complementary strand through base pairing. Hybridization reactions can be sensitive and selective so that a particular sequence of interest can be identified even in samples in which it is present at low concentrations. Suitably stringent conditions can be defined by, for example, the concentrations of salt or formamide in the prehybridization and hybridization solutions, or by the hybridization temperature, and are well known in the art. In particular, stringency can be increased by reducing the concentration of salt, increasing the concentration of formamide, or raising the hybridization temperature.

[0075]For example, hybridization under high stringency conditions could occur in about 50% formamide at about 37° C. to 42° C. Hybridization could occur under reduced stringency conditions in about 35% to 25% formamide at about 30° C. to 35° C. In particular, hybridization could occur under high stringency conditions at 42° C. in 50% formamide, 5× SSPE, 0.3% SDS, and 200 n/ml sheared and denatured salmon sperm DNA. Hybridization could occur under reduced stringency conditions as described above, but in 35% formamide at a reduced temperature of 35° C. The temperature range corresponding to a particular level of stringency can be further narrowed by calculating the purine to pyrimidine ratio of the nucleic acid of interest and adjusting the temperature accordingly. Variations on the above ranges and conditions are well known in the art.

[0076]The term "variant" refers to polynucleotides or polypeptides of the invention modified at one or more base pairs, codons, introns, exons, or amino acid residues (respectively) yet still retain the biological activity of an glycosidase of the invention. Variants can be produced by any number of means included methods such as, for example, error-prone PCR, shuffling, oligonucleotide-directed mutagenesis, assembly PCR, sexual PCR mutagenesis, in vivo mutagenesis, cassette mutagenesis, recursive ensemble mutagenesis, exponential ensemble mutagenesis, site-specific mutagenesis, gene reassembly, GSSM and any combination thereof.

[0077]Enzymes are highly selective catalysts. Their hallmark is the ability to catalyze reactions with exquisite stereo-, regio-, and chemo-selectivities that are unparalleled in conventional synthetic chemistry. Moreover, enzymes are remarkably versatile. They can be tailored to function in organic solvents, operate at extreme pHs (for example, high pHs and low pHs) extreme temperatures (for example, high temperatures and low temperatures), extreme salinity levels (for example, high salinity and low salinity), and catalyze reactions with compounds that are structurally unrelated to their natural, physiological substrates.

[0078]Enzymes are reactive toward a wide range of natural and unnatural substrates, thus enabling the modification of virtually any organic lead compound. Moreover, unlike traditional chemical catalysts, enzymes are highly enantio- and regio-selective. The high degree of functional group specificity exhibited by enzymes enables one to keep track of each reaction in a synthetic sequence leading to a new active compound. Enzymes are also capable of catalyzing many diverse reactions unrelated to their physiological function in nature. For example, peroxidases catalyze the oxidation of phenols by hydrogen peroxide. Peroxidases can also catalyze hydroxylation reactions that are not related to the native function of the enzyme. Other examples are proteases which catalyze the breakdown of polypeptides. In organic solution some proteases can also acylate sugars, a function unrelated to the native function of these enzymes.

[0079]The present invention exploits the unique catalytic properties of enzymes. Whereas the use of biocatalysts (i.e., purified or crude enzymes, non-living or living cells) in chemical transformations normally requires the identification of a particular biocatalyst that reacts with a specific starting compound, the present invention uses selected biocatalysts and reaction conditions that are specific for functional groups that are present in many starting compounds.

[0080]Each biocatalyst is specific for one functional group, or several related functional groups, and can react with many starting compounds containing this functional group.

[0081]The biocatalytic reactions produce a population of derivatives from a single starting compound. These derivatives can be subjected to another round of biocatalytic reactions to produce a second population of derivative compounds. Thousands of variations of the original compound can be produced with each iteration of biocatalytic derivatization.

[0082]Enzymes react at specific sites of a starting compound without affecting the rest of the molecule, a process which is very difficult to achieve using traditional chemical methods. This high degree of biocatalytic specificity provides the means to identify a single active compound within the library. The library is characterized by the series of biocatalytic reactions used to produce it, a so-called "biosynthetic history". Screening the library for biological activities and tracing the biosynthetic history identifies the specific reaction sequence producing the active compound. The reaction sequence is repeated and the structure of the synthesized compound determined. This mode of identification, unlike other synthesis and screening approaches, does not require immobilization technologies, and compounds can be synthesized and tested free in solution using virtually any type of screening assay. It is important to note, that the high degree of specificity of enzyme reactions on functional groups allows for the "tracking" of specific enzymatic reactions that make up the biocatalytically produced library.

[0083]Many of the procedural steps are performed using robotic automation enabling the execution of many thousands of biocatalytic reactions and screening assays per day as well as ensuring a high level of accuracy and reproducibility. As a result, a library of derivative compounds can be produced in a matter of weeks which would take years to produce using current chemical methods. (For further teachings on modification of molecules, including small molecules, see PCT/US94/09174, herein incorporated by reference in its entirety).

[0084]In one aspect, the present invention provides a non-stochastic method termed synthetic gene reassembly, that is somewhat related to stochastic shuffling, save that the nucleic acid building blocks are not shuffled or concatenated or chimerized randomly, but rather are assembled non-stochastically.

[0085]The synthetic gene reassembly method does not depend on the presence of a high level of homology between polynucleotides to be shuffled. The invention can be used to non-stochastically generate libraries (or sets) of progeny molecules comprised of over 10100 different chimeras. Conceivably, synthetic gene reassembly can even be used to generate libraries comprised of over 101000 different progeny chimeras.

[0086]Thus, in one aspect, the invention provides a non-stochastic method of producing a set of finalized chimeric nucleic acid molecules having an overall assembly order that is chosen by design, which method is comprised of the steps of generating by design a plurality of specific nucleic acid building blocks having serviceable mutually compatible ligatable ends, and assembling these nucleic acid building blocks, such that a designed overall assembly order is achieved.

[0087]The mutually compatible ligatable ends of the nucleic acid building blocks to be assembled are considered to be "serviceable" for this type of ordered assembly if they enable the building blocks to be coupled in predetermined orders. Thus, in one aspect, the overall assembly order in which the nucleic acid building blocks can be coupled is specified by the design of the ligatable ends and, if more than one assembly step is to be used, then the overall assembly order in which the nucleic acid building blocks can be coupled is also specified by the sequential order of the assembly step(s). In a one embodiment of the invention, the annealed building pieces are treated with an enzyme, such as a ligase (e.g., T4 DNA ligase) to achieve covalent bonding of the building pieces.

[0088]In a another embodiment, the design of nucleic acid building blocks is obtained upon analysis of the sequences of a set of progenitor nucleic acid templates that serve as a basis for producing a progeny set of finalized chimeric nucleic acid molecules. These progenitor nucleic acid templates thus serve as a source of sequence information that aids in the design of the nucleic acid building blocks that are to be mutagenized, i.e. chimerized or shuffled.

[0089]In one exemplification, the invention provides for the chimerization of a family of related genes and their encoded family of related products. In a particular exemplification, the encoded products are enzymes. The glycosidases of the present invention can be mutagenized in accordance with the methods described herein.

[0090]Thus according to one aspect of the invention, the sequences of a plurality of progenitor nucleic acid templates (e.g., polynucleotides of Group A nucleic acid sequences) are aligned in order to select one or more demarcation points, which demarcation points can be located at an area of homology. The demarcation points can be used to delineate the boundaries of nucleic acid building blocks to be generated. Thus, the demarcation points identified and selected in the progenitor molecules serve as potential chimerization points in the assembly of the progeny molecules.

[0091]Typically a serviceable demarcation point is an area of homology (comprised of at least one homologous nucleotide base) shared by at least two progenitor templates, but the demarcation point can be an area of homology that is shared by at least half of the progenitor templates, at least two thirds of the progenitor templates, at least three fourths of the progenitor templates, and preferably at almost all of the progenitor templates. Even more preferably still a serviceable demarcation point is an area of homology that is shared by all of the progenitor templates.

[0092]In a one embodiment, the gene reassembly process is performed exhaustively in order to generate an exhaustive library. In other words, all possible ordered combinations of the nucleic acid building blocks are represented in the set of finalized chimeric nucleic acid molecules. At the same time, the assembly order (i.e. the order of assembly of each building block in the 5' to 3 sequence of each finalized chimeric nucleic acid) in each combination is by design (or non-stochastic). Because of the non-stochastic nature of the method, the possibility of unwanted side products is greatly reduced.

[0093]In another embodiment, the method provides that the gene reassembly process is performed systematically, for example to generate a systematically compartmentalized library, with compartments that can be screened systematically, e.g., one by one. In other words the invention provides that, through the selective and judicious use of specific nucleic acid building blocks, coupled with the selective and judicious use of sequentially stepped assembly reactions, an experimental design can be achieved where specific sets of progeny products are made in each of several reaction vessels. This allows a systematic examination and screening procedure to be performed. Thus, it allows a potentially very large number of progeny molecules to be examined systematically in smaller groups.

[0094]Because of its ability to perform chimerizations in a manner that is highly flexible yet exhaustive and systematic as well, particularly when there is a low level of homology among the progenitor molecules, the instant invention provides for the generation of a library (or set) comprised of a large number of progeny molecules. Because of the non-stochastic nature of the instant gene reassembly invention, the progeny molecules generated preferably comprise a library of finalized chimeric nucleic acid molecules having an overall assembly order that is chosen by design. In a particularly embodiment, such a generated library is comprised of greater than 10³ to greater than 10.sup. 1000 different progeny molecular species.

[0095]In one aspect, a set of finalized chimeric nucleic acid molecules, produced as described is comprised of a polynucleotide encoding a polypeptide. According to one embodiment, this polynucleotide is a gene, which may be a man-made gene. According to another embodiment, this polynucleotide is a gene pathway, which may be a man-made gene pathway. The invention provides that one or more man-made genes generated by the invention may be incorporated into a man-made gene pathway, such as pathway operable in a eukaryotic organism (including a plant).

[0096]In another exemplification, the synthetic nature of the step in which the building blocks are generated allows the design and introduction of nucleotides (e.g., one or more nucleotides, which may be, for example, codons or introns or regulatory sequences) that can later be optionally removed in an in vitro process (e.g., by mutagenesis) or in an in vivo process (e.g., by utilizing the gene splicing ability of a host organism). It is appreciated that in many instances the introduction of these nucleotides may also be desirable for many other reasons in addition to the potential benefit of creating a serviceable demarcation point.

[0097]Thus, According to another embodiment, the invention provides that a nucleic acid building block can be used to introduce an intron. Thus, the invention provides that functional introns may be introduced into a man-made gene of the invention. The invention also provides that functional introns may be introduced into a man-made gene pathway of the invention. Accordingly, the invention provides for the generation of a chimeric polynucleotide that is a man-made gene containing one (or more) artificially introduced intron(s).

[0098]Accordingly, the invention also provides for the generation of a chimeric polynucleotide that is a man-made gene pathway containing one (or more) artificially introduced intron(s). Preferably, the artificially introduced intron(s) are functional in one or more host cells for gene splicing much in the way that naturally-occurring introns serve functionally in gene splicing. The invention provides a process of producing man-made intron-containing polynucleotides to be introduced into host organisms for recombination and/or splicing.

[0099]A man-made gene produced using the invention can also serve as a substrate for recombination with another nucleic acid. Likewise, a man-made gene pathway produced using the invention can also serve as a substrate for recombination with another nucleic acid. In a preferred instance, the recombination is facilitated by, or occurs at, areas of homology between the man-made, intron-containing gene and a nucleic acid, which serves as a recombination partner. In a particularly preferred instance, the recombination partner may also be a nucleic acid generated by the invention, including a man-made gene or a man-made gene pathway. Recombination may be facilitated by or may occur at areas of homology that exist at the one (or more) artificially introduced intron(s) in the man-made gene.

[0100]The synthetic gene reassembly method of the invention utilizes a plurality of nucleic acid building blocks, each of which preferably has two ligatable ends. The two ligatable ends on each nucleic acid building block may be two blunt ends (i.e. each having an overhang of zero nucleotides), or preferably one blunt end and one overhang, or more preferably still two overhangs.

[0101]A useful overhang for this purpose may be a 3' overhang or a 5' overhang. Thus, a nucleic acid building block may have a 3' overhang or alternatively a 5' overhang or alternatively two 3' overhangs or alternatively two 5' overhangs. The overall order in which the nucleic acid building blocks are assembled to form a finalized chimeric nucleic acid molecule is determined by purposeful experimental design and is not random.

[0102]According to one preferred embodiment, a nucleic acid building block is generated by chemical synthesis of two single-stranded nucleic acids (also referred to as single-stranded oligos) and contacting them so as to allow them to anneal to form a double-stranded nucleic acid building block.

[0103]A double-stranded nucleic acid building block can be of variable size. The sizes of these building blocks can be small or large. Preferred sizes for building block range from 1 base pair (not including any overhangs) to 100,000 base pairs (not including any overhangs). Other preferred size ranges are also provided, which have lower limits of from 1 bp to 10,000 bp (including every integer value in between), and upper limits of from 2 bp to 100,000 bp (including every integer value in between).

[0104]Many methods exist by which a double-stranded nucleic acid building block can be generated that is serviceable for the invention; and these are known in the art and can be readily performed by the skilled artisan.

[0105]According to one embodiment, a double-stranded nucleic acid building block is generated by first generating two single stranded nucleic acids and allowing them to anneal to form a double-stranded nucleic acid building block. The two strands of a double-stranded nucleic acid building block may be complementary at every nucleotide apart from any that form an overhang; thus containing no mismatches, apart from any overhang(s). According to another embodiment, the two strands of a double-stranded nucleic acid building block are complementary at fewer than every nucleotide apart from any that form an overhang. Thus, according to this embodiment, a double-stranded nucleic acid building block can be used to introduce codon degeneracy. Preferably the codon degeneracy is introduced using the site-saturation mutagenesis described herein, using one or more N,N,G/T cassettes or alternatively using one or more N,N,N cassettes.

[0106]The in vivo recombination method of the invention can be performed blindly on a pool of unknown hybrids or alleles of a specific polynucleotide or sequence. However, it is not necessary to know the actual DNA or RNA sequence of the specific polynucleotide.

[0107]The approach of using recombination within a mixed population of genes can be useful for the generation of any useful proteins, for example, interleukin I, antibodies, tPA and growth hormone. This approach may be used to generate proteins having altered specificity or activity. The approach may also be useful for the generation of hybrid nucleic acid sequences, for example, promoter regions, introns, exons, enhancer sequences, 31 untranslated regions or 51 untranslated regions of genes. Thus this approach may be used to generate genes having increased rates of expression. This approach may also be useful in the study of repetitive DNA sequences. Finally, this approach may be useful to mutate ribozymes or aptamers.

[0108]In one aspect the invention described herein is directed to the use of repeated cycles of reductive reassortment, recombination and selection which allow for the directed molecular evolution of highly complex linear sequences, such as DNA, RNA or proteins thorough recombination.

[0109]In vivo shuffling of molecules is useful in providing variants and can be performed utilizing the natural property of cells to recombine multimers. While recombination in vivo has provided the major natural route to molecular diversity, genetic recombination remains a relatively complex process that involves 1) the recognition of homologies; 2) strand cleavage, strand invasion, and metabolic steps leading to the production of recombinant chiasma; and finally 3) the resolution of chiasma into discrete recombined molecules. The formation of the chiasma requires the recognition of homologous sequences.

[0110]In another embodiment, the invention includes a method for producing a hybrid polynucleotide from at least a first polynucleotide and a second polynucleotide. The invention can be used to produce a hybrid polynucleotide by introducing at least a first polynucleotide and a second polynucleotide which share at least one region of partial sequence homology into a suitable host cell. The regions of partial sequence homology promote processes which result in sequence reorganization producing a hybrid polynucleotide. The term "hybrid polynucleotide", as used herein, is any nucleotide sequence which results from the method of the present invention and contains sequence from at least two original polynucleotide sequences. Such hybrid polynucleotides can result from intermolecular recombination events which promote sequence integration between DNA molecules. In addition, such hybrid polynucleotides can result from intramolecular reductive reassortment processes which utilize repeated sequences to alter a nucleotide sequence within a DNA molecule.

[0111]The invention provides a means for generating hybrid polynucleotides which may encode biologically active hybrid polypeptides (e.g., hybrid glycosidases). In one aspect, the original polynucleotides encode biologically active polypeptides. The method of the invention produces new hybrid polypeptides by utilizing cellular processes which integrate the sequence of the original polynucleotides such that the resulting hybrid polynucleotide encodes a polypeptide demonstrating activities derived from the original biologically active polypeptides. For example, the original polynucleotides may encode a particular enzyme from different microorganisms. An enzyme encoded by a first polynucleotide from one organism or variant may, for example, function effectively under a particular environmental condition, e.g. high salinity. An enzyme encoded by a second polynucleotide from a different organism or variant may function effectively under a different environmental condition, such as extremely high temperatures. A hybrid polynucleotide containing sequences from the first and second original polynucleotides may encode an enzyme which exhibits characteristics of both enzymes encoded by the original polynucleotides. Thus, the enzyme encoded by the hybrid polynucleotide may function effectively under environmental conditions shared by each of the enzymes encoded by the first and second polynucleotides, e.g., high salinity and extreme temperatures.

[0112]Enzymes encoded by the polynucleotides of the invention include, but are not limited to, hydrolases, such as glycosidases. A hybrid polypeptide resulting from the method of the invention may exhibit specialized enzyme activity not displayed in the original enzymes. For example, following recombination and/or reductive reassortment of polynucleotides encoding hydrolase activities, the resulting hybrid polypeptide encoded by a hybrid polynucleotide can be screened for specialized hydrolase activities obtained from each of the original enzymes, i.e. the type of bond on which the hydrolase acts and the temperature at which the hydrolase functions. Thus, for example, the hydrolase may be screened to ascertain those chemical functionalities which distinguish the hybrid hydrolase from the original hydrolases, such as: (a) amide (peptide bonds), i.e., proteases; (b) ester bonds, i.e., esterases and lipases; (c) acetals, i.e., glycosidases and, for example, the temperature, pH or salt concentration at which the hybrid polypeptide functions.

[0113]Sources of the original polynucleotides may be isolated from individual organisms ("isolates"), collections of organisms that have been grown in defined media ("enrichment cultures"), or, uncultivated organisms ("environmental samples"). The use of a culture-independent approach to derive polynucleotides encoding novel bioactivities from environmental samples is most preferable since it allows one to access untapped resources of biodiversity.

[0114]Environmental libraries" are generated from environmental samples and represent the collective genomes of naturally occurring organisms archived in cloning vectors that can be propagated in suitable prokaryotic hosts. Because the cloned DNA is initially extracted directly from environmental samples, the libraries are not limited to the small fraction of prokaryotes that can be grown in pure culture. Additionally, a normalization of the environmental DNA present in these samples could allow more equal representation of the DNA from all of the species present in the original sample. This can dramatically increase the efficiency of finding interesting genes from minor constituents of the sample which may be under-represented by several orders of magnitude compared to the dominant species.

[0115]For example, gene libraries generated from one or more uncultivated microorganisms are screened for an activity of interest. Potential pathways encoding bioactive molecules of interest are first captured in prokaryotic cells in the form of gene expression libraries. Polynucleotides encoding activities of interest are isolated from such libraries and introduced into a host cell. The host cell is grown under conditions which promote recombination and/or reductive reassortment creating potentially active biomolecules with novel or enhanced activities.

[0116]The microorganisms from which the polynucleotide may be prepared include prokaryotic microorganisms, such as Eubacteria and Archaebacteria, and lower eukaryotic microorganisms such as fungi, some algae and protozoa. Polynucleotides may be isolated from environmental samples in which case the nucleic acid may be recovered without culturing of an organism or recovered from one or more cultured organisms. In one aspect, such microorganisms may be extremophiles, such as hyperthermophiles, psychrophiles, psychrotrophs, halophiles, barophiles and acidophiles. Polynucleotides encoding enzymes isolated from extremophilic microorganisms are particularly preferred. Such enzymes may function at temperatures above 100° C. in terrestrial hot springs and deep sea thermal vents, at temperatures below 0° C. in arctic waters, in the saturated salt environment of the Dead Sea, at pH values around 0 in coal deposits and geothermal sulfur-rich springs, or at pH values greater than 11 in sewage sludge. For example, several esterases and lipases cloned and expressed from extremophilic organisms show high activity throughout a wide range of temperatures and pHs.

[0117]Polynucleotides selected and isolated as hereinabove described are introduced into a suitable host cell. A suitable host cell is any cell which is capable of promoting recombination and/or reductive reassortment. The selected polynucleotides are preferably already in a vector which includes appropriate control sequences. The host cell can be a higher eukaryotic cell, such as a mammalian cell, or a lower eukaryotic cell, such as a yeast cell, or preferably, the host cell can be a prokaryotic cell, such as a bacterial cell. Introduction of the construct into the host cell can be effected by calcium phosphate transfection, DEAE-Dextran mediated transfection, or electroporation (Davis et al., 1986).

[0118]As representative examples of appropriate hosts, there may be mentioned: bacterial cells, such as E. coli, Streptomyces, Salmonella typhimurium; fungal cells, such as yeast; insect cells such as Drosophila S2 and Spodoptera Sf9; animal cells such as CHO, COS or Bowes melanoma; adenoviruses; and plant cells. The selection of an appropriate host is deemed to be within the scope of those skilled in the art from the teachings herein.

[0119]With particular references to various mammalian cell culture systems that can be employed to express recombinant protein, examples of mammalian expression systems include the COS-7 lines of monkey kidney fibroblasts, described in "SV40-transformed simian cells support the replication of early SV40 mutants" (Gluzman, 1981), and other cell lines capable of expressing a compatible vector, for example, the C127, 3T3, CHO, HeLa and BHK cell lines. Mammalian expression vectors will comprise an origin of replication, a suitable promoter and enhancer, and also any necessary ribosome binding sites, polyadenylation site, splice donor and acceptor sites, transcriptional termination sequences, and 5' flanking nontranscribed sequences. DNA sequences derived from the SV40 splice, and polyadenylation sites may be used to provide the required nontranscribed genetic elements.

[0120]Host cells containing the polynucleotides of interest can be cultured in conventional nutrient media modified as appropriate for activating promoters, selecting transformants or amplifying genes. The culture conditions, such as temperature, pH and the like, are those previously used with the host cell selected for expression, and will be apparent to the ordinarily skilled artisan. The clones which are identified as having the specified enzyme activity may then be sequenced to identify the polynucleotide sequence encoding an enzyme having the enhanced activity.

[0121]In another aspect, it is envisioned the method of the present invention can be used to generate novel polynucleotides encoding biochemical pathways from one or more operons or gene clusters or portions thereof. For example, bacteria and many eukaryotes have a coordinated mechanism for regulating genes whose products are involved in related processes. The genes are clustered, in structures referred to as "gene clusters," on a single chromosome and are transcribed together under the control of a single regulatory sequence, including a single promoter which initiates transcription of the entire cluster. Thus, a gene cluster is a group of adjacent genes that are either identical or related, usually as to their function. An example of a biochemical pathway encoded by gene clusters are polyketides. Polyketides are molecules which are an extremely rich source of bioactivities, including antibiotics (such as tetracyclines and erythromycin), anti-cancer agents (daunomycin), immunosuppressants (FK506 and rapamycin), and veterinary products (monensin). Many polyketides (produced by polyketide synthases) are valuable as therapeutic agents. Polyketide synthases are multifunctional enzymes that catalyze the biosynthesis of an enormous variety of carbon chains differing in length and patterns of functionality and cyclization. Polyketide synthase genes fall into gene clusters and at least one type (designated type I) of polyketide synthases have large size genes and enzymes, complicating genetic manipulation and in vitro studies of these genes/proteins.

[0122]Gene cluster DNA can be isolated from different organisms and ligated into vectors, particularly vectors containing expression regulatory sequences which can control and regulate the production of a detectable protein or protein-related array activity from the ligated gene clusters. Use of vectors which have an exceptionally large capacity for exogenous DNA introduction are particularly appropriate for use with such gene clusters and are described by way of example herein to include the f-factor (or fertility factor) of E. coli. This f-factor of E. coli is a plasmid which affect high-frequency transfer of itself during conjugation and is ideal to achieve and stably propagate large DNA fragments, such as gene clusters from mixed microbial samples. A particularly preferred embodiment is to use cloning vectors, referred to as "fosmids" or bacterial artificial chromosome (BAC) vectors. These are derived from E. coli f-factor which is able to stably integrate large segments of genomic DNA. When integrated with DNA from a mixed uncultured environmental sample, this makes it possible to achieve large genomic fragments in the form of a stable "environmental DNA library." Another type of vector for use in the present invention is a cosmid vector. Cosmid vectors were originally designed to clone and propagate large segments of genomic DNA. Cloning into cosmid vectors is described in detail in Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory Press (1989). Once ligated into an appropriate vector, two or more vectors containing different polyketide synthase gene clusters can be introduced into a suitable host cell. Regions of partial sequence homology shared by the gene clusters will promote processes which result in sequence reorganization resulting in a hybrid gene cluster. The novel hybrid gene cluster can then be screened for enhanced activities not found in the original gene clusters.

[0123]Therefore, in a one embodiment, the invention relates to a method for producing a biologically active hybrid polypeptide and screening such a polypeptide for enhanced activity by:

[0124]1) introducing at least a first polynucleotide in operable linkage and a second polynucleotide in operable linkage, said at least first polynucleotide and second polynucleotide sharing at least one region of partial sequence homology, into a suitable host cell;

[0125]2) growing the host cell under conditions which promote sequence reorganization resulting in a hybrid polynucleotide in operable linkage;

[0126]3) expressing a hybrid polypeptide encoded by the hybrid polynucleotide;

[0127]4) screening the hybrid polypeptide under conditions which promote identification of enhanced biological activity; and

[0128]5) isolating the a polynucleotide encoding the hybrid polypeptide.

[0129]Methods for screening for various enzyme activities are known to those of skill in the art and are discussed throughout the present specification. Such methods may be employed when isolating the polypeptides and polynucleotides of the invention.

[0130]As representative examples of expression vectors which may be used, there may be mentioned viral particles, baculovirus, phage, plasmids, phagemids, cosmids, fosmids, bacterial artificial chromosomes, viral DNA (e.g., vaccinia, adenovirus, foul pox virus, pseudorabies and derivatives of SV40), P1-based artificial chromosomes, yeast plasmids, yeast artificial chromosomes, and any other vectors specific for specific hosts of interest (such as bacillus, aspergillus and yeast). Thus, for example, the DNA may be included in any one of a variety of expression vectors for expressing a polypeptide. Such vectors include chromosomal, nonchromosomal and synthetic DNA sequences. Large numbers of suitable vectors are known to those of skill in the art, and are commercially available. The following vectors are provided by way of example; Bacterial: pQE vectors (Qiagen), pBluescript plasmids, pNH vectors, (lambda-ZAP vectors (Stratagene); ptrc99a, pKK223-3, pDR540, pRIT2T (Pharmacia); Eukaryotic: pXT1, pSG5 (Stratagene), pSVK3, pBPV, pMSG, pSVLSV40 (Pharmacia). However, any other plasmid or other vector may be used so long as they are replicable and viable in the host. Low copy number or high copy number vectors may be employed with the present invention.

[0131]The DNA sequence in the expression vector is operatively linked to an appropriate expression control sequence(s) (promoter) to direct RNA synthesis. Particular named bacterial promoters include lac, lacZ, T3, T7, gpt, lambda PR, PL and trp. Eukaryotic promoters include CMV immediate early, HSV thymidine kinase, early and late SV40, LTRs from retrovirus, and mouse metallothionein-I. Selection of the appropriate vector and promoter is well within the level of ordinary skill in the art. The expression vector also contains a ribosome binding site for translation initiation and a transcription terminator. The vector may also include appropriate sequences for amplifying expression. Promoter regions can be selected from any desired gene using chloramphenicol transferase (CAT) vectors or other vectors with selectable markers. In addition, the expression vectors preferably contain one or more selectable marker genes to provide a phenotypic trait for selection of transformed host cells such as dihydrofolate reductase or neomycin resistance for eukaryotic cell culture, or such as tetracycline or ampicillin resistance in E. coli.

[0132]In vivo reassortment is focused on "inter-molecular" processes collectively referred to as "recombination" which in bacteria, is generally viewed as a "RecA-dependent" phenomenon. The invention can rely on recombination processes of a host cell to recombine and re-assort sequences, or the cells' ability to mediate reductive processes to decrease the complexity of quasi-repeated sequences in the cell by deletion. This process of "reductive reassortment" occurs by an "intra-molecular", RecA-independent process.

[0133]Therefore, in another aspect of the invention, novel polynucleotides can be generated by the process of reductive reassortment. The method involves the generation of constructs containing consecutive sequences (original encoding sequences), their insertion into an appropriate vector, and their subsequent introduction into an appropriate host cell. The reassortment of the individual molecular identities occurs by combinatorial processes between the consecutive sequences in the construct possessing regions of homology, or between quasi-repeated units. The reassortment process recombines and/or reduces the complexity and extent of the repeated sequences, and results in the production of novel molecular species. Various treatments may be applied to enhance the rate of reassortment. These could include treatment with ultra-violet light, or DNA damaging chemicals, and/or the use of host cell lines displaying enhanced levels of "genetic instability". Thus the reassortment process may involve homologous recombination or the natural property of quasi-repeated sequences to direct their own evolution.

[0134]Repeated or "quasi-repeated" sequences play a role in genetic instability. In the present invention, "quasi-repeats" are repeats that are not restricted to their original unit structure. Quasi-repeated units can be presented as an array of sequences in a construct; consecutive units of similar sequences. Once ligated, the junctions between the consecutive sequences become essentially invisible and the quasi-repetitive nature of the resulting construct is now continuous at the molecular level. The deletion process the cell performs to reduce the complexity of the resulting construct operates between the quasi-repeated sequences. The quasi-repeated units provide a practically limitless repertoire of templates upon which slippage events can occur. The constructs containing the quasi-repeats thus effectively provide sufficient molecular elasticity that deletion (and potentially insertion) events can occur virtually anywhere within the quasi-repetitive units.

[0135]When the quasi-repeated sequences are all ligated in the same orientation, for instance head to tail or vice versa, the cell cannot distinguish individual units. Consequently, the reductive process can occur throughout the sequences. In contrast, when for example, the units are presented head to head, rather than head to tail, the inversion delineates the endpoints of the adjacent unit so that deletion formation will favor the loss of discrete units. Thus, it is preferable with the present method that the sequences are in the same orientation. Random orientation of quasi-repeated sequences will result in the loss of reassortment efficiency, while consistent orientation of the sequences will offer the highest efficiency. However, while having fewer of the contiguous sequences in the same orientation decreases the efficiency, it may still provide sufficient elasticity for the effective recovery of novel molecules. Constructs can be made with the quasi-repeated sequences in the same orientation to allow higher efficiency.

[0136]Sequences can be assembled in a head to tail orientation using any of a variety of methods, including the following:

[0137]a) Primers that include a poly-A head and poly-T tail which when made single-stranded would provide orientation can be utilized. This is accomplished by having the first few bases of the primers made from RNA and hence easily removed RNAseH.

[0138]b) Primers that include unique restriction cleavage sites can be utilized. Multiple sites, a battery of unique sequences, and repeated synthesis and ligation steps would be required.

[0139]c) The inner few bases of the primer could be thiolated and an exonuclease used to produce properly tailed molecules.

[0140]The recovery of the re-assorted sequences relies on the identification of cloning vectors with a reduced repetitive index (RI). The re-assorted encoding sequences can then be recovered by amplification. The products are re-cloned and expressed. The recovery of cloning vectors with reduced RI can be affected by:

[0141]1) The use of vectors only stably maintained when the construct is reduced in complexity.

[0142]2) The physical recovery of shortened vectors by physical procedures. In this case, the cloning vector would be recovered using standard plasmid isolation procedures and size fractionated on either an agarose gel, or column with a low molecular weight cut off utilizing standard procedures.

[0143]3) The recovery of vectors containing interrupted genes which can be selected when insert size decreases.

[0144]4) The use of direct selection techniques with an expression vector and the appropriate selection.

[0145]Encoding sequences (for example, genes) from related organisms may demonstrate a high degree of homology and encode quite diverse protein products. These types of sequences are particularly useful in the present invention as quasi-repeats. However, while the examples illustrated below demonstrate the reassortment of nearly identical original encoding sequences (quasi-repeats), this process is not limited to such nearly identical repeats.

[0146]The following example demonstrates a method of the invention. Encoding nucleic acid sequences (quasi-repeats) derived from three (3) unique species are described. Each sequence encodes a protein with a distinct set of properties. Each of the sequences differs by a single or a few base pairs at a unique position in the sequence. The quasi-repeated sequences are separately or collectively amplified and ligated into random assemblies such that all possible permutations and combinations are available in the population of ligated molecules. The number of quasi-repeat units can be controlled by the assembly conditions. The average number of quasi-repeated units in a construct is defined as the repetitive index (RI).

[0147]Once formed, the constructs may, or may not be size fractionated on an agarose gel according to published protocols, inserted into a cloning vector, and transfected into an appropriate host cell. The cells are then propagated and "reductive reassortment" is effected. The rate of the reductive reassortment process may be stimulated by the introduction of DNA damage if desired. Whether the reduction in RI is mediated by deletion formation between repeated sequences by an "intra-molecular" mechanism, or mediated by recombination-like events through "inter-molecular" mechanisms is immaterial. The end result is a reassortment of the molecules into all possible combinations.

[0148]Optionally, the method comprises the additional step of screening the library members of the shuffled pool to identify individual shuffled library members having the ability to bind or otherwise interact, or catalyze a particular reaction (e.g., such as catalytic domain of an enzyme) with a predetermined macromolecule, such as for example a proteinaceous receptor, an oligosaccharide, viron, or other predetermined compound or structure.

[0149]The polypeptides that are identified from such libraries can be used for therapeutic, diagnostic, research and related purposes (e.g., catalysts, solutes for increasing osmolarity of an aqueous solution, and the like), and/or can be subjected to one or more additional cycles of shuffling and/or selection.

[0150]In another aspect, it is envisioned that prior to or during recombination or reassortment, polynucleotides generated by the method of the invention can be subjected to agents or processes which promote the introduction of mutations into the original polynucleotides. The introduction of such mutations would increase the diversity of resulting hybrid polynucleotides and polypeptides encoded therefrom. The agents or processes which promote mutagenesis can include, but are not limited to: (+)-CC-1065, or a synthetic analog such as (+)-CC-1065-(N3-Adenine (See Sun and Hurley, (1992); an N-acetylated or deacetylated 4'-fluoro-4-aminobiphenyl adduct capable of inhibiting DNA synthesis (See, for example, van de Poll et al. (1992)); or a N-acetylated or deacetylated 4-aminobiphenyl adduct capable of inhibiting DNA synthesis (See also, van de Poll et al. (1992), pp. 751-758); trivalent chromium, a trivalent chromium salt, a polycyclic aromatic hydrocarbon (PAH) DNA adduct capable of inhibiting DNA replication, such as 7-bromomethyl-benz[α]anthracene ("BMA"), tris(2,3-dibromopropyl)pho-sphate ("Tris-BP"), 1,2-dibromo-3-chloropropane ("DBCP"), 2-bromoacrolein (2BA), benzo[α]pyrene-7,8-dihydrodiol-9-10-epoxide ("BPDE"), a platinum(II) halogen salt, N-hydroxy-2-amino-3-methylimidazo[4,5-g]-quino-line ("N-hydroxy-IQ"), and N-hydroxy-2-amino-1-methyl-6-phenylimidazo[4,5-f]-pyridine ("N-hydroxy-PhIP"). Especially preferred means for slowing or halting PCR amplification consist of UV light (+)-CC-1065 and (+)-CC-1065-(N3-Adenine). Particularly encompassed means are DNA adducts or polynucleotides comprising the DNA adducts from the polynucleotides or polynucleotides pool, which can be released or removed by a process including heating the solution comprising the polynucleotides prior to further processing.

[0151]In another aspect the invention is directed to a method of producing recombinant proteins having biological activity by treating a sample comprising double-stranded template polynucleotides encoding a wild-type protein under conditions according to the invention which provide for the production of hybrid or re-assorted polynucleotides.

[0152]The invention also provides for the use of proprietary codon primers (containing a degenerate N,N,N sequence) to introduce point mutations into a polynucleotide, so as to generate a set of progeny polypeptides in which a full range of single amino acid substitutions is represented at each amino acid position (gene site saturated mutagenesis (GSSM)). The oligos used are comprised contiguously of a first homologous sequence, a degenerate N,N,N sequence, and preferably but not necessarily a second homologous sequence. The downstream progeny translational products from the use of such oligos include all possible amino acid changes at each amino acid site along the polypeptide, because the degeneracy of the N,N,N sequence includes codons for all 20 amino acids.

[0153]In one aspect, one such degenerate oligo (comprised of one degenerate N,N,N cassette) is used for subjecting each original codon in a parental polynucleotide template to a full range of codon substitutions. In another aspect, at least two degenerate N,N,N cassettes are used--either in the same oligo or not, for subjecting at least two original codons in a parental polynucleotide template to a full range of codon substitutions. Thus, more than one N,N,N sequence can be contained in one oligo to introduce amino acid mutations at more than one site. This plurality of N,N,N sequences can be directly contiguous, or separated by one or more additional nucleotide sequence(s). In another aspect, oligos serviceable for introducing additions and deletions can be used either alone or in combination with the codons containing an N,N,N sequence, to introduce any combination or permutation of amino acid additions, deletions, and/or substitutions.

[0154]In a particular exemplification, it is possible to simultaneously mutagenize two or more contiguous amino acid positions using an oligo that contains contiguous N,N,N triplets, i.e. a degenerate (N,N,N)n sequence.

[0155]In another aspect, the present invention provides for the use of degenerate cassettes having less degeneracy than the N,N,N sequence. For example, it may be desirable in some instances to use (e.g. in an oligo) a degenerate triplet sequence comprised of only one N, where said N can be in the first second or third position of the triplet. Any other bases including any combinations and permutations thereof can be used in the remaining two positions of the triplet. Alternatively, it may be desirable in some instances to use (e.g., in an oligo) a degenerate N,N,N triplet sequence, N,N,G/T, or an N,N, G/C triplet sequence.

[0156]It is appreciated, however, that the use of a degenerate triplet (such as N,N,G/T or an N,N, G/C triplet sequence) as disclosed in the instant invention is advantageous for several reasons. In one aspect, this invention provides a means to systematically and fairly easily generate the substitution of the full range of possible amino acids (for a total of 20 amino acids) into each and every amino acid position in a polypeptide. Thus, for a 100 amino acid polypeptide, the invention provides a way to systematically and fairly easily generate 2000 distinct species (i.e., 20 possible amino acids per position times 100 amino acid positions). It is appreciated that there is provided, through the use of an oligo containing a degenerate N,N,G/T or an N,N, G/C triplet sequence, 32 individual sequences that code for 20 possible amino acids. Thus, in a reaction vessel in which a parental polynucleotide sequence is subjected to saturation mutagenesis using one such oligo, there are generated 32 distinct progeny polynucleotides encoding 20 distinct polypeptides. In contrast, the use of a non-degenerate oligo in site-directed mutagenesis leads to only one progeny polypeptide product per reaction vessel.

[0157]This invention also provides for the use of nondegenerate oligos, which can optionally be used in combination with degenerate primers disclosed. It is appreciated that in some situations, it is advantageous to use nondegenerate oligos to generate specific point mutations in a working polynucleotide. This provides a means to generate specific silent point mutations, point mutations leading to corresponding amino acid changes, and point mutations that cause the generation of stop codons and the corresponding expression of polypeptide fragments.

[0158]Thus, in a preferred embodiment of this invention, each saturation mutagenesis reaction vessel contains polynucleotides encoding at least 20 progeny polypeptide molecules such that all 20 amino acids are represented at the one specific amino acid position corresponding to the codon position mutagenized in the parental polynucleotide. The 32-fold degenerate progeny polypeptides generated from each saturation mutagenesis reaction vessel can be subjected to clonal amplification (e.g., cloned into a suitable E. coli host using an expression vector) and subjected to expression screening. When an individual progeny polypeptide is identified by screening to display a favorable change in property (when compared to the parental polypeptide), it can be sequenced to identify the correspondingly favorable amino acid substitution contained therein.

[0159]It is appreciated that upon mutagenizing each and every amino acid position in a parental polypeptide using saturation mutagenesis as disclosed herein, favorable amino acid changes may be identified at more than one amino acid position. One or more new progeny molecules can be generated that contain a combination of all or part of these favorable amino acid substitutions. For example, if 2 specific favorable amino acid changes are identified in each of 3 amino acid positions in a polypeptide, the permutations include 3 possibilities at each position (no change from the original amino acid, and each of two favorable changes) and 3 positions. Thus, there are 3×3×3 or 27 total possibilities, including 7 that were previously examined--6 single point mutations (i.e., 2 at each of three positions) and no change at any position.

[0160]In yet another aspect, site-saturation mutagenesis can be used together with shuffling, chimerization, recombination and other mutagenizing processes, along with screening. This invention provides for the use of any mutagenizing process(es), including saturation mutagenesis, in an iterative manner. In one exemplification, the iterative use of any mutagenizing process(es) is used in combination with screening.

[0161]Thus, in a non-limiting exemplification, this invention provides for the use of saturation mutagenesis in combination with additional mutagenization processes, such as process where two or more related polynucleotides are introduced into a suitable host cell such that a hybrid polynucleotide is generated by recombination and reductive reassortment.

[0162]In addition to performing mutagenesis along the entire sequence of a gene, the instant invention provides that mutagenesis can be use to replace each of any number of bases in a polynucleotide sequence, wherein the number of bases to be mutagenized is preferably every integer from 15 to 100,000. Thus, instead of mutagenizing every position along a molecule, one can subject every or a discrete number of bases (preferably a subset totaling from 15 to 100,000) to mutagenesis. Preferably, a separate nucleotide is used for mutagenizing each position or group of positions along a polynucleotide sequence. A group of 3 positions to be mutagenized may be a codon. The mutations are preferably introduced using a mutagenic primer, containing a heterologous cassette, also referred to as a mutagenic cassette. Preferred cassettes can have from 1 to 500 bases. Each nucleotide position in such heterologous cassettes be N, A, C, G, T, A/C, A/G, A/T, C/G, C/T, G/T, C/G/T, A/G/T, A/C/T, A/C/G, or E, where E is any base that is not A, C, G, or T (E can be referred to as a designer oligo).

[0163]In a general sense, saturation mutagenesis is comprised of mutagenizing a complete set of mutagenic cassettes (wherein each cassette is preferably about 1-500 bases in length) in defined polynucleotide sequence to be mutagenized (wherein the sequence to be mutagenized is preferably from about 15 to 100,000 bases in length). Thus, a group of mutations (ranging from 1 to 100 mutations) is introduced into each cassette to be mutagenized. A grouping of mutations to be introduced into one cassette can be different or the same from a second grouping of mutations to be introduced into a second cassette during the application of one round of saturation mutagenesis. Such groupings are exemplified by deletions, additions, groupings of particular codons, and groupings of particular nucleotide cassettes.

[0164]Defined sequences to be mutagenized include a whole gene, pathway, cDNA, an entire open reading frame (ORF), and entire promoter, enhancer, repressor/transactivator, origin of replication, intron, operator, or any polynucleotide functional group. Generally, a "defined sequences" for this purpose may be any polynucleotide that a 15 base-polynucleotide sequence, and polynucleotide sequences of lengths between 15 bases and 15,000 bases (this invention specifically names every integer in between). Considerations in choosing groupings of codons include types of amino acids encoded by a degenerate mutagenic cassette.

[0165]In a particularly preferred exemplification a grouping of mutations that can be introduced into a mutagenic cassette, this invention specifically provides for degenerate codon substitutions (using degenerate oligos) that code for 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, and 20 amino acids a teach position, and a library of polypeptides encoded thereby.

[0166]One aspect of the invention is an isolated nucleic acid comprising one of the sequences of Group A nucleic acid sequences, and sequences substantially identical thereto, the sequences complementary thereto, or a fragment comprising at least 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, 150, 200, 300, 400, or 500 consecutive bases of one of the sequences of a Group A nucleic acid sequence (or the sequences complementary thereto). The isolated, nucleic acids may comprise DNA, including cDNA, genomic DNA, and synthetic DNA. The DNA may be double-stranded or single-stranded, and if single stranded may be the coding strand or non-coding (anti-sense) strand. Alternatively, the isolated nucleic acids may comprise RNA.

[0167]As discussed in more detail below, the isolated nucleic acids of one of the Group A nucleic acid sequences, and sequences substantially identical thereto, may be used to prepare one of the polypeptides of a Group B amino acid sequence, and sequences substantially identical thereto, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids of one of the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto.

[0168]Accordingly, another aspect of the invention is an isolated nucleic acid which encodes one of the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids of one of the polypeptides of the Group B amino acid sequences. The coding sequences of these nucleic acids may be identical to one of the coding sequences of one of the nucleic acids of Group A nucleic acid sequences, or a fragment thereof or may be different coding sequences which encode one of the polypeptides of Group B amino acid sequences, sequences substantially identical thereto, and fragments having at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids of one of the polypeptides of Group B amino acid sequences, as a result of the redundancy or degeneracy of the genetic code. The genetic code is well known to those of skill in the art and can be obtained, for example, on page 214 of B. Lewin, Genes VI, Oxford University Press, 1997, the disclosure of which is incorporated herein by reference.

[0169]The isolated nucleic acid which encodes one of the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto, may include, but is not limited to: only the coding sequence of one of Group A nucleic acid sequences, and sequences substantially identical thereto, and additional coding sequences, such as leader sequences or proprotein sequences and non-coding sequences, such as introns or non-coding sequences 5' and/or 3' of the coding sequence. Thus, as used herein, the term "polynucleotide encoding a polypeptide" encompasses a polynucleotide which includes only the coding sequence for the polypeptide as well as a polynucleotide which includes additional coding and/or non-coding sequence.

[0170]Alternatively, the nucleic acid sequences of Group A nucleic acid sequences, and sequences substantially identical thereto, may be mutagenized using conventional techniques, such as site directed mutagenesis, or other techniques familiar to those skilled in the art, to introduce silent changes into the polynucleotides of Group A nucleic acid sequences, and sequences substantially identical thereto. As used herein, "silent changes" include, for example, changes which do not alter the amino acid sequence encoded by the polynucleotide. Such changes may be desirable in order to increase the level of the polypeptide produced by host cells containing a vector encoding the polypeptide by introducing codons or codon pairs which occur frequently in the host organism.

[0171]The invention also relates to polynucleotides which have nucleotide changes which result in amino acid substitutions, additions, deletions, fusions and truncations in the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto. Such nucleotide changes may be introduced using techniques such as site directed mutagenesis, random chemical mutagenesis, exonuclease III deletion, and other recombinant DNA techniques. Alternatively, such nucleotide changes may be naturally occurring allelic variants which are isolated by identifying nucleic acids which specifically hybridize to probes comprising at least 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, 150, 200, 300, 400, or 500 consecutive bases of one of the sequences of Group A nucleic acid sequences, and sequences substantially identical thereto (or the sequences complementary thereto) under conditions of high, moderate, or low stringency as provided herein.

[0172]The isolated nucleic acids of Group A nucleic acid sequences, and sequences substantially identical thereto, the sequences complementary thereto, or a fragment comprising at least 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, 150, 200, 300, 400, or 500 consecutive bases of one of the sequences of Group A nucleic acid sequences, and sequences substantially identical thereto, or the sequences complementary thereto may also be used as probes to determine whether a biological sample, such as a soil sample, contains an organism having a nucleic acid sequence of the invention or an organism from which the nucleic acid was obtained. In such procedures, a biological sample potentially harboring the organism from which the nucleic acid was isolated is obtained and nucleic acids are obtained from the sample. The nucleic acids are contacted with the probe under conditions which permit the probe to specifically hybridize to any complementary sequences from which are present therein.

[0173]Where necessary, conditions which permit the probe to specifically hybridize to complementary sequences may be determined by placing the probe in contact with complementary sequences from samples known to contain the complementary sequence as well as control sequences which do not contain the complementary sequence. Hybridization conditions, such as the salt concentration of the hybridization buffer, the formamide concentration of the hybridization buffer, or the hybridization temperature, may be varied to identify conditions which allow the probe to hybridize specifically to complementary nucleic acids.

[0174]If the sample contains the organism from which the nucleic acid was isolated, specific hybridization of the probe is then detected. Hybridization may be detected by labeling the probe with a detectable agent such as a radioactive isotope, a fluorescent dye or an enzyme capable of catalyzing the formation of a detectable product.

[0175]Many methods for using the labeled probes to detect the presence of complementary nucleic acids in a sample are familiar to those skilled in the art. These include Southern Blots, Northern Blots, colony hybridization procedures, and dot blots. Protocols for each of these procedures are provided in Ausubel et al. Current Protocols in Molecular Biology, John Wiley 503 Sons, Inc. and Sambrook et al., Molecular Cloning: A Laboratory Manual 2nd Ed., Cold Spring Harbor Laboratory Press (1989), the entire disclosures of which are incorporated herein by reference.

[0176]Alternatively, more than one probe (at least one of which is capable of specifically hybridizing to any complementary sequences which are present in the nucleic acid sample), may be used in an amplification reaction to determine whether the sample contains an organism containing a nucleic acid sequence of the invention (e.g., an organism from which the nucleic acid was isolated). Typically, the probes comprise oligonucleotides. In one embodiment, the amplification reaction may comprise a PCR reaction. PCR protocols are described in Ausubel and Sambrook, supra. Alternatively, the amplification may comprise a ligase chain reaction, 3SR, or strand displacement reaction. (See Barany, F., "The Ligase Chain Reaction in a PCR World", PCR Methods and Applications 1:5-16, 1991; E. Fahy et al., "Self-sustained Sequence Replication (3SR): An Isothermal Transcription-based Amplification System Alternative to PCR", PCR Methods and Applications 1:25-33, 1991; and Walker G. T. et al., "Strand Displacement Amplification--an Isothermal in vitro DNA Amplification Technique", Nucleic Acid Research 20:1691-1696, 1992, the disclosures of which are incorporated herein by reference in their entireties). In such procedures, the nucleic acids in the sample are contacted with the probes, the amplification reaction is performed, and any resulting amplification product is detected. The amplification product may be detected by performing gel electrophoresis on the reaction products and staining the gel with an interculator such as ethidium bromide. Alternatively, one or more of the probes may be labeled with a radioactive isotope and the presence of a radioactive amplification product may be detected by autoradiography after gel electrophoresis.

[0177]Probes derived from sequences near the ends of the sequences of Group A nucleic acid sequences, and sequences substantially identical thereto, may also be used in chromosome walking procedures to identify clones containing genomic sequences located adjacent to the sequences of Group A nucleic acid sequences, and sequences substantially identical thereto. Such methods allow the isolation of genes which encode additional proteins from the host organism.

[0178]The isolated nucleic acids of Group A nucleic acid sequences, and sequences substantially identical thereto, the sequences complementary thereto, or a fragment comprising at least 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, 150, 200, 300, 400, or 500 consecutive bases of one of the sequences of Group A nucleic acid sequences, and sequences substantially identical thereto, or the sequences complementary thereto may be used as probes to identify and isolate related nucleic acids. In some embodiments, the related nucleic acids may be cDNAs or genomic DNAs from organisms other than the one from which the nucleic acid was isolated. For example, the other organisms may be related organisms. In such procedures, a nucleic acid sample is contacted with the probe under conditions which permit the probe to specifically hybridize to related sequences. Hybridization of the probe to nucleic acids from the related organism is then detected using any of the methods described above.

[0179]In nucleic acid hybridization reactions, the conditions used to achieve a particular level of stringency will vary, depending on the nature of the nucleic acids being hybridized. For example, the length, degree of complementarity, nucleotide sequence composition (e.g., GC v. AT content), and nucleic acid type (e.g., RNA v. DNA) of the hybridizing regions of the nucleic acids can be considered in selecting hybridization conditions. An additional consideration is whether one of the nucleic acids is immobilized, for example, on a filter.

[0180]Hybridization may be carried out under conditions of low stringency, moderate stringency or high stringency. As an example of nucleic acid hybridization, a polymer membrane containing immobilized denatured nucleic acids is first prehybridized for 30 minutes at 45° C. in a solution consisting of 0.9 M NaCl, 50 mM NaH₂PO₄, pH 7.0, 5.0 mM Na₂EDTA, 0.5% SDS, 10× Denhardt's, and 0.5 mg/ml polyriboadenylic acid. Approximately 2×10⁷ cpm (specific activity 4-9×10⁸ cpm/ug) of ³²P end-labeled oligonucleotide probe are then added to the solution. After 12-16 hours of incubation, the membrane is washed for 30 minutes at room temperature in IX SET (150 mM NaCl, 20 mM Tris hydrochloride, pH 7.8, 1 mM Na₂EDTA) containing 0.5% SDS, followed by a 30 minute wash in fresh IX SET at T_m-10° C. for the oligonucleotide probe. The membrane is then exposed to auto-radiographic film for detection of hybridization signals.

[0181]By varying the stringency of the hybridization conditions used to identify nucleic acids, such as cDNAs or genomic DNAs, which hybridize to the detectable probe, nucleic acids having different levels of homology to the probe can be identified and isolated. Stringency may be varied by conducting the hybridization at varying temperatures below the melting temperatures of the probes. The melting temperature, T_m, is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly complementary probe. Very stringent conditions are selected to be equal to or about 5° C. lower than the T_m for a particular probe. The melting temperature of the probe may be calculated using the following formulas:

[0182]For probes between 14 and 70 nucleotides in length the melting temperature (T_m) is calculated using the formula: T_m=81.5+16.6(log [Na+])+0.41 (fraction G+C)-(600/N) where N is the length of the probe.

[0183]If the hybridization is carried out in a solution containing formamide, the melting temperature may be calculated using the equation: T_m=81.5+16.6(log [Na+])+0.41(fraction G+C)-(0.63% formamide)-(600/N) where N is the length of the probe.

[0184]Prehybridization may be carried out in 6× SSC, 5× Denhardt's reagent, 0.5% SDS, 100% g denatured fragmented salmon sperm DNA or 6× SSC, 5× Denhardt's reagent, 0.5% SDS, 100μg denatured fragmented salmon sperm DNA, 50% formamide. The formulas for SSC and Denhardt's solutions are listed in Sambrook et al, supra.

[0185]Hybridization is conducted by adding the detectable probe to the prehybridization solutions listed above. Where the probe comprises double stranded DNA, it is denatured before addition to the hybridization solution. The filter is contacted with the hybridization solution for a sufficient period of time to allow the probe to hybridize to cDNAs or genomic DNAs containing sequences complementary thereto or homologous thereto. For probes over 200 nucleotides in length, the hybridization may be carried out at 15-25° C. below the T_m. For shorter probes, such as oligonucleotide probes, the hybridization may be conducted at 5-10 C below the T_m. Typically, for hybridizations in 6× SSC, the hybridization is conducted at approximately 68° C. Usually, for hybridizations in 50% formamide containing solutions, the hybridization is conducted at approximately 42° C.

[0186]All of the foregoing hybridizations would be considered to be under conditions of high stringency.

[0187]Following hybridization, the filter is washed to remove any non-specifically bound detectable probe. The stringency used to wash the filters can also be varied depending on the nature of the nucleic acids being hybridized, the length of the nucleic acids being hybridized, the degree of complementarity, the nucleotide sequence composition (e.g., GC v. AT content), and the nucleic acid type (e.g., RNA v. DNA). Examples of progressively higher stringency condition washes are as follows: 2× SSC, 0.1% SDS at room temperature for 15 minutes (low stringency); 0.1× SSC, 0.5% SDS at room temperature for 30 minutes to 1 hour (moderate stringency); 0.1× SSC, 0.5% SDS for 15 to 30 minutes at between the hybridization temperature and 68° C. (high stringency); and 0.15M NaCl for 15 minutes at 72° C. (very high stringency). A final low stringency wash can be conducted in 0.1× SSC at room temperature. The examples above are merely illustrative of one set of conditions that can be used to wash filters. One of skill in the art would know that there are numerous recipes for different stringency washes. Some other examples are given below.

[0188]Nucleic acids which have hybridized to the probe are identified by autoradiography or other conventional techniques.

[0189]The above procedure may be modified to identify nucleic acids having decreasing levels of homology to the probe sequence. For example, to obtain nucleic acids of decreasing homology to the detectable probe, less stringent conditions may be used. For example, the hybridization temperature may be decreased in increments of 5° C. from 68° C. to 42° C. in a hybridization buffer having a Na+ concentration of approximately 1 M. Following hybridization, the filter may be washed with 2× SSC, 0.5% SDS at the temperature of hybridization. These conditions are considered to be "moderate" conditions above 50° C. and "low" conditions below 50° C. A specific example of "moderate" hybridization conditions is when the above hybridization is conducted at 55° C. A specific example of "low stringency" hybridization conditions is when the above hybridization is conducted at 45° C.

[0190]Alternatively, the hybridization may be carried out in buffers, such as 6× SSC, containing formamide at a temperature of 42° C. In this case, the concentration of formamide in the hybridization buffer may be reduced in 5% increments from 50% to 0% to identify clones having decreasing levels of homology to the probe. Following hybridization, the filter may be washed with 6× SSC, 0.5% SDS at 50° C. These conditions are considered to be "moderate" conditions above 25% formamide and "low" conditions below 25% formamide. A specific example of "moderate" hybridization conditions is when the above hybridization is conducted at 30% formamide. A specific example of "low stringency" hybridization conditions is when the above hybridization is conducted at 10% formamide.

[0191]For example, the preceding methods may be used to isolate nucleic acids having a sequence with at least about 97%, at least 95%, at least 90%, at least 85%, at least 80%, at least 70%, at least 65%, at least 60%, at least 55%, or at least 50% homology to a nucleic acid sequence selected from the group consisting of one of the sequences of Group A nucleic acid sequences, and sequences substantially identical thereto, or fragments comprising at least about 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, 150, 200, 300, 400, or 500 consecutive bases thereof, and the sequences complementary thereto. Homology may be measured using the alignment algorithm. For example, the homologous polynucleotides may have a coding sequence which is a naturally occurring allelic variant of one of the coding sequences described herein. Such allelic variants may have a substitution, deletion or addition of one or more nucleotides when compared to the nucleic acids of Group A nucleic acid sequences or the sequences complementary thereto.

[0192]Additionally, the above procedures may be used to isolate nucleic acids which encode polypeptides having at least about 99%, 95%, at least 90%, at least 85%, at least 80%, at least 75%, at least 70%, at least 65%, at least 60%, at least 55%, or at least 50% homology to a polypeptide having the sequence of one of Group B amino acid sequences, and sequences substantially identical thereto, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof as determined using a sequence alignment algorithm (e.g., such as the FASTA version 3.0t78 algorithm with the default parameters).

[0193]Another aspect of the invention is an isolated or purified polypeptide comprising the sequence of one of Group A nucleic acid sequences, and sequences substantially identical thereto, or fragments comprising at least about 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof. As discussed above, such polypeptides may be obtained by inserting a nucleic acid encoding the polypeptide into a vector such that the coding sequence is operably linked to a sequence capable of driving the expression of the encoded polypeptide in a suitable host cell. For example, the expression vector may comprise a promoter, a ribosome binding site for translation initiation and a transcription terminator. The vector may also include appropriate sequences for amplifying expression.

[0194]Promoters suitable for expressing the polypeptide or fragment thereof in bacteria include the E. coli lac or trp promoters, the lacI promoter, the lacZ promoter, the T3 promoter, the T7 promoter, the gpt promoter, the lambda P_R promoter, the lambda P_L promoter, promoters from operons encoding glycolytic enzymes such as 3-phosphoglycerate kinase (PGK), and the acid phosphatase promoter. Fungal promoters include the V factor promoter. Eukaryotic promoters include the CMV immediate early promoter, the HSV thymidine kinase promoter, heat shock promoters, the early and late SV40 promoter, LTRs from retroviruses, and the mouse metallothionein-I promoter. Other promoters known to control expression of genes in prokaryotic or eukaryotic cells or their viruses may also be used.

[0195]Mammalian expression vectors may also comprise an origin of replication, any necessary ribosome binding sites, a polyadenylation site, splice donor and acceptor sites, transcriptional termination sequences, and 5' flanking nontranscribed sequences. In some embodiments, DNA sequences derived from the SV40 splice and polyadenylation sites may be used to provide the required nontranscribed genetic elements.

[0196]Vectors for expressing the polypeptide or fragment thereof in eukaryotic cells may also contain enhancers to increase expression levels. Enhancers are cis-acting elements of DNA, usually from about 10 to about 300 bp in length that act on a promoter to increase its transcription. Examples include the SV40 enhancer on the late side of the replication origin bp 100 to 270, the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and the adenovirus enhancers.

[0197]In addition, the expression vectors typically contain one or more selectable marker genes to permit selection of host cells containing the vector. Such selectable markers include genes encoding dihydrofolate reductase or genes conferring neomycin resistance for eukaryotic cell culture, genes conferring tetracycline or ampicillin resistance in E. coli, and the S. cerevisiae TRP1 gene.

[0198]In some embodiments, the nucleic acid encoding one of the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto, or fragments comprising at least about 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof is assembled in appropriate phase with a leader sequence capable of directing secretion of the translated polypeptide or fragment thereof. Optionally, the nucleic acid can encode a fusion polypeptide in which one of the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof is fused to heterologous peptides or polypeptides, such as N-terminal identification peptides which impart desired characteristics, such as increased stability or simplified purification.

[0199]The appropriate DNA sequence may be inserted into the vector by a variety of procedures. In general, the DNA sequence is ligated to the desired position in the vector following digestion of the insert and the vector with appropriate restriction endonucleases. Alternatively, blunt ends in both the insert and the vector may be ligated. A variety of cloning techniques are disclosed in Ausubel et al. Current Protocols in Molecular Biology, John Wiley 503 Sons, Inc. 1997 and Sambrook et al., Molecular Cloning: A Laboratory Manual 2nd Ed., Cold Spring Harbor Laboratory Press (1989), the entire disclosures of which are incorporated herein by reference. Such procedures and others are deemed to be within the scope of those skilled in the art.

[0200]The vector may be, for example, in the form of a plasmid, a viral particle, or a phage. Other vectors include chromosomal, nonchromosomal and synthetic DNA sequences, derivatives of SV40; bacterial plasmids, phage DNA, baculovirus, yeast plasmids, vectors derived from combinations of plasmids and phage DNA, viral DNA such as vaccinia, adenovirus, fowl pox virus, and pseudorabies. A variety of cloning and expression vectors for use with prokaryotic and eukaryotic hosts are described by Sambrook, et al., Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor, N.Y., (1989), the disclosure of which is hereby incorporated by reference.

[0201]Particular bacterial vectors which may be used include the commercially available plasmids comprising genetic elements of the well known cloning vector pBR322 (ATCC 37017), pKK223-3 (Pharmacia Fine Chemicals, Uppsala, Sweden), GEMI (Promega Biotec, Madison, Wis., USA) pQE70, pQE60, pQE-9 (Qiagen), pD10, psiX174 pBluescript II KS, pNH8A, pNH16a, pNH18A, pNH46A (Stratagene), ptrc99a, pKK223-3, pKK233-3, pDR540, pRIT5 (Pharmacia), pKK232-8 and pCM7. Particular eukaryotic vectors include pSV2CAT, pOG44, pXT1, pSG (Stratagene) pSVK3, pBPV, pMSG, and pSVL (Pharmacia). However, any other vector may be used as long as it is replicable and viable in the host cell.

[0202]The host cell may be any of the host cells familiar to those skilled in the art, including prokaryotic cells, eukaryotic cells, mammalian cells, insect cells, or plant cells. As representative examples of appropriate hosts, there may be mentioned: bacterial cells, such as E. coli, Streptomyces, Bacillus subtilis, Salmonella typhimurium and various species within the genera Pseudomonas, Streptomyces, and Staphylococcus, fungal cells, such as yeast, insect cells such as Drosophila S2 and Spodoptera SJ9, animal cells such as CHO, COS or Bowes melanoma, and adenoviruses. The selection of an appropriate host is within the abilities of those skilled in the art.

[0203]The vector may be introduced into the host cells using any of a variety of techniques, including transformation, transfection, transduction, viral infection, gene guns, or Ti-mediated gene transfer. Particular methods include calcium phosphate transfection, DEAE-Dextran mediated transfection, lipofection, or electroporation (Davis, L., Dibner, M., Battey, I., Basic Methods in Molecular Biology, (1986)).

[0204]Where appropriate, the engineered host cells can be cultured in conventional nutrient media modified as appropriate for activating promoters, selecting transformants or amplifying the genes of the invention. Following transformation of a suitable host strain and growth of the host strain to an appropriate cell density, the selected promoter may be induced by appropriate means (e.g., temperature shift or chemical induction) and the cells may be cultured for an additional period to allow them to produce the desired polypeptide or fragment thereof.

[0205]Cells are typically harvested by centrifugation, disrupted by physical or chemical means, and the resulting crude extract is retained for further purification. Microbial cells employed for expression of proteins can be disrupted by any convenient method, including freeze-thaw cycling, sonication, mechanical disruption, or use of cell lysing agents. Such methods are well known to those skilled in the art. The expressed polypeptide or fragment thereof can be recovered and purified from recombinant cell cultures by methods including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography and lectin chromatography. Protein refolding steps can be used, as necessary, in completing configuration of the polypeptide. If desired, high performance liquid chromatography (HPLC) can be employed for final purification steps.

[0206]Various mammalian cell culture systems can also be employed to express recombinant protein. Examples of mammalian expression systems include the COS-7 lines of monkey kidney fibroblasts (described by Gluzman, Cell, 23:175, 1981), and other cell lines capable of expressing proteins from a compatible vector, such as the C127, 3T3, CHO, HeLa and BHK cell lines.

[0207]The constructs in host cells can be used in a conventional manner to produce the gene product encoded by the recombinant sequence. Depending upon the host employed in a recombinant production procedure, the polypeptides produced by host cells containing the vector may be glycosylated or may be non-glycosylated. Polypeptides of the invention may or may not also include an initial methionine amino acid residue.

[0208]Alternatively, the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof can be synthetically produced by conventional peptide synthesizers. In other embodiments, fragments or portions of the polypeptides may be employed for producing the corresponding full-length polypeptide by peptide synthesis; therefore, the fragments may be employed as intermediates for producing the full-length polypeptides.

[0209]Cell-free translation systems can also be employed to produce one of the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof using mRNAs transcribed from a DNA construct comprising a promoter operably linked to a nucleic acid encoding the polypeptide or fragment thereof. In some embodiments, the DNA construct may be linearized prior to conducting an in vitro transcription reaction. The transcribed mRNA is then incubated with an appropriate cell-free translation extract, such as a rabbit reticulocyte extract, to produce the desired polypeptide or fragment thereof.

[0210]The invention also relates to variants of the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof. The term "variant" includes derivatives or analogs of these polypeptides. In particular, the variants may differ in amino acid sequence from the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto, by one or more substitutions, additions, deletions, fusions and truncations, which may be present in any combination.

[0211]The variants may be naturally occurring or created in vitro. In particular, such variants may be created using genetic engineering techniques such as site directed mutagenesis, random chemical mutagenesis, Exonuclease III deletion procedures, and standard cloning techniques. Alternatively, such variants, fragments, analogs, or derivatives may be created using chemical synthesis or modification procedures.

[0212]Other methods of making variants are also familiar to those skilled in the art. These include procedures in which nucleic acid sequences obtained from natural isolates are modified to generate nucleic acids which encode polypeptides having characteristics which enhance their value in industrial or laboratory applications. In such procedures, a large number of variant sequences having one or more nucleotide differences with respect to the sequence obtained from the natural isolate are generated and characterized. Typically, these nucleotide differences result in amino acid changes with respect to the polypeptides encoded by the nucleic acids from the natural isolates.

[0213]For example, variants may be created using error prone PCR. In error prone PCR, PCR is performed under conditions where the copying fidelity of the DNA polymerase is low, such that a high rate of point mutations is obtained along the entire length of the PCR product. Error prone PCR is described in Leung, D. W., et al., Technique, 1:11-15, 1989) and Caldwell, R. C. & Joyce G. F., PCR Methods Applic., 2:28-33, 1992, the disclosure of which is incorporated herein by reference in its entirety. Briefly, in such procedures, nucleic acids to be mutagenized are mixed with PCR primers, reaction buffer, MgCl₂, MnCl₂, Taq polymerase and an appropriate concentration of dNTPs for achieving a high rate of point mutation along the entire length of the PCR product. For example, the reaction may be performed using 20 fmoles of nucleic acid to be mutagenized, 30 pmole of each PCR primer, a reaction buffer comprising 50 mM KCl, 10 mM Tris HCl (pH 8.3) and 0.01% gelatin, 7 mM MgCl₂, 0.5 mM MnCl₂, 5 units of Taq polymerase, 0.2 mM dGTP, 0.2 mM dATP, 1 mM dCTP, and 1 mM dTTP. PCR may be performed for 30 cycles of 94° C. for 1 min, 45° C. for 1 min, and 72° C. for 1 min. However, it will be appreciated that these parameters may be varied as appropriate. The mutagenized nucleic acids are cloned into an appropriate vector and the activities of the polypeptides encoded by the mutagenized nucleic acids is evaluated.

[0214]Variants may also be created using oligonucleotide directed mutagenesis to generate site-specific mutations in any cloned DNA of interest. Oligonucleotide mutagenesis is described in Reidhaar-Olson, J. F. & Sauer, R. T., et al., Science, 241:53-57, 1988, the disclosure of which is incorporated herein by reference in its entirety. Briefly, in such procedures a plurality of double stranded oligonucleotides bearing one or more mutations to be introduced into the cloned DNA are synthesized and inserted into the cloned DNA to be mutagenized. Clones containing the mutagenized DNA are recovered and the activities of the polypeptides they encode are assessed.

[0215]Another method for generating variants is assembly PCR. Assembly PCR involves the assembly of a PCR product from a mixture of small DNA fragments. A large number of different PCR reactions occur in parallel in the same vial, with the products of one reaction priming the products of another reaction. Assembly PCR is described in U.S. Pat. No. 5,965,408, filed Jul. 9, 1996, entitled, "Method of DNA Reassembly by Interrupting Synthesis", the disclosure of which is incorporated herein by reference in its entirety.

[0216]Still another method of generating variants is sexual PCR mutagenesis. In sexual PCR mutagenesis, forced homologous recombination occurs between DNA molecules of different but highly related DNA sequence in vitro, as a result of random fragmentation of the DNA molecule based on sequence homology, followed by fixation of the crossover by primer extension in a PCR reaction. Sexual PCR mutagenesis is described in Stemmer, W. P., PNAS, USA, 91:10747-10751, 1994, the disclosure of which is incorporated herein by reference. Briefly, in such procedures a plurality of nucleic acids to be recombined are digested with DNAse to generate fragments having an average size of 50-200 nucleotides. Fragments of the desired average size are purified and resuspended in a PCR mixture. PCR is conducted under conditions which facilitate recombination between the nucleic acid fragments. For example, PCR may be performed by resuspending the purified fragments at a concentration of 10-30 ng/:l in a solution of 0.2 mM of each dNTP, 2.2 mM MgCl2, 50 mM KCL, 10 mM Tris HCl, pH 9.0, and 0.1% Triton X-100. 2.5 units of Taq polymerase per 100:1 of reaction mixture is added and PCR is performed using the following regime: 94° C. for 60 seconds, 94° C. for 30 seconds, 50-55° C. for 30 seconds, 72° C. for 30 seconds (30-45 times) and 72° C. for 5 minutes. However, it will be appreciated that these parameters may be varied as appropriate. In some embodiments, oligonucleotides may be included in the PCR reactions. In other embodiments, the Klenow fragment of DNA polymerase I may be used in a first set of PCR reactions and Taq polymerase may be used in a subsequent set of PCR reactions. Recombinant sequences are isolated and the activities of the polypeptides they encode are assessed.

[0217]Variants may also be created by in vivo mutagenesis. In some embodiments, random mutations in a sequence of interest are generated by propagating the sequence of interest in a bacterial strain, such as an E. coli strain, which carries mutations in one or more of the DNA repair pathways. Such "mutator" strains have a higher random mutation rate than that of a wild-type parent. Propagating the DNA in one of these strains will eventually generate random mutations within the DNA. Mutator strains suitable for use for in vivo mutagenesis are described in PCT Publication No. WO 91/16427, published Oct. 31, 1991, entitled "Methods for Phenotype Creation from Multiple Gene Populations" the disclosure of which is incorporated herein by reference in its entirety.

[0218]Variants may also be generated using cassette mutagenesis. In cassette mutagenesis a small region of a double stranded DNA molecule is replaced with a synthetic oligonucleotide "cassette" that differs from the native sequence. The oligonucleotide often contains completely and/or partially randomized native sequence.

[0219]Recursive ensemble mutagenesis may also be used to generate variants. Recursive ensemble mutagenesis is an algorithm for protein engineering (protein mutagenesis) developed to produce diverse populations of phenotypically related mutants whose members differ in amino acid sequence. This method uses a feedback mechanism to control successive rounds of combinatorial cassette mutagenesis. Recursive ensemble mutagenesis is described in Arkin, A. P. and Youvan, D. C., PNAS, USA, 89:7811-7815, 1992, the disclosure of which is incorporated herein by reference in its entirety.

[0220]In some embodiments, variants are created using exponential ensemble mutagenesis. Exponential ensemble mutagenesis is a process for generating combinatorial libraries with a high percentage of unique and functional mutants, wherein small groups of residues are randomized in parallel to identify, at each altered position, amino acids which lead to functional proteins. Exponential ensemble mutagenesis is described in Delegrave, S, and Youvan, D. C., Biotechnology Research, 11: 1548-1552, 1993, the disclosure of which incorporated herein by reference in its entirety. Random and site-directed mutagenesis are described in Arnold, F. H., Current Opinion in Biotechnology, 4:450-455, 1993, the disclosure of which is incorporated herein by reference in its entirety.

[0221]In some embodiments, the variants are created using shuffling procedures wherein portions of a plurality of nucleic acids which encode distinct polypeptides are fused together to create chimeric nucleic acid sequences which encode chimeric polypeptides as described in U.S. Pat. No. 5,965,408, filed Jul. 9, 1996, entitled, "Method of DNA Reassembly by Interrupting Synthesis", and U.S. Pat. No. 5,939,250, filed May 22, 1996, entitled, "Production of Enzymes Having Desired Activities by Mutagenesis", both of which are incorporated herein by reference.

[0222]The variants of the polypeptides of Group B amino acid sequences may be variants in which one or more of the amino acid residues of the polypeptides of the Group B amino acid sequences are substituted with a conserved or non-conserved amino acid residue (preferably a conserved amino acid residue) and such substituted amino acid residue may or may not be one encoded by the genetic code.

[0223]Conservative substitutions are those that substitute a given amino acid in a polypeptide by another amino acid of like characteristics. Typically seen as conservative substitutions are the following replacements: replacements of an aliphatic amino acid such as Alanine, Valine, Leucine and Isoleucine with another aliphatic amino acid; replacement of a Serine with a Threonine or vice versa; replacement of an acidic residue such as Aspartic acid and Glutamic acid with another acidic residue; replacement of a residue bearing an amide group, such as Asparagine and Glutamine, with another residue bearing an amide group; exchange of a basic residue such as Lysine and Arginine with another basic residue; and replacement of an aromatic residue such as Phenylalanine, Tyrosine with another aromatic residue.

[0224]Other variants are those in which one or more of the amino acid residues of the polypeptides of the Group B amino acid sequences includes a substituent group.

[0225]Still other variants are those in which the polypeptide is associated with another compound, such as a compound to increase the half-life of the polypeptide (for example, polyethylene glycol).

[0226]Additional variants are those in which additional amino acids are fused to the polypeptide, such as a leader sequence, a secretory sequence, a proprotein sequence or a sequence which facilitates purification, enrichment, or stabilization of the polypeptide.

[0227]In some embodiments, the fragments, derivatives and analogs retain the same biological function or activity as the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto. In other embodiments, the fragment, derivative, or analog includes a proprotein, such that the fragment, derivative, or analog can be activated by cleavage of the proprotein portion to produce an active polypeptide.

[0228]Another aspect of the invention is polypeptides or fragments thereof which have at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or more than about 95% homology to one of the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto, or a fragment comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof. Homology may be determined using any of the programs described above which aligns the polypeptides or fragments being compared and determines the extent of amino acid identity or similarity between them. It will be appreciated that amino acid "homology" includes conservative amino acid substitutions such as those described above.

[0229]The polypeptides or fragments having homology to one of the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto, or a fragment comprising at least about 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof may be obtained by isolating the nucleic acids encoding them using the techniques described above.

[0230]Alternatively, the homologous polypeptides or fragments may be obtained through biochemical enrichment or purification procedures. The sequence of potentially homologous polypeptides or fragments may be determined by proteolytic digestion, gel electrophoresis and/or microsequencing. The sequence of the prospective homologous polypeptide or fragment can be compared to one of the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto, or a fragment comprising at least about 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof using any of the programs described above.

[0231]Another aspect of the invention is an assay for identifying fragments or variants of Group B amino acid sequences, and sequences substantially identical thereto, which retain the enzymatic function of the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto. For example the fragments or variants of said polypeptides, may be used to catalyze biochemical reactions, which indicate that the fragment or variant retains the enzymatic activity of the polypeptides in the Group B amino acid sequences.

[0232]The assay for determining if fragments of variants retain the enzymatic activity of the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto includes the steps of: contacting the polypeptide fragment or variant with a substrate molecule under conditions which allow the polypeptide fragment or variant to function, and detecting either a decrease in the level of substrate or an increase in the level of the specific reaction product of the reaction between the polypeptide and substrate.

[0233]The polypeptides of Group B amino acid sequences, and sequences substantially identical thereto or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof may be used in a variety of applications. For example, the polypeptides or fragments thereof may be used to catalyze biochemical reactions. In accordance with one aspect of the invention, there is provided a process for utilizing the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto or polynucleotides encoding such polypeptides for hydrolyzing glycosidic linkages. In such procedures, a substance containing a glycosidic linkage (e.g., a starch) is contacted with one of the polypeptides of Group B amino acid sequences, or sequences substantially identical thereto under conditions which facilitate the hydrolysis of the glycosidic linkage.

[0234]The polypeptides of Group B amino acid sequences, and sequences substantially identical thereto or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof, may also be used to generate antibodies which bind specifically to the polypeptides or fragments. The resulting antibodies may be used in immunoaffinity chromatography procedures to isolate or purify the polypeptide or to determine whether the polypeptide is present in a biological sample. In such procedures, a protein preparation, such as an extract, or a biological sample is contacted with an antibody capable of specifically binding to one of the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof.

[0235]In immunoaffinity procedures, the antibody is attached to a solid support, such as a bead or other column matrix. The protein preparation is placed in contact with the antibody under conditions in which the antibody specifically binds to one of the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto, or fragment thereof. After a wash to remove non-specifically bound proteins, the specifically bound polypeptides are eluted.

[0236]The ability of proteins in a biological sample to bind to the antibody may be determined using any of a variety of procedures familiar to those skilled in the art. For example, binding may be determined by labeling the antibody with a detectable label such as a fluorescent agent, an enzymatic label, or a radioisotope. Alternatively, binding of the antibody to the sample may be detected using a secondary antibody having such a detectable label thereon. Particular assays include ELISA assays, sandwich assays, radioimmunoassays, and Western Blots.

[0237]Polyclonal antibodies generated against the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof can be obtained by direct injection of the polypeptides into an animal or by administering the polypeptides to an animal, for example, a nonhuman. The antibody so obtained will then bind the polypeptide itself. In this manner, even a sequence encoding only a fragment of the polypeptide can be used to generate antibodies which may bind to the whole native polypeptide. Such antibodies can then be used to isolate the polypeptide from cells expressing that polypeptide.

[0238]For preparation of monoclonal antibodies, any technique which provides antibodies produced by continuous cell line cultures can be used. Examples include the hybridoma technique (Kohler and Milstein, Nature, 256:495-497, 1975, the disclosure of which is incorporated herein by reference), the trioma technique, the human B-cell hybridoma technique (Kozbor et al., Immunology Today 4:72, 1983, the disclosure of which is incorporated herein by reference), and the EBV-hybridoma technique (Cole, et al., 1985, in Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96, the disclosure of which is incorporated herein by reference).

[0239]Techniques described for the production of single chain antibodies (U.S. Pat. No. 4,946,778, the disclosure of which is incorporated herein by reference) can be adapted to produce single chain antibodies to the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof. Alternatively, transgenic mice may be used to express humanized antibodies to these polypeptides or fragments thereof.

[0240]Antibodies generated against the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto, or fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids thereof may be used in screening for similar polypeptides from other organisms and samples. In such techniques, polypeptides from the organism are contacted with the antibody and those polypeptides which specifically bind the antibody are detected. Any of the procedures described above may be used to detect antibody binding. One such screening assay is described in "Methods for Measuring Cellulase Activities", Methods in Enzymology, Vol 160, pp. 87-116, which is hereby incorporated by reference in its entirety.

[0241]As used herein the term "nucleic acid sequence as set forth in SEQ ID Nos.: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 57, 58, 59 and 60" encompasses the nucleotide sequences of Group A nucleic acid sequences, and sequences substantially identical thereto, as well as sequences homologous to Group A nucleic acid sequences, and fragments thereof and sequences complementary to all of the preceding sequences. The fragments include portions of SEQ ID Nos.: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 57, 58, 59 and 60 comprising at least 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, 150, 200, 300, 400, or 500 consecutive nucleotides of Group A nucleic acid sequences, and sequences substantially identical thereto. Homologous sequences and fragments of Group A nucleic acid sequences, and sequences substantially identical thereto, refer to a sequence having at least 99%, 98%, 97%, 96%, 95%, 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, or 50% homology to these sequences. Homology may be determined using any of the computer programs and parameters described herein, including FASTA version 3.0t78 with the default parameters. Homologous sequences also include RNA sequences in which uridines replace the thymines in the nucleic acid sequences as set forth in the Group A nucleic acid sequences. The homologous sequences may be obtained using any of the procedures described herein or may result from the correction of a sequencing error. It will be appreciated that the nucleic acid sequences as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto, can be represented in the traditional single character format (See the inside back cover of Stryer, Lubert. Biochemistry 3rd Ed., W. H Freeman & Co., New York.) or in any other format which records the identity of the nucleotides in a sequence.

[0242]As used herein the term "a polypeptide sequence as set forth in SEQ ID Nos.: 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 61, 62, 63 and 64" encompasses the polypeptide sequence of Group B amino acid sequences, and sequences substantially identical thereto, which are encoded by a sequence as set forth in SEQ ID Nos.: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 57, 58, 59 and 60, polypeptide sequences homologous to the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto, or fragments of any of the preceding sequences. Homologous polypeptide sequences refer to a polypeptide sequence having at least 99%, 98%, 97%, 96%, 95%, 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55% or 50% homology to one of the polypeptide sequences of the Group B amino acid sequences. Homology may be determined using any of the computer programs and parameters described herein, including FASTA version 3.0t78 with the default parameters or with any modified parameters. The homologous sequences may be obtained using any of the procedures described herein or may result from the correction of a sequencing error. The polypeptide fragments comprise at least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 consecutive amino acids of the polypeptides of Group B amino acid sequences, and sequences substantially identical thereto. It will be appreciated that the polypeptide codes as set forth in Group B amino acid sequences, and sequences substantially identical thereto, can be represented in the traditional single character format or three letter format (See the inside back cover of Stryer, Lubert. Biochemistry, 3rd Ed., W. H Freeman & Co., New York.) or in any other format which relates the identity of the polypeptides in a sequence.

[0243]It will be appreciated by those skilled in the art that a nucleic acid sequence as set forth in SEQ ID Nos.: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 57, 58, 59 and 60 and a polypeptide sequence as set forth in SEQ ID Nos.: 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 61, 62, 63 and 64 can be stored, recorded, and manipulated on any medium which can be read and accessed by a computer. As used herein, the words "recorded" and "stored" refer to a process for storing information on a computer medium. A skilled artisan can readily adopt any of the presently known methods for recording information on a computer readable medium to generate manufactures comprising one or more of the nucleic acid sequences as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto, one or more of the polypeptide sequences as set forth in Group B amino acid sequences, and sequences substantially identical thereto. Another aspect of the invention is a computer readable medium having recorded thereon at least 2, 5, 10, 15, or 20 nucleic acid sequences as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto.

[0244]Another aspect of the invention is a computer readable medium having recorded thereon one or more of the nucleic acid sequences as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto. Another aspect of the invention is a computer readable medium having recorded thereon one or more of the polypeptide sequences as set forth in Group B amino acid sequences, and sequences substantially identical thereto. Another aspect of the invention is a computer readable medium having recorded thereon at least 2, 5, 10, 15, or 20 of the sequences as set forth above.

[0245]Computer readable media include magnetically readable media, optically readable media, electronically readable media and magnetic/optical media. For example, the computer readable media may be a hard disk, a floppy disk, a magnetic tape, CD-ROM, Digital Versatile Disk (DVD), Random Access Memory (RAM), or Read Only Memory (ROM) as well as other types of other media known to those skilled in the art.

[0246]Embodiments of the invention include systems (e.g., internet based systems), particularly computer systems which store and manipulate the sequence information described herein. One example of a computer system 100 is illustrated in block diagram form in FIG. 1. As used herein, "a computer system" refers to the hardware components, software components, and data storage components used to analyze a nucleotide sequence of a nucleic acid sequence as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto, or a polypeptide sequence as set forth in the Group B amino acid sequences. The computer system 100 typically includes a processor for processing, accessing and manipulating the sequence data. The processor 105 can be any well-known type of central processing unit, such as, for example, the Pentium III from Intel Corporation, or similar processor from Sun, Motorola, Compaq, AMD or International Business Machines.

[0247]Typically the computer system 100 is a general purpose system that comprises the processor 105 and one or more internal data storage components 110 for storing data, and one or more data retrieving devices for retrieving the data stored on the data storage components. A skilled artisan can readily appreciate that any one of the currently available computer systems are suitable.

[0248]In one particular embodiment, the computer system 100 includes a processor 105 connected to a bus which is connected to a main memory 115 (preferably implemented as RAM) and one or more internal data storage devices 110, such as a hard drive and/or other computer readable media having data recorded thereon. In some embodiments, the computer system 100 further includes one or more data retrieving device 118 for reading the data stored on the internal data storage devices 110.

[0249]The data retrieving device 118 may represent, for example, a floppy disk drive, a compact disk drive, a magnetic tape drive, or a modem capable of connection to a remote data storage system (e.g., via the internet) etc. In some embodiments, the internal data storage device 110 is a removable computer readable medium such as a floppy disk, a compact disk, a magnetic tape, etc. containing control logic and/or data recorded thereon. The computer system 100 may advantageously include or be programmed by appropriate software for reading the control logic and/or the data from the data storage component once inserted in the data retrieving device.

[0250]The computer system 100 includes a display 120 which is used to display output to a computer user. It should also be noted that the computer system 100 can be linked to other computer systems 125a-c in a network or wide area network to provide centralized access to the computer system 100.

[0251]Software for accessing and processing the nucleotide sequences of a nucleic acid sequence as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto, or a polypeptide sequence as set forth in Group B amino acid sequences, and sequences substantially identical thereto, (such as search tools, compare tools, and modeling tools etc.) may reside in main memory 115 during execution.

[0252]In some embodiments, the computer system 100 may further comprise a sequence comparison algorithm for comparing a nucleic acid sequence as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto, or a polypeptide sequence as set forth in Group B amino acid sequences, and sequences substantially identical thereto, stored on a computer readable medium to a reference nucleotide or polypeptide sequence(s) stored on a computer readable medium. A "sequence comparison algorithm" refers to one or more programs which are implemented (locally or remotely) on the computer system 100 to compare a nucleotide sequence with other nucleotide sequences and/or compounds stored within a data storage means. For example, the sequence comparison algorithm may compare the nucleotide sequences of a nucleic acid sequence as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto, or a polypeptide sequence as set forth in Group B amino acid sequences, and sequences substantially identical thereto, stored on a computer readable medium to reference sequences stored on a computer readable medium to identify homologies or structural motifs. Various sequence comparison programs identified elsewhere in this patent specification are particularly contemplated for use in this aspect of the invention. Protein and/or nucleic acid sequence homologies may be evaluated using any of the variety of sequence comparison algorithms and programs known in the art. Such algorithms and programs include, but are by no means limited to, TBLASTN, BLASTP, FASTA, TFASTA, and CLUSTALW (Pearson and Lipman, Proc. Natl. Acad. Sci. USA 85(8):2444-2448, 1988; Altschul et al., J. Mol. Biol. 215(3):403-410, 1990; Thompson et al., Nucleic Acids Res. 22(2):4673-4680, 1994; Higgins et al., Methods Enzymol. 266:383-402, 1996; Altschul et al., J. Mol. Biol. 215(3):403-410, 1990; Altschul et al., Nature Genetics 3:266-272, 1993).

[0253]Homology or identity is often measured using sequence analysis software (e.g., Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, 1710 University Avenue, Madison, Wis. 53705). Such software matches similar sequences by assigning degrees of homology to various deletions, substitutions and other modifications. The terms "homology" and "identity" in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same when compared and aligned for maximum correspondence over a comparison window or designated region as measured using any number of sequence comparison algorithms or by manual alignment and visual inspection.

[0254]For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters.

[0255]A "comparison window", as used herein, includes reference to a segment of any one of the number of contiguous positions selected from the group consisting of from 20 to 600, usually about 50 to about 200, more usually about 100 to about 150 in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. Methods of alignment of sequence for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482, 1981, by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol 48:443, 1970, by the search for similarity method of person & Lipman, Proc. Nat'l. Acad. Sci. USA 85:2444, 1988, by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by manual alignment and visual inspection. Other algorithms for determining homology or identity include, for example, in addition to a BLAST program (Basic Local Alignment Search Tool at the National Center for Biological Information), ALIGN, AMAS (Analysis of Multiply Aligned Sequences), AMPS (Protein Multiple Sequence Alignment), ASSET (Aligned Segment Statistical Evaluation Tool), BANDS, BESTSCOR, BIOSCAN (Biological Sequence Comparative Analysis Node), BLIMPS (BLocks IMProved Searcher), FASTA, Intervals & Points, BMB, CLUSTAL V, CLUSTAL W, CONSENSUS, LCONSENSUS, WCONSENSUS, Smith-Waterman algorithm, DARWIN, Las Vegas algorithm, FNAT (Forced Nucleotide Alignment Tool), Framealign, Framesearch, DYNAMIC, FILTER, FSAP (Fristensky Sequence Analysis Package), GAP (Global Alignment Program), GENAL, GIBBS, GenQuest, ISSC (Sensitive Sequence Comparison), LALIGN (Local Sequence Alignment), LCP (Local Content Program), MACAW (Multiple Alignment Construction & Analysis Workbench), MAP (Multiple Alignment Program), MBLKP, MBLKN, PIMA (Pattern-Induced Multi-sequence Alignment), SAGA (Sequence Alignment by Genetic Algorithm) and WHAT-IF. Such alignment programs can also be used to screen genome databases to identify polynucleotide sequences having substantially identical sequences. A number of genome databases are available, for example, a substantial portion of the human genome is available as part of the Human Genome Sequencing Project. At least twenty-one other genomes have already been sequenced, including, for example, M. geiiitalium (Fraser et al., 1995), M. jannaschii (Bult et al., 1996), H. influenzae (Fleischmann et al., 1995), E. coli (Blattner et al., 1997), and yeast (S. cerevisiae) (Mewes et al., 1997), and D. melanogaster (Adams et al., 2000). Significant progress has also been made in sequencing the genomes of model organism, such as mouse, C. elegans, and Arabadopsis sp. Several databases containing genomic information annotated with some functional information are maintained by different organization, and are accessible via the internet, for example.

[0256]One example of a useful algorithm is BLAST and BLAST 2.0 algorithms, which are described in Altschul et al., Nuc. Acids Res. 25:3389-3402, 1977, and Altschul et al., J. Mol. Biol. 215:403-410, 1990, respectively. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/). This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, M=5, N=-4 and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength of 3, and expectations (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915, 1989) alignments (B) of 50, expectation (E) of 10, M=5, N=-4, and a comparison of both strands.

[0257]The BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Natl. Acad. Sci. USA 90:5873, 1993). One measure of similarity provided by BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a references sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.2, more preferably less than about 0.01, and most preferably less than about 0.001.

[0258]In one embodiment, protein and nucleic acid sequence homologies are evaluated using the Basic Local Alignment Search Tool ("BLAST") In particular, five specific BLAST programs are used to perform the following task:

[0259](1) BLASTP and BLAST3 compare an amino acid query sequence against a protein sequence database;

[0260](2) BLASTN compares a nucleotide query sequence against a nucleotide sequence database;

[0261](3) BLASTX compares the six-frame conceptual translation products of a query nucleotide sequence (both strands) against a protein sequence database;

[0262](4) TBLASTN compares a query protein sequence against a nucleotide sequence database translated in all six reading frames (both strands); and

[0263](5) TBLASTX compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.

[0264]The BLAST programs identify homologous sequences by identifying similar segments, which are referred to herein as "high-scoring segment pairs," between a query amino or nucleic acid sequence and a test sequence which is preferably obtained from a protein or nucleic acid sequence database. High-scoring segment pairs are preferably identified (i.e., aligned) by means of a scoring matrix, many of which are known in the art. Preferably, the scoring matrix used is the BLOSUM62 matrix (Gonnet et al., Science 256: 1443-1445, 1992; Henikoff and Henikoff, Proteins 17:49-61, 1993). Less preferably, the PAM or PAM250 matrices may also be used (see, e.g., Schwartz and Dayhoff, eds., 1978, Matrices for Detecting Distance Relationships: Atlas of Protein Sequence and Structure, Washington: National Biomedical Research Foundation). BLAST programs are accessible through the U.S. National Library of Medicine.

[0265]The parameters used with the above algorithms may be adapted depending on the sequence length and degree of homology studied. In some embodiments, the parameters may be the default parameters used by the algorithms in the absence of instructions from the user.

[0266]FIG. 2 is a flow diagram illustrating one embodiment of a process 200 for comparing a new nucleotide or protein sequence with a database of sequences in order to determine the homology levels between the new sequence and the sequences in the database. The database of sequences can be a private database stored within the computer system 100, or a public database such as GENBANK that is available through the Internet.

[0267]The process 200 begins at a start state 201 and then moves to a state 202 wherein the new sequence to be compared is stored to a memory in a computer system 100. As discussed above, the memory could be any type of memory, including RAM or an internal storage device.

[0268]The process 200 then moves to a state 204 wherein a database of sequences is opened for analysis and comparison. The process 200 then moves to a state 206 wherein the first sequence stored in the database is read into a memory on the computer. A comparison is then performed at a state 210 to determine if the first sequence is the same as the second sequence. It is important to note that this step is not limited to performing an exact comparison between the new sequence and the first sequence in the database. Well-known methods are known to those of skill in the art for comparing two nucleotide or protein sequences, even if they are not identical. For example, gaps can be introduced into one sequence in order to raise the homology level between the two tested sequences. The parameters that control whether gaps or other features are introduced into a sequence during comparison are normally entered by the user of the computer system.

[0269]Once a comparison of the two sequences has been performed at the state 210, a determination is made at a decision state 210 whether the two sequences are the same. Of course, the term "same" is not limited to sequences that are absolutely identical. Sequences that are within the homology parameters entered by the user will be marked as "same" in the process 200.

[0270]If a determination is made that the two sequences are the same, the process 200 moves to a state 214 wherein the name of the sequence from the database is displayed to the user. This state notifies the user that the sequence with the displayed name fulfills the homology constraints that were entered. Once the name of the stored sequence is displayed to the user, the process 200 moves to a decision state 218 wherein a determination is made whether more sequences exist in the database. If no more sequences exist in the database, then the process 200 terminates at an end state 220. However, if more sequences do exist in the database, then the process 200 moves to a state 224 wherein a pointer is moved to the next sequence in the database so that it can be compared to the new sequence. In this manner, the new sequence is aligned and compared with every sequence in the database.

[0271]It should be noted that if a determination had been made at the decision state 212 that the sequences were not homologous, then the process 200 would move immediately to the decision state 218 in order to determine if any other sequences were available in the database for comparison.

[0272]Accordingly, one aspect of the invention is a computer system comprising a processor, a data storage device having stored thereon a nucleic acid sequence as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto, or a polypeptide sequence as set forth in Group B amino acid sequences, and sequences substantially identical thereto, a data storage device having retrievably stored thereon reference nucleotide sequences or polypeptide sequences to be compared to a nucleic acid sequence as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto, or a polypeptide sequence as set forth in Group B amino acid sequences, and sequences substantially identical thereto, and a sequence comparer for conducting the comparison. The sequence comparer may indicate a homology level between the sequences compared or identify structural motifs in the above described nucleic acid code of Group A nucleic acid sequences, and sequences substantially identical thereto, or a polypeptide sequence as set forth in Group B amino acid sequences, and sequences substantially identical thereto, or it may identify structural motifs in sequences which are compared to these nucleic acid codes and polypeptide codes. In some embodiments, the data storage device may have stored thereon the sequences of at least 2, 5, 10, 15, 20, 25, 30 or 40 or more of the nucleic acid sequences as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto, or the polypeptide sequences as set forth in Group B amino acid sequences, and sequences substantially identical thereto.

[0273]Another aspect of the invention is a method for determining the level of homology between a nucleic acid sequence as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto, or a polypeptide sequence as set forth in Group B amino acid sequences, and sequences substantially identical thereto, and a reference nucleotide sequence. The method including reading the nucleic acid code or the polypeptide code and the reference nucleotide or polypeptide sequence through the use of a computer program which determines homology levels and determining homology between the nucleic acid code or polypeptide code and the reference nucleotide or polypeptide sequence with the computer program. The computer program may be any of a number of computer programs for determining homology levels, including those specifically enumerated herein, (e.g., BLAST2N with the default parameters or with any modified parameters). The method may be implemented using the computer systems described above. The method may also be performed by reading at least 2, 5, 10, 15, 20, 25, 30 or 40 or more of the above described nucleic acid sequences as set forth in the Group A nucleic acid sequences, or the polypeptide sequences as set forth in the Group B amino acid sequences through use of the computer program and determining homology between the nucleic acid codes or polypeptide codes and reference nucleotide sequences or polypeptide sequences.

[0274]FIG. 3 is a flow diagram illustrating one embodiment of a process 250 in a computer for determining whether two sequences are homologous. The process 250 begins at a start state 252 and then moves to a state 254 wherein a first sequence to be compared is stored to a memory. The second sequence to be compared is then stored to a memory at a state 256. The process 250 then moves to a state 260 wherein the first character in the first sequence is read and then to a state 262 wherein the first character of the second sequence is read. It should be understood that if the sequence is a nucleotide sequence, then the character would normally be either A, T, C, G or U. If the sequence is a protein sequence, then it is preferably in the single letter amino acid code so that the first and sequence sequences can be easily compared.

[0275]A determination is then made at a decision state 264 whether the two characters are the same. If they are the same, then the process 250 moves to a state 268 wherein the next characters in the first and second sequences are read. A determination is then made whether the next characters are the same. If they are, then the process 250 continues this loop until two characters are not the same. If a determination is made that the next two characters are not the same, the process 250 moves to a decision state 274 to determine whether there are any more characters either sequence to read.

[0276]If there are not any more characters to read, then the process 250 moves to a state 276 wherein the level of homology between the first and second sequences is displayed to the user. The level of homology is determined by calculating the proportion of characters between the sequences that were the same out of the total number of sequences in the first sequence. Thus, if every character in a first 100 nucleotide sequence aligned with a every character in a second sequence, the homology level would be 100%.

[0277]Alternatively, the computer program may be a computer program which compares the nucleotide sequences of a nucleic acid sequence as set forth in the invention, to one or more reference nucleotide sequences in order to determine whether the nucleic acid code of Group A nucleic acid sequences, and sequences substantially identical thereto, differs from a reference nucleic acid sequence at one or more positions. Optionally such a program records the length and identity of inserted, deleted or substituted nucleotides with respect to the sequence of either the reference polynucleotide or a nucleic acid sequence as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto. In one embodiment, the computer program may be a program which determines whether a nucleic acid sequence as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto, contains a single nucleotide polymorphism (SNP) with respect to a reference nucleotide sequence.

[0278]Accordingly, another aspect of the invention is a method for determining whether a nucleic acid sequence as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto, differs at one or more nucleotides from a reference nucleotide sequence comprising the steps of reading the nucleic acid code and the reference nucleotide sequence through use of a computer program which identifies differences between nucleic acid sequences and identifying differences between the nucleic acid code and the reference nucleotide sequence with the computer program. In some embodiments, the computer program is a program which identifies single nucleotide polymorphisms. The method may be implemented by the computer systems described above and the method illustrated in FIG. 3. The method may also be performed by reading at least 2, 5, 10, 15, 20, 25, 30, or 40 or more of the nucleic acid sequences as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto, and the reference nucleotide sequences through the use of the computer program and identifying differences between the nucleic acid codes and the reference nucleotide sequences with the computer program.

[0279]In other embodiments the computer based system may further comprise an identifier for identifying features within a nucleic acid sequence as set forth in the Group A nucleic acid sequences or a polypeptide sequence as set forth in Group B amino acid sequences, and sequences substantially identical thereto.

[0280]An "identifier" refers to one or more programs which identifies certain features within a nucleic acid sequence as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto, or a polypeptide sequence as set forth in Group B amino acid sequences, and sequences substantially identical thereto. In one embodiment, the identifier may comprise a program which identifies an open reading frame in a nucleic acid sequence as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto.

[0281]FIG. 5 is a flow diagram illustrating one embodiment of an identifier process 300 for detecting the presence of a feature in a sequence. The process 300 begins at a start state 302 and then moves to a state 304 wherein a first sequence that is to be checked for features is stored to a memory 115 in the computer system 100. The process 300 then moves to a state 306 wherein a database of sequence features is opened. Such a database would include a list of each feature's attributes along with the name of the feature. For example, a feature name could be "Initiation Codon" and the attribute would be "ATG". Another example would be the feature name "TAATAA Box" and the feature attribute would be "TAATAA". An example of such a database is produced by the University of Wisconsin Genetics Computer Group. Alternatively, the features may be structural polypeptide motifs such as alpha helices, beta sheets, or functional polypeptide motifs such as enzymatic active sites, helix-turn-helix motifs or other motifs known to those skilled in the art.

[0282]Once the database of features is opened at the state 306, the process 300 moves to a state 308 wherein the first feature is read from the database. A comparison of the attribute of the first feature with the first sequence is then made at a state 310. A determination is then made at a decision state 316 whether the attribute of the feature was found in the first sequence. If the attribute was found, then the process 300 moves to a state 318 wherein the name of the found feature is displayed to the user.

[0283]The process 300 then moves to a decision state 320 wherein a determination is made whether move features exist in the database. If no more features do exist, then the process 300 terminates at an end state 324. However, if more features do exist in the database, then the process 300 reads the next sequence feature at a state 326 and loops back to the state 310 wherein the attribute of the next feature is compared against the first sequence.

[0284]It should be noted, that if the feature attribute is not found in the first sequence at the decision state 316, the process 300 moves directly to the decision state 320 in order to determine if any more features exist in the database.

[0285]Accordingly, another aspect of the invention is a method of identifying a feature within a nucleic acid sequence as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto, or a polypeptide sequence as set forth in Group B amino acid sequences, and sequences substantially identical thereto, comprising reading the nucleic acid code(s) or polypeptide code(s) through the use of a computer program which identifies features therein and identifying features within the nucleic acid code(s) with the computer program. In one embodiment, computer program comprises a computer program which identifies open reading frames. The method may be performed by reading a single sequence or at least 2, 5, 10, 15, 20, 25, 30, or 40 of the nucleic acid sequences as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto, or the polypeptide sequences as set forth in Group B amino acid sequences, and sequences substantially identical thereto, through the use of the computer program and identifying features within the nucleic acid codes or polypeptide codes with the computer program.

[0286]A nucleic acid sequence as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto, or a polypeptide sequence as set forth in Group B amino acid sequences, and sequences substantially identical thereto, may be stored and manipulated in a variety of data processor programs in a variety of formats. For example, a nucleic acid sequence as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto, or a polypeptide sequence as set forth in Group B amino acid sequences, and sequences substantially identical thereto, may be stored as text in a word processing file, such as MicrosoftWORD or WORDPERFECT or as an ASCII file in a variety of database programs familiar to those of skill in the art, such as DB2, SYBASE, or ORACLE. In addition, many computer programs and databases may be used as sequence comparison algorithms, identifiers, or sources of reference nucleotide sequences or polypeptide sequences to be compared to a nucleic acid sequence as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto, or a polypeptide sequence as set forth in Group B amino acid sequences, and sequences substantially identical thereto. The following list is intended not to limit the invention but to provide guidance to programs and databases which are useful with the nucleic acid sequences as set forth in Group A nucleic acid sequences, and sequences substantially identical thereto, or the polypeptide sequences as set forth in Group B amino acid sequences, and sequences substantially identical thereto.

[0287]The programs and databases which may be used include, but are not limited to: MacPattern (EMBL), DiscoveryBase (Molecular Applications Group), GeneMine (Molecular Applications Group), Look (Molecular Applications Group), MacLook (Molecular Applications Group), BLAST and BLAST2 (NCBI), BLASTN and BLASTX (Altschul et al, J. Mol. Biol. 215: 403, 1990), FASTA (Pearson and Lipman, Proc. Natl. Acad. Sci. USA, 85: 2444, 1988), FASTDB (Brutlag et al. Comp. App. Biosci. 6:237-245, 1990), Catalyst (Molecular Simulations Inc.), Catalyst/SHAPE (Molecular Simulations Inc.), Cerius².DBAccess (Molecular Simulations Inc.), HypoGen (Molecular Simulations Inc.), Insight II, (Molecular Simulations Inc.), Discover (Molecular Simulations Inc.), CHARMM (Molecular Simulations Inc.), Felix (Molecular Simulations Inc.), DelPhi, (Molecular Simulations Inc.), QuanteMM, (Molecular Simulations Inc.), Homology (Molecular Simulations Inc.), Modeler (Molecular Simulations Inc.), ISIS (Molecular Simulations Inc.), Quanta/Protein Design (Molecular Simulations Inc.), WebLab (Molecular Simulations Inc.), WebLab Diversity Explorer (Molecular Simulations Inc.), Gene Explorer (Molecular Simulations Inc.), SeqFold (Molecular Simulations Inc.), the MDL Available Chemicals Directory database, the MDL Drug Data Report data base, the Comprehensive Medicinal Chemistry database, Derwent's World Drug Index database, the BioByteMasterFile database, the Genbank database, and the Genseqn database. Many other programs and data bases would be apparent to one of skill in the art given the present disclosure.

[0288]Motifs which may be detected using the above programs include sequences encoding leucine zippers, helix-turn-helix motifs, glycosylation sites, ubiquitination sites, alpha helices, and beta sheets, signal sequences encoding signal peptides which direct the secretion of the encoded proteins, sequences implicated in transcription regulation such as homeoboxes, acidic stretches, enzymatic active sites, substrate binding sites, and enzymatic cleavage sites.

[0289]The present invention exploits the unique catalytic properties of enzymes. Whereas the use of biocatalysts (i.e., purified or crude enzymes, non-living or living cells) in chemical transformations normally requires the identification of a particular biocatalyst that reacts with a specific starting compound, the present invention uses selected biocatalysts and reaction conditions that are specific for functional groups that are present in many starting compounds, such as small molecules. Each biocatalyst is specific for one functional group, or several related functional groups, and can react with many starting compounds containing this functional group.

[0290]The biocatalytic reactions produce a population of derivatives from a single starting compound. These derivatives can be subjected to another round of biocatalytic reactions to produce a second population of derivative compounds. Thousands of variations of the original small molecule or compound can be produced with each iteration of biocatalytic derivatization.

[0291]Enzymes react at specific sites of a starting compound without affecting the rest of the molecule, a process which is very difficult to achieve using traditional chemical methods. This high degree of biocatalytic specificity provides the means to identify a single active compound within the library. The library is characterized by the series of biocatalytic reactions used to produce it, a so called "biosynthetic history". Screening the library for biological activities and tracing the biosynthetic history identifies the specific reaction sequence producing the active compound. The reaction sequence is repeated and the structure of the synthesized compound determined. This mode of identification, unlike other synthesis and screening approaches, does not require immobilization technologies, and compounds can be synthesized and tested free in solution using virtually any type of screening assay. It is important to note, that the high degree of specificity of enzyme reactions on functional groups allows for the "tracking" of specific enzymatic reactions that make up the biocatalytically produced library.

[0292]Many of the procedural steps are performed using robotic automation enabling the execution of many thousands of biocatalytic reactions and screening assays per day as well as ensuring a high level of accuracy and reproducibility. As a result, a library of derivative compounds can be produced in a matter of weeks which would take years to produce using current chemical methods.

[0293]In a particular embodiment, the invention provides a method for modifying small molecules, comprising contacting a polypeptide encoded by a polynucleotide described herein or enzymatically active fragments thereof with a small molecule to produce a modified small molecule. A library of modified small molecules is tested to determine if a modified small molecule is present within the library which exhibits a desired activity. A specific biocatalytic reaction which produces the modified small molecule of desired activity is identified by systematically eliminating each of the biocatalytic reactions used to produce a portion of the library, and then testing the small molecules produced in the portion of the library for the presence or absence of the modified small molecule with the desired activity. The specific biocatalytic reactions which produce the modified small molecule of desired activity is optionally repeated. The biocatalytic reactions are conducted with a group of biocatalysts that react with distinct structural moieties found within the structure of a small molecule, each biocatalyst is specific for one structural moiety or a group of related structural moieties; and each biocatalyst reacts with many different small molecules which contain the distinct structural moiety.

[0294]The invention will be further described with reference to the following examples; however, it is to be understood that the invention is not limited to such examples.

EXAMPLES

Example 1

Bacterial Expression and Purification of Glycosidase Enzymes

[0295]DNA encoding the enzymes of the present invention, SEQ ID NOS: 1-14 and 57-60 were initially amplified from a pBluescript vector containing the DNA by the PCR technique using the primers noted herein. The amplified sequences were then inserted into the respective PQE vector listed beneath the primer sequences, and the enzyme was expressed according to the protocols set forth herein. The 5' and 3' primer sequences for the respective genes are as follows:

TABLE-US-00002 1 Thermococcus AEDII12RA-18B/G (SEQ ID NO:29) 5'CCGAGAATTCATTAAAGAGGAGAAA-TTAACTATGGTGAATGCTATGA TTGTC 3' (SEQ ID NO:30) 3'CGGAAGATCTTCATAGCTCCGGAAGCCCATA 5' Vector: pQE12; and contains the following restriction enzyme sites 5' EcoRI and 3' Big II. . . OC1/4V-33B/G (SEQ ID NO:31) 5'CCGAGAATTCATTAAAGAGGAGAA-ATTAACTATGATAAGAAGGTCCG ATTTTCC 3' (SEQ ID NO:32) 3'CGGAAGATCTTTAAGATTTTAGAAATTCCTT 5' Vector: pQE12; and contains the following restriction enzyme sites 5' EcoRI and 3' Bgl II. Thermococcus 9N2-31B/G (SEQ ID NO:33) 5'CCGAGAATTCATTAAAGAGGAGAAATTAACTATGCTACCAGAAGGCTT TCTC 3' (SEQ ID NO:34) 3'CGGAGGTACCTCACCCAAGTCCGAACTTCTC 5; Vector: pQE30; and contains the following restriction enzyme sites 5; EcoRI and 3' KpnI. Staphylothermus marinus F1-12G (SEQ ID NO:35) 5'CCGAGAATTCATTAAAGAGGAGAAATTAACTATGATAAGGTTTCCTGA TTAT 3' (SEQ ID NO:36) 3'CGGAAGATCTTTATTCGAGGTTCTTTAATCC 5' Vector: pQE12; and contains the following restriction enzyme sites 5' EcoRI and 3' Bld II. Thermococcus chitonophagus GC74-22G (SEQ ID NO:37) 5'CCGAGAATTCATTCATTAAAGAGGAGAAATTAACTATGCTTCGAGGAG AACTTTCTC 3' (SEQ ID NO:38) 3'CGGAGGATCCCTACCCCTCCTCTAAGATGTC 5' Vector: pQE12; and contains the following restriction enzyme sites 5' EcoRI and 3' BamHI. M11TL (SEQ ID NO:39) 5'ATAATCTAGAGCATGCAATTCCCCAAAGACTTCATGATAG 3' (SEQ ID NO:40) 3'AATAAAAGCTTACTGGATCAGTGTAAGATGCT 5' Vector: pQE70; and contains the following restriction enzyme sites 5' SphI and 3' Hind III. Thermotoga maritime MSB8-6G (SEQ ID NO:41) 5'CCGACAATTGATTAAAGAGGAGAAATTAACTATGGAAAGGATCGATGA AATT 3' (SEQ ID NO:42) 3'CGGAGGTACCTCATGGTTTGAATCTCTTCTC 5' Vector: pQE12; and contains the following restriction enzyme sites 5' EcoRI and 3' KpnI. Pyrococcus furiosus VC1-7G1 (SEQ ID NO:43) 5'CCGACAATTGATTAAAGAGGAGAAATTAACTATGTTCCCTGAAAAGTT CCTT 3' (SEQ ID NO:44) 3'CGGAGGTACCTCATCCCCTCAGCAATTCCTC 5' Vector: pQE12; and contains the following restriction enzyme sites 5' EcoRI and 3' KpnI. Bankia gouldi endoglucanase (37GP1) (SEQ ID NO:45) 5'AATAAGGATCCGTTTAGCGACGCTCGC 3' (SEQ ID NO:46) 3'AATAAAAGCTTCCGGGTTGTACAGCGGTAATAGGC 5' Vector: pQE52; and contains the following restriction enzyme sites 5' Bam HI and 3' Hind III. Thermotoga maritimaα-galactosidase (6GC2) (SEQ ID NO:47) 5'TTTATTGAATTCATTAAAGAGGAGAAATTAACTAT-GATCTGTGTGGA AATATTCGGAAAG 3' (SEQ ID NO:48) 3'TCTATAAAGCTTTCATTCTCT-CTCACCCTCTTCGTAGAAG 5' Vector: pQET; and contains the following restriction enzyme sites 5' EcoRi and 3' Hind III. Thermotoga maritimaα-galactosidase (6GP2) (SEQ ID NO:49) 5'TTTATTCAATTGATTAAAGAGGAGAAATTAACTATGGGGATTGGTGGG GACGAC 3' (SEQ ID NO:50) 3'TTTATTAAGCTTATCTTTTCATATTCACATACCTCC 5' Vector: pQEt; and contains the following restriction enzyme sites 5' Hind III and 3' EcoRI. AEPII 1αβ-mannanase (63GB1) (SEQ ID NO:51) 5'TTTATTGAATTCATTAAAGAGGAGAAATTAA-CTATGCTACCAGAAGA GTTCCTATGGGGC 3' (SEQ ID NO:52) 3'TTTATTAAGCTTCTCATCAACGGCTATGGTCTTCATTTC 5' Vector: pQEt; and contains the following restriction enzyme sites 5' Hind III and 3' EcoRI. OC1/4V endoglucanase (33GP1) (SEQ ID NO:53) 5'AAAAAACAATTGAATTCATTAAAGAGGAGAAATTAACTATGGTAGAAA GACACTTCAGATATGTTCTT 3' (SEQ ID NO:54) 3'TTTTTCGGATCCAATTCTTCATTTACTCTTTGCCTG 5' Vector: pQEt; and contains the following restriction enzyme sites 5' BamHI and 3' EcoRI. Thermotoga maritima pullalanase (6GP3) (SEQ ID NO:55) 5'TTTTGGAATTCATTAAAGAGGAGAAATTAACTATGG-AACTGATCATA GAAGGTTAC 3' (SEQ ID NO:56) 3'ATAAGAAGCTTTTCACTCTCTGTACA-GAACGTACGC 5' Vector: pQEt; and contains the following restriction enzyme sites 5' EcoRI and 3' Hind III. Thermotoga maritima MSB8-6GP2 (SEQ ID NO:65) 5'CCGACAATTGATTAAAGAGGAGAA-ATTAACTATGGAAAGGATCGATG AAATT 3' (SEQ ID NO:66) 3'CGGAGGTACCTCATGGTTTGAATCTCTTCTC 5' Vector: pQE12; and contains the following restriction enzyme sites 5' EcoRI and 3' KpnI. Pyrococcus furiosus VC1-7EG1 (SEQ ID NO:67) 5'CCGACAATTGATTAAAGAGGAGAAATTAACTATGTTCCCTGAAAAGTT CCTT 3' (SEQ ID NO:68) 3'CGGAGGTACCTCATCCCCTCAGCAATTCCTC 5' Vector: pQE12; and contains the following restriction enzyme sites 5' EcoRI and 3' Kpn I. Bankia gouldi endoglucanase (37GP4) (SEQ ID NO:69) 5'AATAAGGATCCGTTTAGCGACGCTCGC 3' (SEQ ID NO:70) 3'AATAAAAGCTTCCGGGTTGTACAGCGGTAATAGGC 5' Vector: pQE52; and contains the following restriction enzyme sites 5' BamHI and 3' Hind III. Thermotoga maritime MSB8-6GP4 (SEQ ID NO:71) AATAACAATTGAAGGAGGAATTTAAATGGCTTATCATACCTCTGAGGACA AG (SEQ ID NO:72) AATAAGTCGACTTAGGAAATAAGAGGTCTATC Vector: and contains the following restriction enzyme sites 5' and 3' .

[0296]The restriction enzyme sites indicated correspond to the restriction enzyme sites on the bacterial expression vector indicated for the respective gene (Qiagen, Inc. Chatsworth, Calif.). The pQE vector encodes antibiotic resistance (Amp'), a bacterial origin of replication (ori), an IPTG-regulatable promoter operator (P/O), a ribosome binding site (RBS), a 6-His tag and restriction enzyme sites.

[0297]The pQE vector was digested with the restriction enzymes indicated. The amplified sequences were ligated into the respective pQE vector and inserted in frame with the sequence encoding for the RBS. The ligation mixture was then used to transform the E. coli strain M15/pREP4 (Qiagen, Inc.) by electroporation. M15/pREP4 contains multiple copies of the plasmid pREP4, which expresses the lacI repressor and also confers kanamycin resistance (Kan'). Transformants were identified by their ability to grow on LB plates and ampicillin/kanamycin resistant colonies were selected. Plasmid DNA was isolated and confirmed by restriction analysis. Clones containing the desired constructs were grown overnight (O/N) in liquid culture in LB media supplemented with both Amp (100μg/ml) and Kan (25μg/ml). The O/N culture was used to inoculate a large culture at a ratio of 1:100 to 1:250. The cells were grown to an optical density 600 (O.D⁶⁰⁰) of between 0.4 and 0.6. IPTG ("Isopropyl-B-D-thiogalacto pyranoside") was then added to a final concentration of 1 mM. IPTG induces by inactivating the lacI repressor, clearing the P/O leading to increased gene expression. Cells were grown an extra 3 to 4 hours. Cells were then harvested by centrifugation.

[0298]The primer sequences set out above may also be employed to isolate the target gene from the deposited material by hybridization techniques described above.

Example 2

Isolation of a Selected Clone from the Deposited Genomic Clones

[0299]A clone is isolated directly by screening the deposited material using the oligonucleotide primers set forth in Example 1 for the particular gene desired to be isolated. The specific oligonucleotides are synthesized using an Applied Biosystems DNA synthesizer. The oligonucleotides are labeled with ³²P-ATP using T4 polynucleotide kinase and purified according to a standard protocol (Maniatis et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press, Cold Spring, N.Y., 1982). The deposited clones in the pBluescript vectors may be employed to transform bacterial hosts which are then plated on 1.5% agar plates to the density of 20,000-50,000 pfu/150 mm plate. These plates are screened using Nylon membranes according to the standard screening protocol (Stratagene, 1993). Specifically, the Nylon membrane with denatured and fixed DNA is prehybridized in 6× SSC, 20 mM NaJ₂PO₄, 0.4% SDS, 5× Denhardt's 500μg/ml denatured, sonicated salmon sperm DNA; and 6× SSC, 0.1% SDS. After one hour of prehybridization, the membrane is hybridized with hybridization buffer 6× SSC, 20 mM NaH₂PO₄, 0.4% SDS, 500 ug/ml denatured, sonicated salmon sperm DNA with 1× 10⁶ cpm/ml ³²P-probe overnight at 42° C. The membrane is washed at 45-50° C. with washing buffer 6× SSC, 0.1% SDS for 20-30 minutes dried and exposed to Kodak X-ray film overnight. Positive clones are isolated and purified by secondary and tertiary screening the purified clone is sequenced to verify its identity to the primer source.

[0300]Once the clone is isolated, the two oligonucleotide primers corresponding to the gene of interest are used to amplify the gene from the deposited material. A polymerase chain reaction is carried out in 25μl of reaction mixture with 0.5 ug of the DNA of the gene of interest. The reaction mixture is 1.5-5 mM MgCl₂₀.01% (w/v) gelatin, 20μM each of dATP, dCTP, dGTP dTTP, 25 pmol of each primer and 0.25 Unit of Taq polymerase. Thirty five cycles of PCR (denaturation at 94° C. for 1 min; annealing at 55° C. for 1 min; elongation at 72° C. for 1 min) are performed with the Perkin-Elmer Cetus automated thermal cycler. The amplified product is analyzed by agarose gel electrophoresis and the DNA band with expected molecular weight is excised and purified. The PCR product is verified to be the gene of interest by subcloning and sequencing the DNA product. The ends of the newly purified genes are nucleotide sequenced to identify full length sequences. Complete sequencing of full length genes is then performed by Exonuclease III digestion or primer walking.

Example 3

Screening for Galactosidase Activity

[0301]Screening procedures for α-galactosidase protein activity may be assayed for as follows:

[0302]Substrate plates were provided by a standard plating procedure. Dilute LX1-Blue MRF E. coli host of (Stratagene Cloning Systems, La Jolla, Calif.) of O.D₆₀₀=10.0 with NZY media. In 15 ml tubes, inoculate 200μl diluted host cells with phage. Mix gently and incubate tubes at 37° C. for 15 min. Add approximately 3.5 nil LB top agarose (0.7%) containing 1 mM 1PTG to each tube and pour onto all NYZ plate surface. Allow to cool and incubate at 37° C. overnight. The assay plates are obtained as substrate p-Nitrophenyl cc-galactosidase (Sigma) (200 nig/100 ml)(100 mM NaCl, 100 mM Potassium-Phosphate) 1% (w/v) agarose. The plaques are overlayed with nitrocellulose and incubated at 4° C. for 30 minutes whereupon the nitrocellulose is removed and overlayed onto the substrate plates. The substrate plates are then incubated at 70° C. for 20 minutes.

Example 4

Screening of Clones for Mannanase Activity

[0303]A solid phase screening assay was utilized as a primary screening method to test clones for β-mannanase activity.

[0304]A culture solution of the Y1090-E. coli host strain (Stratagene Cloning Systems, La Jolla, Calif.) was diluted to O.D₆₀₀=1.0 with NZY media. The amplified library from Thermotoga maritima lambda gtl 1 library was diluted in SM (phage dilution buffer): 5×10⁷ pfu/μl diluted 1:1000 then 1:100 to 5×10² pfu/μl. Then 8μl of phage dilution (5×10² pfu/μl) was plated in 200μl host cells. They were then incubated in 15 ml tubes at 37° C. for 15 minutes.

[0305]Approximately 4 ml of molten, LP top agarose (0.7%) at approximately 52° C. was added to each tube and the mixture was poured onto the surface of LP agar plates. The agar plates were then incubated at 37° C. for five hours. The plates were replicated and induced with 10 mM IPTG-soaked Duralon-UV® nylon membranes (Stratagene Cloning Systems, La Jolla, Calif.) overnight. The nylon membranes and plates were marked with a needle to keep their orientation and the nylon membranes were then removed and stored at 4° C.

[0306]An Azo-galactomannan overlay was applied to the LB plates containing the lambda plaques. The overlay contains 1% agarose, 50 mM potassium-phosphate buffer pH 7, 0.4% Azocarob-galactomannan. (Megazyme, Australia). The plates were incubated at 72° C. The Azocarob-galactomannan treated plates were observed after 4 hours then returned to incubation overnight. Putative positives were identified by clearing zones on the Azocarob-galactomannan plates. Two positive clones were observed.

[0307]The nylon membranes referred to above, which correspond to the positive clones were retrieved, oriented over the plate and the portions matching the locations of the clearing zones for positive clones were cut out. Phage was eluted from the membrane cut-out portions by soaking the individual portions in 500μl SM (phage dilution buffer) and 25μl CHCl₃.

Example 5

Screening for Clones for Mannosidase Activity

[0308]A solid phase screening assay was utilized as a primary screening method to test clones for β-mannosidase activity. 103251 A culture solution of the Y1090-E. coli host strain (Stratagene Cloning Systems, La Jolla, Calif.) was diluted to O.D₆₀₀=1.0 with NZY media. The amplified library from AEPII la lambda gtl 1 library was diluted in SM (phage dilution buffer): 5×10⁷ pfu/μl diluted 1:1000 then 1:100 to 5×10² pfu/μl. Then 8μl of phage dilution (5×10² pfu/μl) was plated in 200μl host cells. They were then incubated in 15 ml tubes at 37° C. for 15 minutes.

[0309]Approximately 4 ml of molten, LP top agarose (0.7%) at approximately 52° C. was added to each tube and the mixture was poured onto the surface of LP agar plates. The agar plates were then incubated at 37° C. for five hours. The plates were replicated and induced with 10 mM IPTG-soaked Duralon-UV.sup.® nylon membranes (Stratagene Cloning Systems, La Jolla, Calif.) overnight. The nylon membranes and plates were marked with a needle to keep their orientation and the nylon membranes were then removed and stored at 4° C.

[0310]A p-nitrophenyl-β-manno-pyranoside overlay was applied to the LB plates containing the lambda plaques. The overlay contains 1% agarose, 50 mM potassium-phosphate buffer pH 7, 0.4% p-nitrophenyl-β-manno-py-ranoside. (Megazyme, Australia). The plates were incubated at 72° C. The p-nitrophenyl-β-manno-pyranoside treated plates were observed after 4 hours then returned to incubation overnight. Putative positives were identified by clearing zones on the p-nitrophenyl-β-manno-pyran-oside plates. Two positive clones were observed.

[0311]The nylon membranes referred to above, which correspond to the positive clones were retrieved, oriented over the plate and the portions matching the locations of the clearing zones for positive clones were cut out. Phage was eluted from the membrane cut-out portions by soaking the individual portions in 500μl SM (phage dilution buffer) and 25μl CHCl₃.

Example 6

Screening for Pullulanase Activity

[0312]Screening procedures for pullulanase protein activity may be assayed for as follows:

[0313]Substrate plates were provided by a standard plating procedure. Host cells are diluted to O.D₆₀₀=1.0 with NZY media. In 15 ml tubes, inoculate 200μl diluted host cells with phage. Mix gently and incubate tubes at 37° C. for 15 minutes. Add approximately 3.5 ml LB top agarose (0.7%) is added to each tube and the mixture is plated, allowed to cool, and incubated at 37° C. for 28 hours. Overlays of 4.5 mls of the following substrate are poured:

2 100 ml total volume 0.5 g Red Pullulan Red (Megazyme, Australia) 1.0 g Agarose 5 ml Buffer (Tris-HCL pH 7.2 @ 75° C.) 2 ml 5M NaCl 5 ml CaCl₂ (100 mM) 85 ml dH₂O

[0314]Plates are cooled at room temperature, and then incubated at 75° C. for 2 hours. Positives are observed as showing substrate degradation.

Example 7

Screening for Endoglucanase Activity

[0315]Screening procedures for endoglucanase protein activity may be assayed for as follows:

[0316]i. The gene library is plated onto 6 LB/GelRite/0.1% CMC/NZY agar plates (˜4,800 plaque forming units/plate) in E. coli host with LP agarose as top agarose. The plates are incubated at 37° C. overnight.

[0317]ii. Plates are chilled at 4° C. for one hour.

[0318]iii. The plates are overlayed with Duralon membranes (Stratagene) at room temperature for one hour and the membranes are oriented and lifted off the plates and stored at 4° C.

[0319]iv. The top agarose layer is removed and plates are incubated at 37° C. for 3 hours.

[0320]v. The plate surface is rinsed with NaCl.

[0321]vi. The plate is stained with 0.1% Congo Red for 15 minutes.

[0322]vii. The plate is destained with 1M NaCl

[0323]viii. The putative positives identified on plate are isolated from the Duralon membrane (positives are identified by clearing zones around clones). The phage is eluted from the membrane by incubating 500μl SM+25μl CHCl₃ to elute.

[0324]ix. Insert DNA is subcloned into any appropriate cloning vector and subclones are reassayed for CMCase activity using the following protocol:

[0325]a) Spin 1 ml overnight miniprep of clone at maximum speed for 3 minutes.

[0326]b) Decant the supernatant and use it to fill "wells" that have been made in an LB/GelRite/0.1% CMC plate.

[0327]c) Incubate at 37° C. for 2 hours.

[0328]d) Stain with 0.1% Congo Red for 15 minutes.

[0329]e) Destain with 1 M NaCl for 15 minutes.

[0330]f) Identify positives by clearing zone around clone.

[0331]While the invention has been described in detail with reference to certain preferred embodiments thereof, it will be understood that modifications and variations are within the spirit and scope of that which is described and claimed.

Sequence CWU 1

7211446DNADesulfurococcus sp. 1ttgaaattcc ccaaagactt catgataggc tactcatctt caccgtttca atttgaagct 60ggtattcccg ggtccgagga tccgaatagt gattggtggg tatgggtgca tgatccggag 120aacacagcag ctggactagt cagcggcgat tttcccgaga acggcccagg ttactggaat 180ttaaaccaaa atgaccacga cctggctgag aagctggggg ttaacactat tagagtaggc 240gttgagtgga gtaggatttt tccaaagcca actttcaatg ttaaagtccc tgtagagaga 300gatgagaacg gcagcattgt tcacgtagat gtcgatgata aagcggttga aagacttgat 360gaattagcca acaaggaggc cgtaaaccat tacgtagaaa tgtataaaga ctgggttgaa 420agaggtagaa aacttatact caatttatac cattggcccc tgcctctctg gcttcacaac 480ccaatcatgg tgagaagaat gggcccggac agagcgccct caggctggct taacgaggag 540tccgtggtgg agtttgccaa atacgccgca tacattgctt ggaaaatggg cgagctacct 600gttatgtgga gcaccatgaa cgaacccaac gtcgtttatg agcaaggata catgttcgtt 660aaagggggtt tcccacccgg ctacttgagt ttggaagctg ctgataaggc caggagaaat 720atgatccagg ctcatgcacg ggcctatgac aatattaaac gcttcagtaa gaaacctgtt 780ggactaatat acgctttcca atggttcgaa ctattagagg gtccagcaga agtatttgat 840aagtttaaga gctctaagtt atactatttc acagacatag tatcgaaggg tagttcaatc 900atcaatgttg aatacaggag agatcttgcc aataggctag actggttggg cgttaactac 960tatagccgtt tagtctacaa aatcgtcgat gacaaaccta taatcctgca cgggtatgga 1020ttcctttgta cacctggggg gatcagcccg gctgaaaatc cttgtagcga ttttgggtgg 1080gaggtgtatc ctgaaggact ctacctactt ctaaaagaac tttacaaccg atacggggta 1140gacttgatcg tgaccgagaa cggtgtttca gacagcaggg atgcgttgag accggcatac 1200ctggtctcgc atgtttacag cgtatggaaa gccgctaacg agggcattcc cgtcaaaggc 1260tacctccact ggagcttgac agacaattac gagtgggccc agggcttcag gcagaaattc 1320ggtttagtca tggttgactt caaaactaag aaaaggtatc tccgcccaag cgccctagtg 1380ttccgggaga tcgcaacgca taacggaata ccggatgagc tacagcatct tacactgatc 1440cagtaa 144621317DNAThermotoga sp. 2atgataagaa ggtccgattt tccaaaagat tttatcttcg gaacggctac ggcagcatac 60cagattgaag gtgcagcaaa cgaagatggc agagggccat caatttggga tgtcttttca 120cacacgcctg gcaaaaccct gaacggtgac acaggagacg ttgcgtgtga ccattatcac 180cgatacaagg aagatatcca gctgatgaaa gaaatagggt tagacgctta caggttctct 240atctcctggc ccagaattat gccagatggg aagaacatca accaaaaggg tgtggatttc 300tacaacagac tcgttgatga gcttttgaag aatgatatca taccattcgt aacactctat 360cactgggact taccctacgc actttatgaa aaaggtggat ggcttaaccc agatatagcg 420ctctatttca gagcatacgc aacgtttatg ttcaacgaac tcggtgatcg tgtgaaacat 480tggattacac tgaacgaacc atggtgttct tctttctcgg gttattacac gggagagcat 540gccccgggtc atcaaaattt acaagaagcg ataatcgcgg cgcacaacct gttgagggaa 600catggacatg ccgtccaggc gtccagagaa gaagtaaaag atggggaagt tggcttaacc 660aacgttgtga tgaaaataga accgggcgat gcaaaacccg aaagtttctt ggtcgcaagt 720cttgttgata agttcgttaa tgcatggtcc catgaccctg ttgttttcgg aaaatatccc 780gaagaagcag ttgcacttta tacggaaaaa gggttgcaag ttctcgatag cgatatgaat 840attatttcga ctcctataga cttctttggt gtgaattatt acacaagaac acttgttgtt 900tttgatatga acaatcctct tggattttcg tatgttcagg gagaccttcc caaaacggag 960atgggatggg aaatctaccc gcagggatta tttgatatgc tggtctatct gaaggaaaga 1020tataaactac cactttatat cacagagaac gggatggctg gacctgataa attggaaaac 1080ggaagagttc atgataatta ccgaattgaa tatttggaaa agcactttga aaaagcactt 1140gaagcaatca atgcagatgt tgatttgaaa ggttacttca tttggtcttt gatggataac 1200ttcgaatggg cgtgcggata ctccaaacgt ttcggtataa tctacgtaga ttacaatacc 1260ccaaaaagga tattgaaaga ttcagcgatg tggttgaagg aatttctaaa atcttaa 131731266DNAStaphylothermus marinus 3ttgataaggt ttcctgatta tttcttgttt ggaacagcta catcatcgca ccagatcgag 60ggtaataaca tatttaatga ttggtgggag tgggagacta aaggcaggat taaggtgaga 120tcgggtaagg catgtaatca ttgggaactc tataaagaag acatagagct tatggctgag 180ctgggatata atgcttatag gttctccata gagtggagta gaatatttcc cagaaaagat 240catatagatt atgagtcgct taataagtat aaggaaatag ttaatctact tagaaaatac 300gggatagaac ctgtaatcac tcttcaccac ttcacaaacc cgcaatggtt tatgaaaatt 360ggtggatgga ctagggaaga gaacataaaa tattttataa aatatgtaga acttatagct 420tccgagataa aagacgtgaa aatatggatc actattaatg aaccaataat atatgtttta 480caaggatata tttccggcga atggccacct ggaattaaaa atttaaaaat agctgatcaa 540gtaactaaga atcttttaaa agcacataat gaagcctata atatacttca taaacacggt 600attgtaggca tagctaaaaa catgatagca tttaaaccag gatctaatag aggaaaagac 660attaatattt atcataaagt cgataaagca ttcaactggg gatttctcaa cggaatatta 720aggggagaac tagaaactct ccgtggaaaa taccgagttg agcccggaaa tattgatttc 780ataggcataa actattattc atcatatatt gtaaaatata cttggaatcc ttttaaacta 840catattaaag tcgaaccatt agatacaggt ctatggacaa ctatgggtta ctgcatatat 900cctagaggaa tatatgaagt tgtaatgaaa actcatgaga aatacggcaa agaaataatc 960attacagaga acggtgttgc agtagaaaat gatgaattaa ggattttatc cattatcagg 1020cacttacaat acttatataa agccatgaat gaaggagcaa aggtgaaagg atatttctac 1080tggagcttca tggataattt tgagtgggat aaaggattta accaaaggtt cggactagta 1140gaagttgatt ataagacttt tgagagaaaa cctagaaaaa gcgcatatgt atatagtcaa 1200atagcacgta ccaagactat aagtgatgaa tacctagaaa aatatggatt aaagaacctc 1260gaataa 126641530DNAThermococcus sp. 4atgctaccag aaggctttct ctggggcgtg tcccagtccg gctttcagtt cgagatgggc 60gacaagctca ggaggaacat tgatccgaac acagactggt ggaagtgggt cagggatccc 120ttcaacataa agagggaact cgtcagcggc gacctgcccg aggaggggat aaacaactac 180gaactttacg agaaggatca ccgcctcgcc agagacctcg gtctgaacgt ttacaggatt 240ggaatagagt ggagcaggat ctttccctgg ccaacgtggt ttgtggaggt tgacgttgag 300cgggacagct acggactcgt gaaggacgtc aaaatcgata aagacacgct cgaagagctc 360gacgagatag cgaatcatca ggagatagcc tactaccgcc gcgttataga gcacctcagg 420gagctgggct tcaaggtcat cgtgaacctc aaccacttca cgctccccct ctggcttcac 480gatccgataa tcgcgaggga gaaggccctc accaacggta ggattggctg ggtcgggcag 540gagagcgtgg tggagttcgc caagtacgcg gcgtacatcg cgaacgcact cggggacctc 600gttgatatgt ggagcacctt caacgagccg atggtcgttg tggagctcgg ttacctcgcg 660ccctactccg gctttccgcc gggggttatg aaccccgagg cggcaaagct ggcaatcctc 720aacatgataa acgcccacgc actggcctac aagatgataa agaagttcga cagggtaaag 780gccgataagg attcccgctc cgaggccgag gtcgggataa tctacaacaa cataggcgtt 840gcctatccat acgactccaa cgacccaaag gacgtgaaag ctgcagaaaa cgacaactac 900ttccacagcg ggctcttctt cgacgcaatc cacaagggca agctcaacat cgagttcgac 960ggtgagacct tcgtcaaagt tcggcatctc agggggaacg actggatagg cgttaactac 1020tacacgagag aagtcgtcag gtattcggag cccaagttcc cgagcatacc cctgatatcc 1080ttccggggag ttcacaacta cggctacgcc tgcaggcccg ggagttcttc cgccgacgga 1140aggcccgtaa gcgacatcgg ctgggagatc tatccggagg ggatctacga ctcgataaga 1200gaggccaaca aatacggggt cccggtttac gtcaccgaaa acggaatagc cgattcaact 1260gacaccctgc ggccgtacta cctcgcgagc catgtagcga agattgagga ggcgtacgag 1320gcgggttacg acgtcagggg ctacctctac tgggcgctga ccgacaacta cgagtgggcc 1380ctcggtttca ggatgaggtt cggcctctat aaagtggatc tcataaccaa ggagagaaca 1440ccgcgggagg aaagcgtaaa ggtttatagg ggcatcgtgg agaacaacgg agtgagcaag 1500gaaatccggg agaagttcgg acttgggtga 153052166DNAThermotoga maritima 5atggaaagga tcgatgaaat tctctctcag ttaactacag aggaaaaggt gaagctcgtt 60gtgggggttg gtcttccagg actttttggg aacccacatt ccagagtggc gggtgcggct 120ggagaaacac atcccgttcc aagacttgga attcctgcgt ttgtcctggc agatggtccc 180gcaggactca gaataaatcc cacaagggaa aacgatgaaa acacttacta cacgacggca 240tttcccgttg aaatcatgct cgcttctacc tggaacagag accttctgga agaagtggga 300aaagccatgg gagaagaagt tagggaatac ggtgtcgatg tgcttcttgc acctgcgatg 360aacattcaca gaaaccctct ttgtggaagg aatttcgagt actactcaga agatcctgtc 420ctttccggtg aaatggcttc agcctttgtc aagggagttc aatctcaagg ggtgggagcc 480tgcataaaac actttgtcgc gaacaaccag gaaacgaaca ggatggtagt ggacacgatc 540gtgtccgagc gagccctcag agaaatatat ctgaaaggtt ttgaaattgc tgtcaagaaa 600gcaagaccct ggaccgtgat gagcgcttac aacaaactga atggaaaata ctgttcacag 660aacgaatggc ttttgaagaa ggttctcagg gaagaatggg gatttggcgg tttcgtgatg 720agcgactggt acgcgggaga caaccctgta gaacagctca aggccggaaa cgatatgatc 780atgcctggga aagcgtatca ggtgaacaca gaaagaagag atgaaataga agaaatcatg 840gaggcgttga aggagggaaa attgagtgag gaggttctcg atgagtgtgt gagaaacatt 900ctcaaagttc ttgtgaacgc gccttccttc aaagggtaca ggtactcaaa caagccggat 960ctcgaatctc acgcggaagt cgcctacgaa gcaggtgcgg agggtgttgt ccttcttgag 1020aacaacggtg ttcttccgtt cgatgaaaat acccatgtcg ccgtctttgg caccggtcaa 1080atcgaaacaa taaagggagg aacgggaagt ggagacaccc atccgagata cacgatctct 1140atccttgaag gcataaaaga aagaaacatg aagttcgacg aagaactcgc ttccacttat 1200gaggagtaca taaaaaagat gagagaaaca gaggaatata aacccagaac cgactcttgg 1260ggaacggtca taaaaccgaa actcccagag aatttcctct cagaaaaaga gataaagaaa 1320cctccaaaga aaaacgatgt tgcagttgtt gtgatcagta ggatctccgg tgagggatac 1380gacagaaagc cggtgaaagg tgacttctac ctctccgatg acgagctgga actcataaaa 1440accgtctcga aagaattcca cgatcagggt aagaaagttg tggttcttct gaacatcgga 1500agtcccatcg aagtcgcaag ctggagagac cttgtggatg gaattcttct cgtctggcag 1560gcgggacagg agatgggaag aatagtggcc gatgttcttg tgggaaagat taatccctcc 1620ggaaaacttc caacgacctt cccgaaggat tactcggacg ttccatcctg gacgttccca 1680ggagagccaa aggacaatcc gcaaagagtg gtgtacgagg aagacatcta cgtgggatac 1740aggtactacg acaccttcgg tgtggaacct gcctacgaat tcggctacgg cctctcttac 1800acaaagtttg aatacaaaga tttaaaaatc gctatcgacg gtgagacgct cagagtgtcg 1860tacacgatca caaacactgg ggacagagct ggaaaggaag tctcacaggt ctacatcaaa 1920gctccaaaag gaaaaataga caaacccttc caggagctga aagcgtttca caaaacaaaa 1980cttttgaacc cgggtgaatc agaagaaatc tccttggaaa ttcctctcag agatcttgcg 2040agtttcgatg ggaaagaatg ggttgtcgag tcaggagaat acgaggtcag ggtcggtgca 2100tcttcgaggg atataaggtt gagagatatt tttctggttg agggagagaa gagattcaaa 2160ccatga 216661365DNAThermococcus alcaliphilus 6atgatccact gcccggttaa agggattata tctgaggctc gcggcataac catcacaata 60gatttaagtt ttcaaggcca aataaataat ttggtgaatg ctatgattgt ctttccggag 120ttcttcctct ttggaaccgc cacatcttct catcagatcg agggagataa taaatggaac 180gactggtggt attatgagga gataggtaag ctcccctaca aatccggtaa agcctgcaat 240cactgggagc tttacaggga agatatagag ctaatggcac agctcggcta caatgcctac 300cgcttttcga tagagtggag ccgtctcttc ccggaagagg gcaaattcaa tgaagaagcc 360ttcaaccgct accgtgaaat aattgaaatc ctccttgaga aggggattac tccaaacgtt 420acactgcacc acttcacatc accgctgtgg ttcatgcgga agggaggctt tttgaaggaa 480gaaaacctca agtactggga gcagtacgtt gataaagccg cggagctcct caagggagtc 540aagcttgtag ctacattcaa cgagccgatg gtctatgtta tgatgggcta cctcacagcc 600tactggccgc ccttcatcaa gagtcccttt aaagccttta aagttgccgc aaacctcctt 660aaggcccatg caatggcata tgatatcctc catggtaact ttgatgtggg gatagttaaa 720aacatcccca taatgctccc tgcaagcaac agagagaaag acgtagaagc tgcccaaaag 780gcggataacc tctttaactg gaacttcctt gatgcaatat ggagcggaaa atataaagga 840gcttttggaa cttacaaaac tccagaaagc gatgcagact tcatagggat aaactactac 900acagccagcg aggtaaggca tagctggaat ccgctaaagt ttttcttcga tgccaagctt 960gcagacttaa gcgagagaaa aacagatatg ggttggagtg tctatccaaa gggcatatac 1020gaagctatag caaaggtttc acactacgga aagccaatgt acatcacgga aaacgggata 1080gctaccttag acgatgagtg gaggatagag tttatcatcc agcacctcca gtacgttcac 1140aaagccttaa acgatggctt tgacttgaga ggctacttct attggtcttt tatggataac 1200ttcgagtggg ctgagggttt tagaccacgc tttgggctgg tcgaggtgga ctacacgacc 1260ttcaagagga gaccgagaaa gagtgcttac atatatggag aaattgcaag ggaaaagaaa 1320ataaaagacg aactgctggc aaagtatggg cttccggagc tatga 136571536DNAThermococcus chitonophagus 7ttgcttccag agaactttct ctggggagtt tcacagtccg gattccagtt tgaaatgggg 60gacagactga ggaggcacat tgatccaaac acagattggt ggtactgggt aagagatgaa 120tataatatca aaaaaggact agtaagtggg gatcttcccg aagacggtat aaattcatat 180gaattatatg agagagacca agaaattgca aaggatttag ggctcaacac atataggatc 240ggaattgaat ggagcagagt atttccatgg ccaacgactt ttgtcgacgt ggagtatgaa 300attgatgagt cttacgggtt ggtaaaggat gtgaagattt ctaaagacgc attagaaaaa 360cttgatgaaa tcgctaacca aagggaaata atatattata ggaacctaat aaattcccta 420agaaagaggg gttttaaggt aatactaaac ctaaatcatt ttaccctccc aatatggctt 480catgatccta tcgaatctag agaaaaagcc ctgaccaata agagaaacgg atgggtaagc 540gaaaggagtg ttatagagtt tgcaaaattt gccgcgtatt tagcatataa attcggagac 600atagtagaca tgtggagcac atttaatgaa cctatggtgg tcgccgagtt ggggtattta 660gccccatact caggattccc cccgggagtc atgaatccag aagcagcaaa gttagttatg 720ctacatatga taaacgccca tgctttagca tataggatga taaagaaatt tgacagaaaa 780aaagctgatc cagaatcaaa agaaccagct gaaataggaa ttatatacaa taacatcggc 840gtcacatatc cgtttaatcc gaaagactca aaggatctac aagcatccga taatgccaat 900ttcttccaca gtgggctatt cttaacggct atccacaggg gaaaattaaa tatcgaattt 960gacggagaga catttgttta ccttccatat ttaaagggca atgattggct gggagtgaat 1020tattatacaa gagaagtcgt taaataccaa gatcccatgt ttccaagtat ccctctcata 1080agcttcaagg gcgttccaga ttatggatac ggatgtagac caggaacgac gtcaaaggac 1140ggtaatcctg ttagtgacat tggatgggag gtatatccca aaggcatgta cgactctata 1200gtagctgcca atgaatatgg agttcctgta tacgtaacag aaaacggaat agcagattca 1260aaagatgtat taaggcccta ttacatcgca tctcacattg aagccatgga agaggcttac 1320gaaaatggtt atgacgtgag aggatactta cactgggcat taaccgataa ttacgaatgg 1380gccttagggt tcagaatgag gtttggcttg tacgaagtaa acttgataac caaagagaga 1440aaacccagga aaaagagtgt aagagtattc agagagatag ttattaataa tgggctaaca 1500agcaacatca ggaaagagat cttagaggag gggtag 153681533DNAPyrococcus furiosus 8atgttccctg aaaagttcct ttggggtgtg gcacaatcgg gttttcagtt tgaaatgggg 60gataaactca ggaggaatat tgacactaac actgattggt ggcactgggt aagggataag 120acaaatatag agaaaggcct cgttagtgga gatcttcccg aggaggggat taacaattac 180gagctttatg agaaggacca tgagattgca agaaagctgg gtcttaatgc ttacagaata 240ggcatagagt ggagcagaat attcccatgg ccaacgacat ttattgatgt tgattatagc 300tataatgaat catataacct tatagaagat gtaaagatca ccaaggacac tttggaggag 360ttagatgaga tcgccaacaa gagggaggtg gcctactata ggtcagtcat aaacagcctg 420aggagcaagg ggtttaaggt tatagttaat ctaaatcact tcacccttcc atattggttg 480catgatccca ttgaggctag ggagagggcg ttaactaata agaggaacgg ctgggttaac 540ccaagaacag ttatagagtt tgcaaagtat gccgcttaca tagcctataa gtttggagat 600atagtggata tgtggagcac gtttaatgag cctatggtgg ttgttgagct tggctaccta 660gccccctact ctggcttccc tccaggggtt ctaaatccag aggccgcaaa gctggcgata 720cttcacatga taaatgcaca tgctttagct tataggcaga taaagaagtt tgacactgag 780aaagctgata aggattctaa agagcctgca gaagttggta taatttacaa caacattgga 840gttgcttatc ccaaggatcc gaacgattcc aaggatgtta aggcagcaga aaacgacaac 900ttcttccact cagggctgtt cttcgaggcc atacacaaag gaaaacttaa tatagagttt 960gacggtgaaa cgtttataga tgccccctat ctaaagggca atgactggat aggggttaat 1020tactacacaa gggaagtagt tacgtatcag gaaccaatgt ttccttcaat cccgctgatc 1080acctttaagg gagttcaagg atatggctat gcctgcagac ctggaactct gtcaaaggat 1140gacagacccg tcagcgacat aggatgggaa ctctatccag aggggatgta cgattcaata 1200gttgaagctc acaagtacgg cgttccagtt tacgtgacgg agaacggaat agcggattca 1260aaggacatcc taagacctta ctacatagcg agccacataa agatgataga gaaggccttt 1320gaggatgggt atgaagttaa gggctacttc cactgggcat taactgacaa cttcgagtgg 1380gctctcgggt ttagaatgcg ctttggcctc tacgaagtca acctaattac aaaggagaga 1440attcccaggg agaagagcgt gtcgatattc agagagatag tagccaataa tggtgttacg 1500aaaaagattg aagaggaatt gctgagggga tga 153391614DNABankia gouldi 9atgagaatac gtttagcgac gctcgcgctc tgcgcagcgc tgagcccagt cacctttgca 60gataatgtaa ccgtacaaat cgacgccgac ggcggtaaaa aactcatcag ccgagccctt 120tacggcatga ataactccaa cgcagaaagc cttaccgata ctgactggca gcgttttcgc 180gatgcaggtg tgcgcatgct gcgggaaaat ggcggcaaca acagcaccaa atataactgg 240caactgcacc tgagcagtca tccggattgg tacaacaatg tctacgccgg caacaacaac 300tgggacaacc gggtagccct gattcaggaa aacctgcccg gcgccgacac catgtgggca 360ttccagctca tcggtaaggt cgcggcgact tctgcctaca actttaacga ttgggaattc 420aaccagtcgc aatggtggac cggcgtcgct cagaatctcg ctggcggcgg tgaacccaat 480ctggacggcg gcggcgaagc gctggttgaa ggagacccca atctctacct catggattgg 540tcgccagccg acactgtggg tattctcgac cactggtttg gcgtaaacgg gctgggcgtg 600cggcgtggca aagccaaata ctggagtatg gataacgagc ccggcatctg ggttggcacc 660cacgacgatg tagtgaaaga acaaacgccg gtagaagatt tcctgcacac ctatttcgaa 720accgccaaaa aagcccgcgc caaatttccc ggtattaaaa tcaccggtcc ggtgcccgct 780aatgagtggc agtggtatgc ctggggcggt ttctcggtac cccaggaaca agggtttatg 840agctggatgg agtatttcat caagcgggtg tctgaagagc aacgcgcaag tggtgttcgc 900ctcctcgatg tactcgatct gcactactac cccggcgctt acaatgcgga agatatcgtg 960caattacatc gcacgttctt cgaccgcgac tttgtttcac tggatgccaa cggggtgaaa 1020atggtagaag gtggctggga tgacagcatc aacaaggaat atattttcgg gcgagtgaac 1080gattggctcg aggaatatat ggggccagac catggtgtaa ccctgggctt aaccgaaatg 1140tgcgtgcgca atgtgaatcc gatgactacc gccatctggt atgcctccat gctcggcacc 1200ttcgcggata acggcgtcga aatattcacc ccatggtgct ggaacaccgg aatgtgggaa 1260acactccacc tcttcagccg ctacaacaaa ccttatcggg tcgcctccag ctccagtctt 1320gaagagtttg tcagcgccta cagctccatt aacgaagcag aagacgccat gacggtactt 1380ctggtgaatc gttccactag cgagacccac accgccactg tcgctatcga cgatttccca 1440ctggatggcc cctaccgcac cctgcgctta cacaacctgc cgggggagga aaccttcgta 1500tctcaccgag acaacgccct ggaaaaaggt acagtgcgcg ccagcgacaa tacggtaaca 1560ctggagttgc cccctctgtc cgttactgca atattgctca aggcccggcc ctaa 1614101668DNAThermotoga maritima 10gtgatctgtg tggaaatatt cggaaagacc ttcagagagg gaagattcgt tctcaaagag 60aaaaacttca cagttgagtt cgcggtggag aagatacacc ttggctggaa gatctccggc 120agggtgaagg gaagtccggg aaggcttgag gttcttcgaa cgaaagcacc ggaaaaggta 180cttgtgaaca actggcagtc ctggggaccg tgcagggtgg tcgatgcctt ttctttcaaa 240ccacctgaaa tagatccgaa ctggagatac accgcttcgg tggtgcccga tgtacttgaa 300aggaacctcc agagcgacta tttcgtggct gaagaaggaa aagtgtacgg ttttctgagt 360tcgaaaatcg cacatccttt cttcgctgtg gaagatgggg aacttgtggc atacctcgaa 420tatttcgatg tcgagttcga cgactttgtt cctcttgaac ctctcgttgt actcgaggat 480cccaacacac cccttcttct ggagaaatac gcggaactcg tcggaatgga aaacaacgcg 540agagttccaa aacacacacc cactggatgg tgcagctggt accattactt ccttgatctc 600acctgggaag agaccctcaa gaacctgaag ctcgcgaaga atttcccgtt cgaggtcttc 660cagatagacg acgcctacga aaaggacata ggtgactggc tcgtgacaag aggagacttt 720ccatcggtgg aagagatggc aaaagttata

gcggaaaacg gtttcatccc gggcatatgg 780accgccccgt tcagtgtttc tgaaacctcg gatgtattca acgaacatcc ggactgggta 840gtgaaggaaa acggagagcc gaagatggct tacagaaact ggaacaaaaa gatatacgcc 900ctcgatcttt cgaaagatga ggttctgaac tggcttttcg atctcttctc atctctgaga 960aagatgggct acaggtactt caagatcgac tttctcttcg cgggtgccgt tccaggagaa 1020agaaaaaaga acataacacc aattcaggcg ttcagaaaag ggattgagac gatcagaaaa 1080gcggtgggag aagattcttt catcctcgga tgcggctctc cccttcttcc cgcagtggga 1140tgcgtcgacg ggatgaggat aggacctgac actgcgccgt tctggggaga acatatagaa 1200gacaacggag ctcccgctgc aagatgggcg ctgagaaacg ccataacgag gtacttcatg 1260cacgacaggt tctggctgaa cgaccccgac tgtctgatac tgagagagga gaaaacggat 1320ctcacacaga aggaaaagga gctctactcg tacacgtgtg gagtgctcga caacatgatc 1380atagaaagcg atgatctctc gctcgtcaga gatcatggaa aaaaggttct gaaagaaacg 1440ctcgaactcc tcggtggaag accacgggtt caaaacatca tgtcggagga tctgagatac 1500gagatcgtct cgtctggcac tctctcagga aacgtcaaga tcgtggtcga tctgaacagc 1560agagagtacc acctggaaaa agaaggaaag tcctccctga aaaaaagagt cgtcaaaaga 1620gaagacggaa gaaacttcta cttctacgaa gagggtgaga gagaatga 1668112043DNAThermotoga maritima 11atggggattg gtggcgacga ctcctggagc ccgtcagtat cggcggaatt ccttttattg 60atcgttgagc tctctttcgt tctctttgca agtgacgagt tcgtgaaagt ggaaaacgga 120aaattcgctc tgaacggaaa agaattcaga ttcattggaa gcaacaacta ctacatgcac 180tacaagagca acggaatgat agacagtgtt ctggagagtg ccagagacat gggtataaag 240gtcctcagaa tctggggttt cctcgacggg gagagttact gcagagacaa gaacacctac 300atgcatcctg agcccggtgt tttcggggtg ccagaaggaa tatcgaacgc ccagagcggt 360ttcgaaagac tcgactacac agttgcgaaa gcgaaagaac tcggtataaa acttgtcatt 420gttcttgtga acaactggga cgacttcggt ggaatgaacc agtacgtgag gtggtttgga 480ggaacccatc acgacgattt ctacagagat gagaagatca aagaagagta caaaaagtac 540gtctcctttc tcgtaaacca tgtcaatacc tacacgggag ttccttacag ggaagagccc 600accatcatgg cctgggagct tgcaaacgaa ccgcgctgtg agacggacaa atcggggaac 660acgctcgttg agtgggtgaa ggagatgagc tcctacataa agagtctgga tcccaaccac 720ctcgtggctg tgggggacga aggattcttc agcaactacg aaggattcaa accttacggt 780ggagaagccg agtgggccta caacggctgg tccggtgttg actggaagaa gctcctttcg 840atagagacgg tggacttcgg cacgttccac ctctatccgt cccactgggg tgtcagtcca 900gagaactatg cccagtgggg agcgaagtgg atagaagacc acataaagat cgcaaaagag 960atcggaaaac ccgttgttct ggaagaatat ggaattccaa agagtgcgcc agttaacaga 1020acggccatct acagactctg gaacgatctg gtctacgatc tcggtggaga tggagcgatg 1080ttctggatgc tcgcgggaat cggggaaggt tcggacagag acgagagagg gtactatccg 1140gactacgacg gtttcagaat agtgaacgac gacagtccag aagcggaact gataagagaa 1200tacgcgaagc tgttcaacac aggtgaagac ataagagaag acacctgctc tttcatcctt 1260ccaaaagacg gcatggagat caaaaagacc gtggaagtga gggctggtgt tttcgactac 1320agcaacacgt ttgaaaagtt gtctgtcaaa gtcgaagatc tggtttttga aaatgagata 1380gagcatctcg gatacggaat ttacggcttt gatctcgaca caacccggat cccggatgga 1440gaacatgaaa tgttccttga aggccacttt cagggaaaaa cggtgaaaga ctctatcaaa 1500gcgaaagtgg tgaacgaagc acggtacgtg ctcgcagagg aagttgattt ttcctctcca 1560gaagaggtga aaaactggtg gaacagcgga acctggcagg cagagttcgg gtcacctgac 1620attgaatgga acggtgaggt gggaaatgga gcactgcagc tgaacgtgaa actgcccgga 1680aagagcgact gggaagaagt gagagtagca aggaagttcg aaagactctc agaatgtgag 1740atcctcgagt acgacatcta cattccaaac gtcgagggac tcaagggaag gttgaggccg 1800tacgcggttc tgaaccccgg ctgggtgaag ataggcctcg acatgaacaa cgcgaacgtg 1860gaaagtgcgg agatcatcac tttcggcgga aaagagtaca gaagattcca tgtaagaatt 1920gagttcgaca gaacagcggg ggtgaaagaa cttcacatag gagttgtcgg tgatcatctg 1980aggtacgatg gaccgatttt catcgataat gtgagacttt ataaaagaac aggaggtatg 2040tga 2043121539DNAThermococcus chitonophagus 12atgctaccag aagagttcct atggggcgtt gggcagtcag gctttcagtt cgaaatgggc 60gacaagctca ggaggcacat cgatccaaat accgactggt ggaagtgggt tcgcgatcct 120ttcaacataa aaaaggagct tgtgagtggg gaccttcccg aggacggcat caacaactac 180gaactttttg aaaacgatca caagctcgct aaaggccttg gactcaacgc atacaggatt 240ggaatagagt ggagcagaat ctttccctgg ccgacgtgga cggtcgatac cgaggtcgag 300ttcgacactt acggtttagt aaaggacgtt aagatagaca agtccaccct tgctgaactc 360gacaggctgg ccaacaagga ggaggtaatg tactacaggc gcgttattca gcatttgagg 420gagctcggct tcaaggtctt cgttaacctc aaccacttca cgcttccaat atggctccac 480gacccgatag tggcaaggga gaaggccctc acaaacgaca gaatcggctg ggtctcccag 540aggacagttg ttgagtttgc caagtatgct gcttacatcg cccatgcgct cggagacctc 600gtggacacat ggagcacctt caacgaacct atggtagttg tggagctcgg ctacctcgcc 660ccctactcag gatttccccc gggagtcatg aaccccgagg ccgcgaagct ggcgatcctc 720aacatgataa acgcccacgc cttggcatat aagatgataa agaggttcga caccaagaag 780gccgatgagg atagcaagtc ccctgcggac gttggcataa tttacaacaa catcggtgtt 840gcctacccta aagaccctaa cgatcccaag gacgttaaag cagccgaaaa cgacaactac 900ttccacagcg gactgttctt tgatgccatc cacaagggta agctcaacat agagttcgac 960ggcgaaaact ttgtaaaagt tagacaccta aaaggcaatg actggatagg cctcaactac 1020tacacccgcg aggttgttag atattcggag cccaagttcc caagtatacc cctcatatcc 1080ttcaagggcg ttcccaacta cggctactcc tgcaggcccg gcacgacctc cgccgatggc 1140atgcccgtca gcgatatcgg ctgggaagtc tatccccagg gaatctacga ctcgatagtc 1200gaggccacca agtacagtgt tcctgtttac gtcaccgaga acggtgttgc ggattccgcg 1260gacacgctga ggccatacta catagtcagc cacgtctcaa agatagagga agccattgag 1320aatggatacc ccgtaaaagg ctacatgtac tgggcgctta cggataacta cgagtgggcc 1380ctcggcttca gcatgaggtt tggtctctac aaggtcgacc tcatctccaa ggagaggatc 1440ccgagggaga gaagcgttga gatatatcgc aggatagtgc agtccaacgg tgttcctaag 1500gatatcaaag aggagttcct gaagggtgag gagaaatga 1539131083DNAThermotoga sp. 13atggtagaaa gacacttcag atatgttctt atttgcaccc tgtttcttgt tatgctccta 60atctcatcca ctcagtgtgg aaaaaatgaa ccaaacaaaa gagtgaatag catggaacag 120tcagttgctg aaagtgatag caactcagca tttgaataca acaaaatggt aggtaaagga 180gtaaatattg gaaatgcttt agaagctcct ttcgaaggag cttggggagt aagaattgag 240gatgaatatt ttgagataat aaagaaaagg ggatttgatt ctgttaggat tcccataaga 300tggtcagcac atatatccga aaagccacca tatgatattg acaggaattt cctcgaaaga 360gttaaccatg ttgtcgatag ggctcttgag aataatttaa cagtaatcat caatacgcac 420cattttgaag aactctatca agaaccggat aaatacggcg atgttttggt ggaaatttgg 480agacagattg caaaattctt taaagattac ccggaaaatc tgttctttga aatctacaac 540gagcctgctc agaacttgac agctgaaaaa tggaacgcac tttatccaaa agtgctcaaa 600gttatcaggg agagcaatcc aacccggatt gtcattatcg atgctccaaa ctgggcacac 660tatagcgcag tgagaagtct aaaattagtc aacgacaaac gcatcattgt ttccttccat 720tactacgaac ctttcaaatt cacacatcag ggtgccgaat gggttaatcc catcccacct 780gttagggtta agtggaatgg cgaggaatgg gaaattaacc aaatcagaag tcatttcaaa 840tacgtgagtg actgggcaaa gcaaaataac gtaccaatct ttcttggtga attcggtgct 900tattcaaaag cagacatgga ctcaagggtt aagtggaccg aaagtgtgag aaaaatggcg 960gaagaatttg gattttcata cgcgtattgg gaattttgtg caggatttgg catatacgat 1020agatggtctc aaaactggat cgaaccattg gcaacagctg tggttggcac aggcaaagag 1080taa 1083142319DNAThermotoga maritima 14atggatctta caaaggtggg gatcatagtg aggctgaacg agtggcaggc aaaagacgtg 60gcaaaagaca ggttcataga gataaaagac ggaaaggctg aagtgtggat actccaggga 120gtggaagaga ttttctacga aaaaccagac acatctccca gaatcttctt cgcacaggca 180aggtcgaaca aggtgatcga ggcttttctg accaatcctg tggatacgaa aaagaaagaa 240ctcttcaagg ttactgttga cggaaaagag attcccgtct caagagtgga aaaggccgat 300cccacggaca tagacgtgac gaactacgtg agaatcgtcc tttctgaatc cctgaaagaa 360gaagacctca gaaaagacgt ggaactgatc atagaaggtt acaaaccggc aagagtcatc 420atgatggaga tcctggacga ctactattac gatggagagc tcggagccgt atattctcca 480gagaagacga tattcagagt ctggtccccc gtttctaagt gggtaaaggt gcttctcttc 540aaaaacggag aagacacaga accgtaccag gttgtgaaca tggaatacaa gggaaacggg 600gtctgggaag cggttgttga aggcgatctc gacggagtgt tctacctcta tcagctggaa 660aactacggaa agatcagaac aaccgtcgat ccttattcga aagcggttta cgcaaacagc 720aaaaagagcg ccgttgtgaa tcttgccagg acaaacccag aaggatggga aaacgacagg 780ggaccgaaaa tcgaaggata cgaagacgcg ataatctatg aaatacacat agcggacatc 840acaggactcg aaaactccgg ggtaaaaaac aaaggcctct atctcgggct caccgaagaa 900aacacgaaag gaccgggcgg tgtgacaaca ggcctttcgc accttgtgga actcggtgtt 960acacacgttc atatacttcc tttctttgat ttctacacag gcgacgaact cgataaagat 1020ttcgagaagt actacaactg gggttacgat ccttacctgt tcatggttcc ggagggcaga 1080tactcaaccg atcccaaaaa cccacacacg agaatcagag aagtcaaaga aatggtcaaa 1140gcccttcaca aacacggtat aggtgtgatt atggacatgg tgttccctca cacctacggt 1200ataggcgaac tctctgcgtt cgatcagacg gtgccgtact acttctacag aatcgacaag 1260acaggtgcct atttgaacga aagcggatgt ggtaacgtca tcgcaagcga aagacccatg 1320atgagaaaat tcatagtcga taccgtcacc tactgggtaa aggagtatca catagacgga 1380ttcaggttcg atcagatggg tctcatcgac aaaaagacaa tgctcgaagt cgaaagagct 1440cttcataaaa tcgatccaac tatcattctc tacggcgaac cgtggggtgg atggggagca 1500ccgatcaggt ttggaaagag cgatgtcgcc ggcacacacg tggcagcttt caacgatgag 1560ttcagagacg caataagggg ttccgtgttc aacccgagcg tcaagggatt cgtcatggga 1620ggatacggaa aggaaaccaa gatcaaaagg ggtgttgttg gaagcataaa ctacgacgga 1680aaactcatca aaagtctcgc ccttgatcca gaagaaacta taaactacgc agcgtgtcac 1740gacaaccaca cactgtggga caagaactac cttgccgcca aagctgataa gaaaaaggaa 1800tggaccgaag aagaactgaa aaacgcccag aaactggctg gtgcgatact tctcacttct 1860caaggtgttc ctttcctcca cggagggcag gacttctgca ggacgaagaa tttcaacgac 1920aactcctaca acgcccctat ctcgataaac ggcttcgatt acgaaagaaa acttcagttc 1980atagacgtgt tcaattacca caagggtctc ataaaactca gaaaagaaca ccctgctttc 2040aggctgaaaa acgctgaaga gatcaaaaaa cacctggaat ttctcccggg cgggagaaga 2100atagttgcgt tcatgcttaa agaccacgca ggtggtgatc cctggaaaga catcgtggtg 2160atttacaatg gaaacttaga gaagacaaca tacaaactgc cagaaggaaa atggaatgtg 2220gttgtgaaca gccagaaagc cggaacagaa gtgatagaaa ccgtcgaagg aacaatagaa 2280ctcgatccgc tttccgcgta cgttctgtac agagagtga 231915481PRTDesulfurococcus sp. 15Leu Lys Phe Pro Lys Asp Phe Met Ile Gly Tyr Ser Ser Ser Pro Phe1 5 10 15Gln Phe Glu Ala Gly Ile Pro Gly Ser Glu Asp Pro Asn Ser Asp Trp 20 25 30Trp Val Trp Val His Asp Pro Glu Asn Thr Ala Ala Gly Leu Val Ser 35 40 45Gly Asp Phe Pro Glu Asn Gly Pro Gly Tyr Trp Asn Leu Asn Gln Asn 50 55 60Asp His Asp Leu Ala Glu Lys Leu Gly Val Asn Thr Ile Arg Val Gly65 70 75 80Val Glu Trp Ser Arg Ile Phe Pro Lys Pro Thr Phe Asn Val Lys Val 85 90 95Pro Val Glu Arg Asp Glu Asn Gly Ser Ile Val His Val Asp Val Asp 100 105 110Asp Lys Ala Val Glu Arg Leu Asp Glu Leu Ala Asn Lys Glu Ala Val 115 120 125Asn His Tyr Val Glu Met Tyr Lys Asp Trp Val Glu Arg Gly Arg Lys 130 135 140Leu Ile Leu Asn Leu Tyr His Trp Pro Leu Pro Leu Trp Leu His Asn145 150 155 160Pro Ile Met Val Arg Arg Met Gly Pro Asp Arg Ala Pro Ser Gly Trp 165 170 175Leu Asn Glu Glu Ser Val Val Glu Phe Ala Lys Tyr Ala Ala Tyr Ile 180 185 190Ala Trp Lys Met Gly Glu Leu Pro Val Met Trp Ser Thr Met Asn Glu 195 200 205Pro Asn Val Val Tyr Glu Gln Gly Tyr Met Phe Val Lys Gly Gly Phe 210 215 220Pro Pro Gly Tyr Leu Ser Leu Glu Ala Ala Asp Lys Ala Arg Arg Asn225 230 235 240Met Ile Gln Ala His Ala Arg Ala Tyr Asp Asn Ile Lys Arg Phe Ser 245 250 255Lys Lys Pro Val Gly Leu Ile Tyr Ala Phe Gln Trp Phe Glu Leu Leu 260 265 270Glu Gly Pro Ala Glu Val Phe Asp Lys Phe Lys Ser Ser Lys Leu Tyr 275 280 285Tyr Phe Thr Asp Ile Val Ser Lys Gly Ser Ser Ile Ile Asn Val Glu 290 295 300Tyr Arg Arg Asp Leu Ala Asn Arg Leu Asp Trp Leu Gly Val Asn Tyr305 310 315 320Tyr Ser Arg Leu Val Tyr Lys Ile Val Asp Asp Lys Pro Ile Ile Leu 325 330 335His Gly Tyr Gly Phe Leu Cys Thr Pro Gly Gly Ile Ser Pro Ala Glu 340 345 350Asn Pro Cys Ser Asp Phe Gly Trp Glu Val Tyr Pro Glu Gly Leu Tyr 355 360 365Leu Leu Leu Lys Glu Leu Tyr Asn Arg Tyr Gly Val Asp Leu Ile Val 370 375 380Thr Glu Asn Gly Val Ser Asp Ser Arg Asp Ala Leu Arg Pro Ala Tyr385 390 395 400Leu Val Ser His Val Tyr Ser Val Trp Lys Ala Ala Asn Glu Gly Ile 405 410 415Pro Val Lys Gly Tyr Leu His Trp Ser Leu Thr Asp Asn Tyr Glu Trp 420 425 430Ala Gln Gly Phe Arg Gln Lys Phe Gly Leu Val Met Val Asp Phe Lys 435 440 445Thr Lys Lys Arg Tyr Leu Arg Pro Ser Ala Leu Val Phe Arg Glu Ile 450 455 460Ala Thr His Asn Gly Ile Pro Asp Glu Leu Gln His Leu Thr Leu Ile465 470 475 480Gln16438PRTThermotoga sp. 16Met Ile Arg Arg Ser Asp Phe Pro Lys Asp Phe Ile Phe Gly Thr Ala1 5 10 15Thr Ala Ala Tyr Gln Ile Glu Gly Ala Ala Asn Glu Asp Gly Arg Gly 20 25 30Pro Ser Ile Trp Asp Val Phe Ser His Thr Pro Gly Lys Thr Leu Asn 35 40 45Gly Asp Thr Gly Asp Val Ala Cys Asp His Tyr His Arg Tyr Lys Glu 50 55 60Asp Ile Gln Leu Met Lys Glu Ile Gly Leu Asp Ala Tyr Arg Phe Ser65 70 75 80Ile Ser Trp Pro Arg Ile Met Pro Asp Gly Lys Asn Ile Asn Gln Lys 85 90 95Gly Val Asp Phe Tyr Asn Arg Leu Val Asp Glu Leu Leu Lys Asn Asp 100 105 110Ile Ile Pro Phe Val Thr Leu Tyr His Trp Asp Leu Pro Tyr Ala Leu 115 120 125Tyr Glu Lys Gly Gly Trp Leu Asn Pro Asp Ile Ala Leu Tyr Phe Arg 130 135 140Ala Tyr Ala Thr Phe Met Phe Asn Glu Leu Gly Asp Arg Val Lys His145 150 155 160Trp Ile Thr Leu Asn Glu Pro Trp Cys Ser Ser Phe Ser Gly Tyr Tyr 165 170 175Thr Gly Glu His Ala Pro Gly His Gln Asn Leu Gln Glu Ala Ile Ile 180 185 190Ala Ala His Asn Leu Leu Arg Glu His Gly His Ala Val Gln Ala Ser 195 200 205Arg Glu Glu Val Lys Asp Gly Glu Val Gly Leu Thr Asn Val Val Met 210 215 220Lys Ile Glu Pro Gly Asp Ala Lys Pro Glu Ser Phe Leu Val Ala Ser225 230 235 240Leu Val Asp Lys Phe Val Asn Ala Trp Ser His Asp Pro Val Val Phe 245 250 255Gly Lys Tyr Pro Glu Glu Ala Val Ala Leu Tyr Thr Glu Lys Gly Leu 260 265 270Gln Val Leu Asp Ser Asp Met Asn Ile Ile Ser Thr Pro Ile Asp Phe 275 280 285Phe Gly Val Asn Tyr Tyr Thr Arg Thr Leu Val Val Phe Asp Met Asn 290 295 300Asn Pro Leu Gly Phe Ser Tyr Val Gln Gly Asp Leu Pro Lys Thr Glu305 310 315 320Met Gly Trp Glu Ile Tyr Pro Gln Gly Leu Phe Asp Met Leu Val Tyr 325 330 335Leu Lys Glu Arg Tyr Lys Leu Pro Leu Tyr Ile Thr Glu Asn Gly Met 340 345 350Ala Gly Pro Asp Lys Leu Glu Asn Gly Arg Val His Asp Asn Tyr Arg 355 360 365Ile Glu Tyr Leu Glu Lys His Phe Glu Lys Ala Leu Glu Ala Ile Asn 370 375 380Ala Asp Val Asp Leu Lys Gly Tyr Phe Ile Trp Ser Leu Met Asp Asn385 390 395 400Phe Glu Trp Ala Cys Gly Tyr Ser Lys Arg Phe Gly Ile Ile Tyr Val 405 410 415Asp Tyr Asn Thr Pro Lys Arg Ile Leu Lys Asp Ser Ala Met Trp Leu 420 425 430Lys Glu Phe Leu Lys Ser 43517421PRTStaphylothermus marinus 17Leu Ile Arg Phe Pro Asp Tyr Phe Leu Phe Gly Thr Ala Thr Ser Ser1 5 10 15His Gln Ile Glu Gly Asn Asn Ile Phe Asn Asp Trp Trp Glu Trp Glu 20 25 30Thr Lys Gly Arg Ile Lys Val Arg Ser Gly Lys Ala Cys Asn His Trp 35 40 45Glu Leu Tyr Lys Glu Asp Ile Glu Leu Met Ala Glu Leu Gly Tyr Asn 50 55 60Ala Tyr Arg Phe Ser Ile Glu Trp Ser Arg Ile Phe Pro Arg Lys Asp65 70 75 80His Ile Asp Tyr Glu Ser Leu Asn Lys Tyr Lys Glu Ile Val Asn Leu 85 90 95Leu Arg Lys Tyr Gly Ile Glu Pro Val Ile Thr Leu His His Phe Thr 100 105 110Asn Pro Gln Trp Phe Met Lys Ile Gly Gly Trp Thr Arg Glu Glu Asn 115 120 125Ile Lys Tyr Phe Ile Lys Tyr Val Glu Leu Ile Ala Ser Glu Ile Lys 130 135 140Asp Val Lys Ile Trp Ile Thr Ile Asn Glu Pro Ile Ile Tyr Val Leu145 150 155 160Gln Gly Tyr Ile Ser Gly Glu Trp Pro Pro Gly Ile Lys Asn Leu Lys 165 170 175Ile Ala Asp Gln Val Thr Lys Asn Leu Leu Lys Ala His Asn Glu Ala 180 185 190Tyr Asn Ile Leu His Lys His Gly Ile Val Gly Ile Ala Lys

Asn Met 195 200 205Ile Ala Phe Lys Pro Gly Ser Asn Arg Gly Lys Asp Ile Asn Ile Tyr 210 215 220His Lys Val Asp Lys Ala Phe Asn Trp Gly Phe Leu Asn Gly Ile Leu225 230 235 240Arg Gly Glu Leu Glu Thr Leu Arg Gly Lys Tyr Arg Val Glu Pro Gly 245 250 255Asn Ile Asp Phe Ile Gly Ile Asn Tyr Tyr Ser Ser Tyr Ile Val Lys 260 265 270Tyr Thr Trp Asn Pro Phe Lys Leu His Ile Lys Val Glu Pro Leu Asp 275 280 285Thr Gly Leu Trp Thr Thr Met Gly Tyr Cys Ile Tyr Pro Arg Gly Ile 290 295 300Tyr Glu Val Val Met Lys Thr His Glu Lys Tyr Gly Lys Glu Ile Ile305 310 315 320Ile Thr Glu Asn Gly Val Ala Val Glu Asn Asp Glu Leu Arg Ile Leu 325 330 335Ser Ile Ile Arg His Leu Gln Tyr Leu Tyr Lys Ala Met Asn Glu Gly 340 345 350Ala Lys Val Lys Gly Tyr Phe Tyr Trp Ser Phe Met Asp Asn Phe Glu 355 360 365Trp Asp Lys Gly Phe Asn Gln Arg Phe Gly Leu Val Glu Val Asp Tyr 370 375 380Lys Thr Phe Glu Arg Lys Pro Arg Lys Ser Ala Tyr Val Tyr Ser Gln385 390 395 400Ile Ala Arg Thr Lys Thr Ile Ser Asp Glu Tyr Leu Glu Lys Tyr Gly 405 410 415Leu Lys Asn Leu Glu 42018509PRTThermococcus sp. 18Met Leu Pro Glu Gly Phe Leu Trp Gly Val Ser Gln Ser Gly Phe Gln1 5 10 15Phe Glu Met Gly Asp Lys Leu Arg Arg Asn Ile Asp Pro Asn Thr Asp 20 25 30Trp Trp Lys Trp Val Arg Asp Pro Phe Asn Ile Lys Arg Glu Leu Val 35 40 45Ser Gly Asp Leu Pro Glu Glu Gly Ile Asn Asn Tyr Glu Leu Tyr Glu 50 55 60Lys Asp His Arg Leu Ala Arg Asp Leu Gly Leu Asn Val Tyr Arg Ile65 70 75 80Gly Ile Glu Trp Ser Arg Ile Phe Pro Trp Pro Thr Trp Phe Val Glu 85 90 95Val Asp Val Glu Arg Asp Ser Tyr Gly Leu Val Lys Asp Val Lys Ile 100 105 110Asp Lys Asp Thr Leu Glu Glu Leu Asp Glu Ile Ala Asn His Gln Glu 115 120 125Ile Ala Tyr Tyr Arg Arg Val Ile Glu His Leu Arg Glu Leu Gly Phe 130 135 140Lys Val Ile Val Asn Leu Asn His Phe Thr Leu Pro Leu Trp Leu His145 150 155 160Asp Pro Ile Ile Ala Arg Glu Lys Ala Leu Thr Asn Gly Arg Ile Gly 165 170 175Trp Val Gly Gln Glu Ser Val Val Glu Phe Ala Lys Tyr Ala Ala Tyr 180 185 190Ile Ala Asn Ala Leu Gly Asp Leu Val Asp Met Trp Ser Thr Phe Asn 195 200 205Glu Pro Met Val Val Val Glu Leu Gly Tyr Leu Ala Pro Tyr Ser Gly 210 215 220Phe Pro Pro Gly Val Met Asn Pro Glu Ala Ala Lys Leu Ala Ile Leu225 230 235 240Asn Met Ile Asn Ala His Ala Leu Ala Tyr Lys Met Ile Lys Lys Phe 245 250 255Asp Arg Val Lys Ala Asp Lys Asp Ser Arg Ser Glu Ala Glu Val Gly 260 265 270Ile Ile Tyr Asn Asn Ile Gly Val Ala Tyr Pro Tyr Asp Ser Asn Asp 275 280 285Pro Lys Asp Val Lys Ala Ala Glu Asn Asp Asn Tyr Phe His Ser Gly 290 295 300Leu Phe Phe Asp Ala Ile His Lys Gly Lys Leu Asn Ile Glu Phe Asp305 310 315 320Gly Glu Thr Phe Val Lys Val Arg His Leu Arg Gly Asn Asp Trp Ile 325 330 335Gly Val Asn Tyr Tyr Thr Arg Glu Val Val Arg Tyr Ser Glu Pro Lys 340 345 350Phe Pro Ser Ile Pro Leu Ile Ser Phe Arg Gly Val His Asn Tyr Gly 355 360 365Tyr Ala Cys Arg Pro Gly Ser Ser Ser Ala Asp Gly Arg Pro Val Ser 370 375 380Asp Ile Gly Trp Glu Ile Tyr Pro Glu Gly Ile Tyr Asp Ser Ile Arg385 390 395 400Glu Ala Asn Lys Tyr Gly Val Pro Val Tyr Val Thr Glu Asn Gly Ile 405 410 415Ala Asp Ser Thr Asp Thr Leu Arg Pro Tyr Tyr Leu Ala Ser His Val 420 425 430Ala Lys Ile Glu Glu Ala Tyr Glu Ala Gly Tyr Asp Val Arg Gly Tyr 435 440 445Leu Tyr Trp Ala Leu Thr Asp Asn Tyr Glu Trp Ala Leu Gly Phe Arg 450 455 460Met Arg Phe Gly Leu Tyr Lys Val Asp Leu Ile Thr Lys Glu Arg Thr465 470 475 480Pro Arg Glu Glu Ser Val Lys Val Tyr Arg Gly Ile Val Glu Asn Asn 485 490 495Gly Val Ser Lys Glu Ile Arg Glu Lys Phe Gly Leu Gly 500 50519721PRTThermotoga maritima 19Met Glu Arg Ile Asp Glu Ile Leu Ser Gln Leu Thr Thr Glu Glu Lys1 5 10 15Val Lys Leu Val Val Gly Val Gly Leu Pro Gly Leu Phe Gly Asn Pro 20 25 30His Ser Arg Val Ala Gly Ala Ala Gly Glu Thr His Pro Val Pro Arg 35 40 45Leu Gly Ile Pro Ala Phe Val Leu Ala Asp Gly Pro Ala Gly Leu Arg 50 55 60Ile Asn Pro Thr Arg Glu Asn Asp Glu Asn Thr Tyr Tyr Thr Thr Ala65 70 75 80Phe Pro Val Glu Ile Met Leu Ala Ser Thr Trp Asn Arg Asp Leu Leu 85 90 95Glu Glu Val Gly Lys Ala Met Gly Glu Glu Val Arg Glu Tyr Gly Val 100 105 110Asp Val Leu Leu Ala Pro Ala Met Asn Ile His Arg Asn Pro Leu Cys 115 120 125Gly Arg Asn Phe Glu Tyr Tyr Ser Glu Asp Pro Val Leu Ser Gly Glu 130 135 140Met Ala Ser Ala Phe Val Lys Gly Val Gln Ser Gln Gly Val Gly Ala145 150 155 160Cys Ile Lys His Phe Val Ala Asn Asn Gln Glu Thr Asn Arg Met Val 165 170 175Val Asp Thr Ile Val Ser Glu Arg Ala Leu Arg Glu Ile Tyr Leu Lys 180 185 190Gly Phe Glu Ile Ala Val Lys Lys Ala Arg Pro Trp Thr Val Met Ser 195 200 205Ala Tyr Asn Lys Leu Asn Gly Lys Tyr Cys Ser Gln Asn Glu Trp Leu 210 215 220Leu Lys Lys Val Leu Arg Glu Glu Trp Gly Phe Gly Gly Phe Val Met225 230 235 240Ser Asp Trp Tyr Ala Gly Asp Asn Pro Val Glu Gln Leu Lys Ala Gly 245 250 255Asn Asp Met Ile Met Pro Gly Lys Ala Tyr Gln Val Asn Thr Glu Arg 260 265 270Arg Asp Glu Ile Glu Glu Ile Met Glu Ala Leu Lys Glu Gly Lys Leu 275 280 285Ser Glu Glu Val Leu Asp Glu Cys Val Arg Asn Ile Leu Lys Val Leu 290 295 300Val Asn Ala Pro Ser Phe Lys Gly Tyr Arg Tyr Ser Asn Lys Pro Asp305 310 315 320Leu Glu Ser His Ala Glu Val Ala Tyr Glu Ala Gly Ala Glu Gly Val 325 330 335Val Leu Leu Glu Asn Asn Gly Val Leu Pro Phe Asp Glu Asn Thr His 340 345 350Val Ala Val Phe Gly Thr Gly Gln Ile Glu Thr Ile Lys Gly Gly Thr 355 360 365Gly Ser Gly Asp Thr His Pro Arg Tyr Thr Ile Ser Ile Leu Glu Gly 370 375 380Ile Lys Glu Arg Asn Met Lys Phe Asp Glu Glu Leu Ala Ser Thr Tyr385 390 395 400Glu Glu Tyr Ile Lys Lys Met Arg Glu Thr Glu Glu Tyr Lys Pro Arg 405 410 415Thr Asp Ser Trp Gly Thr Val Ile Lys Pro Lys Leu Pro Glu Asn Phe 420 425 430Leu Ser Glu Lys Glu Ile Lys Lys Pro Pro Lys Lys Asn Asp Val Ala 435 440 445Val Val Val Ile Ser Arg Ile Ser Gly Glu Gly Tyr Asp Arg Lys Pro 450 455 460Val Lys Gly Asp Phe Tyr Leu Ser Asp Asp Glu Leu Glu Leu Ile Lys465 470 475 480Thr Val Ser Lys Glu Phe His Asp Gln Gly Lys Lys Val Val Val Leu 485 490 495Leu Asn Ile Gly Ser Pro Ile Glu Val Ala Ser Trp Arg Asp Leu Val 500 505 510Asp Gly Ile Leu Leu Val Trp Gln Ala Gly Gln Glu Met Gly Arg Ile 515 520 525Val Ala Asp Val Leu Val Gly Lys Ile Asn Pro Ser Gly Lys Leu Pro 530 535 540Thr Thr Phe Pro Lys Asp Tyr Ser Asp Val Pro Ser Trp Thr Phe Pro545 550 555 560Gly Glu Pro Lys Asp Asn Pro Gln Arg Val Val Tyr Glu Glu Asp Ile 565 570 575Tyr Val Gly Tyr Arg Tyr Tyr Asp Thr Phe Gly Val Glu Pro Ala Tyr 580 585 590Glu Phe Gly Tyr Gly Leu Ser Tyr Thr Lys Phe Glu Tyr Lys Asp Leu 595 600 605Lys Ile Ala Ile Asp Gly Glu Thr Leu Arg Val Ser Tyr Thr Ile Thr 610 615 620Asn Thr Gly Asp Arg Ala Gly Lys Glu Val Ser Gln Val Tyr Ile Lys625 630 635 640Ala Pro Lys Gly Lys Ile Asp Lys Pro Phe Gln Glu Leu Lys Ala Phe 645 650 655His Lys Thr Lys Leu Leu Asn Pro Gly Glu Ser Glu Glu Ile Ser Leu 660 665 670Glu Ile Pro Leu Arg Asp Leu Ala Ser Phe Asp Gly Lys Glu Trp Val 675 680 685Val Glu Ser Gly Glu Tyr Glu Val Arg Val Gly Ala Ser Ser Arg Asp 690 695 700Ile Arg Leu Arg Asp Ile Phe Leu Val Glu Gly Glu Lys Arg Phe Lys705 710 715 720Pro20454PRTThermococcus alcaliphilus 20Met Ile His Cys Pro Val Lys Gly Ile Ile Ser Glu Ala Arg Gly Ile1 5 10 15Thr Ile Thr Ile Asp Leu Ser Phe Gln Gly Gln Ile Asn Asn Leu Val 20 25 30Asn Ala Met Ile Val Phe Pro Glu Phe Phe Leu Phe Gly Thr Ala Thr 35 40 45Ser Ser His Gln Ile Glu Gly Asp Asn Lys Trp Asn Asp Trp Trp Tyr 50 55 60Tyr Glu Glu Ile Gly Lys Leu Pro Tyr Lys Ser Gly Lys Ala Cys Asn65 70 75 80His Trp Glu Leu Tyr Arg Glu Asp Ile Glu Leu Met Ala Gln Leu Gly 85 90 95Tyr Asn Ala Tyr Arg Phe Ser Ile Glu Trp Ser Arg Leu Phe Pro Glu 100 105 110Glu Gly Lys Phe Asn Glu Glu Ala Phe Asn Arg Tyr Arg Glu Ile Ile 115 120 125Glu Ile Leu Leu Glu Lys Gly Ile Thr Pro Asn Val Thr Leu His His 130 135 140Phe Thr Ser Pro Leu Trp Phe Met Arg Lys Gly Gly Phe Leu Lys Glu145 150 155 160Glu Asn Leu Lys Tyr Trp Glu Gln Tyr Val Asp Lys Ala Ala Glu Leu 165 170 175Leu Lys Gly Val Lys Leu Val Ala Thr Phe Asn Glu Pro Met Val Tyr 180 185 190Val Met Met Gly Tyr Leu Thr Ala Tyr Trp Pro Pro Phe Ile Lys Ser 195 200 205Pro Phe Lys Ala Phe Lys Val Ala Ala Asn Leu Leu Lys Ala His Ala 210 215 220Met Ala Tyr Asp Ile Leu His Gly Asn Phe Asp Val Gly Ile Val Lys225 230 235 240Asn Ile Pro Ile Met Leu Pro Ala Ser Asn Arg Glu Lys Asp Val Glu 245 250 255Ala Ala Gln Lys Ala Asp Asn Leu Phe Asn Trp Asn Phe Leu Asp Ala 260 265 270Ile Trp Ser Gly Lys Tyr Lys Gly Ala Phe Gly Thr Tyr Lys Thr Pro 275 280 285Glu Ser Asp Ala Asp Phe Ile Gly Ile Asn Tyr Tyr Thr Ala Ser Glu 290 295 300Val Arg His Ser Trp Asn Pro Leu Lys Phe Phe Phe Asp Ala Lys Leu305 310 315 320Ala Asp Leu Ser Glu Arg Lys Thr Asp Met Gly Trp Ser Val Tyr Pro 325 330 335Lys Gly Ile Tyr Glu Ala Ile Ala Lys Val Ser His Tyr Gly Lys Pro 340 345 350Met Tyr Ile Thr Glu Asn Gly Ile Ala Thr Leu Asp Asp Glu Trp Arg 355 360 365Ile Glu Phe Ile Ile Gln His Leu Gln Tyr Val His Lys Ala Leu Asn 370 375 380Asp Gly Phe Asp Leu Arg Gly Tyr Phe Tyr Trp Ser Phe Met Asp Asn385 390 395 400Phe Glu Trp Ala Glu Gly Phe Arg Pro Arg Phe Gly Leu Val Glu Val 405 410 415Asp Tyr Thr Thr Phe Lys Arg Arg Pro Arg Lys Ser Ala Tyr Ile Tyr 420 425 430Gly Glu Ile Ala Arg Glu Lys Lys Ile Lys Asp Glu Leu Leu Ala Lys 435 440 445Tyr Gly Leu Pro Glu Leu 45021511PRTThermococcus chitonophagus 21Leu Leu Pro Glu Asn Phe Leu Trp Gly Val Ser Gln Ser Gly Phe Gln1 5 10 15Phe Glu Met Gly Asp Arg Leu Arg Arg His Ile Asp Pro Asn Thr Asp 20 25 30Trp Trp Tyr Trp Val Arg Asp Glu Tyr Asn Ile Lys Lys Gly Leu Val 35 40 45Ser Gly Asp Leu Pro Glu Asp Gly Ile Asn Ser Tyr Glu Leu Tyr Glu 50 55 60Arg Asp Gln Glu Ile Ala Lys Asp Leu Gly Leu Asn Thr Tyr Arg Ile65 70 75 80Gly Ile Glu Trp Ser Arg Val Phe Pro Trp Pro Thr Thr Phe Val Asp 85 90 95Val Glu Tyr Glu Ile Asp Glu Ser Tyr Gly Leu Val Lys Asp Val Lys 100 105 110Ile Ser Lys Asp Ala Leu Glu Lys Leu Asp Glu Ile Ala Asn Gln Arg 115 120 125Glu Ile Ile Tyr Tyr Arg Asn Leu Ile Asn Ser Leu Arg Lys Arg Gly 130 135 140Phe Lys Val Ile Leu Asn Leu Asn His Phe Thr Leu Pro Ile Trp Leu145 150 155 160His Asp Pro Ile Glu Ser Arg Glu Lys Ala Leu Thr Asn Lys Arg Asn 165 170 175Gly Trp Val Ser Glu Arg Ser Val Ile Glu Phe Ala Lys Phe Ala Ala 180 185 190Tyr Leu Ala Tyr Lys Phe Gly Asp Ile Val Asp Met Trp Ser Thr Phe 195 200 205Asn Glu Pro Met Val Val Ala Glu Leu Gly Tyr Leu Ala Pro Tyr Ser 210 215 220Gly Phe Pro Pro Gly Val Met Asn Pro Glu Ala Ala Lys Leu Val Met225 230 235 240Leu His Met Ile Asn Ala His Ala Leu Ala Tyr Arg Met Ile Lys Lys 245 250 255Phe Asp Arg Lys Lys Ala Asp Pro Glu Ser Lys Glu Pro Ala Glu Ile 260 265 270Gly Ile Ile Tyr Asn Asn Ile Gly Val Thr Tyr Pro Phe Asn Pro Lys 275 280 285Asp Ser Lys Asp Leu Gln Ala Ser Asp Asn Ala Asn Phe Phe His Ser 290 295 300Gly Leu Phe Leu Thr Ala Ile His Arg Gly Lys Leu Asn Ile Glu Phe305 310 315 320Asp Gly Glu Thr Phe Val Tyr Leu Pro Tyr Leu Lys Gly Asn Asp Trp 325 330 335Leu Gly Val Asn Tyr Tyr Thr Arg Glu Val Val Lys Tyr Gln Asp Pro 340 345 350Met Phe Pro Ser Ile Pro Leu Ile Ser Phe Lys Gly Val Pro Asp Tyr 355 360 365Gly Tyr Gly Cys Arg Pro Gly Thr Thr Ser Lys Asp Gly Asn Pro Val 370 375 380Ser Asp Ile Gly Trp Glu Val Tyr Pro Lys Gly Met Tyr Asp Ser Ile385 390 395 400Val Ala Ala Asn Glu Tyr Gly Val Pro Val Tyr Val Thr Glu Asn Gly 405 410 415Ile Ala Asp Ser Lys Asp Val Leu Arg Pro Tyr Tyr Ile Ala Ser His 420 425 430Ile Glu Ala Met Glu Glu Ala Tyr Glu Asn Gly Tyr Asp Val Arg Gly 435 440 445Tyr Leu His Trp Ala Leu Thr Asp Asn Tyr Glu Trp Ala Leu Gly Phe 450 455 460Arg Met Arg Phe Gly Leu Tyr Glu Val Asn Leu Ile Thr Lys Glu Arg465 470 475 480Lys Pro Arg Lys Lys Ser Val Arg Val Phe Arg Glu Ile Val Ile Asn 485 490 495Asn Gly Leu Thr Ser Asn Ile Arg Lys Glu Ile Leu Glu Glu Gly 500 505 51022510PRTPyrococcus furiosus 22Met Phe Pro Glu Lys Phe Leu Trp Gly Val Ala Gln Ser Gly Phe Gln1 5 10 15Phe Glu Met Gly Asp Lys Leu Arg Arg Asn Ile Asp Thr Asn Thr Asp 20 25 30Trp Trp His Trp Val Arg Asp Lys Thr Asn Ile Glu Lys Gly Leu Val

35 40 45Ser Gly Asp Leu Pro Glu Glu Gly Ile Asn Asn Tyr Glu Leu Tyr Glu 50 55 60Lys Asp His Glu Ile Ala Arg Lys Leu Gly Leu Asn Ala Tyr Arg Ile65 70 75 80Gly Ile Glu Trp Ser Arg Ile Phe Pro Trp Pro Thr Thr Phe Ile Asp 85 90 95Val Asp Tyr Ser Tyr Asn Glu Ser Tyr Asn Leu Ile Glu Asp Val Lys 100 105 110Ile Thr Lys Asp Thr Leu Glu Glu Leu Asp Glu Ile Ala Asn Lys Arg 115 120 125Glu Val Ala Tyr Tyr Arg Ser Val Ile Asn Ser Leu Arg Ser Lys Gly 130 135 140Phe Lys Val Ile Val Asn Leu Asn His Phe Thr Leu Pro Tyr Trp Leu145 150 155 160His Asp Pro Ile Glu Ala Arg Glu Arg Ala Leu Thr Asn Lys Arg Asn 165 170 175Gly Trp Val Asn Pro Arg Thr Val Ile Glu Phe Ala Lys Tyr Ala Ala 180 185 190Tyr Ile Ala Tyr Lys Phe Gly Asp Ile Val Asp Met Trp Ser Thr Phe 195 200 205Asn Glu Pro Met Val Val Val Glu Leu Gly Tyr Leu Ala Pro Tyr Ser 210 215 220Gly Phe Pro Pro Gly Val Leu Asn Pro Glu Ala Ala Lys Leu Ala Ile225 230 235 240Leu His Met Ile Asn Ala His Ala Leu Ala Tyr Arg Gln Ile Lys Lys 245 250 255Phe Asp Thr Glu Lys Ala Asp Lys Asp Ser Lys Glu Pro Ala Glu Val 260 265 270Gly Ile Ile Tyr Asn Asn Ile Gly Val Ala Tyr Pro Lys Asp Pro Asn 275 280 285Asp Ser Lys Asp Val Lys Ala Ala Glu Asn Asp Asn Phe Phe His Ser 290 295 300Gly Leu Phe Phe Glu Ala Ile His Lys Gly Lys Leu Asn Ile Glu Phe305 310 315 320Asp Gly Glu Thr Phe Ile Asp Ala Pro Tyr Leu Lys Gly Asn Asp Trp 325 330 335Ile Gly Val Asn Tyr Tyr Thr Arg Glu Val Val Thr Tyr Gln Glu Pro 340 345 350Met Phe Pro Ser Ile Pro Leu Ile Thr Phe Lys Gly Val Gln Gly Tyr 355 360 365Gly Tyr Ala Cys Arg Pro Gly Thr Leu Ser Lys Asp Asp Arg Pro Val 370 375 380Ser Asp Ile Gly Trp Glu Leu Tyr Pro Glu Gly Met Tyr Asp Ser Ile385 390 395 400Val Glu Ala His Lys Tyr Gly Val Pro Val Tyr Val Thr Glu Asn Gly 405 410 415Ile Ala Asp Ser Lys Asp Ile Leu Arg Pro Tyr Tyr Ile Ala Ser His 420 425 430Ile Lys Met Ile Glu Lys Ala Phe Glu Asp Gly Tyr Glu Val Lys Gly 435 440 445Tyr Phe His Trp Ala Leu Thr Asp Asn Phe Glu Trp Ala Leu Gly Phe 450 455 460Arg Met Arg Phe Gly Leu Tyr Glu Val Asn Leu Ile Thr Lys Glu Arg465 470 475 480Ile Pro Arg Glu Lys Ser Val Ser Ile Phe Arg Glu Ile Val Ala Asn 485 490 495Asn Gly Val Thr Lys Lys Ile Glu Glu Glu Leu Leu Arg Gly 500 505 51023537PRTBankia gouldi 23Met Arg Ile Arg Leu Ala Thr Leu Ala Leu Cys Ala Ala Leu Ser Pro1 5 10 15Val Thr Phe Ala Asp Asn Val Thr Val Gln Ile Asp Ala Asp Gly Gly 20 25 30Lys Lys Leu Ile Ser Arg Ala Leu Tyr Gly Met Asn Asn Ser Asn Ala 35 40 45Glu Ser Leu Thr Asp Thr Asp Trp Gln Arg Phe Arg Asp Ala Gly Val 50 55 60Arg Met Leu Arg Glu Asn Gly Gly Asn Asn Ser Thr Lys Tyr Asn Trp65 70 75 80Gln Leu His Leu Ser Ser His Pro Asp Trp Tyr Asn Asn Val Tyr Ala 85 90 95Gly Asn Asn Asn Trp Asp Asn Arg Val Ala Leu Ile Gln Glu Asn Leu 100 105 110Pro Gly Ala Asp Thr Met Trp Ala Phe Gln Leu Ile Gly Lys Val Ala 115 120 125Ala Thr Ser Ala Tyr Asn Phe Asn Asp Trp Glu Phe Asn Gln Ser Gln 130 135 140Trp Trp Thr Gly Val Ala Gln Asn Leu Ala Gly Gly Gly Glu Pro Asn145 150 155 160Leu Asp Gly Gly Gly Glu Ala Leu Val Glu Gly Asp Pro Asn Leu Tyr 165 170 175Leu Met Asp Trp Ser Pro Ala Asp Thr Val Gly Ile Leu Asp His Trp 180 185 190Phe Gly Val Asn Gly Leu Gly Val Arg Arg Gly Lys Ala Lys Tyr Trp 195 200 205Ser Met Asp Asn Glu Pro Gly Ile Trp Val Gly Thr His Asp Asp Val 210 215 220Val Lys Glu Gln Thr Pro Val Glu Asp Phe Leu His Thr Tyr Phe Glu225 230 235 240Thr Ala Lys Lys Ala Arg Ala Lys Phe Pro Gly Ile Lys Ile Thr Gly 245 250 255Pro Val Pro Ala Asn Glu Trp Gln Trp Tyr Ala Trp Gly Gly Phe Ser 260 265 270Val Pro Gln Glu Gln Gly Phe Met Ser Trp Met Glu Tyr Phe Ile Lys 275 280 285Arg Val Ser Glu Glu Gln Arg Ala Ser Gly Val Arg Leu Leu Asp Val 290 295 300Leu Asp Leu His Tyr Tyr Pro Gly Ala Tyr Asn Ala Glu Asp Ile Val305 310 315 320Gln Leu His Arg Thr Phe Phe Asp Arg Asp Phe Val Ser Leu Asp Ala 325 330 335Asn Gly Val Lys Met Val Glu Gly Gly Trp Asp Asp Ser Ile Asn Lys 340 345 350Glu Tyr Ile Phe Gly Arg Val Asn Asp Trp Leu Glu Glu Tyr Met Gly 355 360 365Pro Asp His Gly Val Thr Leu Gly Leu Thr Glu Met Cys Val Arg Asn 370 375 380Val Asn Pro Met Thr Thr Ala Ile Trp Tyr Ala Ser Met Leu Gly Thr385 390 395 400Phe Ala Asp Asn Gly Val Glu Ile Phe Thr Pro Trp Cys Trp Asn Thr 405 410 415Gly Met Trp Glu Thr Leu His Leu Phe Ser Arg Tyr Asn Lys Pro Tyr 420 425 430Arg Val Ala Ser Ser Ser Ser Leu Glu Glu Phe Val Ser Ala Tyr Ser 435 440 445Ser Ile Asn Glu Ala Glu Asp Ala Met Thr Val Leu Leu Val Asn Arg 450 455 460Ser Thr Ser Glu Thr His Thr Ala Thr Val Ala Ile Asp Asp Phe Pro465 470 475 480Leu Asp Gly Pro Tyr Arg Thr Leu Arg Leu His Asn Leu Pro Gly Glu 485 490 495Glu Thr Phe Val Ser His Arg Asp Asn Ala Leu Glu Lys Gly Thr Val 500 505 510Arg Ala Ser Asp Asn Thr Val Thr Leu Glu Leu Pro Pro Leu Ser Val 515 520 525Thr Ala Ile Leu Leu Lys Ala Arg Pro 530 53524555PRTThermotoga maritima 24Val Ile Cys Val Glu Ile Phe Gly Lys Thr Phe Arg Glu Gly Arg Phe1 5 10 15Val Leu Lys Glu Lys Asn Phe Thr Val Glu Phe Ala Val Glu Lys Ile 20 25 30His Leu Gly Trp Lys Ile Ser Gly Arg Val Lys Gly Ser Pro Gly Arg 35 40 45Leu Glu Val Leu Arg Thr Lys Ala Pro Glu Lys Val Leu Val Asn Asn 50 55 60Trp Gln Ser Trp Gly Pro Cys Arg Val Val Asp Ala Phe Ser Phe Lys65 70 75 80Pro Pro Glu Ile Asp Pro Asn Trp Arg Tyr Thr Ala Ser Val Val Pro 85 90 95Asp Val Leu Glu Arg Asn Leu Gln Ser Asp Tyr Phe Val Ala Glu Glu 100 105 110Gly Lys Val Tyr Gly Phe Leu Ser Ser Lys Ile Ala His Pro Phe Phe 115 120 125Ala Val Glu Asp Gly Glu Leu Val Ala Tyr Leu Glu Tyr Phe Asp Val 130 135 140Glu Phe Asp Asp Phe Val Pro Leu Glu Pro Leu Val Val Leu Glu Asp145 150 155 160Pro Asn Thr Pro Leu Leu Leu Glu Lys Tyr Ala Glu Leu Val Gly Met 165 170 175Glu Asn Asn Ala Arg Val Pro Lys His Thr Pro Thr Gly Trp Cys Ser 180 185 190Trp Tyr His Tyr Phe Leu Asp Leu Thr Trp Glu Glu Thr Leu Lys Asn 195 200 205Leu Lys Leu Ala Lys Asn Phe Pro Phe Glu Val Phe Gln Ile Asp Asp 210 215 220Ala Tyr Glu Lys Asp Ile Gly Asp Trp Leu Val Thr Arg Gly Asp Phe225 230 235 240Pro Ser Val Glu Glu Met Ala Lys Val Ile Ala Glu Asn Gly Phe Ile 245 250 255Pro Gly Ile Trp Thr Ala Pro Phe Ser Val Ser Glu Thr Ser Asp Val 260 265 270Phe Asn Glu His Pro Asp Trp Val Val Lys Glu Asn Gly Glu Pro Lys 275 280 285Met Ala Tyr Arg Asn Trp Asn Lys Lys Ile Tyr Ala Leu Asp Leu Ser 290 295 300Lys Asp Glu Val Leu Asn Trp Leu Phe Asp Leu Phe Ser Ser Leu Arg305 310 315 320Lys Met Gly Tyr Arg Tyr Phe Lys Ile Asp Phe Leu Phe Ala Gly Ala 325 330 335Val Pro Gly Glu Arg Lys Lys Asn Ile Thr Pro Ile Gln Ala Phe Arg 340 345 350Lys Gly Ile Glu Thr Ile Arg Lys Ala Val Gly Glu Asp Ser Phe Ile 355 360 365Leu Gly Cys Gly Ser Pro Leu Leu Pro Ala Val Gly Cys Val Asp Gly 370 375 380Met Arg Ile Gly Pro Asp Thr Ala Pro Phe Trp Gly Glu His Ile Glu385 390 395 400Asp Asn Gly Ala Pro Ala Ala Arg Trp Ala Leu Arg Asn Ala Ile Thr 405 410 415Arg Tyr Phe Met His Asp Arg Phe Trp Leu Asn Asp Pro Asp Cys Leu 420 425 430Ile Leu Arg Glu Glu Lys Thr Asp Leu Thr Gln Lys Glu Lys Glu Leu 435 440 445Tyr Ser Tyr Thr Cys Gly Val Leu Asp Asn Met Ile Ile Glu Ser Asp 450 455 460Asp Leu Ser Leu Val Arg Asp His Gly Lys Lys Val Leu Lys Glu Thr465 470 475 480Leu Glu Leu Leu Gly Gly Arg Pro Arg Val Gln Asn Ile Met Ser Glu 485 490 495Asp Leu Arg Tyr Glu Ile Val Ser Ser Gly Thr Leu Ser Gly Asn Val 500 505 510Lys Ile Val Val Asp Leu Asn Ser Arg Glu Tyr His Leu Glu Lys Glu 515 520 525Gly Lys Ser Ser Leu Lys Lys Arg Val Val Lys Arg Glu Asp Gly Arg 530 535 540Asn Phe Tyr Phe Tyr Glu Glu Gly Glu Arg Glu545 550 55525680PRTThermotoga maritima 25Met Gly Ile Gly Gly Asp Asp Ser Trp Ser Pro Ser Val Ser Ala Glu1 5 10 15Phe Leu Leu Leu Ile Val Glu Leu Ser Phe Val Leu Phe Ala Ser Asp 20 25 30Glu Phe Val Lys Val Glu Asn Gly Lys Phe Ala Leu Asn Gly Lys Glu 35 40 45Phe Arg Phe Ile Gly Ser Asn Asn Tyr Tyr Met His Tyr Lys Ser Asn 50 55 60Gly Met Ile Asp Ser Val Leu Glu Ser Ala Arg Asp Met Gly Ile Lys65 70 75 80Val Leu Arg Ile Trp Gly Phe Leu Asp Gly Glu Ser Tyr Cys Arg Asp 85 90 95Lys Asn Thr Tyr Met His Pro Glu Pro Gly Val Phe Gly Val Pro Glu 100 105 110Gly Ile Ser Asn Ala Gln Ser Gly Phe Glu Arg Leu Asp Tyr Thr Val 115 120 125Ala Lys Ala Lys Glu Leu Gly Ile Lys Leu Val Ile Val Leu Val Asn 130 135 140Asn Trp Asp Asp Phe Gly Gly Met Asn Gln Tyr Val Arg Trp Phe Gly145 150 155 160Gly Thr His His Asp Asp Phe Tyr Arg Asp Glu Lys Ile Lys Glu Glu 165 170 175Tyr Lys Lys Tyr Val Ser Phe Leu Val Asn His Val Asn Thr Tyr Thr 180 185 190Gly Val Pro Tyr Arg Glu Glu Pro Thr Ile Met Ala Trp Glu Leu Ala 195 200 205Asn Glu Pro Arg Cys Glu Thr Asp Lys Ser Gly Asn Thr Leu Val Glu 210 215 220Trp Val Lys Glu Met Ser Ser Tyr Ile Lys Ser Leu Asp Pro Asn His225 230 235 240Leu Val Ala Val Gly Asp Glu Gly Phe Phe Ser Asn Tyr Glu Gly Phe 245 250 255Lys Pro Tyr Gly Gly Glu Ala Glu Trp Ala Tyr Asn Gly Trp Ser Gly 260 265 270Val Asp Trp Lys Lys Leu Leu Ser Ile Glu Thr Val Asp Phe Gly Thr 275 280 285Phe His Leu Tyr Pro Ser His Trp Gly Val Ser Pro Glu Asn Tyr Ala 290 295 300Gln Trp Gly Ala Lys Trp Ile Glu Asp His Ile Lys Ile Ala Lys Glu305 310 315 320Ile Gly Lys Pro Val Val Leu Glu Glu Tyr Gly Ile Pro Lys Ser Ala 325 330 335Pro Val Asn Arg Thr Ala Ile Tyr Arg Leu Trp Asn Asp Leu Val Tyr 340 345 350Asp Leu Gly Gly Asp Gly Ala Met Phe Trp Met Leu Ala Gly Ile Gly 355 360 365Glu Gly Ser Asp Arg Asp Glu Arg Gly Tyr Tyr Pro Asp Tyr Asp Gly 370 375 380Phe Arg Ile Val Asn Asp Asp Ser Pro Glu Ala Glu Leu Ile Arg Glu385 390 395 400Tyr Ala Lys Leu Phe Asn Thr Gly Glu Asp Ile Arg Glu Asp Thr Cys 405 410 415Ser Phe Ile Leu Pro Lys Asp Gly Met Glu Ile Lys Lys Thr Val Glu 420 425 430Val Arg Ala Gly Val Phe Asp Tyr Ser Asn Thr Phe Glu Lys Leu Ser 435 440 445Val Lys Val Glu Asp Leu Val Phe Glu Asn Glu Ile Glu His Leu Gly 450 455 460Tyr Gly Ile Tyr Gly Phe Asp Leu Asp Thr Thr Arg Ile Pro Asp Gly465 470 475 480Glu His Glu Met Phe Leu Glu Gly His Phe Gln Gly Lys Thr Val Lys 485 490 495Asp Ser Ile Lys Ala Lys Val Val Asn Glu Ala Arg Tyr Val Leu Ala 500 505 510Glu Glu Val Asp Phe Ser Ser Pro Glu Glu Val Lys Asn Trp Trp Asn 515 520 525Ser Gly Thr Trp Gln Ala Glu Phe Gly Ser Pro Asp Ile Glu Trp Asn 530 535 540Gly Glu Val Gly Asn Gly Ala Leu Gln Leu Asn Val Lys Leu Pro Gly545 550 555 560Lys Ser Asp Trp Glu Glu Val Arg Val Ala Arg Lys Phe Glu Arg Leu 565 570 575Ser Glu Cys Glu Ile Leu Glu Tyr Asp Ile Tyr Ile Pro Asn Val Glu 580 585 590Gly Leu Lys Gly Arg Leu Arg Pro Tyr Ala Val Leu Asn Pro Gly Trp 595 600 605Val Lys Ile Gly Leu Asp Met Asn Asn Ala Asn Val Glu Ser Ala Glu 610 615 620Ile Ile Thr Phe Gly Gly Lys Glu Tyr Arg Arg Phe His Val Arg Ile625 630 635 640Glu Phe Asp Arg Thr Ala Gly Val Lys Glu Leu His Ile Gly Val Val 645 650 655Gly Asp His Leu Arg Tyr Asp Gly Pro Ile Phe Ile Asp Asn Val Arg 660 665 670Leu Tyr Lys Arg Thr Gly Gly Met 675 68026512PRTThermococcus chitonophagus 26Met Leu Pro Glu Glu Phe Leu Trp Gly Val Gly Gln Ser Gly Phe Gln1 5 10 15Phe Glu Met Gly Asp Lys Leu Arg Arg His Ile Asp Pro Asn Thr Asp 20 25 30Trp Trp Lys Trp Val Arg Asp Pro Phe Asn Ile Lys Lys Glu Leu Val 35 40 45Ser Gly Asp Leu Pro Glu Asp Gly Ile Asn Asn Tyr Glu Leu Phe Glu 50 55 60Asn Asp His Lys Leu Ala Lys Gly Leu Gly Leu Asn Ala Tyr Arg Ile65 70 75 80Gly Ile Glu Trp Ser Arg Ile Phe Pro Trp Pro Thr Trp Thr Val Asp 85 90 95Thr Glu Val Glu Phe Asp Thr Tyr Gly Leu Val Lys Asp Val Lys Ile 100 105 110Asp Lys Ser Thr Leu Ala Glu Leu Asp Arg Leu Ala Asn Lys Glu Glu 115 120 125Val Met Tyr Tyr Arg Arg Val Ile Gln His Leu Arg Glu Leu Gly Phe 130 135 140Lys Val Phe Val Asn Leu Asn His Phe Thr Leu Pro Ile Trp Leu His145 150 155 160Asp Pro Ile Val Ala Arg Glu Lys Ala Leu Thr Asn Asp Arg Ile Gly 165 170 175Trp Val Ser Gln Arg Thr Val Val Glu Phe Ala Lys Tyr Ala Ala Tyr 180 185 190Ile Ala His Ala Leu Gly Asp Leu Val Asp Thr Trp Ser Thr Phe Asn 195 200 205Glu Pro Met Val Val Val Glu Leu Gly Tyr Leu Ala Pro Tyr Ser Gly 210 215

220Phe Pro Pro Gly Val Met Asn Pro Glu Ala Ala Lys Leu Ala Ile Leu225 230 235 240Asn Met Ile Asn Ala His Ala Leu Ala Tyr Lys Met Ile Lys Arg Phe 245 250 255Asp Thr Lys Lys Ala Asp Glu Asp Ser Lys Ser Pro Ala Asp Val Gly 260 265 270Ile Ile Tyr Asn Asn Ile Gly Val Ala Tyr Pro Lys Asp Pro Asn Asp 275 280 285Pro Lys Asp Val Lys Ala Ala Glu Asn Asp Asn Tyr Phe His Ser Gly 290 295 300Leu Phe Phe Asp Ala Ile His Lys Gly Lys Leu Asn Ile Glu Phe Asp305 310 315 320Gly Glu Asn Phe Val Lys Val Arg His Leu Lys Gly Asn Asp Trp Ile 325 330 335Gly Leu Asn Tyr Tyr Thr Arg Glu Val Val Arg Tyr Ser Glu Pro Lys 340 345 350Phe Pro Ser Ile Pro Leu Ile Ser Phe Lys Gly Val Pro Asn Tyr Gly 355 360 365Tyr Ser Cys Arg Pro Gly Thr Thr Ser Ala Asp Gly Met Pro Val Ser 370 375 380Asp Ile Gly Trp Glu Val Tyr Pro Gln Gly Ile Tyr Asp Ser Ile Val385 390 395 400Glu Ala Thr Lys Tyr Ser Val Pro Val Tyr Val Thr Glu Asn Gly Val 405 410 415Ala Asp Ser Ala Asp Thr Leu Arg Pro Tyr Tyr Ile Val Ser His Val 420 425 430Ser Lys Ile Glu Glu Ala Ile Glu Asn Gly Tyr Pro Val Lys Gly Tyr 435 440 445Met Tyr Trp Ala Leu Thr Asp Asn Tyr Glu Trp Ala Leu Gly Phe Ser 450 455 460Met Arg Phe Gly Leu Tyr Lys Val Asp Leu Ile Ser Lys Glu Arg Ile465 470 475 480Pro Arg Glu Arg Ser Val Glu Ile Tyr Arg Arg Ile Val Gln Ser Asn 485 490 495Gly Val Pro Lys Asp Ile Lys Glu Glu Phe Leu Lys Gly Glu Glu Lys 500 505 51027360PRTThermotoga sp. 27Met Val Glu Arg His Phe Arg Tyr Val Leu Ile Cys Thr Leu Phe Leu1 5 10 15Val Met Leu Leu Ile Ser Ser Thr Gln Cys Gly Lys Asn Glu Pro Asn 20 25 30Lys Arg Val Asn Ser Met Glu Gln Ser Val Ala Glu Ser Asp Ser Asn 35 40 45Ser Ala Phe Glu Tyr Asn Lys Met Val Gly Lys Gly Val Asn Ile Gly 50 55 60Asn Ala Leu Glu Ala Pro Phe Glu Gly Ala Trp Gly Val Arg Ile Glu65 70 75 80Asp Glu Tyr Phe Glu Ile Ile Lys Lys Arg Gly Phe Asp Ser Val Arg 85 90 95Ile Pro Ile Arg Trp Ser Ala His Ile Ser Glu Lys Pro Pro Tyr Asp 100 105 110Ile Asp Arg Asn Phe Leu Glu Arg Val Asn His Val Val Asp Arg Ala 115 120 125Leu Glu Asn Asn Leu Thr Val Ile Ile Asn Thr His His Phe Glu Glu 130 135 140Leu Tyr Gln Glu Pro Asp Lys Tyr Gly Asp Val Leu Val Glu Ile Trp145 150 155 160Arg Gln Ile Ala Lys Phe Phe Lys Asp Tyr Pro Glu Asn Leu Phe Phe 165 170 175Glu Ile Tyr Asn Glu Pro Ala Gln Asn Leu Thr Ala Glu Lys Trp Asn 180 185 190Ala Leu Tyr Pro Lys Val Leu Lys Val Ile Arg Glu Ser Asn Pro Thr 195 200 205Arg Ile Val Ile Ile Asp Ala Pro Asn Trp Ala His Tyr Ser Ala Val 210 215 220Arg Ser Leu Lys Leu Val Asn Asp Lys Arg Ile Ile Val Ser Phe His225 230 235 240Tyr Tyr Glu Pro Phe Lys Phe Thr His Gln Gly Ala Glu Trp Val Asn 245 250 255Pro Ile Pro Pro Val Arg Val Lys Trp Asn Gly Glu Glu Trp Glu Ile 260 265 270Asn Gln Ile Arg Ser His Phe Lys Tyr Val Ser Asp Trp Ala Lys Gln 275 280 285Asn Asn Val Pro Ile Phe Leu Gly Glu Phe Gly Ala Tyr Ser Lys Ala 290 295 300Asp Met Asp Ser Arg Val Lys Trp Thr Glu Ser Val Arg Lys Met Ala305 310 315 320Glu Glu Phe Gly Phe Ser Tyr Ala Tyr Trp Glu Phe Cys Ala Gly Phe 325 330 335Gly Ile Tyr Asp Arg Trp Ser Gln Asn Trp Ile Glu Pro Leu Ala Thr 340 345 350Ala Val Val Gly Thr Gly Lys Glu 355 36028772PRTThermotoga maritima 28Met Asp Leu Thr Lys Val Gly Ile Ile Val Arg Leu Asn Glu Trp Gln1 5 10 15Ala Lys Asp Val Ala Lys Asp Arg Phe Ile Glu Ile Lys Asp Gly Lys 20 25 30Ala Glu Val Trp Ile Leu Gln Gly Val Glu Glu Ile Phe Tyr Glu Lys 35 40 45Pro Asp Thr Ser Pro Arg Ile Phe Phe Ala Gln Ala Arg Ser Asn Lys 50 55 60Val Ile Glu Ala Phe Leu Thr Asn Pro Val Asp Thr Lys Lys Lys Glu65 70 75 80Leu Phe Lys Val Thr Val Asp Gly Lys Glu Ile Pro Val Ser Arg Val 85 90 95Glu Lys Ala Asp Pro Thr Asp Ile Asp Val Thr Asn Tyr Val Arg Ile 100 105 110Val Leu Ser Glu Ser Leu Lys Glu Glu Asp Leu Arg Lys Asp Val Glu 115 120 125Leu Ile Ile Glu Gly Tyr Lys Pro Ala Arg Val Ile Met Met Glu Ile 130 135 140Leu Asp Asp Tyr Tyr Tyr Asp Gly Glu Leu Gly Ala Val Tyr Ser Pro145 150 155 160Glu Lys Thr Ile Phe Arg Val Trp Ser Pro Val Ser Lys Trp Val Lys 165 170 175Val Leu Leu Phe Lys Asn Gly Glu Asp Thr Glu Pro Tyr Gln Val Val 180 185 190Asn Met Glu Tyr Lys Gly Asn Gly Val Trp Glu Ala Val Val Glu Gly 195 200 205Asp Leu Asp Gly Val Phe Tyr Leu Tyr Gln Leu Glu Asn Tyr Gly Lys 210 215 220Ile Arg Thr Thr Val Asp Pro Tyr Ser Lys Ala Val Tyr Ala Asn Ser225 230 235 240Lys Lys Ser Ala Val Val Asn Leu Ala Arg Thr Asn Pro Glu Gly Trp 245 250 255Glu Asn Asp Arg Gly Pro Lys Ile Glu Gly Tyr Glu Asp Ala Ile Ile 260 265 270Tyr Glu Ile His Ile Ala Asp Ile Thr Gly Leu Glu Asn Ser Gly Val 275 280 285Lys Asn Lys Gly Leu Tyr Leu Gly Leu Thr Glu Glu Asn Thr Lys Gly 290 295 300Pro Gly Gly Val Thr Thr Gly Leu Ser His Leu Val Glu Leu Gly Val305 310 315 320Thr His Val His Ile Leu Pro Phe Phe Asp Phe Tyr Thr Gly Asp Glu 325 330 335Leu Asp Lys Asp Phe Glu Lys Tyr Tyr Asn Trp Gly Tyr Asp Pro Tyr 340 345 350Leu Phe Met Val Pro Glu Gly Arg Tyr Ser Thr Asp Pro Lys Asn Pro 355 360 365His Thr Arg Ile Arg Glu Val Lys Glu Met Val Lys Ala Leu His Lys 370 375 380His Gly Ile Gly Val Ile Met Asp Met Val Phe Pro His Thr Tyr Gly385 390 395 400Ile Gly Glu Leu Ser Ala Phe Asp Gln Thr Val Pro Tyr Tyr Phe Tyr 405 410 415Arg Ile Asp Lys Thr Gly Ala Tyr Leu Asn Glu Ser Gly Cys Gly Asn 420 425 430Val Ile Ala Ser Glu Arg Pro Met Met Arg Lys Phe Ile Val Asp Thr 435 440 445Val Thr Tyr Trp Val Lys Glu Tyr His Ile Asp Gly Phe Arg Phe Asp 450 455 460Gln Met Gly Leu Ile Asp Lys Lys Thr Met Leu Glu Val Glu Arg Ala465 470 475 480Leu His Lys Ile Asp Pro Thr Ile Ile Leu Tyr Gly Glu Pro Trp Gly 485 490 495Gly Trp Gly Ala Pro Ile Arg Phe Gly Lys Ser Asp Val Ala Gly Thr 500 505 510His Val Ala Ala Phe Asn Asp Glu Phe Arg Asp Ala Ile Arg Gly Ser 515 520 525Val Phe Asn Pro Ser Val Lys Gly Phe Val Met Gly Gly Tyr Gly Lys 530 535 540Glu Thr Lys Ile Lys Arg Gly Val Val Gly Ser Ile Asn Tyr Asp Gly545 550 555 560Lys Leu Ile Lys Ser Leu Ala Leu Asp Pro Glu Glu Thr Ile Asn Tyr 565 570 575Ala Ala Cys His Asp Asn His Thr Leu Trp Asp Lys Asn Tyr Leu Ala 580 585 590Ala Lys Ala Asp Lys Lys Lys Glu Trp Thr Glu Glu Glu Leu Lys Asn 595 600 605Ala Gln Lys Leu Ala Gly Ala Ile Leu Leu Thr Ser Gln Gly Val Pro 610 615 620Phe Leu His Gly Gly Gln Asp Phe Cys Arg Thr Lys Asn Phe Asn Asp625 630 635 640Asn Ser Tyr Asn Ala Pro Ile Ser Ile Asn Gly Phe Asp Tyr Glu Arg 645 650 655Lys Leu Gln Phe Ile Asp Val Phe Asn Tyr His Lys Gly Leu Ile Lys 660 665 670Leu Arg Lys Glu His Pro Ala Phe Arg Leu Lys Asn Ala Glu Glu Ile 675 680 685Lys Lys His Leu Glu Phe Leu Pro Gly Gly Arg Arg Ile Val Ala Phe 690 695 700Met Leu Lys Asp His Ala Gly Gly Asp Pro Trp Lys Asp Ile Val Val705 710 715 720Ile Tyr Asn Gly Asn Leu Glu Lys Thr Thr Tyr Lys Leu Pro Glu Gly 725 730 735Lys Trp Asn Val Val Val Asn Ser Gln Lys Ala Gly Thr Glu Val Ile 740 745 750Glu Thr Val Glu Gly Thr Ile Glu Leu Asp Pro Leu Ser Ala Tyr Val 755 760 765Leu Tyr Arg Glu 7702952DNAArtificial sequencesynthetically generated oligonucleotide 29ccgagaattc attaaagagg agaaattaac tatggtgaat gctatgattg tc 523031DNAArtificial sequencesynthetically generated oligonucleotide 30atacccgaag gcctcgatac ttctagaagg c 313154DNAArtificial sequencesynthetically generated oligonucleotide 31ccgagaattc attaaagagg agaaattaac tatgataaga aggtccgatt ttcc 543231DNAArtificial sequencesynthetically generated oligonucleotide 32ttccttaaag attttagaat ttctagaagg c 313352DNAArtificial sequencesynthetically generated oligonucleotide 33ccgagaattc attaaagagg agaaattaac tatgctacca gaaggctttc tc 523431DNAArtificial sequencesynthetically generated oligonucleotide 34ctcttcaagc ctgaacccac tccatggagg c 313552DNAArtificial sequencesynthetically generated oligonucleotide 35ccgagaattc attaaagagg agaaattaac tatgataagg tttcctgatt at 523631DNAArtificial sequencesynthetically generated oligonucleotide 36cctaatttct tggagcttat ttctagaagg c 313757DNAArtificial sequencesynthetically generated oligonucleotide 37ccgagaattc attcattaaa gaggagaaat taactatgct tccaggagaa ctttctc 573831DNAArtificial sequencesynthetically generated oligonucleotide 38ctctagaatc tcctccccat ccctaggagg c 313940DNAArtificial sequencesynthetically generated oligonucleotide 39ataatctaga gcatgcaatt ccccaaagac ttcatgatag 404032DNAArtificial sequencesynthetically generated oligonucleotide 40tcgtagaatg tgactaggtc attcgaaaat aa 324152DNAArtificial sequencesynthetically generated oligonucleotide 41ccgacaattg attaaagagg agaaattaac tatggaaagg atcgatgaaa tt 524231DNAArtificial sequencesynthetically generated oligonucleotide 42ctcttctcta agtttggtac tccatggagg c 314352DNAArtificial sequencesynthetically generated oligonucleotide 43ccgacaattg attaaagagg agaaattaac tatgttccct gaaaagttcc tt 524431DNAArtificial sequencesynthetically generated oligonucleotide 44ctccttaacg actcccctac tccatggagg c 314527DNAArtificial sequencesynthetically generated oligonucleotide 45aataaggatc cgtttagcga cgctcgc 274635DNAArtificial sequencesynthetically generated oligonucleotide 46cggataatgg cgacatgttg ggccttcgaa aataa 354760DNAArtificial sequencesynthetically generated oligonucleotide 47tttattgaat tcattaaaga ggagaaatta actatgatct gtgtggaaat attcggaaag 604840DNAArtificial sequenceprimer sequence 48gaagatgctt ctcccactct ctcttacttt cgaaatatct 404954DNAArtificial sequencesynthetically generated oligonucleotide 49tttattcaat tgattaaaga ggagaaatta actatgggga ttggtggcga cgac 545036DNAArtificial sequencesynthetically generated oligonucleotide 50cctccataca cttatacttt tctattcgaa ttattt 365160DNAArtificial sequencesynthetically generated oligonucleotide 51tttattgaat tcattaaaga ggagaaatta actatgctac cagaagagtt cctatggggc 605239DNAArtificial sequencesynthetically generated oligonucleotide 52ctttacttct ggtatcggca actactcttc gaattattt 395368DNAArtificial sequencesynthetically generated oligonucleotide 53aaaaaacaat tgaattcatt aaagaggaga aattaactat ggtagaaaga cacttcagat 60atgttctt 685436DNAArtificial sequencesynthetically generated oligonucleotide 54gtccgtttct catttacttc ttaacctagg cttttt 365556DNAArtificial sequencesynthetically generated oligonucleotide 55ttttggaatt cattaaagag gagaaattaa ctatggaact gatcatagaa ggttac 565636DNAArtificial sequencesynthetically generated oligonucleotide 56cgcatgcaag acatgtctct cacttttcga agaata 36571992DNAThermotoga maritima 57cttttattga tcgttgagct ctctttcgtt ctctttgcaa gtgacgagtt cgtgaaagtg 60gaaaacggaa aattcgctct gaacggaaaa gaattcagat tcattggaag caacaactac 120tacatgcact acaagagcaa cggaatgata gacagtgttc tggagagtgc cagagacatg 180ggtataaagg tcctcagaat ctggggtttc ctcgacgggg agagttactg cagagacaag 240aacacctaca tgcatcctga gcccggtgtt ttcggggtgc cagaaggaat atcgaacgcc 300cagagcggtt tcgaaagact cgactacaca gttgcgaaag cgaaagaact cggtataaaa 360cttgtcattg ttcttgtgaa caactgggac gacttcggtg gaatgaacca gtacgtgagg 420tggtttggag gaacccatca cgacgatttc tacagagatg agaagatcaa agaagagtac 480aaaaagtacg tctcctttct cgtaaaccat gtcaatacct acacgggagt tccttacagg 540gaagagccca ccatcatggc ctgggagctt gcaaacgaac cgcgctgtga gacggacaaa 600tcggggaaca cgctcgttga gtgggtgaag gagatgagct cctacataaa gagtctggat 660cccaaccacc tcgtggctgt gggggacgaa ggattcttca gcaactacga aggattcaaa 720ccttacggtg gagaagccga gtgggcctac aacggctggt ccggtgttga ctggaagaag 780ctcctttcga tagagacggt ggacttcggc acgttccacc tctatccgtc ccactggggt 840gtcagtccag agaactatgc ccagtgggga gcgaagtgga tagaagacca cataaagatc 900gcaaaagaga tcggaaaacc cgttgttctg gaagaatatg gaattccaaa gagtgcgcca 960gttaacagaa cggccatcta cagactctgg aacgatctgg tctacgatct cggtggagat 1020ggagcgatgt tctggatgct cgcgggaatc ggggaaggtt cggacagaga cgagagaggg 1080tactatccgg actacgacgg tttcagaata gtgaacgacg acagtccaga agcggaactg 1140ataagagaat acgcgaagct gttcaacaca ggtgaagaca taagagaaga cacctgctct 1200ttcatccttc caaaagacgg catggagatc aaaaagaccg tggaagtgag ggctggtgtt 1260ttcgactaca gcaacacgtt tgaaaagttg tctgtcaaag tcgaagatct ggtttttgaa 1320aatgagatag agcatctcgg atacggaatt tacggctttg atctcgacac aacccggatc 1380ccggatggag aacatgaaat gttccttgaa ggccactttc agggaaaaac ggtgaaagac 1440tctatcaaag cgaaagtggt gaacgaagca cggtacgtgc tcgcagagga agttgatttt 1500tcctctccag aagaggtgaa aaactggtgg aacagcggaa cctggcaggc agagttcggg 1560tcacctgaca ttgaatggaa cggtgaggtg ggaaatggag cactgcagct gaacgtgaaa 1620ctgcccggaa agagcgactg ggaagaagtg agagtagcaa ggaagttcga aagactctca 1680gaatgtgaga tcctcgagta cgacatctac attccaaacg tcgagggact caagggaagg 1740ttgaggccgt acgcggttct gaaccccggc tgggtgaaga taggcctcga catgaacaac 1800gcgaacgtgg aaagtgcgga gatcatcact ttcggcggaa aagagtacag aagattccat 1860gtaagaattg agttcgacag aacagcgggg gtgaaagaac ttcacatagg agttgtcggt 1920gatcatctga ggtacgatgg accgattttc atcgataatg tgagacttta taaaagaaca 1980ggaggtatgt ga 1992582055DNAThermotoga maritima 58atgaaaagaa tcgacctgaa tggtttctgg agcgttaggg ataacgaagg gagattttcg 60tttgaaggga ctgtgccagg ggttgtccag gcagatctgg tcagaaaagg tcttcttcca 120cacccgtacg ttgggatgaa cgaagatctc ttcaaggaaa tagaagacag agagtggatc 180tacgagaggg agttcgagtt caaagaagat gtgaaagagg gggaacgtgt cgatctcgtt 240tttgagggcg tcgacacgct gtcggatgtt tatctgaacg gtgtttacct tggaagcacc 300gaagacatgt tcatcgagta tcgcttcgat gtcacgaacg tgttgaaaga aaagaatcac 360ctgaaggtgt acataaaatc tcccatcaga gttccgaaaa ctctcgagca gaactacggg 420gtcctcggcg gtcctgaaga tcccatcaga ggatacataa gaaaagccca gtattcgtac 480ggatgggact ggggtgccag aatcgttaca agcggtattt ggaaacccgt ctacctcgag 540gtgtacaggg cacgtcttca ggattcaacg gcttatctgt tggaacttga ggggaaagat 600gcccttgtga gggtgaacgg tttcgtacac ggggaaggaa atctcattgt ggaagtttat 660gtaaacggtg aaaagatagg ggagtttcct gttcttgaaa agaacggaga aaagctcttc 720gatggagtgt tccacctgaa agatgtgaaa ctatggtatc cgtggaacgt ggggaaaccg 780tacctgtacg atttcgtttt cgtgttgaaa gacttaaacg gagagatcta cagagaagaa 840aagaaaatcg gtttgagaag

agtcagaatc gttcaggagc ccgatgaaga aggaaaaact 900ttcatattcg aaatcaacgg tgagaaagtc ttcgctaagg gtgctaactg gattccctca 960gaaaacatcc tcacgtggtt gaaggaggaa gattacgaaa agctcgtcaa aatggcaagg 1020agtgccaata tgaacatgct cagggtctgg ggaggaggaa tctacgagag agagatcttc 1080tacagactct gtgatgaact cggtatcatg gtgtggcagg atttcatgta cgcgtgtctt 1140gaatatccgg atcatcttcc gtggttcaga aaactcgcga acgaagaggc aagaaagatt 1200gtgagaaaac tcagatacca tccctccatt gttctctggt gcggaaacaa cgaaaacaac 1260tggggattcg atgaatgggg aaatatggcc agaaaagtgg atggtatcaa cctcggaaac 1320aggctctacc tcttcgattt tcctgagatt tgtgccgaag aagacccgtc cactccctat 1380tggccatcca gtccatacgg cggtgaaaaa gcgaacagcg aaaaggaagg agacaggcac 1440gtctggtacg tgtggagtgg ctggatgaac tacgaaaact acgaaaaaga caccggaagg 1500ttcatcagcg agtttggatt tcagggtgct ccccatccag agacgataga gttcttttca 1560aaacccgagg aaagagagat attccatccc gtcatgctga agcacaacaa acaggtggaa 1620ggacaggaaa gattgatcag gttcatattc ggaaattttg gaaagtgtaa agatttcgac 1680agttttgtgt atctgtccca gctcaaccag gcggaggcga tcaagttcgg tgttgaacac 1740tggcgaagca ggaagtacaa aacggccggc gctctcttct ggcagttcaa cgacagctgg 1800ccggtcttca gctggtccgc agtcgattac ttcaaaaggc ccaaagctct ctactactat 1860gcgagaagat tcttcgctga agttctaccc gttttgaaga agagagacaa caaaatagaa 1920ctgctggtgg gtgagcgatc tgagggagac aaaagaagtc tctctcaggc ttgcagccta 1980cgagaagaag ggagaaaagg tattcgaaaa gacttacaga acggtactcc cagcagacgg 2040tgtgagtttg gttga 2055592870DNABankia gouldi 59atgaaaaaaa atctactaat gtttaaaagg cttacgtatc tacctttgtt tttaatgctg 60ctctcactaa gttcagtagc tcaatctcct gtagaaaaac atggccgttt acaagttgac 120ggaaaccgca ttcttaatgc gtctggagaa attacgagct tagctggtaa cagcctcttt 180tggagtaatg ctggagacac ctccgatttt tataatgcag aaactgttga ttttttagca 240gaaaactgga atagctcact tattagaata gctatgggcg taaaagaaaa ttgggatggc 300ggaaatggct atattgatag tccgcaggag caagaagcta aaattagaaa agttattgat 360gcagctattg ctaacggcat atatgtaata atagactggc acactcacga agcagagtta 420tacacagatg aggctgttga cttttttacc agaatggcag acctatacgg agatactccc 480aatgtaatgt atgaaattta taacgagcct atataccaaa gttggcctgt tattaagaat 540tatgcagagc aagtaattgc tggtatacgt tctaaagacc cagataattt aataattgta 600ggtactagca attattctca gcaagttgat gtagcatcag cagacccaat atctgatact 660aatgtggcat atactttaca tttttatgca gcatttaacc cgcatgataa cttaagaaat 720gtagcacaga cagcattaga taataatgtt gctttgtttg ttacagaatg gggtacaatt 780ttaaataccg gacaaggaga accagacaaa gaaagcacta atacttggat ggcctttttg 840aaagaaaaag gtataagtca cgctaattgg tctttgagtg acaaagcttt tcctgaaaca 900gggtctgtag ttcaagcagg acaaggtgta tctggtttaa ttagcaataa acttacagcc 960tctggtgaaa ttgtaaaaaa catcatccaa aactgggata cagagacctc tacaggacct 1020aaaacaacac aatgtagtac tatagaatgt attagagctg caatggaaac agcacaagca 1080ggagatgaaa ttataattgc ccctggaaac tacaattttc aagacaagat acaaggtgcc 1140tttaaccgta gtgtttacct ttatggtagt gctaacggaa acagtacaaa ccctattata 1200ttaagaggcg aaagcgctac aaaccctcct gttttctcag gattagatta taacaatggc 1260tacctattaa gtattgaagg tgattattgg aatattaaag atatagagtt taaaactggg 1320tctaaaggta ttgttcttga caattctaat ggtagtaaat taaaaaacct tgttgttcat 1380gatattggag aagaagctat tcacttgcgt gatggatcta gcaataatag tatagatggt 1440tgcactatat acaatacagg tagaactaaa cctggttttg gtgaaggttt atatgtaggc 1500tcagataaag gacaacatga cacttatgaa agagcttgta acaataacac tattgaaaac 1560tgtaccgttg gacccaatgt aacagcagaa ggcgtagatg ttaaggaagg tacaatgaac 1620actattataa gaaattgcgt gttttctgca gaaggaattt caggagaaaa tagctcagat 1680gcttttattg atttaaaagg agcctatggt tttgtataca gaaacacgtt taatgttgat 1740ggttctgaag taataaatac tggagtagac tttttagata gaggtacagg atttaataca 1800ggttttagaa atgcaatatt tgaaaataca tataaccttg gcagtagagc ttcagaaatt 1860tcaactgctc gtaaaaaaca aggttctcct gaacaaactc acgtttggga taatattaga 1920aaccctaatt ctgttgattt tccaataagt gatggtacag aaaatctagt aaataaattc 1980tgcccagatt ggaatataga accatgtaat cctgtagacg aaaccaacca agcacctaca 2040ataagcttcc tatctcctgt taacaatatt actttagttg aaggttataa tttacaagtt 2100gaagttaatg ctactgatgc agatggaact attgataatg taaaacttta tatagataac 2160aatttagtta ggcaaataaa ttctacttca tataaatggg gccattctga ttctccaaat 2220acagatgaac ttaatggtct tacagaagga acttatacct taaaagcaat tgcaactgat 2280aacgacgggg cttctacaga aacgcaattt acgttaactg taataacaga acaaagtccg 2340tctgagaatt gtgactttaa tacaccttct tcaactggtt tagaagattt tgacattaaa 2400aagttttcta acgtttttga gttaggatct ggcggaccat ctttaagtaa tttaaaaaca 2460tttactatta attggaattc gcaatacaat gggttatatc aattttcaat aaacacaaac 2520aacggtgtac ctgattatta tataaattta aaaccaaaaa ttacctttca gtttaaaaat 2580gcaaatccag aaatatctat tagcaatagc ttaattccta attttgatgg tgattactgg 2640gtaacatcag ataacggtaa ttttgtgatg gtatctaaaa ctaataattt tacgatatac 2700tttagtaatg acgctactgc tcctatttgt aatgttacgc ctagtaacca aataagtaaa 2760attactgatg attctagtat taattttaag ctttacccta atcctgcttt agacgaaact 2820atttttgtga gcgctgaaga tgaaaaacta gctttggtgc ttgtaccagt 287060960DNAPyrococcus furiosus 60atgagcaaga aaaagttcgt catcgtatct atcttaacaa tccttttagt acaggcaata 60tattttgtag aaaagtatca tacctctgag gacaagtcaa cttcaaatac ctcatctaca 120ccaccccaaa caacactttc cactaccaag gttctcaaga ttagataccc tgatgacggt 180gagtggccag gagctcctat tgataaggat ggtgatggga acccagaatt ctacattgaa 240ataaacctat ggaacattct taatgctact ggatttgctg agatgacgta caatttaacc 300agcggcgtcc ttcactacgt ccaacaactt gacaacattg tcttgaggga tagaagtaat 360tgggtgcatg gataccccga aatattctat ggaaacaagc catggaatgc aaactacgca 420actgatggcc caataccatt acccagtaaa gtttcaaacc taacagactt ctatctaaca 480atctcctata aacttgagcc caagaacggc ctgccaatta acttcgcaat agaatcctgg 540ttaacgagag aagcttggag aacaacagga attaacagcg atgagcaaga agtaatgata 600tggatttact atgacggatt acaaccggct ggctccaaag ttaaggagat tgtagtccca 660ataatagtta acggaacacc agtaaatgct acatttgaag tatggaaggc aaacattggt 720tgggagtatg ttgcatttag aataaagacc ccaatcaaag agggaacagt gacaattcca 780tacggagcat ttataagtgt tgcagccaac atttcaagct taccaaatta cacagaactt 840tacttagagg acgtggagat tggaactgag tttggaacgc caagcactac ctccgcccac 900ctagagtggt ggatcacaaa cataacacta actcctctag atagacctct tatttcctaa 96061663PRTThermotoga maritima 61Leu Leu Leu Ile Val Glu Leu Ser Phe Val Leu Phe Ala Ser Asp Glu1 5 10 15Phe Val Lys Val Glu Asn Gly Lys Phe Ala Leu Asn Gly Lys Glu Phe 20 25 30Arg Phe Ile Gly Ser Asn Asn Tyr Tyr Met His Tyr Lys Ser Asn Gly 35 40 45Met Ile Asp Ser Val Leu Glu Ser Ala Arg Asp Met Gly Ile Lys Val 50 55 60Leu Arg Ile Trp Gly Phe Leu Asp Gly Glu Ser Tyr Cys Arg Asp Lys65 70 75 80Asn Thr Tyr Met His Pro Glu Pro Gly Val Phe Gly Val Pro Glu Gly 85 90 95Ile Ser Asn Ala Gln Ser Gly Phe Glu Arg Leu Asp Tyr Thr Val Ala 100 105 110Lys Ala Lys Glu Leu Gly Ile Lys Leu Val Ile Val Leu Val Asn Asn 115 120 125Trp Asp Asp Phe Gly Gly Met Asn Gln Tyr Val Arg Trp Phe Gly Gly 130 135 140Thr His His Asp Asp Phe Tyr Arg Asp Glu Lys Ile Lys Glu Glu Tyr145 150 155 160Lys Lys Tyr Val Ser Phe Leu Val Asn His Val Asn Thr Tyr Thr Gly 165 170 175Val Pro Tyr Arg Glu Glu Pro Thr Ile Met Ala Trp Glu Leu Ala Asn 180 185 190Glu Pro Arg Cys Glu Thr Asp Lys Ser Gly Asn Thr Leu Val Glu Trp 195 200 205Val Lys Glu Met Ser Ser Tyr Ile Lys Ser Leu Asp Pro Asn His Leu 210 215 220Val Ala Val Gly Asp Glu Gly Phe Phe Ser Asn Tyr Glu Gly Phe Lys225 230 235 240Pro Tyr Gly Gly Glu Ala Glu Trp Ala Tyr Asn Gly Trp Ser Gly Val 245 250 255Asp Trp Lys Lys Leu Leu Ser Ile Glu Thr Val Asp Phe Gly Thr Phe 260 265 270His Leu Tyr Pro Ser His Trp Gly Val Ser Pro Glu Asn Tyr Ala Gln 275 280 285Trp Gly Ala Lys Trp Ile Glu Asp His Ile Lys Ile Ala Lys Glu Ile 290 295 300Gly Lys Pro Val Val Leu Glu Glu Tyr Gly Ile Pro Lys Ser Ala Pro305 310 315 320Val Asn Arg Thr Ala Ile Tyr Arg Leu Trp Asn Asp Leu Val Tyr Asp 325 330 335Leu Gly Gly Asp Gly Ala Met Phe Trp Met Leu Ala Gly Ile Gly Glu 340 345 350Gly Ser Asp Arg Asp Glu Arg Gly Tyr Tyr Pro Asp Tyr Asp Gly Phe 355 360 365Arg Ile Val Asn Asp Asp Ser Pro Glu Ala Glu Leu Ile Arg Glu Tyr 370 375 380Ala Lys Leu Phe Asn Thr Gly Glu Asp Ile Arg Glu Asp Thr Cys Ser385 390 395 400Phe Ile Leu Pro Lys Asp Gly Met Glu Ile Lys Lys Thr Val Glu Val 405 410 415Arg Ala Gly Val Phe Asp Tyr Ser Asn Thr Phe Glu Lys Leu Ser Val 420 425 430Lys Val Glu Asp Leu Val Phe Glu Asn Glu Ile Glu His Leu Gly Tyr 435 440 445Gly Ile Tyr Gly Phe Asp Leu Asp Thr Thr Arg Ile Pro Asp Gly Glu 450 455 460His Glu Met Phe Leu Glu Gly His Phe Gln Gly Lys Thr Val Lys Asp465 470 475 480Ser Ile Lys Ala Lys Val Val Asn Glu Ala Arg Tyr Val Leu Ala Glu 485 490 495Glu Val Asp Phe Ser Ser Pro Glu Glu Val Lys Asn Trp Trp Asn Ser 500 505 510Gly Thr Trp Gln Ala Glu Phe Gly Ser Pro Asp Ile Glu Trp Asn Gly 515 520 525Glu Val Gly Asn Gly Ala Leu Gln Leu Asn Val Lys Leu Pro Gly Lys 530 535 540Ser Asp Trp Glu Glu Val Arg Val Ala Arg Lys Phe Glu Arg Leu Ser545 550 555 560Glu Cys Glu Ile Leu Glu Tyr Asp Ile Tyr Ile Pro Asn Val Glu Gly 565 570 575Leu Lys Gly Arg Leu Arg Pro Tyr Ala Val Leu Asn Pro Gly Trp Val 580 585 590Lys Ile Gly Leu Asp Met Asn Asn Ala Asn Val Glu Ser Ala Glu Ile 595 600 605Ile Thr Phe Gly Gly Lys Glu Tyr Arg Arg Phe His Val Arg Ile Glu 610 615 620Phe Asp Arg Thr Ala Gly Val Lys Glu Leu His Ile Gly Val Val Gly625 630 635 640Asp His Leu Arg Tyr Asp Gly Pro Ile Phe Ile Asp Asn Val Arg Leu 645 650 655Tyr Lys Arg Thr Gly Gly Met 66062684PRTThermotoga maritima 62Met Lys Arg Ile Asp Leu Asn Gly Phe Trp Ser Val Arg Asp Asn Glu1 5 10 15Gly Arg Phe Ser Phe Glu Gly Thr Val Pro Gly Val Val Gln Ala Asp 20 25 30Leu Val Arg Lys Gly Leu Leu Pro His Pro Tyr Val Gly Met Asn Glu 35 40 45Asp Leu Phe Lys Glu Ile Glu Asp Arg Glu Trp Ile Tyr Glu Arg Glu 50 55 60Phe Glu Phe Lys Glu Asp Val Lys Glu Gly Glu Arg Val Asp Leu Val65 70 75 80Phe Glu Gly Val Asp Thr Leu Ser Asp Val Tyr Leu Asn Gly Val Tyr 85 90 95Leu Gly Ser Thr Glu Asp Met Phe Ile Glu Tyr Arg Phe Asp Val Thr 100 105 110Asn Val Leu Lys Glu Lys Asn His Leu Lys Val Tyr Ile Lys Ser Pro 115 120 125Ile Arg Val Pro Lys Thr Leu Glu Gln Asn Tyr Gly Val Leu Gly Gly 130 135 140Pro Glu Asp Pro Ile Arg Gly Tyr Ile Arg Lys Ala Gln Tyr Ser Tyr145 150 155 160Gly Trp Asp Trp Gly Ala Arg Ile Val Thr Ser Gly Ile Trp Lys Pro 165 170 175Val Tyr Leu Glu Val Tyr Arg Ala Arg Leu Gln Asp Ser Thr Ala Tyr 180 185 190Leu Leu Glu Leu Glu Gly Lys Asp Ala Leu Val Arg Val Asn Gly Phe 195 200 205Val His Gly Glu Gly Asn Leu Ile Val Glu Val Tyr Val Asn Gly Glu 210 215 220Lys Ile Gly Glu Phe Pro Val Leu Glu Lys Asn Gly Glu Lys Leu Phe225 230 235 240Asp Gly Val Phe His Leu Lys Asp Val Lys Leu Trp Tyr Pro Trp Asn 245 250 255Val Gly Lys Pro Tyr Leu Tyr Asp Phe Val Phe Val Leu Lys Asp Leu 260 265 270Asn Gly Glu Ile Tyr Arg Glu Glu Lys Lys Ile Gly Leu Arg Arg Val 275 280 285Arg Ile Val Gln Glu Pro Asp Glu Glu Gly Lys Thr Phe Ile Phe Glu 290 295 300Ile Asn Gly Glu Lys Val Phe Ala Lys Gly Ala Asn Trp Ile Pro Ser305 310 315 320Glu Asn Ile Leu Thr Trp Leu Lys Glu Glu Asp Tyr Glu Lys Leu Val 325 330 335Lys Met Ala Arg Ser Ala Asn Met Asn Met Leu Arg Val Trp Gly Gly 340 345 350Gly Ile Tyr Glu Arg Glu Ile Phe Tyr Arg Leu Cys Asp Glu Leu Gly 355 360 365Ile Met Val Trp Gln Asp Phe Met Tyr Ala Cys Leu Glu Tyr Pro Asp 370 375 380His Leu Pro Trp Phe Arg Lys Leu Ala Asn Glu Glu Ala Arg Lys Ile385 390 395 400Val Arg Lys Leu Arg Tyr His Pro Ser Ile Val Leu Trp Cys Gly Asn 405 410 415Asn Glu Asn Asn Trp Gly Phe Asp Glu Trp Gly Asn Met Ala Arg Lys 420 425 430Val Asp Gly Ile Asn Leu Gly Asn Arg Leu Tyr Leu Phe Asp Phe Pro 435 440 445Glu Ile Cys Ala Glu Glu Asp Pro Ser Thr Pro Tyr Trp Pro Ser Ser 450 455 460Pro Tyr Gly Gly Glu Lys Ala Asn Ser Glu Lys Glu Gly Asp Arg His465 470 475 480Val Trp Tyr Val Trp Ser Gly Trp Met Asn Tyr Glu Asn Tyr Glu Lys 485 490 495Asp Thr Gly Arg Phe Ile Ser Glu Phe Gly Phe Gln Gly Ala Pro His 500 505 510Pro Glu Thr Ile Glu Phe Phe Ser Lys Pro Glu Glu Arg Glu Ile Phe 515 520 525His Pro Val Met Leu Lys His Asn Lys Gln Val Glu Gly Gln Glu Arg 530 535 540Leu Ile Arg Phe Ile Phe Gly Asn Phe Gly Lys Cys Lys Asp Phe Asp545 550 555 560Ser Phe Val Tyr Leu Ser Gln Leu Asn Gln Ala Glu Ala Ile Lys Phe 565 570 575Gly Val Glu His Trp Arg Ser Arg Lys Tyr Lys Thr Ala Gly Ala Leu 580 585 590Phe Trp Gln Phe Asn Asp Ser Trp Pro Val Phe Ser Trp Ser Ala Val 595 600 605Asp Tyr Phe Lys Arg Pro Lys Ala Leu Tyr Tyr Tyr Ala Arg Arg Phe 610 615 620Phe Ala Glu Val Leu Pro Val Leu Lys Lys Arg Asp Asn Lys Ile Glu625 630 635 640Leu Leu Val Gly Glu Arg Ser Glu Gly Asp Lys Arg Ser Leu Ser Gln 645 650 655Ala Cys Ser Leu Arg Glu Glu Gly Arg Lys Gly Ile Arg Lys Asp Leu 660 665 670Gln Asn Gly Thr Pro Ser Arg Arg Cys Glu Phe Gly 675 68063956PRTBankia gouldi 63Met Lys Lys Asn Leu Leu Met Phe Lys Arg Leu Thr Tyr Leu Pro Leu1 5 10 15Phe Leu Met Leu Leu Ser Leu Ser Ser Val Ala Gln Ser Pro Val Glu 20 25 30Lys His Gly Arg Leu Gln Val Asp Gly Asn Arg Ile Leu Asn Ala Ser 35 40 45Gly Glu Ile Thr Ser Leu Ala Gly Asn Ser Leu Phe Trp Ser Asn Ala 50 55 60Gly Asp Thr Ser Asp Phe Tyr Asn Ala Glu Thr Val Asp Phe Leu Ala65 70 75 80Glu Asn Trp Asn Ser Ser Leu Ile Arg Ile Ala Met Gly Val Lys Glu 85 90 95Asn Trp Asp Gly Gly Asn Gly Tyr Ile Asp Ser Pro Gln Glu Gln Glu 100 105 110Ala Lys Ile Arg Lys Val Ile Asp Ala Ala Ile Ala Asn Gly Ile Tyr 115 120 125Val Ile Ile Asp Trp His Thr His Glu Ala Glu Leu Tyr Thr Asp Glu 130 135 140Ala Val Asp Phe Phe Thr Arg Met Ala Asp Leu Tyr Gly Asp Thr Pro145 150 155 160Asn Val Met Tyr Glu Ile Tyr Asn Glu Pro Ile Tyr Gln Ser Trp Pro 165 170 175Val Ile Lys Asn Tyr Ala Glu Gln Val Ile Ala Gly Ile Arg Ser Lys 180 185 190Asp Pro Asp Asn Leu Ile Ile Val Gly Thr Ser Asn Tyr Ser Gln Gln 195 200 205Val Asp Val Ala Ser Ala Asp Pro Ile Ser Asp Thr Asn Val Ala Tyr 210 215 220Thr Leu His Phe Tyr Ala Ala Phe Asn Pro His Asp Asn Leu Arg Asn225 230 235 240Val Ala Gln Thr Ala Leu Asp Asn Asn Val Ala Leu Phe Val Thr Glu 245 250 255Trp Gly Thr Ile Leu Asn Thr Gly Gln Gly Glu Pro Asp Lys Glu Ser 260 265 270Thr Asn Thr Trp Met

Ala Phe Leu Lys Glu Lys Gly Ile Ser His Ala 275 280 285Asn Trp Ser Leu Ser Asp Lys Ala Phe Pro Glu Thr Gly Ser Val Val 290 295 300Gln Ala Gly Gln Gly Val Ser Gly Leu Ile Ser Asn Lys Leu Thr Ala305 310 315 320Ser Gly Glu Ile Val Lys Asn Ile Ile Gln Asn Trp Asp Thr Glu Thr 325 330 335Ser Thr Gly Pro Lys Thr Thr Gln Cys Ser Thr Ile Glu Cys Ile Arg 340 345 350Ala Ala Met Glu Thr Ala Gln Ala Gly Asp Glu Ile Ile Ile Ala Pro 355 360 365Gly Asn Tyr Asn Phe Gln Asp Lys Ile Gln Gly Ala Phe Asn Arg Ser 370 375 380Val Tyr Leu Tyr Gly Ser Ala Asn Gly Asn Ser Thr Asn Pro Ile Ile385 390 395 400Leu Arg Gly Glu Ser Ala Thr Asn Pro Pro Val Phe Ser Gly Leu Asp 405 410 415Tyr Asn Asn Gly Tyr Leu Leu Ser Ile Glu Gly Asp Tyr Trp Asn Ile 420 425 430Lys Asp Ile Glu Phe Lys Thr Gly Ser Lys Gly Ile Val Leu Asp Asn 435 440 445Ser Asn Gly Ser Lys Leu Lys Asn Leu Val Val His Asp Ile Gly Glu 450 455 460Glu Ala Ile His Leu Arg Asp Gly Ser Ser Asn Asn Ser Ile Asp Gly465 470 475 480Cys Thr Ile Tyr Asn Thr Gly Arg Thr Lys Pro Gly Phe Gly Glu Gly 485 490 495Leu Tyr Val Gly Ser Asp Lys Gly Gln His Asp Thr Tyr Glu Arg Ala 500 505 510Cys Asn Asn Asn Thr Ile Glu Asn Cys Thr Val Gly Pro Asn Val Thr 515 520 525Ala Glu Gly Val Asp Val Lys Glu Gly Thr Met Asn Thr Ile Ile Arg 530 535 540Asn Cys Val Phe Ser Ala Glu Gly Ile Ser Gly Glu Asn Ser Ser Asp545 550 555 560Ala Phe Ile Asp Leu Lys Gly Ala Tyr Gly Phe Val Tyr Arg Asn Thr 565 570 575Phe Asn Val Asp Gly Ser Glu Val Ile Asn Thr Gly Val Asp Phe Leu 580 585 590Asp Arg Gly Thr Gly Phe Asn Thr Gly Phe Arg Asn Ala Ile Phe Glu 595 600 605Asn Thr Tyr Asn Leu Gly Ser Arg Ala Ser Glu Ile Ser Thr Ala Arg 610 615 620Lys Lys Gln Gly Ser Pro Glu Gln Thr His Val Trp Asp Asn Ile Arg625 630 635 640Asn Pro Asn Ser Val Asp Phe Pro Ile Ser Asp Gly Thr Glu Asn Leu 645 650 655Val Asn Lys Phe Cys Pro Asp Trp Asn Ile Glu Pro Cys Asn Pro Val 660 665 670Asp Glu Thr Asn Gln Ala Pro Thr Ile Ser Phe Leu Ser Pro Val Asn 675 680 685Asn Ile Thr Leu Val Glu Gly Tyr Asn Leu Gln Val Glu Val Asn Ala 690 695 700Thr Asp Ala Asp Gly Thr Ile Asp Asn Val Lys Leu Tyr Ile Asp Asn705 710 715 720Asn Leu Val Arg Gln Ile Asn Ser Thr Ser Tyr Lys Trp Gly His Ser 725 730 735Asp Ser Pro Asn Thr Asp Glu Leu Asn Gly Leu Thr Glu Gly Thr Tyr 740 745 750Thr Leu Lys Ala Ile Ala Thr Asp Asn Asp Gly Ala Ser Thr Glu Thr 755 760 765Gln Phe Thr Leu Thr Val Ile Thr Glu Gln Ser Pro Ser Glu Asn Cys 770 775 780Asp Phe Asn Thr Pro Ser Ser Thr Gly Leu Glu Asp Phe Asp Ile Lys785 790 795 800Lys Phe Ser Asn Val Phe Glu Leu Gly Ser Gly Gly Pro Ser Leu Ser 805 810 815Asn Leu Lys Thr Phe Thr Ile Asn Trp Asn Ser Gln Tyr Asn Gly Leu 820 825 830Tyr Gln Phe Ser Ile Asn Thr Asn Asn Gly Val Pro Asp Tyr Tyr Ile 835 840 845Asn Leu Lys Pro Lys Ile Thr Phe Gln Phe Lys Asn Ala Asn Pro Glu 850 855 860Ile Ser Ile Ser Asn Ser Leu Ile Pro Asn Phe Asp Gly Asp Tyr Trp865 870 875 880Val Thr Ser Asp Asn Gly Asn Phe Val Met Val Ser Lys Thr Asn Asn 885 890 895Phe Thr Ile Tyr Phe Ser Asn Asp Ala Thr Ala Pro Ile Cys Asn Val 900 905 910Thr Pro Ser Asn Gln Ile Ser Lys Ile Thr Asp Asp Ser Ser Ile Asn 915 920 925Phe Lys Leu Tyr Pro Asn Pro Ala Leu Asp Glu Thr Ile Phe Val Ser 930 935 940Ala Glu Asp Glu Lys Leu Ala Leu Val Leu Val Pro945 950 95564319PRTPyrococcus furiosus 64Met Ser Lys Lys Lys Phe Val Ile Val Ser Ile Leu Thr Ile Leu Leu1 5 10 15Val Gln Ala Ile Tyr Phe Val Glu Lys Tyr His Thr Ser Glu Asp Lys 20 25 30Ser Thr Ser Asn Thr Ser Ser Thr Pro Pro Gln Thr Thr Leu Ser Thr 35 40 45Thr Lys Val Leu Lys Ile Arg Tyr Pro Asp Asp Gly Glu Trp Pro Gly 50 55 60Ala Pro Ile Asp Lys Asp Gly Asp Gly Asn Pro Glu Phe Tyr Ile Glu65 70 75 80Ile Asn Leu Trp Asn Ile Leu Asn Ala Thr Gly Phe Ala Glu Met Thr 85 90 95Tyr Asn Leu Thr Ser Gly Val Leu His Tyr Val Gln Gln Leu Asp Asn 100 105 110Ile Val Leu Arg Asp Arg Ser Asn Trp Val His Gly Tyr Pro Glu Ile 115 120 125Phe Tyr Gly Asn Lys Pro Trp Asn Ala Asn Tyr Ala Thr Asp Gly Pro 130 135 140Ile Pro Leu Pro Ser Lys Val Ser Asn Leu Thr Asp Phe Tyr Leu Thr145 150 155 160Ile Ser Tyr Lys Leu Glu Pro Lys Asn Gly Leu Pro Ile Asn Phe Ala 165 170 175Ile Glu Ser Trp Leu Thr Arg Glu Ala Trp Arg Thr Thr Gly Ile Asn 180 185 190Ser Asp Glu Gln Glu Val Met Ile Trp Ile Tyr Tyr Asp Gly Leu Gln 195 200 205Pro Ala Gly Ser Lys Val Lys Glu Ile Val Val Pro Ile Ile Val Asn 210 215 220Gly Thr Pro Val Asn Ala Thr Phe Glu Val Trp Lys Ala Asn Ile Gly225 230 235 240Trp Glu Tyr Val Ala Phe Arg Ile Lys Thr Pro Ile Lys Glu Gly Thr 245 250 255Val Thr Ile Pro Tyr Gly Ala Phe Ile Ser Val Ala Ala Asn Ile Ser 260 265 270Ser Leu Pro Asn Tyr Thr Glu Leu Tyr Leu Glu Asp Val Glu Ile Gly 275 280 285Thr Glu Phe Gly Thr Pro Ser Thr Thr Ser Ala His Leu Glu Trp Trp 290 295 300Ile Thr Asn Ile Thr Leu Thr Pro Leu Asp Arg Pro Leu Ile Ser305 310 3156552DNAArtificial Sequencesynthetically generated oligonucleotide 65ccgacaattg attaaagagg agaaattaac tatggaaagg atcgatgaaa tt 526631DNAArtificial Sequencesynthetically generated oligonucleotide 66ctcttctcta agtttggtac tccatggagg c 316752DNAArtificial Sequencesynthetically generated oligonucleotide 67ccgacaattg attaaagagg agaaattaac tatgttccct gaaaagttcc tt 526831DNAArtificial Sequencesynthetically generated oligonucleotide 68ctccttaacg actcccctac tccatggagg c 316927DNAArtificial Sequencesynthetically generated oligonucleotide 69aataaggatc cgtttagcga cgctcgc 277035DNAArtificial Sequencesynthetically generated oligonucleotide 70cggataatgg cgacatgttg ggccttcgaa aataa 357152DNAArtificial Sequencesynthetically generated oligonucleotide 71aataacaatt gaaggaggaa tttaaatggc ttatcatacc tctgaggaca ag 527232DNAArtificial Sequencesynthetically generated oligonucleotide 72ctatctggag aataaaggat tcagctgaat aa 32

Claims

1. An isolated, synthetic or recombinant polypeptide having glycosidase activity comprising:(a) a sequence having the sequence of SEQ ID NO:28, or an enzymatically active fragment thereof;(b) a polypeptide comprising a sequence having at least 70% sequence identity to the sequence SEQ ID NO:28, or an enzymatically active fragment thereof;(c) a polypeptide comprising a sequence having at least 75% sequence identity to the sequence SEQ ID NO:28, or an enzymatically active fragment thereof;(d) a polypeptide comprising a sequence having at least 80% sequence identity to the sequence SEQ ID NO:28, or an enzymatically active fragment thereof;(e) a polypeptide comprising a sequence having at least 85% sequence identity to the sequence SEQ ID NO:28, or an enzymatically active fragment thereof;(f) a polypeptide comprising a sequence having at least 90% sequence identity to the sequence SEQ ID NO:28, or an enzymatically active fragment thereof;(g) a polypeptide comprising a sequence having at least 95% sequence identity to the sequence SEQ ID NO:28, or an enzymatically active fragment thereof(h) a polypeptide comprising a sequence having at least 96% sequence identity to the sequence SEQ ID NO:28, or an enzymatically active fragment thereof;(i) a polypeptide comprising a sequence having at least 97% sequence identity to the sequence SEQ ID NO:28, or an enzymatically active fragment thereof;(j) a polypeptide comprising a sequence having at least 98% sequence identity to the sequence SEQ ID NO:28, or an enzymatically active fragment thereof; or(k) a polypeptide comprising a sequence having at least 99% sequence identity to the sequence SEQ ID NO:28, or an enzymatically active fragment thereof.

2. A method of producing a polypeptide having a glycosidase activity comprising: (a) introducing a nucleic acid that encodes the polypeptide of claim 1 into an isolated host cell, (b) culturing the host cell, (c) expressing from the host cell a polypeptide, wherein the polypeptide has glycosidase activity, and (d) isolating the polypeptide.

3. A method for degrading a starch comprising use of the polypeptide of claim 1.

4. A method for generating a glucose or a maltose comprising use of the polypeptide of claim 1.

5. A method for conversion of biomass into a fuel or a chemical comprising use of the polypeptide of claim 1.

6. A method for hydrolyzing a guar gum comprising use of the polypeptide of claim 1.

7. A method for waste treatment comprising use of the polypeptide of claim 1.

8. A method for making low lactose content milk comprising use of the polypeptide of claim 1.

9. A method for drilling or well stimulation comprising use of the polypeptide of claim 1.

10. A method for making a fuel comprising use of the polypeptide of claim 1.

11. A detergent comprising a polypeptide of claim 1.

12. A composition comprising a polypeptide of claim 1, wherein optionally, the composition comprises a starch, a juice, a food, a feed, a fuel, or a textile.

13. A juice comprising a polypeptide of claim 1.

14. A feed or food comprising a polypeptide of claim 1.

15. A fuel comprising a polypeptide of claim 1.

16. An oil- or gas-comprising composition comprising a polypeptide of claim 1.

17. A waste composition comprising a polypeptide of claim 1.

18. The isolated, synthetic, or recombinant polypeptide of claim 1, wherein the glycosidase activity comprises a pullulanase activity.

19. The method of claim 2, wherein the glycosidase activity comprises a pullulanase activity.

20. The method of claim 3, wherein the glycosidase activity comprises a pullulanase activity.

21. The method of claim 4, wherein the glycosidase activity comprises a pullulanase activity.

22. The method of claim 5, wherein the glycosidase activity comprises a pullulanase activity.

23. The method of claim 6, wherein the glycosidase activity comprises a pullulanase activity.

24. The method of claim 7, wherein the glycosidase activity comprises a pullulanase activity.

25. The method of claim 8, wherein the glycosidase activity comprises a pullulanase activity.

26. The method of claim 9, wherein the glycosidase activity comprises a pullulanase activity.

27. The method of claim 10, wherein the glycosidase activity comprises a pullulanase activity.

28. A method of generating a variant of a polypeptide having glycosidase activity comprising:(a) providing a template nucleic acid comprising a sequence encoding the polypeptide of claim 1, and(b) modifying, deleting or adding one or more nucleotides in the template sequence, or a combination thereof, to generate a variant of the template nucleic acid,wherein the variant nucleic acid encodes a polypeptide having glycosidase activity, and expressing the variant nucleic acid, thereby generating a variant polypeptide having glycosidase activity.

29. The method of claim 28, wherein the modifications are introduced by a method selected from the group consisting of error-prone PCR, shuffling, oligonucleotide-directed mutagenesis, assembly PCR, sexual PCR mutagenesis, in vivo mutagenesis, cassette mutagenesis, recursive ensemble mutagenesis, exponential ensemble mutagenesis, site specific mutagenesis, gene reassembly, gene site saturated mutagenesis or a combination thereof.

30. The method of claim 28, wherein the method is iteratively repeated.

31. A method for comparing a first sequence to a reference sequence wherein said first sequence is a polypeptide sequence of claim 1 comprising: reading the first sequence and the reference sequence through use of a computer program which compares sequences; and determining differences between the first sequence and the reference sequence with the computer program.

32. A method for identifying a feature in a sequence wherein the sequence is a polypeptide sequence of claim 1 comprising: reading the sequence through the use of a computer program which identifies features in sequences; and identifying features in the sequences with the computer program.

33. The isolated, synthetic or recombinant polypeptide of claim 1, wherein the polypeptide is an enzyme which is stable to heat, is heat resistant and catalyzes the hydrolysis of glycoside bonds, and wherein the enzyme is able to renature and regain activity after exposure to temperatures of from about 60.degree. C. to 105.degree. C.

34. A method of catalyzing the hydrolysis of glycoside bonds comprising contacting a sample containing glycoside bonds with the polypeptide of claim 1 under conditions which facilitate the hydrolysis of the glycoside bonds.

35. An enzyme preparation comprising the polypeptide of claim 1, wherein optionally, the enzyme preparation is liquid or is dry.

36. A method for modifying small molecules, comprising mixing the polypeptide of claim 1 with a small molecule to produce a modified small molecule.

37. The method of claim 36 wherein a library of modified small molecules is tested to determine if a modified small molecule is present within the library which exhibits a desired activity.

38. The method of claim 36 wherein a specific biocatalytic reaction which produces the modified small molecule of desired activity is identified by systematically eliminating each of the biocatalytic reactions used to produce a portion of the library, and then testing the small molecules produced in the portion of the library for the presence or absence of the modified small molecule with the desired activity.

39. The method of claim 38 wherein the specific biocatalytic reactions which produce the modified small molecule of desired activity is optionally repeated.

40. The method of claim 38 or 39 wherein (a) the biocatalytic reactions are conducted with a group of biocatalysts that react with distinct structural moieties found within the structure of a small molecule, (b) each biocatalyst is specific for one structural moiety or a group of related structural moieties; and each biocatalyst reacts with many different small molecules which contain the distinct structural moiety.

41. The method of claim 28, wherein the glycosidase activity comprises a pullulanase activity.

42. The isolated, synthetic or recombinant polypeptide of claim 33, wherein the glycosidase activity comprises a pullulanase activity.

43. The composition of claim 12, wherein the glycosidase activity comprises a pullulanase activity.

44. The enzyme preparation of claim 35, wherein the glycosidase activity comprises a pullulanase activity.

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