TECHNOLOGY FOCUS - BIOTECHNOLOGY - Preferred Sequences: The nucleic acid sequence comprises a sequence of ODD SEQ ID NOS: 1-251. The sequence comparison algorithm is a BLAST version 2.2.2 algorithm where a filtering setting is set to blastall -p blastp -d "nr pataa" -F F, and all other options are set to default. The lyase activity comprises an ammonia lyase activity. The ammonia lyase activity comprises a phenylalanine ammonia lyase activity. The ammonia lyase activity comprises catalyzing the deamination of phenylalanine. The ammonia lyase activity comprises tyrosine ammonia lyase activity. The lyase activity comprises catalyzing the deamination of tyrosine. The ammonia lyase activity comprises histidine ammonia lyase activity, where the histidine ammonia lyase activity comprises generation of urocanoic acid or urocanoic acid derivatives. The lyase activity comprises catalyzing the deamination of histidine. The lyase activity comprises catalysis of the deamination of phenylalanine, tyrosine, histidine or their derivatives to generate cinnamic acid, para-hydroxycinnamic acid, para-hydroxyl styrene or their derivatives. The ammonia lyase activity comprises phenylalanine ammonia lyase, histidine ammonia lyase or tyrosine ammonia lyase activity or their combination. The lyase activity comprises catalysis of the deamination of phenylalanine, tyrosine, histidine or their derivatives to generate L- or D-beta-amino acids, or their derivatives. The lyase activity comprises catalysis of the deamination of histidine or their derivatives to generate L- and D-beta-histidine, or their derivatives. The lyase activity comprises catalyzing the deamination of phenylalanine, tyrosine or histidine to generate a 3,5-dihydro-5-methylidine-4H-imidazol-4-one (MIO). The lyase activity comprises carboxy-lyase activity. The lyase activity comprises argininosuccinate lyase activity. The lyase activity comprises hydroxynitrile lyase activity. The lyase activity comprises C17,20-lyase activity, where the lyase substrate is progesterone or 17-hydroxyprogesterone. The lyase activity comprises dimethylsulphoniopropionate (DMSP) lyase activity. The lyase activity comprises 5'-deoxyribose phosphate lyase activity. The lyase activity comprises isocitrate lyase activity, catalyzing the formation of succinate and glyoxylate from isocitrate, where the lyase activity comprises oxalomalate lyase activity, catalyzing the formation of oxaloacetate and glyoxylate. The lyase activity comprises hydroxymethylglutaryl-CoA lyase activity. The lyase activity is thermostable, where the polypeptide retains a lyase activity under conditions comprising a temperature of 37-99degreesC. The lyase activity is thermotolerant, where the polypeptide retains a lyase activity after exposure to a temperature of greater than 37-99degreesC. A lyase-encoding nucleic acid is generated by amplification of a polynucleotide using an amplification primer pair, where optionally the amplification is by PCR, where the nucleic acid generated by amplification of a gene library, and optionally the gene library is an environmental library. An isolated or recombinant lyase is encoded by the lyase-encoding nucleic acid. The isolated or recombinant polypeptide comprises a polypeptide and lacking a signal or leader sequence or a prepro sequence. An isolated or recombinant polypeptide comprises a polypeptide and having a heterologous signal or leader sequence or a heterologous prepro sequence. The lyase activity comprises a specific activity at 37degreesC in the range of 100-1000 units/mg protein. The thermotolerance comprises retention of at least half of the specific activity of the lyase at 37degreesC after being heated to an elevated temperature, or, where the thermotolerance comprises retention of specific activity at 37degreesC in 500-1200 units/mg protein after being heated to an elevated temperature. The polypeptide comprises at least one glycosylation site, and optionally the glycosylation is an N-linked glycosylation, and optionally the polypeptide is glycosylated after being expressed in a yeast cell or mammalian cell, and optionally the yeast cell is P. pastoris or a S. pombe. The polypeptide retains a lyase activity under conditions comprising pH 4.0-6.5, or more acidic, or after exposure to conditions comprising pH 4.0-6.5, or more acidic. The polypeptide retains a lyase activity under conditions comprising pH 7.5-10.5, or more basic, or after exposure to conditions comprising pH 7.5-10.5 or more basic. Preparation (claimed): Isolating or recovering a nucleic acid encoding a polypeptide with a lyase activity from a sample comprises (a) providing an amplification primer pair, (b) isolating a nucleic acid from the sample or treating the environmental sample such that nucleic acid in the sample is accessible for hybridization to the amplification primer pair, and (c) combining the nucleic acid of step (b) with the amplification primer pair of step (a) and amplifying nucleic acid from the sample, thus isolating or recovering a nucleic acid encoding a polypeptide with a lyase activity from a sample, where optionally the sample is an environmental sample. Isolating or recovering a nucleic acid encoding a polypeptide with a lyase activity from a sample comprises (a) providing a polynucleotide probe, or its subsequence, or a probe, (b) isolating a nucleic acid from the environmental sample or treating the environmental sample such that nucleic acid in the sample is accessible for hybridization to a polynucleotide probe of step (a), (c) combining the isolated nucleic acid or the treated environmental sample of step (b) with the polynucleotide probe of step (a), and (d) isolating a nucleic acid that specifically hybridizes with the polynucleotide probe of step (a), thus isolating or recovering a nucleic acid encoding a polypeptide with a lyase activity from a sample, where optionally the sample is an environmental sample. Preferred Method: Inhibiting the translation of a lyase message in a cell comprises administering to the cell or expressing in the cell an antisense oligonucleotide comprising a nucleic acid sequence complementary to or capable of hybridizing under stringent conditions to a sequence above. Isolating or identifying a polypeptide with a lyase activity comprises providing an antibody, providing a sample comprising polypeptides, and contacting the sample with the antibody under conditions where the antibody can specifically bind to the polypeptide, thus isolating or identifying a polypeptide having a lyase activity. Making an anti-lyase antibody comprises administering to a non-human animal a nucleic acid in an amount to generate a humoral immune response, thus making an anti-lyase antibody, or administering to a non-human animal a polypeptide in an amount to generate a humoral immune response, thus making an anti-lyase antibody. Identifying a polypeptide having a lyase activity comprises providing a polypeptide, providing a lyase substrate, and contacting the polypeptide with the substrate and detecting a decrease in the amount of substrate or an increase in the amount of a reaction product, where a decrease in the amount of the substrate or an increase in the amount of the reaction product detects a polypeptide having a lyase activity. Determining whether a test compound specifically binds to a polypeptide comprises expressing a nucleic acid or a vector comprising the nucleic acid under conditions for translation of the nucleic acid to a polypeptide, providing a test compound, contacting the polypeptide with the test compound, and determining whether the test compound specifically binds to the polypeptide. Identifying a modulator of a lyase activity comprises providing a polypeptide, providing a test compound, contacting the polypeptide with the test compound and measuring an activity of the glucanase, where a change in the lyase activity measured in the presence of the test compound compared to the activity in the absence of the test compound provides a determination that the test compound modulates the lyase activity. Modifying codons in a nucleic acid encoding a polypeptide with a lyase activity to increase its expression in a host cell comprises providing a nucleic acid encoding a polypeptide with a lyase activity, and identifying a non-preferred or a less preferred codon in the nucleic acid and replacing it with a preferred or neutrally used codon encoding the same amino acid as the replaced codon, where a preferred codon is a codon over-represented in coding sequences in genes in the host cell and a non- preferred or less preferred codon is a codon under-represented in coding sequences in genes in the host cell, thus modifying the nucleic acid to increase its expression in a host cell. Whole cell engineering of new or modified phenotypes by using real-time metabolic flux analysis comprises making a modified cell by modifying the genetic composition of a cell, where the genetic composition is modified by addition to the cell of a nucleic acid, culturing the modified cell to generate a plurality of modified cells, measuring at least one metabolic parameter of the cell by monitoring the cell culture in real time; and analyzing the data to determine if the measured parameter differs from a comparable measurement in an unmodified cell under similar conditions, thus identifying an engineered phenotype in the cell using real-time metabolic flux analysis, where optionally the genetic composition of the cell is modified by a method comprising deletion of a sequence or modification of a sequence in the cell, or, knocking out the expression of a gene, and optionally the method further comprises selecting a cell comprising a newly engineered phenotype, and optionally the method further comprises culturing the selected cell, thus generating a new cell strain comprising a newly engineered phenotype. Making a transgenic plant comprises introducing a heterologous nucleic acid sequence into the cell, thus producing a transformed plant cell, producing a transgenic plant from the transformed cell. Optionally the step (a) further comprises introducing the heterologous nucleic acid sequence by electroporation or microinjection of plant cell protoplasts, and optionally step (a) comprises introducing the heterologous nucleic acid sequence directly to plant tissue by DNA particle bombardment or by using an Agrobacterium tumefaciens host. Deaminating a phenylalanine, tyrosine or a histidine comprises providing a polypeptide having a lyase activity, or a polypeptide encoded by a nucleic acid above, providing a composition comprising a phenylalanine, tyrosine or a histidine residue, and contacting the polypeptide with the composition under conditions where the lyase deaminates the phenylalanine, tyrosine or a histidine residue in the composition, where optionally the composition comprises a plant cell, a bacterial cell, a yeast cell, an insect cell, or an animal cell, and optionally the polypeptide has ammonia lyase activity. Dough conditioning comprises contacting a dough or a bread product with at least one polypeptide or a polypeptide encoded by a nucleic acid, under conditions for conditioning the dough. Beverage production comprises administration of at least one polypeptide or a polypeptide encoded by a nucleic acid above to a beverage, drink or a beverage or drink precursor under conditions for decreasing the viscosity of the beverage. Utilizing a lyase as a nutritional supplement in an animal diet comprises preparing a nutritional supplement containing a lyase enzyme comprising at least 30 contiguous amino acids of a polypeptide, or a polypeptide encoded by a nucleic acid above, and administering the nutritional supplement to an animal as an enzyme substitution therapy, where optionally the enzyme substitution therapy is for the treatment of phenylketonuria (PKU), and optionally the animal is a human, a ruminant or a monogastric animal, and optionally the lyase enzyme is prepared by expression of a polynucleotide encoding the lyase in an organism selected from a bacterium, a yeast, a plant, an insect, a fungus and an animal. Decreasing elevated levels of phenylalanine in the bloodstream (hyperphenylalaninemia) comprises providing a pharmaceutical composition or dietary supplement, and administering an amount of the pharmaceutical composition or dietary supplement to an individual. Processing a biomass material comprises contacting a composition with a polypeptide or a polypeptide encoded by a nucleic acid above. Improving texture and flavor of a dairy product comprises providing a polypeptide or a polypeptide encoded by a nucleic acid above, providing a dairy product, and contacting the polypeptide and the dairy product under conditions where the lyase can improve the texture or flavor of the dairy product. Treating solid or liquid animal waste products comprises providing a polypeptide or a polypeptide encoded by a nucleic acid above, where optionally the polypeptide has ammonia lyase activity, or phenylalanine ammonia lyase activity, tyrosine ammonia lyase activity and/or histidine ammonia lyase activity, providing a solid or a liquid animal waste, and contacting the polypeptide and the solid or liquid waste under conditions where the protease can treat the waste. Preferred Pharmaceutical Composition: The pharmaceutical composition or dietary supplement is formulated for the treatment of PKU. The polypeptide is chemically modified to produce a protected form that possesses better specific activity, prolonged half-life, and/or reduced immunogenicity in vivo. The polypeptide is chemically modified by glycosylation, pegylation or their combination. The polypeptide is formulated by encapsulation in a liposome, or a micro- or nano-structure, where optionally the structure is a nanotubule or a nano- or microcapsule. The polypeptide is formulated in a matrix stabilized enzyme crystal.