CA2590662A1

CA2590662A1 - Corynebacterium glutamicum genes encoding metabolic pathway proteins

Info

Publication number: CA2590662A1
Application number: CA002590662A
Authority: CA
Inventors: Markus Pompejus; Burkhard Kroeger; Hartwig Schroeder; Oskar Zelder; Gregor Haberhauer
Original assignee: Individual
Current assignee: BASF SE
Priority date: 1999-06-25
Filing date: 2000-06-23
Publication date: 2001-01-04
Also published as: CA2592965A1

Abstract

Isolated nucleic acid molecules, designated MP nucleic acid molecules, which encode novel MP proteins from Corynebacterium glutamicum are described. The invention also provides antisense nucleic acid molecules, recombinant expression vectors containing MP nucleic acid molecules, and host cells into which the expression vectors have been introduced. The invention still further provides isolated MP
proteins, mutated MP proteins, fusion proteins, antigenic peptides and methods for the improvement of production of a desired compound from C. glutamicum based on genetic engineering of MP genes in this organism.

Description

- ~ ' f CORYNEBACTERIUM GLUTAMICUM GENES ENCODING METABOLIC
PATHWAY PROTEINS

This is a divisional application of Canadian Patent Application Serial No.

2,383,865. In some aspects, this divisional application relates to an isolated nucleic acid from Corynebacterium glutamicum encoding a metabolic pathway protein or a portion thereof, said nucleic acid being charactererized by SEQ ID NO:449. An isolated nucleic acid comprising a nucleotide sequence at least 50% homolgous to SEQ ID NO:449, corresponding polypeptides (SEQ ID NO:450), corresponding vectors, recombinant host cells, production methods, and use in diagnois of C. dipteriae are also contemplated.
However, it should be understood that the expression "the invention" and the like encompass the subject matter of both the parent and this divisional application.

Background of the Invention Certain products and by-products of naturally-occurring metabolic processes in cells have utility in a wide array of industries, including the food, feed, cosmetics, and phannaceutical industries. These molecules, collectively termed 'fine chemicals', include organic acids, both proteinogenic and non-proteinogenic amino acids, nucleotides and nucleosides, lipids and fatty acids, diols, carbohydrates, aromatic compounds, vitamins and cofactors, and enzymes. Their production is most conveniently performed through large-scale culture of bacteria developed to produce and secrete large quantities of a particular desired molecule. One particularly useful organism for this purpose is Corynebacterium glutamicum, a gram positive, nonpathogenic bacterium. Through strain selection, a number of mutant strains have been developed which produce an array of desirable compounds. However, selection of strains improved for the production of a particular molecule is a time-consuming and difficult process.

Summary of the Invention The invention provides novel bacterial nucleic acid molecules which have a variety of uses. These uses include the identification of microorganisms which can be used to produce fine chemicals, the modulation of fine chemical production in C.
glutamicum or related bacteria, the typing or identification of C. glutamicum or related bacteria, as reference points for mapping the C. glutamicum genome, and as markers for transformation. These novel nucleic acid molecules encode proteins, referred to herein as metabolic pathway (MP) proteins.
C. glutamicum is a gram positive, aerobic bacterium which is commonly used in industry for the large-scale production of a variety of fine chemicals, and also for the degradation of hydrocarbons (such as in petroleum spills) and for the oxidation of terpenoids. The MP nucleic acid molecules of the invention, therefore, can be used to identify microorganisms which can be used to produce fine chemicals, e.g., by fermentation processes. Modulation of the expression of the MP nucleic acids of the invention, or modification of the sequence of the MP nucleic acid molecules of the invention, can be used to modulate the production of one or more fine chemicals from a microorganism (e.g., to improve the yield or production of one or more fine chemicals from a Corynebacterium or Brevibacterium species).
The MP nucleic acids of the invention may also be used to identify an organism as being Corynebacterium glutamicum or a close relative thereof, or to identify the presence of C. glutamicum or a relative thereof in a mixed population of microorganisms. The invention provides the nucleic acid sequences of a number of C.
glutamicum genes; by probing the extracted genomic DNA of a culture of a unique or mixed population of microorganisms under stringent conditions with a probe spanning a region of a C. glutamicum gene which is unique to this organism, one can ascertain whether this organism is present. Although Corynebacterium glutamicum itself is nonpathogenic, it is related to species pathogenic in humans, such as Corynebacterium diphtheriae (the causative agent of diphtheria); the detection of such organisms is of significant clinical relevance.
The MP nucleic acid molecules of the invention may also serve as reference points for mapping of the C. glutamicum genome, or of genomes of related organisms.
Similarly, these molecules, or variants or portions thereof, may serve as markers for genetically engineered Corynebacterium or Brevibacterium species.
The MP proteins encoded by the novel nucleic acid molecules of the invention are capable of, for example, performing an enzymatic step involved in the metabolism of certain fine chemicals, including amino acids, vitamins, cofactors, nutraceuticals, nucleotides, nucleosides, and trehalose. Given the availability of cloning vectors for use in Corynebacterium glutamicum, such as those disclosed in Sinskey et al., U.S.
Patent No. 4,649,119, and techniques for genetic manipulation of C. glutamicum and the related Brevibacterium species (e.g., lactofermentum) (Yoshihama et al,.I.
Bacteriol.
162: 591-597 (1985); Katsumata et al,, J. Bacteriol. 159: 306-311 (1984); and Santamaria et al., J. Gen. Microbiol. 130: 2237-2246 (1984)), the nucleic acid molecules of the invention may be utilized in the genetic engineering of this organism to make it a better or more efficient producer of one or more fine chemicals.
This improved production or efficiency of production of a fine chemical may be due to a direct effect of manipulation of a gene of the invention, or it may be due to an indirect effect of such manipulation. Specifically, alterations in C.
glutamicum metabolic pathways for amino acids, vitamins, cofactors, nucleotides, and trehalose may have a direct impact on the overall production of one or more of these desired compounds from this organism. For example, optimizing the activity of a lysine biosynthetic pathway protein or decreasing the activity of a lysine degradative pathway protein may result in an increase in the yield or efficiency of production of lysine from such an engineered organism. Alterations in the proteins involved in these metabolic pathways may also have an indirect impact on the production or efficiency of production of a desired fine chemical. For example, a reaction which is in competition for an intermediate necessary for the production of a desired molecule may be eliminated, or a pathway necessary for the production of a particular intermediate for a desired compound may be optimized. Further, modulations in the biosynthesis or degradation of, for example, an amino acid, a vitamin, or a nucleotide may increase the overall ability of the microorganism to rapidly grow and divide, thus increasing the number and/or production capacities of the microorganism in culture and thereby increasing the possible yield of the desired fine chemical.
The nucleic acid and protein molecules of the invention may be utilized to directly improve the production or efficiency of production of one or more desired fine chemicals from Corynebacterium glutamicum. Using recombinant genetic techniques well known in the art, one or more of the biosynthetic or degradative enzymes of the invention for amino acids, vitamins, cofactors, nutraceuticals, nucleotides, nucleosides, or trehalose may be manipulated such that its function is modulated. For example, a biosynthetic enzyme may be improved in efficiency, or its allosteric control region destroyed such that feedback inhibition of production of the compound is prevented.
Similarly, a degradative enzyme may be deleted or modified by substitution, deletion, or addition such that its degradative activity is lessened for the desired compound without impairing the viability of the cell. In each case, the overall yield or rate of production of the desired fine chemical may be increased.
It is also possible that such alterations in the protein and nucleotide molecules of the invention may improve the production of other fine chemicals besides the amino acids, vitamins, cofactors, nutraceuticals, nucleotides, nucleosides, and trehalose through indirect mechanisms. Metabolism of any one compound is necessarily intertwined with other biosynthetic and degradative pathways within the cell, and necessary cofactors, intermediates, or substrates in one pathway are likely supplied or limited by another such pathway. Therefore, by modulating the activity of one or more of the proteins of the invention, the production or efficiency of activity of another fine chemical biosynthetic or degradative pathway may be impacted. For example, amino acids serve as the structural units of all proteins, yet may be present intracellularly in levels which are limiting for protein synthesis; therefore, by increasing the efficiency of production or the yields of one or more amino acids within the cell, proteins, such as biosynthetic or degradative proteins, may be more readily synthesized.
Likewise, an alteration in a metabolic pathway enzyme such that a particular side reaction becomes more or less favored may result in the over- or under-production of one or more compounds which are utilized as intermediates or substrates for the production of a desired fine chemical.

This invention provides novel nucleic acid molecules which encode proteins, referred to herein as metabolic pathway proteins (MP), which are capable of, for example, performing an enzymatic step involved in the metabolism of molecules important for the normal functioning of cells, such as amino acids, vitamins, cofactors, nucleotides and nucleosides, or trehalose. Nucleic acid molecules encoding an MP
protein are referred to herein as MP nucleic acid molecules. In a preferred embodiment, the MP protein performs an enzymatic step related to the metabolism of one or more of the following: amino acids, vitamins, cofactors, nutraceuticals, nucleotides, nucleosides, and trehalose. Examples of such proteins include those encoded by the genes set forth in Table 1.
Accordingly, one aspect of the invention pertains to isolated nucleic acid molecules (e.g., cDNAs, DNAs, or RNAs) comprising a nucleotide sequence encoding an MP protein or biologically active portions thereof, as well as nucleic acid fragments suitable as primers or hybridization probes for the detection or amplification of MP-encoding nucleic acid (e.g., DNA or mRNA). In particularly preferred embodiments, the isolated nucleic acid molecule comprises orte of the nucleotide sequences set forth as the odd-numbered SEQ ID NOs in the Sequence Listing (e.g., SEQ ID NO:], SEQ ID
NO:3, SEQ ID NO:5, SEQ ID NO:7....), or the coding region or a complement thereof of one of these nucleotide sequences. In other particularly preferred embodiments, the isolated nucleic acid molecule of the invention comprises a nucleotide sequence which hybridizes to or is at least about 50%, preferably at least about 60%, more preferably at least about 70%, 80% or 90%, and even more preferably at least about 95%, 96%, 97%, 98%, 99% or more homologous to a nucleotide sequence set forth as an odd-numbered SEQ ID NO in the Sequence Listing (e.g., SEQ ID NO:I, SEQ ID NO:3, SEQ ID
NO:5, SEQ ID NO:7....), or a portion thereof. In other preferred embodiments, the isolated nucleic acid molecule encodes one of the amino acid sequences set forth as an even-numbered SEQ ID NO in the Sequence Listing (e.g., SEQ ID NO:2, SEQ ID NO:4, SEQ
ID NO:6, SEQ ID NO:8....). The preferred MP proteins of the present invention also preferably possess at least one of the MP activities described herein.
In another embodiment, the isolated nucleic acid molecule encodes a protein or portion thereof wherein the protein or portion thereof includes an amino acid sequence which is sufficiently homologous to an amino acid sequence of the invention (e.g., a sequence having an even-numbered SEQ ID NO: in the Sequence Listing), e.g., sufficiently homologous to an amino acid sequence of the invention such that the protein or portion thereof maintains an MP activity. Preferably, the protein or portion thereof encoded by the nucleic acid molecule maintains the ability to perform an enzymatic reaction in a amino acid, vitamin, cofactor, nutraceutical, nucleotide, nucleoside, or trehalose metabolic pathway. In one embodiment, the protein encoded by the nucleic acid molecule is at least about 50%, preferably at least about 60%, and more preferably at least about 70%, 80%, or 90% and most preferably at least about 95%, 96%, 97%, 98%, or 99% or more homologous to an amino acid sequence of the invention (e.g., an entire amino acid sequence selected from those having an even-numbered SEQ ID
NO
in the Sequence Listing). In another preferred embodiment, the protein is a full length C. glutamicum protein which is substantially homologous to an entire amino acid sequence of the invention (encoded by an open reading frame shown in the corresponding odd-numbered SEQ ID NOs in the Sequence Listing (e.g., SEQ ID
NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7....).
In another preferred embodiment, the isolated nucleic acid molecule is derived from C. glutamicum and encodes a protein (e.g., an MP fusion protein) which includes a biologically active domain which is at least about 50% or more homologous to one of the amino acid sequences of the invention (e.g., a sequence of one of the even-numbered SEQ ID NOs in the Sequence Listing) and is able to catalyze a reaction in a metabolic pathway for an amino acid, vitamin, cofactor, nutraceutical, nucleotide, nucleoside, or trehalose, or one or more of the activities set forth in Table 1, and which also includes heterologous nucleic acid sequences encoding a heterologous polypeptide or regulatory regions.
In another embodiment, the isolated nucleic acid molecule is at least 15 nucleotides in length and hybridizes under stringent conditions to a nucleic acid molecule comprising a nucleotide sequence of the invention (e.g., a sequence of an odd-numbered SEQ ID NO in the Sequence Listing). Preferably, the isolated nucleic acid molecule corresponds to a naturally-occurring nucleic acid molecule. More preferably, the isolated nucleic acid encodes a naturally-occurring C. glutamicum MP
protein, or a biologically active portion thereof.

Another aspect of the invention pertains to vectors, e.g., recombinant expression vectors, containing the nucleic acid molecules of the invention, and host cells into which such vectors have been introduced. In one embodiment, such a host cell is used to produce an MP protein by culturing the host cell in a suitable medium. The MP
protein can be then isolated from the medium or the host cell.
Yet another aspect of the invention pertains to a genetically altered microorganism in which an MP gene has been introduced or altered. In one embodiment, the genome of the microorganism has been altered by introduction of a nucleic acid molecule of the invention encoding wild-type or mutated MP
sequence as a transgene. In another embodiment, an endogenous MP gene within the genome of the microorganism has been altered, e.g., functionally disrupted, by homologous recombination with an altered MP gene. In another embodiment, an endogenous or introduced MP gene in a microorganism has been altered by one or more point mutations, deletions, or inversions, but still encodes a functional MP
protein. In still another embodiment, one or more of the regulatory regions (e.g., a promoter, repressor, or inducer) of an MP gene in a microorganism has been altered (e.g., by deletion, truncation, inversion, or point mutation) such that the expression of the MP
gene is modulated. In a preferred embodiment, the microorganism belongs to the genus Corynebacterium or Brevibacterium, with Corynebacterium glutamicum being particularly preferred. In a preferred embodiment, the microorganism is also utilized for the production of a desired compound, such as an amino acid, with lysine being particularly preferred.
In another aspect, the invention provides a method of identifying the presence or activity of Cornyebacterium diphtheriae in a subject. This method includes detection of one or more of the nucleic acid or amino acid sequences of the invention (e.g., the sequences set forth in the Sequence Listing as SEQ ID NOs 1 through 1156) in a subject, thereby detecting the presence or activity of Corynebacterium diphtheriae in the subject.
Still another aspect of the invention pertains to an isolated MP protein or a portion, e.g., a biologically active portion, thereof. In a preferred embodiment, the isolated MP protein or portion thereof can catalyze an enzymatic reaction involved in one or more pathways for the metabolism of an amino acid, a vitamin, a cofactor, a nutraceutical, a nucleotide, a nucleoside, or trehalose. In another preferred embodiment, the isolated MP protein or portion thereof is sufficiently homologous to an amino acid sequence of the invention (e.g., a sequence of an even-numbered SEQ ID NO: in the Sequence Listing) such that the protein or portion thereof maintains the ability to catalyze an enzymatic reaction involved in one or more pathways for the metabolism of an amino acid, a vitamin, a cofactor, a nutraceutical, a nucleotide, a nucleoside, or trehalose.
The invention also provides an isolated preparation of an MP protein. In preferred embodiments, the MP protein comprises an amino acid sequence of the invention (e.g., a sequence of an even-numbered SEQ ID NO: of the Sequence Listing).
In another preferred embodiment, the invention pertains to an isolated full length protein which is substantially homologous to an entire amino acid sequence of the invention (e.g., a sequence of an even-numbered SEQ ID NO: of the Sequence Listing) (encoded by an open reading frame set forth in a corresponding odd-numbered SEQ ID NO:
of the Sequence Listing). In yet another embodiment, the protein is at least about 50%, preferably at least about 60%, and more preferably at least about 70%, 80%, or 90%, and most preferably at least about 95%, 96%, 97%, 98%, or 99% or more homologous to an entire amino acid sequence of the invention (e.g., a sequence of an even-numbered SEQ ID NO: of the Sequence Listing). In other embodiments, the isolated MP
protein comprises an amino acid sequence which is at least about 50% or more homologous to one of the amino acid sequences of the invention (e.g., a sequence of an even-numbered SEQ ID NO: of the Sequence Listing) and is able to catalyze an enzymatic reaction in an amino acid, vitamin, cofactor, nutraceutical, nucleotide, nucleoside, or trehalose metabolic pathway, or has one or more of the activities set forth in Table 1.
Alternatively, the isolated MP protein can comprise an amino acid sequence which is encoded by a nucleotide sequence which hybridizes, e.g., hybridizes under stringent conditions, or is at least about 50%, preferably at least about 60%, more preferably at least about 70%, 80%, or 90%, and even more preferably at least about 95%, 96%, 97%, 98,%, or 99% or more homologous to a nucleotide sequence of one of the even-numbered SEQ ID NOs set forth in the Sequence Listing. It is also preferred that the preferred forms of MP proteins also have one or more of the MP
bioactivities described herein.

. . =

The MP polypeptide, or a biologically active portion thereof, can be operatively linked to a non-MP polypeptide to form a fusion protein. In preferred embodiments, this fusion protein has an activity which differs from that of the MP protein alone. In other preferred embodiments, this fusion protein, when introduced into a C.
glutamicum pathway for the metabolism of an amino acid, vitamin, cofactor, nutraceutical, results in increased yields and/or efficiency of production of a desired fine chemical from C.
glutamicum. In particularly preferred embodiments, integration of this fusion protein into an amino acid, vitamin, cofactor, nutraceutical, nucleotide, nucleoside, or trehalose metabolic pathway of a host cell modulates production of a desired compound from the cell.
In another aspect, the invention provides methods for screening molecules which modulate the activity of an MP protein, either by interacting with the protein itself or a substrate or binding partner of the MP protein, or by modulating the transcription or translation of an MP nucleic acid molecule of the invention.
Another aspect of the invention pertains to a method for producing a fine chemical. This method involves the culturing of a cell containing a vector directing the expression of an MP nucleic acid molecule of the invention, such that a fine chemical is produced. In a preferred embodiment, this method further includes the step of obtaining a cell containing such a vector, in which a cell is transfected with a vector directing the expression of an MP nucleic acid. In another preferred embodiment, this method further includes the step of recovering the fine chemical from the culture. In a particularly preferred embodiment, the cell is from the genus Corynebacterium or Brevibacterium, or is selected from those strains set forth in Table 3.
Another aspect of the invention pertains to methods for modulating production of a molecule from a microorganism. Such methods include contacting the cell with an agent which modulates MP protein activity or MP nucleic acid expression such that a cell associated activity is altered relative to this same activity in the absence of the agent. In a preferred embodiment, the cell is modulated for one or more C.
glutamicum amino acid, vitamin, cofactor, nutraceutical, nucleotide, nucleoside, or trehalose metabolic pathways, such that the yields or rate of production of a desired fine chemical by this microorganism is improved. The agent which modulates MP protein activity can be an agent which stimulates MP protein activity or MP nucleic acid expression.

-II-Examples of agents which stimulate MP protein activity or MP nucleic acid expression include small molecules, active MP proteins, and nucleic acids encoding MP
proteins that have been introduced into the cell. Examples of agents which inhibit MP
activity or expression include small molecules, and antisense MP nucleic acid molecules.
Another aspect of the invention pertains to methods for modulating yields of a desired compound from a cell, involving the introduction of a wild-type or mutant MP
gene into a cell, either maintained on a separate plasmid or integrated into the genome of the host cell. If integrated into the genome, such integration can be random, or it can take place by homologous recombination such that the native gene is replaced by the introduced copy, causing the production of the desired compound from the cell to be modulated. In a preferred embodiment, said yields are increased. In another preferred embodiment, said chemical is a fine chemical. In a particularly preferred embodiment, said fine chemical is an amino acid. In especially preferred embodiments, said amino acid is L-lysine.
Detailed Description of the Invention The present invention provides MP nucleic acid and protein molecules which are involved in the metabolism of certain fine chemicals in Corynebacterium glutarnicum, including amino acids, vitamins, cofactors, nutraceuticals, nucleotides, nucleosides, and trehalose. The molecules of the invention may be utilized in the modulation of production of fine chemicals from microorganisms, such as C. glutamicum, either directly (e.g., where modulation of the activity of a lysine biosynthesis protein has a direct impact on the production or efficiency of production of lysine from that organism), or may have an indirect impact which nonetheless results in an increase of yield or efficiency of production of the desired compound (e.g., where modulation of the activity of a nucleotide biosynthesis protein has an impact on the production of an organic acid or a fatty acid from the bacterium, perhaps due to improved growth or an increased supply of necessary co-factors, energy compounds, or precursor molecules).
Aspects of the invention are further explicated below.

. ~ ' I. Fine Chemicals The term 'fine chemical' is art-recognized and includes molecules produced by an organism which have applications in various industries, such as, but not limited to, the pharmaceutical, agriculture, and cosmetics industries. Such compounds include organic acids, such as tartaric acid, itaconic acid, and diaminopimelic acid, both proteinogenic and non-proteinogenic amino acids, purine and pyrimidine bases, nucleosides, and nucleotides (as described e.g. in Kuninaka, A. (1996) Nucleotides and related compounds, p. 561-612, in Biotechnology vol. 6, Rehm el al., eds. VCH:
Weinheim, and references contained therein), lipids, both saturated and unsaturated fatty acids (e.g., arachidonic acid), diols (e.g., propane diol, and butane diol), carbohydrates (e.g., hyaluronic acid and trehalose), aromatic compounds (e.g., aromatic amines, vanillin, and indigo), vitamins and cofactors (as described in Ullmann's Encyclopedia of Industrial Chemistry, vol. A27, "Vitamins", p. 443-613 (1996) VCH: Weinheim and references therein; and Ong, A.S., Niki, E. & Packer, L. (1995) "Nutrition, Lipids, Health, and Disease" Proceedings of the UNESCO/Confederation of Scientific and Technological Associations in Malaysia, and the Society for Free Radical Research -Asia, held Sept, 1-3, 1994 at Penang, Malaysia, AOCS Press, (1995)), enzymes, polyketides (Cane et al. (1998) Science 282: 63-68), and all other chemicals described in Gutcho (1983) Chemicals by Fermentation, Noyes Data Corporation, ISBN:
0818805086 and references therein. The metabolism and uses of certain of these fine chemicals are further explicated below.

A. Amino Acid Metabolism and Uses Amino acids comprise the basic structural units of all proteins, and as such are essential for nonnal cellular functioning in all organisms. The term "amino acid" is art-recognized. The proteinogenic amino acids, of which there are 20 species, serve as structural units for proteins, in which they are linked by peptide bonds, while the nonproteinogenic amino acids (hundreds of which are known) are not normally found in proteins (see Ulmann's Encyclopedia of Industrial Chemistry, vol. A2, p. 57-97 VCH:
Weinheim (1985)). Amino acids may be in the D- or L- optical configuration, though L-amino acids are generally the only type found in naturally-occurring proteins.
Biosynthetic and degradative pathways of each of the 20 proteinogenic amino acids have been well characterized in both prokaryotic and eukaryotic cells (see, for example, Stryer, L. Biochemistry, 3'd edition, pages 578-590 (1988)). The 'essential' amino acids (histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine), so named because they are generally a nutritional requirement due to the complexity of their biosyntheses, are readily converted by simple biosynthetic pathways to the remaining 11 'nonessential' amino acids (alanine, arginine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, and tyrosine).
Higher animals do retain the ability to synthesize some of these amino acids, but the essential amino acids must be supplied from the diet in order for normal protein synthesis to occur.
Aside from their function in protein biosynthesis, these amino acids are interesting chemicals in their own right, and many have been found to have various applications in the food, feed, chemical, cosmetics, agriculture, and pharmaceutical industries. Lysine is an important amino acid in the nutrition not only of humans, but also of monogastric animals such as poultry and swine. Glutamate is most commonly used as a flavor additive (mono-sodium glutamate, MSG) and is widely used throughout the food industry, as are aspartate, phenylalanine, glycine, and cysteine.
Glycine, L-methionine and tryptophan are all utilized in the pharmaceutical industry.
Glutamine, valine, leucine, isoleucine, histidine, arginine, proline, serine and alanine are of use in both the pharmaceutical and cosmetics industries. Threonine, tryptophan, and D/ L-methionine are common feed additives. (Leuchtenberger, W. (1996) Amino aids -technical production and use, p. 466-502 in Rehm el al. (eds.) Biotechnology vol. 6, chapter 14a, VCH: Weinheim). Additionally, these amino acids have been found to be useful as precursors for the synthesis of synthetic amino acids and proteins, such as N-acetylcysteine, S-carboxymethyl-L-cysteine, (S)-5-hydroxytryptophan, and others described in Ulmann's Encyclopedia of Industrial Chemistry, vol. A2, p. 57-97, VCH:
Weinheim, 1985.
The biosynthesis of these natural amino acids in organisms capable of producing them, such as bacteria, has been well characterized (for review of bacterial amino acid biosynthesis and regulation thereof, see Umbarger, H.E.(1978) Ann.
Rev.
Biochem. 47: 533-606). Glutamate is synthesized by the reductive amination of a-ketoglutarate, an intermediate in the citric acid cycle. Glutamine, proline, and arginine are each subsequently produced from glutamate. The biosynthesis of serine is a three-step process beginning with 3-phosphoglycerate (an intermediate in glycolysis), and resulting in this amino acid after oxidation, transamination, and hydrolysis steps. Both cysteine and glycine are produced from serine; the former by the condensation of homocysteine with serine, and the latter by the transferal of the side-chain 0-carbon atom to tetrahydrofolate, in a reaction catalyzed by serine transhydroxymethylase.
Phenylalanine, and tyrosine are synthesized from the glycolytic and pentose phosphate pathway precursors erythrose 4-phosphate and phosphoenolpyruvate in a 9-step biosynthetic pathway that differ only at the final two steps after synthesis of prephenate.
Tryptophan is also produced from these two initial molecules, but its synthesis is an 11-step pathway. Tyrosine may also be synthesized from phenylalanine, in a reaction catalyzed by phenylalanine hydroxylase. Alanine, valine, and leucine are all biosynthetic products of pyruvate, the final product of glycolysis. Aspartate is formed from oxaloacetate, an intermediate of the citric acid cycle. Asparagine, methionine, threonine, and lysine are each produced by the conversion of aspartate.
Isoleucine is formed from threonine. A complex 9-step pathway results in the production of histidine from 5-phosphoribosyl-l-pyrophosphate, an activated sugar.
Amino acids in excess of the protein synthesis needs of the cell cannot be stored, and are instead degraded to provide intermediates for the major metabolic pathways of the cell (for review see Stryer, L. Biochemistry 3'd ed. Ch. 21 "Amino Acid Degradation and the Urea Cycle" p. 495-516 (1988)). Although the cell is able to convert unwanted amino acids into useful metabolic intermediates, amino acid production is costly in terms of energy, precursor molecules, and the enzymes necessary to synthesize them.
Thus it is not surprising that amino acid biosynthesis is regulated by feedback inhibition, in which the presence of a particular amino acid serves to slow or entirely stop its own production (for overview of feedback mechanisms in amino acid biosynthetic pathways, see Stryer, L. Biochemistry, 3'd ed. Ch. 24: "Biosynthesis of Amino Acids and Heme" p.
575-600 (1988)). Thus, the output of any particular amino acid is limited by the amount of that amino acid present in the cell.

B. Vitamin, Cofactor, and Nutraceutical Metabolism and Uses Vitamins, cofactors, and nutraceuticals comprise another group of molecules which the higher animals have lost the ability to synthesize and so must ingest, although they are readily synthesized by other organisms, such as bacteria. These molecules are either bioactive substances themselves, or are precursors of biologically active substances which may serve as electron carriers or intermediates in a variety of metabolic pathways. Aside from their nutritive value, these compounds also have significant industrial value as coloring agents, antioxidants, and catalysts or other processing aids. (For an overview of the structure, activity, and industrial applications of these compounds, see, for example, Ullman's Encyclopedia of Industrial Chemistry, "Vitamins" vol. A27, p. 443-613, VCH: Weinheim, 1996.) The term "vitamin" is art-recognized, and includes nutrients which are required by an organism for normal functioning, but which that organism cannot synthesize by itself. The group of vitamins may encompass cofactors and nutraceutical compounds. The language "cofactor"
includes nonproteinaceous compounds required for a normal enzymatic activity to occur. Such compounds may be organic or inorganic; the cofactor molecules of the invention are preferably organic. The term "nutraceutical" includes dietary supplements having health benefits in plants and animals, particularly humans. Examples of such molecules are vitamins, antioxidants, and also certain lipids (e.g., polyunsaturated fatty acids).
The biosynthesis of these molecules in organisms capable of producing them, such as bacteria, has been largely characterized (Ullman's Encyclopedia of Industrial Chemistry, "Vitamins" vol. A27, p. 443-6I3, VCH: Weinheim, 1996; Michal, G.
(1999) Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology, John Wiley & Sons; Ong, A.S., Niki, E. & Packer, L. (1995) "Nutrition, Lipids, Health, and Disease" Proceedings of the UNESCO/Confederation of Scientific and Technological Associations in Malaysia, and the Society for Free Radical Research - Asia, held Sept.
1-3, 1994 at Penang, Malaysia, AOCS Press: Champaign, IL X, 374 S).
Thiamin (vitamin B1) is produced by the chemical coupling of pyrimidine and thiazole moieties. Riboflavin (vitamin Bz) is synthesized from guanosine-5'-triphosphate (GTP) and ribose-5'-phosphate. Riboflavin, in turn, is utilized for the synthesis of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). The family of compounds collectively termed 'vitamin B6' (e.g., pyridoxine, pyridoxamine, pyridoxa-5'-phosphate, and the conunercially used pyridoxin hydrochloride) are all derivatives of the common structural unit, 5-hydroxy-6-methylpyridine. Pantothenate (pantothenic acid, (R)-(+)-N-(2,4-dihydroxy-3,3-dimethyl-l-oxobutyl)-o-alanine) can be produced either by chemical synthesis or by fermentation. The final steps in pantothenate biosynthesis consist of the ATP-driven condensation of P-alanine and pantoic acid. The enzymes responsible for the biosynthesis steps for the conversion to pantoic acid, to (i-alanine and for the condensation to panthotenic acid are known. The metabolically active form of pantothenate is Coenzyme A, for which the biosynthesis proceeds in 5 enzymatic steps. Pantothenate, pyridoxal-5'-phosphate, cysteine and ATP are the precursors of Coenzyme A. These enzymes not only catalyze the formation of panthothante, but also the production of (R)-pantoic acid, (R)-pantolacton, (R)-panthenol (provitamin B5), pantetheine (and its derivatives) and coenzyme A.
Biotin biosynthesis from the precursor molecule pimeloyl-CoA in microorganisms has been studied in detail and several of the genes involved have been identified. Many of the corresponding proteins have been found to also be involved in Fe-cluster synthesis and are members of the nifS class of proteins. Lipoic acid is derived from octanoic acid, and serves as a coenzyme in energy metabolism, where it becomes part of the pyruvate dehydrogenase complex and the a-ketoglutarate dehydrogenase complex. The folates are a group of substances which are all derivatives of folic acid, which is turn is derived from L-glutamic acid, p-amino-benzoic acid and 6-methylpterin. The biosynthesis of folic acid and its derivatives, starting from the metabolism intermediates guanosine-5'-triphosphate (GTP), L-glutamic acid and p-amino-benzoic acid has been studied in detail in certain microorganisms.
Corrinoids (such as the cobalamines and particularly vitamin B12) and porphyrines belong to a group of chemicals characterized by a tetrapyrole ring system.
The biosynthesis of vitamin B12 is sufficiently complex that it has not yet been completely characterized, but many of the enzymes and substrates involved are now known. Nicotinic acid (nicotinate), and nicotinamide are pyridine derivatives which are also termed 'niacin'. Niacin is the precursor of the important coenzymes NAD
(nicotinamide adenine dinucleotide) and NADP (nicotinamide adenine dinucleotide phosphate) and their reduced forms.
The large-scale production of these compounds has largely relied on cell-free chemical syntheses, though some of these chemicals have also been produced by large-scale culture of microorganisms, such as riboflavin, Vitamin B6, pantothenate, and biotin. Only Vitamin B12 is produced solely by fermentation, due to the complexity of its synthesis. In vitro methodologies require significant inputs of materials and time, often at great cost.

C. Purine, Pyrimidine, Nucleoside and Nucleotide Metabolism and Uses Purine and pyrimidine metabolism genes and their corresponding proteins are important targets for the therapy of tumor diseases and viral infections. The language "purine" or "pyrimidine" includes the nitrogenous bases which are constituents of nucleic acids, co-enzymes, and nucleotides. The term "nucleotide" includes the basic structural units of nucleic acid molecules, which are comprised of a nitrogenous base, a pentose sugar (in the case of RNA, the sugar is ribose; in the case of DNA, the sugar is D-deoxyribose), and phosphoric acid. The language "nucleoside" includes molecules which serve as precursors to nucleotides, but which are lacking the phosphoric acid moiety that nucleotides possess. By inhibiting the biosynthesis of these molecules, or their mobilization to form nucleic acid molecules, it is possible to inhibit RNA and DNA
synthesis; by inhibiting this activity in a fashion targeted to cancerous cells, the ability of tumor cells to divide and replicate may be inhibited. Additionally, there are nucleotides which do not form nucleic acid molecules, but rather serve as energy stores (i.e., AMP) or as coenzymes (i.e., FAD and NAD).
Several publications have described the use of these chemicals for these medical indications, by influencing purine and/or pyrimidine metabolism (e.g.
Christopherson, R.I. and Lyons, S.D. (1990) "Potent inhibitors of de novo pyrimidine and purine biosynthesis as chemotherapeutic agents." Med. Res. Reviews 10: 505-548).
Studies of enzymes involved in purine and pyrimidine metabolism have been focused on the development of new drugs which can be used, for example, as immunosuppressants or anti-proliferants (Smith, J.L., (1995) "Enzymes in nucleotide synthesis."
Curr. Opin.
Struct. Biol. 5: 752-757; (1995) Biochem Soc. Transact. 23: 877-902). However, purine and pyrimidine bases, nucleosides and nucleotides have other utilities: as intermediates in the biosynthesis of several fine chemicals (e.g., thiamine, S-adenosyl-methionine, folates, or riboflavin), as energy carriers for the cell (e.g., ATP or GTP), and for chemicals themselves, commonly used as flavor enhancers (e.g., IMP or GMP) or for several medicinal applications (see, for example, Kuninaka, A. (1996) Nucleotides and Related Compounds in Biotechnology vol. 6, Rehm et al., eds. VCH: Weinheim, p.

612). Also, enzymes involved in purine, pyrimidine, nucleoside, or nucleotide metabolism are increasingly serving as targets against which chemicals for crop protection, including fungicides, herbicides and insecticides, are developed.
The metabolism of these compounds in bacteria has been characterized (for reviews see, for example, Zalkin, H. and Dixon, J.E. (1992) "de novo purine nucleotide biosynthesis", in: Progress in Nucleic Acid Research and Molecular Biology, vol. 42, Academic Press:, p. 259-287; and Michal, G. (1999) "Nucleotides and Nucleosides", Chapter 8 in: Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology, Wiley: New York). Purine metabolism has been the subject of intensive research, and is essential to the normal functioning of the cell. Impaired purine metabolism in higher animals can cause severe disease, such as gout. Purine nucleotides are synthesized from ribose-5-phosphate, in a series of steps through the intermediate compound inosine-5'-phosphate (IMP), resulting in the production of guanosine-5'-monophosphate (GMP) or adenosine-5'-monophosphate (AMP), from which the triphosphate forms utilized as nucleotides are readily formed. These compounds are also utilized as energy stores, so their degradation provides energy for many different biochemical processes in the cell.
Pyrimidine biosynthesis proceeds by the formation of uridine-5'-monophosphate (UMP) from ribose-5-phosphate. UMP, in turn, is converted to cytidine-5'-triphosphate (CTP).
The deoxy- forms of all of these nucleotides are produced in a one step reduction reaction from the diphosphate ribose form of the nucleotide to the diphosphate deoxyribose form of the nucleotide. Upon phosphorylation, these molecules are able to participate in DNA synthesis.

D. Trehalose Metabolism and Uses Trehalose consists of two glucose molecules, bound in a, a-l,l linkage. It is commonly used in the food industry as a sweetener, an additive for dried or frozen foods, and in beverages. However, it also has applications in the pharmaceutical, cosmetics and biotechnology industries (see, for example, Nishimoto et al., (1998) U.S.
Patent No. 5,759,610; Singer, M.A. and Lindquist, S. (1998) Trends Biotech.
16: 460-467; Paiva, C.L.A. and Panek, A.D. (1996) Biotech. Ann. Rev. 2: 293-314; and Shiosaka, M. (1997) J. Japan 172: 97-102). Trehalose is produced by enzymes from many microorganisms and is naturally released into the surrounding medium, from which it can be collected using methods known in the art.

II. Elements and Methods of the Invention The present invention is based, at least in part, on the discovery of novel molecules, referred to herein as MP nucleic acid and protein molecules, which play a role in or function in one or more cellular metabolic pathways. In one embodiment, the MP molecules catalyze an enzymatic reaction involving one or more amino acid, vitamin, cofactor, nutraceutical, nucleotide, nucleoside, or trehalose metabolic pathways. In a preferred embodiment, the activity of the MP molecules of the present invention in one or more C. glutamicum metabolic pathways for amino acids, vitamins, cofactors, nutraceuticals, nucleotides, nucleosides or trehalose has an impact on the production of a desired fine chemical by this organism. In a particularly preferred embodiment, the MP molecules of the invention are modulated in activity, such that the C. glutamicum metabolic pathways in which the MP proteins of the invention are involved are modulated in efficiency or output, which either directly or indirectly modulates the production or efficiency of production of a desired fine chemical by C.
glulamicum.
The language, "MP protein" or "MP polypeptide" includes proteins which play a role in, e.g., catalyze an enzymatic reaction, in one or more amino acid, vitamin, cofactor, nutraceutical, nucleotide, nucleoside or trehalose metabolic pathways.
Examples of MP proteins include those encoded by the MP genes set forth in Table 1 and by the odd-numbered SEQ ID NOs. The terms "MP gene" or "MP nucleic acid sequence" include nucleic acid sequences encoding an MP protein, which consist of a coding region and also corresponding untranslated 5' and 3' sequence regions.
Examples of MP genes include those set forth in Table 1. The terms "production" or "productivity" are art-recognized and include the concentration of the fermentation product (for example, the desired fine chemical) formed within a given time and a given fermentation volume (e.g., kg product per hour per liter). The term "efficiency of production" includes the time required for a particular level of production to be achieved (for example, how long it takes for the cell to attain a particular rate of output of a fine chemical). The term "yield" or "product/carbon yield" is art-recognized and includes the efficiency of the conversion of the carbon source into the product (i.e., fine chemical). This is generally written as, for example, kg product per kg carbon source.
By increasing the yield or production of the compound, the quantity of recovered molecules, or of useful recovered molecules of that compound in a given amount of culture over a given amount of time is increased. The terms "biosynthesis" or a "biosynthetic pathway" are art-recognized and include the synthesis of a compound, preferably an organic compound, by a cell from intermediate compounds in what may be a multistep and highly regulated process. The terms "degradation" or a' degradation pathway" are art-recognized and include the breakdown of a compound, preferably an organic compound, by a cell to degradation products (generally speaking, smaller or less complex molecules) in what may be a multistep and highly regulated process.
The language "metabolism" is art-recognized and includes the totality of the biochemical reactions that take place in an organism. The metabolism of a particular compound, then, (e.g., the metabolism of an amino acid such as glycine) comprises the overall biosynthetic, modification, and degradation pathways in the cell related to this compound.
In another embodiment, the MP molecules of the invention are capable of modulating the production of a desired molecule, such as a fine chemical, in a microorganism such as C. glutamicum. Using recombinant genetic techniques, one or more of the biosynthetic or degradative enzymes of the invention for amino acids, vitamins, cofactors, nutraceuticals, nucleotides, nucleosides, or trehalose may be manipulated such that its function is modulated. For example, a biosynthetic enzyme may be improved in efficiency, or its allosteric control region destroyed such that feedback inhibition of production of the compound is prevented. Similarly, a degradative enzyme may be deleted or modified by substitution, deletion, or addition such that its degradative activity is lessened for the desired compound without impairing the viability of the cell. In each case, the overall yield or rate of production of one of these desired fine chemicals may be increased.
It is also possible that such alterations in the protein and nucleotide molecules of the invention may improve the production of other fine chemicals besides the amino acids, vitamins, cofactors, nutraceuticals, nucleotides, nucleosides, and trehalose.
Metabolism of any one compound is necessarily intertwined with other biosynthetic and degradative pathways within the cell, and necessary cofactors, intermediates, or substrates in one pathway are likely supplied or limited by another such pathway.
Therefore, by modulating the activity of one or more of the proteins of the invention, the production or efficiency of activity of another fine chemical biosynthetic or degradative pathway may be impacted. For example, amino acids serve as the structural units of all proteins, yet may be present intracellularly in levels which are limiting for protein synthesis; therefore, by increasing the efficiency of production or the yields of one or more amino acids within the cell, proteins, such as biosynthetic or degradative proteins, may be more readily synthesized. Likewise, an alteration in a metabolic pathway enzyme such that a particular side reaction becomes more or less favored may result in the over- or under-production of one or more compounds which are utilized as intermediates or substrates for the production of a desired fine chemical.
The isolated nucleic acid sequences of the invention are contained within the genome of a Corynebacterium glutamicum strain available through the American Type Culture Collection, given designation ATCC 13032. The nucleotide sequence of the isolated C. glutamicum MP DNAs and the predicted amino acid sequences of the C.
glutamicum MP proteins are shown in the Sequence Listing as odd-numbered SEQ
ID
NOs and even-numbered SEQ ID NOs, respectively. Computational analyses were performed which classified and/or identified these nucleotide sequences as sequences which encode metabolic pathway proteins.
The present invention also pertains to proteins which have an amino acid sequence which is substantially homologous to an amino acid sequence of the invention (e.g., the sequence of an even-numbered SEQ ID NO of the Sequence Listing). As used herein, a protein which has an amino acid sequence which is substantially homologous to a selected amino acid sequence is least about 50% homologous to the selected amino acid sequence, e.g., the entire selected amino acid sequence. A protein which has an amino acid sequence which is substantially homologous to a selected amino acid sequence can also be least about 50-60%, preferably at least about 60-70%, and more preferably at least about 70-80%, 80-90%, or 90-95%, and most preferably at least about 96%, 97%, 98%, 99% or more homologous to the selected amino acid sequence.
The MP protein or a biologically active portion or fragment thereof of the invention can catalyze an enzymatic reaction in one or more amino acid, vitamin, cofactor, nutraceutical, nucleotide, nucleoside, or trehalose metabolic pathways, or have one or more of the activities set forth in Table 1.
Various aspects of the invention are described in further detail in the following subsections:
A. Isolated Nucleic Acid Molecules One aspect of the invention pertains to isolated nucleic acid molecules that encode MP polypeptides or biologically active portions thereof, as well as nucleic acid fragments sufficient for use as hybridization probes or primers for the identification or amplification of MP-encoding nucleic acid (e.g., MP DNA). As used herein, the term "nucleic acid molecule" is intended to include DNA molecules (e.g., cDNA or genomic DNA) and RNA molecules (e.g., mRNA) and analogs of the DNA or RNA generated using nucleotide analogs. This term also encompasses untranslated sequence located at both the 3' and 5' ends of the coding region of the gene: at least about 100 nucleotides of sequence upstream from the 5' end of the coding region and at least about nucleotides of sequence downstream from the 3'end of the coding region of the gene.
The nucleic acid molecule can be single-stranded or double-stranded, but preferably is double-stranded DNA. An "isolated" nucleic acid molecule is one which is separated from other nucleic acid molecules which are present in the natural source of the nucleic acid. Preferably, an "isolated" nucleic acid is free of sequences which naturally flank the nucleic acid (i.e., sequences located at the 5' and 3' ends of the nucleic acid) in the genomic DNA of the organism from which the nucleic acid is derived. For example, in various embodiments, the isolated MP nucleic acid molecule can contain less than about 5 kb, 4kb, 3kb, 2kb, 1 kb, 0.5 kb or 0.1 kb of nucleotide sequences which naturally flank the nucleic acid molecule in genomic DNA of the cell from which the nucleic acid is derived (e.g, a C. glutamicum cell). Moreover, an "isolated" nucleic acid molecule, such as a DNA molecule, can be substantially free of other cellular material, or culture medium when produced by recombinant techniques, or chemical precursors or other chemicals when chemically synthesized.
A nucleic acid molecule of the present invention, e.g., a nucleic acid molecule having a nucleotide sequence of an odd-numbered SEQ ID NO of the Sequence Listing, or a portion thereof, can be isolated using standard molecular biology techniques and the sequence information provided herein. For example, a C. glutamicum MP DNA can be isolated from a C. glutamicum library using all or portion of one of the odd-numbered SEQ ID NO sequences of the Sequence Listing as a hybridization probe and standard hybridization techniques (e.g., as described in Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989).
Moreover, a nucleic acid molecule encompassing all or a portion of one of the nucleic acid sequences of the invention (e.g., an odd-numbered SEQ ID NO:) can be isolated by the polymerase chain reaction using oligonucleotide primers designed based upon this sequence (e.g., a nucleic acid molecule encompassing all or a portion of one of the nucleic acid sequences of the invention (e.g., an odd-numbered SEQ ID NO of the Sequence Listing) can be isolated by the polymerase chain reaction using oligonucleotide primers designed based upon this same sequence). For example, mRNA
can be isolated from normal endothelial cells (e.g., by the guanidinium-thiocyanate extraction procedure of Chirgwin et al. (1979) Biochemistry 18: 5294-5299) and DNA
can be prepared using reverse transcriptase (e.g., Moloney MLV reverse transcriptase, available from GibcoBRL, Bethesda, MD; or AMV reverse transcriptase, available from Seikagaku America, Inc., St. Petersburg, FL). Synthetic oligonucleotide primers for polymerase chain reaction amplification can be designed based upon one of the nucleotide sequences shown in the Sequence Listing. A nucleic acid of the invention can be amplified using cDNA or, altematively, genomic DNA, as a template and appropriate oligonucleotide primers according to standard PCR amplification techniques. The nucleic acid so amplified can be cloned into an appropriate vector and characterized by DNA sequence analysis. Furthermore, oligonucleotides corresponding to an MP nucleotide sequence can be prepared by standard synthetic techniques, e.g., using an automated DNA synthesizer.
In a preferred embodiment, an isolated nucleic acid molecule of the invention comprises one of the nucleotide sequences shown in the Sequence Listing. The nucleic acid sequences of the invention, as set forth in the Sequence Listing, correspond to the Corynebacterium glutamicum MP DNAs of the invention. This DNA comprises sequences encoding MP proteins (i.e., the "coding region", indicated in each odd-numbered SEQ ID NO: sequence in the Sequence Listing), as well as 5' untranslated sequences and 3' untranslated sequences, also indicated in each odd-numbered SEQ ID
NO: in the Sequence Listing. Altematively, the nucleic acid molecule can comprise only the coding region of any of the nucleic acid sequences of the Sequence Listing.
For the purposes of this application, it will be understood that each of the nucleic acid and amino acid sequences set forth in the Sequence Listing has an identifying RXA, RXN, RXS, or RXC number having the designation "RXA", "RXN", "RXS", or "RXC"
followed by 5 digits (i.e., RXA00007, RXN00023, RXS00116, or RXC00128). Each of the nucleic acid sequences comprises up to three parts: a 5' upstream region, a coding region, and a downstream region. Each of these three regions is identified by the same RXA, RXN, RXS, or RXC designation to eliminate confusion. The recitation "one of the odd-numbered sequences of the Sequence Listing", then, refers to any of the nucleic acid sequences in the Sequence Listing, which may also be distinguished by their differing RXA, RXN, RXS, or RXC designations. The coding region of each of these sequences is translated into a corresponding amino acid sequence, which is also set forth in the Sequence Listing, as an even-numbered SEQ ID NO: immediately following the corresponding nucleic acid sequence. For example, the coding region for RXA02229 is set forth in SEQ ID NO:I, while the amino acid sequence which it encodes is set forth as SEQ ID NO:2. The sequences of the nucleic acid molecules of the invention are identified by the same RXA, RXN, RXS, or RXC designations as the amino acid molecules which they encode, such that they can be readily correlated. For example, the amino acid sequences designated RXA02229, RX00351, RXS02970, and RXC02390 are translations of the coding regions of the nucleotide sequences of nucleic acid molecules RXA02229, RX00351, RXS02970, and RXC02390, respectively. The correspondence between the RXA, RXN, RXS, and RXC nucleotide and amino acid sequences of the invention and their assigned SEQ ID NOs is set forth in Table 1.
Several of the genes of the invention are "F-designated genes". An F-designated gene includes those genes set forth in Table I which have an 'F' in front of the RXA, RXN, RXS, or RXC designation. For example, SEQ ID NO:5, designated, as indicated on Table 1, as "F RXA01009", is an F-designated gene, as are SEQ ID NOs: 73, 75, and 77 (designated on Table I as "F RXA00007", "F RXA00364", and "F RXA00367", respectively).

In one embodiment, the nucleic acid molecules of the present invention are not intended to include C. glutamicum those compiled in Table 2. In the case of the dapD
gene, a sequence for this gene was published in Wehrmann, A., et al. (1998) J.
Bacteriol. 180(12): 3159-3165. However, the sequence obtained by the inventors of the present application is significantly longer than the published version. It is believed that the published version relied on an incorrect start codon, and thus represents only a fragment of the actual coding region.
In another preferred embodiment, an isolated nucleic acid molecule of the invention comprises a nucleic acid molecule which is a complement of one of the nucleotide sequences of the invention (e.g., a sequence of an odd-numbered SEQ
ID
NO: of the Sequence Listing), or a portion thereof. A nucleic acid molecule which is complementary to one of the nucleotide sequences of the invention is one which is sufficiently complementary to one of the nucleotide sequences shown in the Sequence Listing (e.g., the sequence of an odd-numbered SEQ ID NO:) such that it can hybridize to one of the nucleotide sequences of the invention, thereby forming a stable duplex.
In still another preferred embodiment, an isolated nucleic acid molecule of the invention comprises a nucleotide sequence which is at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, or 60%, preferably at least about 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, or 70%%, more preferably at least about 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, or 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, or 90%, or 91%, 92%, 93%, 94%, and even more preferably at least about 95%, 96%, 97%, 98%, 99% or more homologous to a nucleotide sequence of the invention (e.g., a sequence of an odd-numbered SEQ ID NO: of the Sequence Listing), or a portion thereof. Ranges and identity values intermediate to the above-recited ranges, (e.g., 70-90% identical or 80-95% identical) are also intended to be encompassed by the present invention. For example, ranges of identity values using a combination of any of the above values recited as upper and/or lower limits are intended to be included. In an additional preferred embodiment, an isolated nucleic acid molecule of the invention comprises a nucleotide sequence which hybridizes, e.g., hybridizes under stringent conditions, to one of the nucleotide sequences of the invention, or a portion thereof.
Moreover, the nucleic acid molecule of the invention can comprise only a portion of the coding region of the sequence of one of the odd-numbered SEQ ID
NOs of the Sequence Listing, for example a fragment which can be used as a probe or primer or a fragment encoding a biologically active portion of an MP protein. The nucleotide sequences determined from the cloning of the MP genes from C. glutamicum allows for the generation of probes and primers designed for use in identifying and/or cloning MP
homologues in other cell types and organisms, as well as MP homologues from other Corynebacteria or related species. The probe/primer typically comprises substantially purified oligonucleotide. The oligonucleotide typically comprises a region of nucleotide sequence that hybridizes under stringent conditions to at least about 12, preferably about 25, more preferably about 40, 50 or 75 consecutive nucleotides of a sense strand of one of the nucleotide sequences of the invention (e.g., a sequence of one of the odd-numbered SEQ ID NOs of the Sequence Listing), an anti-sense sequence of one of these sequences, or naturally occurring mutants thereof. Primers based on a nucleotide sequence of the invention can be used in PCR reactions to clone MP homologues.
Probes based on the MP nucleotide sequences can be used to detect transcripts or genomic sequences encoding the same or homologous proteins. In preferred embodiments, the probe further comprises a label group attached thereto, e.g.
the label group can be a radioisotope, a fluorescent compound, an enzyme, or an enzyme co-factor. Such probes can be used as a part of a diagnostic test kit for identifying cells which misexpress an MP protein, such as by measuring a level of an MP-encoding nucleic acid in a sample of cells from a subject e.g., detecting MP mRNA
levels or determining whether a genomic MP gene has been mutated or deleted.
In one embodiment, the nucleic acid molecule of the invention encodes a protein or portion thereof which includes an amino acid sequence which is sufficiently homologous to an amino acid sequence of the invention (e.g., a sequence of an even-numbered SEQ ID NO of the Sequence Listing) such that the protein or portion thereof maintains the ability to catalyze an enzymatic reaction in an amino acid, vitamin, cofactor, nutraceutical, nucleotide, nucleoside, or trehalose metabolic pathway. As used herein, the language "sufficiently homologous" refers to proteins or portions thereof which have amino acid sequences which include a minimum number of identical or equivalent (e.g., an amino acid residue which has a similar side chain as an amino acid residue in a sequence of one of the even-numbered SEQ ID NOs of the Sequence Listing) amino acid residues to an amino acid sequence of the invention such that the protein or portion thereof is able to catalyze an enzymatic reaction in a C.
glutamicum amino acid, vitamin, cofactor, nutraceutical, nucleotide, nucleoside or trehalose metabolic pathway. Protein members of such metabolic pathways, as described herein, function to catalyze the biosynthesis or degradation of one or more of: amino acids, vitamins, cofactors, nutraceuticals, nucleotides, nucleosides, or trehalose.
Examples of such activities are also described herein. Thus, "the function of an MP
protein"
contributes to the overall functioning of one or more such metabolic pathway and contributes, either directly or indirectly, to the yield, production, and/or efficiency of production of one or more fine chemicals. Examples of MP protein activities are set forth in Table 1.
In another embodiment, the protein is at least about 50-60%, preferably at least about 60-70%, and more preferably at least about 70-80%, 80-90%, 90-95%, and most preferably at least about 96%, 97%, 98%, 99% or more homologous to an entire amino acid sequence of the invention (e.g., a sequence of an even-numbered SEQ ID
NO: of the Sequence Listing).
Portions of proteins encoded by the MP nucleic acid molecules of the invention are preferably biologically active portions of one of the MP proteins. As used herein, the term "biologically active portion of an MP protein" is intended to include a portion, e.g_, a domain/motif, of an MP protein that catalyzes an enzymatic reaction in one or more C. glutamicum amino acid, vitamin, cofactor, nutraceutical, nucleotide, nucleoside, or trehalose metabolic pathways, or has an activity as set forth in Table 1.
To determine whether an MP protein or a biologically active portion thereof can catalyze an enzymatic reaction in an amino acid, vitamin, cofactor, nutraceutical, nucleotide, nucleoside, or trehalose metabolic pathway, an assay of enzymatic activity may be performed.
Such assay methods are well known to those of ordinary skill in the art, as detailed in Example 8 of the Exemplification.
Additional nucleic acid fragments encoding biologically active portions of an MP protein can be prepared by isolating a portion of one of the amino acid sequences of the invention (e.g., a sequence of an even-numbered SEQ ID NO: of the Sequence Listing), expressing the encoded portion of the MP protein or peptide (e.g., by recombinant expression in vitro) and assessing the activity of the encoded portion of the MP protein or peptide.

The invention further encompasses nucleic acid molecules that differ from one of the nucleotide sequences of the invention (e.g., a sequence of an odd-numbered SEQ ID
NO: of the Sequence Listing) (and portions thereof) due to degeneracy of the genetic code and thus encode the same MP protein as that encoded by the nucleotide sequences of the invention. In another embodiment, an isolated nucleic acid molecule of the invention has a nucleotide sequence encoding a protein having an amino acid sequence shown in the Sequence Listing (e.g., an even-numbered SEQ ID NO:). In a still further embodiment, the nucleic acid molecule of the invention encodes a full length C.
glutarnicum protein which is substantially homologous to an amino acid sequence of the invention (encoded by an open reading frame shown in an odd-numbered SEQ ID
NO:
of the Sequence Listing).
It will be understood by one of ordinary skill in the art that in one embodiment the sequences of the invention are not meant to include the sequences of the prior art, such as those Genbank sequences set forth in Tables 2 or 4 which were available prior to the present invention. In one embodiment, the invention includes nucleotide and amino acid sequences having a percent identity to a nucleotide or amino acid sequence of the invention which is greater than that of a sequence of the prior art (e. g. , a Genbank sequence (or the protein encoded by such a sequence) set forth in Tables 2 or 4). For example, the invention includes a nucleotide sequence which is greater than and/or at least 40% identical to the nucleotide sequence designated RXA00115 (SEQ ID
NO: 185), a nucleotide sequence which is greater than and/or at least %
identical to the nucleotide sequence designated RXA00131 (SEQ ID NO:99 1), and a nucleotide sequence which is greater than and/or at least 39% identical to the nucleotide sequence designated RXA00219 (SEQ ID NO:345). One of ordinary skill in the art would be able to calculate the lower threshold of percent identity for any given sequence of the invention by examining the GAP-calculated percent identity scores set forth in Table 4 for each of the three top hits for the given sequence, and by subtracting the highest GAP-calculated percent identity from 100 percent. One of ordinary skill in the art will also appreciate that nucleic acid and amino acid sequences having percent identities greater than the lower threshold so calculated (e.g., at least 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, or 60%, preferably at least about 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, or 70%, more preferably at least about 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, or 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, or 90%, or 91%, 92%, 93%, 94%, and even more preferably at least about 95%, 96%, 97%, 98%, 99% or more identical) are also encompassed by the invention.
In addition to the C. glutamicum MP nucleotide sequences set forth in the Sequence Listing as odd-numbered SEQ ID NOs, it will be appreciated by one of ordinary skill in the art that DNA sequence polymorphisms that lead to changes in the amino acid sequences of MP proteins may exist within a population (e.g,, the C.
glutamicum population). Such genetic polymorphism in the MP gene may exist among individuals within a population due to natural variation. As used herein, the terms "gene" and "recombinant gene" refer to nucleic acid molecules comprising an open reading frame encoding an MP protein, preferably a C. glutamicum MP protein.
Such natural variations can typically result in 1-5% variance in the nucleotide sequence of the MP gene. Any and all such nucleotide variations and resulting amino acid polymorphisms in MP that are the result of natural variation and that do not alter the functional activity of MP proteins are intended to be within the scope of the invention.
Nucleic acid molecules corresponding to natural variants and non-C. glutamicum homologues of the C. glutamicum MP DNA of the invention can be isolated based on their homology to the C. glutamicum MP nucleic acid disclosed herein using the C.
glutamicum DNA, or a portion thereof, as a hybridization probe according to standard hybridization techniques under stringent hybridization conditions.
Accordingly, in another embodiment, an isolated nucleic acid molecule of the invention is at least 15 nucleotides in length and hybridizes under stringent conditions to the nucleic acid molecule comprising a nucleotide sequence of an odd-numbered SEQ ID NO: of the Sequence Listing. In other embodiments, the nucleic acid is at least 30, 50, 100, 250 or more nucleotides in length. As used herein, the term "hybridizes under stringent conditions" is intended to describe conditions for hybridization and washing under which nucleotide sequences at least 60% homologous to each other typically remain hybridized to each other. Preferably, the conditions are such that sequences at least about 65%, more preferably at least about 70%, and even more preferably at least about 75% or more homologous to each other typically remain hybridized to each other. Such stringent conditions are known to one of ordinary skill in the art and can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6.

A preferred, non-limiting example of stringent hybridization conditions are hybridization in 6X sodium chloride/sodium citrate (SSC) at about 45 C, followed by one or more washes in 0.2 X SSC, 0.1% SDS at 50-65 C. Preferably, an isolated nucleic acid molecule of the invention that hybridizes under stringent conditions to a nucleotide sequence of the invention corresponds to a naturally-occurring nucleic acid molecule. As used herein, a "naturally-occurring" nucleic acid molecule refers to an RNA or DNA molecule having a nucleotide sequence that occurs in nature (e.g., encodes a natural protein). In one embodiment, the nucleic acid encodes a natural C.
glutamicum MP protein.
In addition to naturally-occurring variants of the MP sequence that may exist in the population, one of ordinary skill in the art will further appreciate that changes can be introduced by mutation into a nucleotide sequence of the invention, thereby leading to changes in the amino acid sequence of the encoded MP protein, without altering the functional ability of the MP protein. For example, nucleotide substitutions leading to amino acid substitutions at "non-essential" amino acid residues can be made in a nucleotide sequence of the invention. A "non-essential" amino acid residue is a residue that can be altered from the wild-type sequence of one of the MP proteins (e.g., an even-numbered SEQ ID NO: of the Sequence Listing) without altering the activity of said MP
protein, whereas an "essential" amino acid residue is required for MP protein activity.
Other amino acid residues, however, (e.g., those that are not conserved or only semi-conserved in the domain having MP activity) may not be essential for activity and thus are likely to be amenable to alteration without altering MP activity.
Accordingly, another aspect of the invention pertains to nucleic acid molecules encoding MP proteins that contain changes in amino acid residues that are not essential for MP activity. Such MP proteins differ in amino acid sequence from a sequence of an even-numbered SEQ ID NO: of the Sequence Listing yet retain at least one of the MP
activities described herein. In one embodiment, the isolated nucleic acid molecule comprises a nucleotide sequence encoding a protein, wherein the protein comprises an amino acid sequence at least about 50% homologous to an amino acid sequence of the invention and is capable of catalyzing an enzymatic reaction in an amino acid, vitamin, cofactor, nutraceutical, nucleotide, nucleoside, or trehalose metabolic pathway, or has one or more activities set forth in Table 1. Preferably, the protein encoded by the nucleic acid molecule is at least about 50-60% homologous to the amino acid sequence of one of the odd-numbered SEQ ID NOs of the Sequence Listing, more preferably at least about 60-70% homologous to one of these sequences, even more preferably at least about 70-80%, 80-90%, 90-95% homologous to one of these sequences, and most preferably at least about 96%, 97%, 98%, or 99% homologous to one of the amino acid sequences of the invention.
To determine the percent homology of two amino acid sequences (e.g., one of the amino acid sequences of the invention and a mutant form thereof) or of two nucleic acids, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in the sequence of one protein or nucleic acid for optimal alignment with the other protein or nucleic acid). The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in one sequence (e.g., one of the amino acid sequences of the invention) is occupied by the same amino acid residue or nucleotide as the corresponding position in the other sequence (e.g., a mutant form of the amino acid sequence), then the molecules are homologous at that position (i.e., as used herein amino acid or nucleic acid "homology"
is equivalent to amino acid or nucleic acid "identity"). The percent homology between the two sequences is a function of the number of identical positions shared by the sequences (i. e. ,% homology =# of identical positions/total # of positions x 100).
An isolated nucleic acid molecule encoding an MP protein homologous to a protein sequence of the invention (e.g., a sequence of an even-numbered SEQ ID
NO: of the Sequence Listing) can be created by introducing one or more nucleotide substitutions, additions or deletions into a nucleotide sequence of the invention such that one or more amino acid substitutions, additions or deletions are introduced into the encoded protein. Mutations can be introduced into one of the nucleotide sequences of the invention by standard techniques, such as site-directed mutagenesis and PCR-mediated mutagenesis. Preferably, conservative amino acid substitutions are made at one or more predicted non-essential amino acid residues. A "conservative amino acid substitution" is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine). Thus, a predicted nonessential amino acid residue in an MP protein is preferably replaced with another amino acid residue from the same side chain family. Alternatively, in another embodiment, mutations can be introduced randomly along all or part of an MP coding sequence, such as by saturation mutagenesis, and the resultant mutants can be screened for an MP activity described herein to identify mutants that retain MP activity. Following mutagenesis of the nucleotide sequence of one of the odd-numbered SEQ ID NOs of the Sequence Listing, the encoded protein can be expressed recombinantly and the activity of the protein can be determined using, for example, assays described herein (see Example 8 of the Exemplification).
In addition to the nucleic acid molecules encoding MP proteins described above, another aspect of the invention pertains to isolated nucleic acid molecules which are antisense thereto. An "antisense" nucleic acid comprises a nucleotide sequence which is complementary to a "sense" nucleic acid encoding a protein, e.g., complementary to the coding strand of a double-stranded DNA molecule or complementary to an mRNA
sequence. Accordingly, an antisense nucleic acid can hydrogen bond to a sense nucleic acid. The antisense nucleic acid can be complementary to an entire MP coding strand, or to only a portion thereof. In one embodiment, an antisense nucleic acid molecule is antisense to a "coding region" of the coding strand of a nucleotide sequence encoding an MP protein. The term "coding region" refers to the region of the nucleotide sequence comprising codons which are translated into amino acid residues (e.g., the entire coding region of SEQ ID NO. 1(RXA02229) comprises nucleotides 1 to 825). In another embodiment, the antisense nucleic acid molecule is antisense to a "noncoding region" of the coding strand of a nucleotide sequence encoding MP. The term "noncoding region"
refers to 5' and 3' sequences which flank the coding region that are not translated into amino acids (i.e., also referred to as 5' and 3' untranslated regions).
Given the coding strand sequences encoding MP disclosed herein (e.g., the sequences set forth as odd-numbered SEQ ID NOs in the Sequence Listing), antisense nucleic acids of the invention can be designed according to the rules of Watson and Crick base pairing. The antisense nucleic acid molecule can be complementary to the entire coding region of MP mRNA, but more preferably is an oligonucleotide which is antisense to only a portion of the coding or noncoding region of MP mRNA. For example, the antisense oligonucleotide can be complementary to the region surrounding the translation start site of MP mRNA. An antisense oligonucleotide can be, for example, about 5, 10, 15, 20, 25, 30, 35, 40, 45 or 50 nucleotides in length.
An antisense nucleic acid of the invention can be constructed using chemical synthesis and enzymatic ligation reactions using procedures known in the art. For example, an antisense nucleic acid (e.g., an antisense oligonucleotide) can be chemically synthesized using naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecules or to increase the physical stability of the duplex formed between the antisense and sense nucleic acids, e.g., phosphorothioate derivatives and acridine substituted nucleotides can be used. Examples of modified nucleotides which can be used to generate the antisense nucleic acid include 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl) uracil, 5-carboxymethylaminomethyl-2-thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine, 7-methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine, 5'-methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid (v), wybutoxosine, pseudouracil, queosine, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid (v), 5-methyl-2-thiouracil, 3-(3-amino-3-carboxypropyl) uracil, (acp3)w, and 2,6-diaminopurine. Alternatively, the antisense nucleic acid can be produced biologically using an expression vector into which a nucleic acid has been subcloned in an antisense orientation (i.e., RNA
transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest, described further in the following subsection).

The antisense nucleic acid molecules of the invention are typically administered to a cell or generated in situ such that they hybridize with or bind to cellular mRNA
and/or genomic DNA encoding an MCT protein to thereby inhibit expression of the protein, e.g., by inhibiting transcription and/or translation. The hybridization can be by conventional nucleotide complementarity to form a stable duplex, or, for example, in the case of an antisense nucleic acid molecule which binds to DNA duplexes, through specific interactions in the major groove of the double helix. The antisense molecule can be modified such that it specifically binds to a receptor or an antigen expressed on a selected cell surface, e.g., by linking the antisense nucleic acid molecule to a peptide or an antibody which binds to a cell surface receptor or antigen. The antisense nucleic acid molecule can also be delivered to cells using the vectors described herein. To achieve sufficient intracellular concentrations of the antisense molecules, vector constructs in which the antisense nucleic acid molecule is placed under the control of a strong prokaryotic, viral, or eukaryotic promoter are preferred.
In yet another embodiment, the antisense nucleic acid molecule of the invention is an a-anomeric nucleic acid molecule. An a-anomeric nucleic acid molecule fomns specific double-stranded hybrids with complementary RNA in which, contrary to the usual 0-units, the strands run parallel to each other (Gaultier et al. (1987) Nucleic Acids.
Res. 15:6625-6641). The antisense nucleic acid molecule can also comprise a 2'-o-methylribonucleotide (Inoue et al. (1987) Nucleic Acids Res. 15:6131-6148) or a chimeric RNA-DNA analogue (Inoue et al. (1987) FEBS Lett. 215:327-330).
In still another embodiment, an antisense nucleic acid of the invention is a ribozyme. Ribozymes are catalytic RNA molecules with ribonuclease activity which are capable of cleaving a single-stranded nucleic acid, such as an mRNA, to which they have a complementary region. Thus, ribozymes (e.g., hanunerhead ribozymes (described in Haselhoff and Gerlach (1988) Nature 334:585-591)) can be used to catalytically cleave MP mRNA transcripts to thereby inhibit translation of MP
mRNA.
A ribozyme having specificity for an MP-encoding nucleic acid can be designed based upon the nucleotide sequence of an MP DNA disclosed herein (i.e., SEQ ID NO: 1 (RXA02229). For example, a derivative of a Tetrahymena L-19 IVS RNA can be constructed in which the nucleotide sequence of the active site is complementary to the nucleotide sequence to be cleaved in an MP-encoding mRNA. See, e.g., Cech et al.

U.S. Patent No. 4,987,071 and Cech et al. U.S. Patent No. 5,116,742.
Altematively, MP
mRNA can be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules. See, e.g., Bartel, D. and Szostak, J.W. (1993) Science 261:1411-1418.
Alternatively, MP gene expression can be inhibited by targeting nucleotide sequences complementary to the regulatory region of an MP nucleotide sequence (e.g., an MP promoter and/or enhancers) to form triple helical structures that prevent transcription of an MP gene in target cells. See generally, Helene, C. (1991) Anticancer Drug Des. 6(6):569-84; Helene, C. et al. (1992) Ann. N. Y. Acad. Sci. 660:27-36; and Maher, L.J. (1992) Bioassays 14(12):807-15.

B. Recombinant Expression Vectors and Host Cells Another aspect of the invention pertains to vectors, preferably expression vectors, containing a nucleic acid encoding an MP protein (or a portion thereof). As used herein, the term "vector" refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. One type of vector is a "plasmid", which refers to a circular double stranded DNA loop into which additional DNA
segments can be ligated. Another type of vector is a viral vector, wherein additional DNA segments can be ligated into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non-episomal mammalian vectors) are integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. Moreover, certain vectors are capable of directing the expression of genes to which they are operatively linked. Such vectors are referred to herein as "expression vectors". In general, expression vectors of utility in recombinant DNA
techniques are often in the form of plasmids. In the present specification, "plasmid" and "vector" can be used interchangeably as the plasmid is the most commonly used form of vector.
However, the invention is intended to include such other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses), which serve equivalent functions.

The recombinant expression vectors of the invention comprise a nucleic acid of the invention in a form suitable for expression of the nucleic acid in a host cell, which means that the recombinant expression vectors include one or more regulatory sequences, selected on the basis of the host cells to be used for expression, which is operatively linked to the nucleic acid sequence to be expressed. Within a recombinant expression vector, "operably linked" is intended to mean that the nucleotide sequence of interest is linked to the regulatory sequence(s) in a manner which allows for expression of the nucleotide sequence (e.g., in an in vitro transcription/translation system or in a host cell when the vector is introduced into the host cell). The term "regulatory sequence" is intended to include promoters, repressor binding sites, activator binding sites, enhancers and other expression control elements (e.g., terminators, polyadenylation signals, or other elements of mRNA secondary structure). Such regulatory sequences are described, for example, in Goeddel; Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, CA (1990).
Regulatory sequences include those which direct constitutive expression of a nucleotide sequence in many types of host cell and those which direct expression of the nucleotide sequence only in certain host cells. Preferred regulatory sequences are, for example, promoters such as cos-, tac-, trp-, tet-, trp-tet-, lpp-, lac-, ]pp-lac-, lacI9-, T7-, T5-, T3-, gal-, trc-, ara-, SP6-, amy, SP02, X-PR- or ?, PL, which are used preferably in bacteria.
Additional regulatory sequences are, for example, promoters from yeasts and fungi, such as ADC1, MFa, AC, P-60, CYC1, GAPDH, TEF, rp28, ADH, promoters from plants such as CaMV/35S, SSU, OCS, lib4, usp, STLS1, B33, nos or ubiquitin- or phaseolin-promoters. It is also possible to use artificial promoters. It will be appreciated by one of ordinary skill in the art that the design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of protein desired, etc. The expression vectors of the invention can be introduced into host cells to thereby produce proteins or peptides, including fusion proteins or peptides, encoded by nucleic acids as described herein (e.g., MP proteins, mutant forms of MP
proteins, fusion proteins, etc.).
The recombinant expression vectors of the invention can be designed for expression of MP proteins in prokaryotic or eukaryotic cells. For example, MP
genes can be expressed in bacterial cells such as C. glutamicum, insect cells (using baculovirus expression vectors), yeast and other fungal cells (see Romanos, M.A. et al.
(1992) "Foreign gene expression in yeast: a review", Yeast 8: 423-488; van den Hondel, C.A.M.J.J. et al. (1991) "Heterologous gene expression in filamentous fungi"
in: More Gene Manipulations in Fungi, J.W. Bennet & L.L. Lasure, eds., p. 396-428:
Academic Press: San Diego; and van den Hondel, C.A.M.J.J. & Punt, P.J. (1991) "Gene transfer systems and vector development for filamentous fungi, in: Applied Molecular Genetics of Fungi, Peberdy, J.F. e1 al., eds., p. 1-28, Cambridge University Press:
Cambridge), algae and multicellular plant cells (see Schmidt, R. and Willmitzer, L. (1988) High efficiency Agrobacteriurn tumefaciens -mediated transformation of Arabidopsis thaliana leaf and cotyledon explants" Plant Cell Rep.: 583-586), or mammalian cells.
Suitable host cells are discussed further in Goeddel, Gene Expression Technology:
Methods in Enzymology 185, Academic Press, San Diego, CA (1990).
Alternatively, the recombinant expression vector can be transcribed and translated in vitro, for example using T7 promoter regulatory sequences and T7 polymerase.
Expression of proteins in prokaryotes is most often carried out with vectors containing constitutive or inducible promoters directing the expression of either fusion or non-fusion proteins. Fusion vectors add a number of amino acids to a protein encoded therein, usually to the amino terminus of the recombinant protein but also to the C-terminus or fused within suitable regions in the proteins. Such fusion vectors typically serve three purposes: 1) to increase expression of recombinant protein; 2) to increase the solubility of the recombinant protein; and 3) to aid in the purification of the recombinant protein by acting as a ligand in affinity purification. Often, in fusion expression vectors, a proteolytic cleavage site is introduced at the junction of the fusion moiety and the recombinant protein to enable separation of the recombinant protein from the fusion moiety subsequent to purification of the fusion protein. Such enzymes, and their cognate recognition sequences, include Factor Xa, thrombin and enterokinase.
Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith, D.B. and Johnson, K.S. (1988) Gene 67:31-40), pMAL (New England Biolabs, Beverly, MA) and pRIT5 (Pharmacia, Piscataway, NJ) which fuse glutathione S-transferase (GST), maltose E binding protein, or protein A, respectively, to the target recombinant protein. In one embodiment, the coding sequence of the MP protein is cloned into a pGEX expression vector to create a vector encoding a fusion protein comprising, from the N-terminus to the C-terminus, GST-thrombin cleavage site-X protein. The fusion protein can be purified by affinity chromatography using glutathione-agarose resin.
Recombinant MP protein unfused to GST can be recovered by cleavage of the fusion protein with thrombin.
Examples of suitable inducible non-fusion E. coli expression vectors include pTrc (Amann et al., (1988) Gene 69:301-315) pLG338, pACYC184, pBR322, pUC18, pUC19, pKC30, pRep4, pHS1, pHS2, pPLc236, pMBL24, pLG200, pUR290, pIN-III113-B1, ?,gtl1, pBdCl, and pET 1 ld (Studier et al., Gene Expression Technology:
Methods in Enzymology 185, Academic Press, San Diego, California (1990) 60-89;
and Pouwels et al., eds. (1985) Cloning Vectors. Elsevier: New York IBSN 0 444 904018).
Target gene expression from the pTrc vector relies on host RNA polymerase transcription from a hybrid trp-lac fusion promoter. Target gene expression from the pET 1 ld vector relies on transcription from a T7 gn10-lac fusion promoter mediated by a coexpressed viral RNA polymerase (T7 gnl). This viral polymerase is supplied by host strains BL21(DE3) or HMS174(DE3) from a resident X prophage harboring a gnl gene under the transcriptional control of the lacUV 5 promoter. For transformation of other varieties of bacteria, appropriate vectors may be selected. For example, the plasmids pIJ101, pIJ364, pIJ702 and pIJ36l are known to be useful in transforming Streptomyces, while plasmids pUB 110, pC 194, or pBD214 are suited for transformation of Bacillus species. Several plasmids of use in the transfer of genetic information into Corynebacterium include pHM1519, pBLI, pSA77, or pAJ667 (Pouwels et al., eds.
(1985) Cloning Vectors. Elsevier: New York IBSN 0 444 904018).
One strategy to maximize recombinant protein expression is to express the protein in a host bacteria with an impaired capacity to proteolytically cleave the recombinant protein (Gottesman, S., Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Califomia (1990) 119-128). Another strategy is to alter the nucleic acid sequence of the nucleic acid to be inserted into an expression vector so that the individual codons for each amino acid are those preferentially utilized in the bacterium chosen for expression, such as C.
glutamicum (Wada et al. (1992) Nucleic Acids Res. 20:2111-2118). Such alteration of nucleic acid sequences of the invention can be carried out by standard DNA synthesis techniques.

In another embodiment, the MP protein expression vector is a yeast expression vector. Examples of vectors for expression in yeast S cerevisiae include pYepSec 1 (Baldari, et al., (1987) Embo J. 6:229-234),, 2 , pAG-1, Yep6, Yep13, pEMBLYe23, pMFa (Kurjan and Herskowitz, (1982) Cell 30:933-943), pJRY88 (Schultz et al., (1987) Gene 54:113-123), and pYES2 (Invitrogen Corporation, San Diego, CA). Vectors and methods for the construction of vectors appropriate for use in other fungi, such as the filamentous fungi, include those detailed in: van den Hondel, C.A.M.J.J. &
Punt, P.J.
(1991) "Gene transfer systems and vector development for filamentous fungi, in:
Applied Molecular Genetics of Fungi, J.F. Peberdy, et al., eds., p. 1-28, Cambridge University Press: Cambridge, and Pouwels et al., eds. (1985) Cloning Vectors.
Elsevier:
New York (IBSN 0 444 904018).
Alternatively, the MP proteins of the invention can be expressed in insect cells using baculovirus expression vectors. Baculovirus vectors available for expression of proteins in cultured insect cells (e.g., Sf 9 cells) include the pAc series (Smith et al.
(1983) Mol. Cell Biol. 3:2156-2165) and the pVL series (Lucklow and Summers (1989) Virology 170:31-39).
In another embodiment, the MP proteins of the invention may be expressed in unicellular plant cells (such as algae) or in plant cells from higher plants (e.g., the spermatophytes, such as crop plants). Examples of plant expression vectors include those detailed in: Becker, D., Kemper, E., Schell, J. and Masterson, R. (1992) "New plant binary vectors with selectable markers located proximal to the left border", Plant Mol. Biol. 20: 1195-1197; and Bevan, M.W. (1984) "Binary Agrobacterium vectors for plant transformation", Nucl. Acid. Res. 12: 8711-8721, and include pLGV23, pGHlac+, pBIN19, pAK2004, and pDH5I (Pouwels et al., eds. (1985) Cloning Vectors.
Elsevier:
New York IBSN 0 444 904018).
In yet another embodiment, a nucleic acid of the invention is expressed in mammalian cells using a mammalian expression vector. Examples of mammalian expression vectors include pCDM8 (Seed, B. (1987) Nature 329:840) and pMT2PC
(Kaufman et al. (1987) EMBOJ. 6:187-195). When used in mammalian cells, the expression vector's control functions are often provided by viral regulatory elements.
For example, commonly used promoters are derived from polyoma, Adenovirus 2, cytomegalovirus and Simian Virus 40. For other suitable expression systems for both prokaryotic and eukaryotic cells see chapters 16 and 17 of Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989.
In another embodiment, the recombinant mammalian expression vector is capable of directing expression of the nucleic acid preferentially in a particular cell type (e.g., tissue-specific regulatory elements are used to express the nucleic acid). Tissue-specific regulatory elements are known in the art. Non-limiting examples of suitable tissue-specific promoters include the albumin promoter (liver-specific;
Pinkert et al.
(1987) Genes Dev. 1:268-277), lymphoid-specific promoters (Calame and Eaton (1988) Adv. Immunol. 43:235-275), in particular promoters of T cell receptors (Winoto and Baltimore (1989) EMBO J. 8:729-733) and immunoglobulins (Banerji et al. (1983) Cell 33:729-740; Queen and Baltimore (1983) Cell 33:741-748), neuron-specific promoters (e.g., the neurofilament promoter; Byrne and Ruddle (1989) PNAS 86:5473-5477), pancreas-specific promoters (Edlund et al. (1985) Science 230:912-916), and mammary gland-specific promoters (e.g., milk whey promoter; U.S. Patent No. 4,873,316 and European Application Publication No. 264,166). Developmentally-regulated promoters are also encompassed, for example the murine hox promoters (Kessel and Gruss (1990) Science 249:374-3 79) and the a-fetoprotein promoter (Campes and Tilghman (1989) Genes Dev. 3: 53 7-546).
The invention further provides a recombinant expression vector comprising a DNA molecule of the invention cloned into the expression vector in an antisense orientation. That is, the DNA molecule is operatively linked to a regulatory sequence in a manner which allows for expression (by transcription of the DNA molecule) of an RNA molecule which is antisense to MP mRNA. Regulatory sequences operatively linked to a nucleic acid cloned in the antisense orientation can be chosen which direct the continuous expression of the antisense RNA molecule in a variety of cell types, for instance viral promoters and/or enhancers, or regulatory sequences can be chosen which direct constitutive, tissue specific or cell type specific expression of antisense RNA.
The antisense expression vector can be in the form of a recombinant plasmid, phagemid or attenuated virus in which antisense nucleic acids are produced under the control of a high efficiency regulatory region, the activity of which can be determined by the cell type into which the vector is introduced. For a discussion of the regulation of gene expression using antisense genes see Weintraub, H. et al., Antisense RNA as a molecular tool for genetic analysis, Reviews - Trends in Genetics, Vol. 1(1) 1986.
Another aspect of the invention pertains to host cells into which a recombinant expression vector of the invention has been introduced. The terms "host cell"
and "recombinant host cell" are used interchangeably herein. It is understood that such terms refer not only to the particular subject cell but to the progeny or potential progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein.
A host cell can be any prokaryotic or eukaryotic cell. For example, an MP
protein can be expressed in bacterial cells such as C. glutamicum, insect cells, yeast or mammalian cells (such as Chinese hamster ovary cells (CHO) or COS cells).
Other suitable host cells are known to those of ordinary skill in the art.
Microorganisms related to Corynebacterium glutamicum which may be conveniently used as host cells for the nucleic acid and protein molecules of the invention are set forth in Table 3.
Vector DNA can be introduced into prokaryotic or eukaryotic cells via conventional transformation or transfection techniques. As used herein, the terms "transformation" and "transfection", "conjugation" and "transduction" are intended to refer to a variety of art-recognized techniques for introducing foreign nucleic acid (e.g., linear DNA or RNA (e.g., a linearized vector or a gene construct alone without a vector) or nucleic acid in the form of a vector (e.g., a plasmid, phage, phasmid, phagemid, transposon or other DNA) into a host cell, including calcium phosphate or calcium chloride co-precipitation, DEAE-dextran-mediated transfection, lipofection, natural competence, chemical-mediated transfer, or electroporation. Suitable methods for transforming or transfecting host cells can be found in Sambrook, et al.
(Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989), and other laboratory manuals.
For stable transfection of mammalian cells, it is known that, depending upon the expression vector and transfection technique used, only a small fraction of cells may integrate the foreign DNA into their genome. In order to identify and select these integrants, a gene that encodes a selectable marker (e.g., resistance to antibiotics) is generally introduced into the host cells along with the gene of interest.
Preferred selectable markers include those which confer resistance to drugs, such as G418, hygromycin and methotrexate. Nucleic acid encoding a selectable marker can be introduced into a host cell on the same vector as that encoding an MP protein or can be introduced on a separate vector. Cells stably transfected with the introduced nucleic acid can be identified by drug selection (e.g., cells that have incorporated the selectable marker gene will survive, while the other cells die).
To create a homologous recombinant microorganism, a vector is prepared which contains at least a portion of an MP gene into which a deletion, addition or substitution has been introduced to thereby alter, e.g., functionally disrupt, the MP gene.
Preferably, this MP gene is a Corynebacterium glutamicum MP gene, but it can be a homologue from a related bacterium or even from a mammalian, yeast, or insect source. In a preferred embodiment, the vector is designed such that, upon homologous recombination, the endogenous MP gene is functionally disrupted (i.e., no longer encodes a functional protein; also referred to as a "knock out" vector).
Alternatively, the vector can be designed such that, upon homologous recombination, the endogenous MP gene is mutated or otherwise altered but still encodes functional protein (e.g., the upstream regulatory region can be altered to thereby alter the expression of the endogenous MP protein). In the homologous recombination vector, the altered portion of the MP gene is flanked at its 5' and 3' ends by additional nucleic acid of the MP gene to allow for homologous recombination to occur between the exogenous MP gene carried by the vector and an endogenous MP gene in a microorganism. The additional flanking MP nucleic acid is of sufficient length for successful homologous recombination with the endogenous gene. Typically, several kilobases of flanking DNA
(both at the 5' and 3' ends) are included in the vector (see e.g., Thomas, K.R., and Capecchi, M.R. (1987) Cell 51: 503 for a description of homologous recombination vectors). The vector is introduced into a microorganism (e.g., by electroporation) and cells in which the introduced MP gene has homologously recombined with the endogenous MP gene are selected, using art-known techniques.
In another embodiment, recombinant microorganisms can be produced which contain selected systems which allow for regulated expression of the introduced gene.

For example, inclusion of an MP gene on a vector placing it under control of the lac operon permits expression of the MP gene only in the presence of IPTG. Such regulatory systems are well known in the art.
In another embodiment, an endogenous MP gene in a host cell is disrupted (e.g., by homologous recombination or other genetic means known in the art) such that expression of its protein product does not occur. In another embodiment, an endogenous or introduced MP gene in a host cell has been altered by one or more point mutations, deletions, or inversions, but still encodes a functional MP protein. In still another embodiment, one or more of the regulatory regions (e.g., a promoter, repressor, or inducer) of an MP gene in a microorganism has been altered (e.g., by deletion, truncation, inversion, or point mutation) such that the expression of the MP
gene is modulated. One of ordinary skill in the art will appreciate that host cells containing more than one of the described MP gene and protein modifications may be readily produced using the methods of the invention, and are meant to be included in the present invention.
A host cell of the invention, such as a prokaryotic or eukaryotic host cell in culture, can be used to produce (i.e., express) an MP protein. Accordingly, the invention further provides methods for producing MP proteins using the host cells of the invention. In one embodiment, the method comprises culturing the host cell of invention (into which a recombinant expression vector encoding an MP protein has been introduced, or into which genome has been introduced a gene encoding a wild-type or altered MP protein) in a suitable medium until MP protein is produced. In another embodiment, the method further comprises isolating MP proteins from the medium or the host cell.
C. Isolated MP Proteins Another aspect of the invention pertains to isolated MP proteins, and biologically active portions thereof. An "isolated" or "purified" protein or biologically active portion thereof is substantially free of cellular material when produced by recombinant DNA
techniques, or chemical precursors or other chemicals when chemically synthesized.
The language "substantially free of cellular material" includes preparations of MP
protein in which the protein is separated from cellular components of the cells in which it is naturally or recombinantly produced. In one embodiment, the language "substantially free of cellular material" includes preparations of MP protein having less than about 30% (by dry weight) of non-MP protein (also referred to herein as a "contaminating protein"), more preferably less than about 20% of non-MP
protein, still more preferably less than about 10% of non-MP protein, and most preferably less than about 5% non-MP protein. When the MP protein or biologically active portion thereof is recombinantly produced, it is also preferably substantially free of culture medium, i.e., culture medium represents less than about 20%, more preferably less than about 10%, and most preferably less than about 5% of the volume of the protein preparation. The language "substantially free of chemical precursors or other chemicals"
includes preparations of MP protein in which the protein is separated from chemical precursors or other chemicals which are involved in the synthesis of the protein. In one embodiment, the language "substantially free of chemical precursors or other chemicals"
includes preparations of MP protein having less than about 30% (by dry weight) of chemical precursors or non-MP chemicals, more preferably less than about 20% chemical precursors or non-MP chemicals, still more preferably less than about 10%
chemical precursors or non-MP chemicals, and most preferably less than about 5%
chemical precursors or non-MP chemicals. In preferred embodiments, isolated proteins or biologically active portions thereof lack contaminating proteins from the same organism from which the MP protein is derived. Typically, such proteins are produced by recombinant expression of, for example, a C. glutamicum MP protein in a microorganism such as C. glutamicum.
An isolated MP protein or a portion thereof of the invention can catalyze an enzymatic reaction in an amino acid, vitamin, cofactor, nutraceutical, nucleotide, nucleoside, or trehalose metabolic pathway, or has one or more of the activities set forth in Table 1. In preferred embodiments, the protein or portion thereof comprises an amino acid sequence which is sufficiently homologous to an amino acid sequence of the invention (e.g., a sequence of an even-numbered SEQ ID NO: of the Sequence Listing) such that the protein or portion thereof maintains the ability to catalyze an enzymatic reaction in an amino acid, vitamin, cofactor, nutraceutical, nucleotide, nucleoside, or trehalose metabolic pathway. The portion of the protein is preferably a biologically active portion as described herein. In another preferred embodiment, an MP
protein of the invention has an amino acid sequence set forth as an even-numbered SEQ ID
NO: of the Sequence Listing. In yet another preferred embodiment, the MP protein has an amino acid sequence which is encoded by a nucleotide sequence which hybridizes, e.g., hybridizes under stringent conditions, to a ni4cleotide sequence of the invention (e.g., a sequence of an odd-numbered SEQ ID NO: of the Sequence Listing). In still another preferred embodiment, the MP protein has an amino acid sequence which is encoded by a nucleotide sequence that is at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, or 60%, preferably at least about 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, or 70%, more preferably at least about 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, or 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, or 90%, or 91%, 92%, 93%, 94%, and even more preferably at least about 95%, 96%, 97%, 98%, 99% or more homologous to one of the nucleic acid sequences of the invention, or a portion thereof. Ranges and identity values intermediate to the above-recited values, (e.g., 70-90% identical or 80-95% identical) are also intended to be encompassed by the present invention. For example, ranges of identity values using a combination of any of the above values recited as upper and/or lower limits are intended to be included. The preferred MP proteins of the present invention also preferably possess at least one of the MP activities described herein. For example, a preferred MP protein of the present invention includes an amino acid sequence encoded by a nucleotide sequence which hybridizes, e.g., hybridizes under stringent conditions, to a nucleotide sequence of the invention, and which can catalyze an enzymatic reaction in an amino acid, vitamin, cofactor, nutraceutical, nucleotide, nucleoside, or trehalose metabolic pathway, or which has one or more of the activities set forth in Table 1.
In other embodiments, the MP protein is substantially homologous to an amino acid sequence of the invention (e.g., a sequence of an even-numbered SEQ ID
NO: of the Sequence Listing) and retains the functional activity of the protein of one of the amino acid sequences of the invention yet differs in amino acid sequence due to natural variation or mutagenesis, as described in detail in subsection I above.
Accordingly, in another embodiment, the MP protein is a protein which comprises an amino acid sequence which is at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, or 60%, preferably at least about 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, or 70%, more preferably at least about 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, or 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, or 90%, or 91%, 92%, 93%, 94%, and even more preferably at least about 95%, 96%, 97%, 98%, 99% or more homologous to an entire amino acid sequence of the invention and which has at least one of the MP activities described herein. Ranges and identity values intermediate to the above-recited values, (e,g., 70-90% identical or 80-95%
identical) are also intended to be encompassed by the present invention. For example, ranges of identity values using a combination of any of the above values recited as upper and/or lower limits are intended to be included. In another embodiment, the invention pertains to a full length C. glutamicum protein which is substantially homologous to an entire amino acid sequence of the invention.
Biologically active portions of an MP protein include peptides comprising amino acid sequences derived from the amino acid sequence of an MP protein, e.g., an amino acid sequence of an even-numbered SEQ ID NO: of the Sequence Listing or the amino acid sequence of a protein homologous to an MP protein, which include fewer amino acids than a full length MP protein or the full length protein which is homologous to an MP protein, and exhibit at least one activity of an MP protein. Typically, biologically active portions (peptides, e.g., peptides which are, for example, 5, 10, 15, 20, 30, 35, 36, 37, 38, 39, 40, 50, 100 or more amino acids in length) comprise a domain or motif with at least one activity of an MP protein. Moreover, other biologically active portions, in which other regions of the protein are deleted, can be prepared by recombinant techniques and evaluated for one or more of the activities described herein.
Preferably, the biologically active portions of an MP protein include one or more selected domains/motifs or portions thereof having biological activity.
MP proteins are preferably produced by recombinant DNA techniques. For example, a nucleic acid molecule encoding the protein is cloned into an expression vector (as described above), the expression vector is introduced into a host cell (as described above) and the MP protein is expressed in the host cell. The MP
protein can then be isolated from the cells by an appropriate purification scheme using standard protein purification techniques. Alternative to recombinant expression, an MP
protein, polypeptide, or peptide can be synthesized chemically using standard peptide synthesis techniques. Moreover, native MP protein can be isolated from cells (e.g., endothelial cells), for example using an anti-MP antibody, which can be produced by standard techniques utilizing an MP protein or fragment thereof of this invention.
The invention also provides MP chimeric or fusion proteins. As used herein, an MP "chimeric protein" or "fusion protein" comprises an MP polypeptide operatively linked to a non-MP polypeptide. An "MP polypeptide" refers to a polypeptide having an amino acid sequence corresponding to MP, whereas a "non-MP polypeptide" refers to a polypeptide having an amino acid sequence corresponding to a protein which is not substantially homologous to the MP protein, e.g., a protein which is different from the MP protein and which is derived from the same or a different organism. Within the fusion protein, the term "operatively linked" is intended to indicate that the MP
polypeptide and the non-MP polypeptide are fused in-frame to each other. The non-MP
polypeptide can be fused to the N-terminus or C-terminus of the MP
polypeptide. For example, in one embodiment the fusion protein is a GST-MP fusion protein in which the MP sequences are fused to the C-terminus of the GST sequences. Such fusion proteins can facilitate the purification of recombinant MP proteins. In another embodiment, the fusion protein is an MP protein containing a heterologous signal sequence at its N-terminus. In certain host cells (e.g., mammalian host cells), expression and/or secretion of an MP protein can be increased through use of a heterologous signal sequence.
Preferably, an MP chimeric or fusion protein of the invention is produced by standard recombinant DNA techniques. For example, DNA fragments coding for the different polypeptide sequences are ligated together in-frame in accordance with conventional techniques, for example by employing blunt-ended or stagger-ended termini for ligation, restriction enzyme digestion to provide for appropriate termini, filling-in of cohesive ends as appropriate, alkaline phosphatase treatment to avoid undesirable joining, and enzymatic ligation. In another embodiment, the fusion gene can be synthesized by conventional techniques including automated DNA
synthesizers.
Alternatively, PCR amplification of gene fragments can be carried out using anchor primers which give rise to complementary overhangs between two consecutive gene fragments which can subsequently be annealed and reamplified to generate a chimeric gene sequence (see, for example, Current Protocols in Molecular Biology, eds.
Ausubel et al. John Wiley & Sons: 1992). Moreover, many expression vectors are commercially available that already encode a fusion moiety (e.g., a GST polypeptide). An MP-encoding nucleic acid can be cloned into such an expression vector such that the fusion moiety is linked in-frame to the MP protein.
Homologues of the MP protein can be generated by mutagenesis, e.g., discrete point mutation or truncation of the MP protein. As used herein, the term "homologue"
refers to a variant form of the MP protein which acts as an agonist or antagonist of the activity of the MP protein. An agonist of the MP protein can retain substantially the same, or a subset, of the biological activities of the MP protein. An antagonist of the MP protein can inhibit one or more of the activities of the naturally occurring form of the MP protein, by, for example, competitively binding to a downstream or upstream member of the MP cascade which includes the MP protein. Thus, the C.
glutamicum MP protein and homologues thereof of the present invention may modulate the activity of one or more metabolic pathways in which MP proteins play a role in this microorganism.
In an alternative embodiment, homologues of the MP protein can be identified by screening combinatorial libraries of mutants, e.g., truncation mutants, of the MP
protein for MP protein agonist or antagonist activity. In one embodiment, a variegated library of MP variants is generated by combinatorial mutagenesis at the nucleic acid level and is encoded by a variegated gene library. A variegated library of MP
variants can be produced by, for example, enzymatically ligating a mixture of synthetic oligonucleotides into gene sequences such that a degenerate set of potential MP
sequences is expressible as individual polypeptides, or alternatively, as a set of larger fu"sion proteins (e.g., for phage display) containing the set of MP sequences therein.
There are a variety of methods which can be used to produce libraries of potential MP
homologues from a degenerate oligonucleotide sequence. Chemical synthesis of a degenerate gene sequence can be performed in an automatic DNA synthesizer, and the synthetic gene then ligated into an appropriate expression vector. Use of a degenerate set of genes allows for the provision, in one mixture, of all of the sequences encoding the desired set of potential MP sequences. Methods for synthesizing degenerate oligonucleotides are known in the art (see, e.g., Narang, S.A. (1983) Tetrahedron 39:3;
Itakura et al. (1984) Annu. Rev. Biochem. 53:323; Itakura et al. (1984) Science 198:1056; Ike et al. (1983) Nucleic Acid Res. 11:477.

In addition, libraries of fragments of the MP protein coding can be used to generate a variegated population of MP fragments for screening and subsequent selection of homologues of an MP protein. In one embodiment, a library of coding sequence fragments can be generated by treating a double stranded PCR fragment of an MP coding sequence with,a nuclease under conditions wherein nicking occurs only about once per molecule, denaturing the double stranded DNA, renaturing the DNA to form double stranded DNA which can include sense/antisense pairs from different nicked products, removing single stranded portions from reformed duplexes by treatment with S1 nuclease, and ligating the resulting fragment library into an expression vector. By this method, an expression library can be derived which encodes N-terminal, C-terminal and internal fragments of various sizes of the MP protein.
Several techniques are known in the art for screening gene products of combinatorial libraries made by point mutations or truncation, and for screening cDNA
libraries for gene products having a selected property. Such techniques are adaptable for rapid screening of the gene libraries generated by the combinatorial mutagenesis of MP
homologues. The most widely used techniques, which are amenable to high through-put analysis, for screening large gene libraries typically include cloning the gene library into replicable expression vectors, transforming appropriate cells with the resulting library of vectors, and expressing the combinatorial genes under conditions in which detection of a desired activity facilitates isolation of the vector encoding the gene whose product was detected. Recursive ensemble mutagenesis (REM), a new technique which enhances the frequency of functional mutants in the libraries, can be used in combination with the screening assays to identify MP homologues (Arkin and Yourvan (1992) PNAS
89:7811-7815; Delgrave et al. (1993) Protein Engineering 6(3):327-331).
In another embodiment, cell based assays can be exploited to analyze a variegated MP library, using methods well known in the art.

D. Uses and Methods of the Invention The nucleic acid molecules, proteins, protein homologues, fusion proteins, primers, vectors, and host cells described herein can be used in one or more of the following methods: identification of C. glulamicum and related organisms;
mapping of genomes of organisms related to C. glutamicum; identification and localization of C.

glutamicum sequences of interest; evolutionary studies; determination of MP
protein regions required for function; modulation of an MP protein activity;
modulation of the activity of an MP pathway; and modulation of cellular production of a desired compound, such as a fine chemical.
The MP nucleic acid molecules of the invention have a variety of uses. First, they may be used to identify an organism as being Corynebacterium glutamicum or a close relative thereof. Also, they may be used to identify the presence of C.
glutamicum or a relative thereof in a mixed population of microorganisms. The invention provides the nucleic acid sequences of a number of C. glutamicum genes; by probing the extracted genomic DNA of a culture of a unique or mixed population of microorganisms under stringent conditions with a probe spanning a region of a C. glutamicum gene which is unique to this organism, one can ascertain whether this organism is present.
Although Corynebacterium glutamicum itself is not pathogenic to humans, it is related to species which are human pathogens, such as Corynebacterium diphtheriae.
Corynebacterium diphtheriae is the causative agent of diphtheria, a rapidly developing, acute, febrile infection which involves both local and systemic pathology. In this disease, a local lesion develops in the upper respiratory tract and involves necrotic injury to epithelial cells; the bacilli secrete toxin which is disseminated through this lesion to distal susceptible tissues of the body. Degenerative changes brought about by the inhibition of protein synthesis in these tissues, which include heart, muscle, peripheral nerves, adrenals, kidneys, liver and spleen, result in the systemic pathology of the disease. Diphtheria continues to have high incidence in many parts of the world, including Africa, Asia, Eastern Europe and the independent states of the former Soviet Union. An ongoing epidemic of diphtheria in the latter two regions has resulted in at least 5,000 deaths since 1990.
In one embodiment, the invention provides a method of identifying the presence or activity of Cornyebacterium diphtheriae in a subject. This method includes detection of one or more of the nucleic acid or amino acid sequences of the invention (e.g., the sequences set forth as odd-numbered or even-numbered SEQ ID NOs, respectively, in the Sequence Listing) in a subject, thereby detecting the presence or activity of Corynebacterium diphtheriae in the subject. C. glulamicum and C. diphtheriae are related bacteria, and many of the nucleic acid and protein molecules in C.
glutamicum are homologous to C. diphtheriae nucleic acid and protein molecules, and can therefore be used to detect C. diphtheriae in a subject.
The nucleic acid and protein molecules of the invention may also serve as markers for specific regions of the genome. This has utility not only in the mapping of the genome, but also for functional studies of C. glutamicum proteins. For example, to identify the region of the genome to which a particular C. glutamicum DNA-binding protein binds, the C. glutamicum genome could be digested, and the fragments incubated with the DNA-binding protein. Those which bind the protein may be additionally probed with the nucleic acid molecules of the invention, preferably with readily detectable labels; binding of such a nucleic acid molecule to the genome fragment enables the localization of the fragment to the genome map of C. glutamicum, and, when performed multiple times with different enzymes, facilitates a rapid determination of the nucleic acid sequence to which the protein binds. Further, the nucleic acid molecules of the invention may be sufficiently homologous to the sequences of related species such that these nucleic acid molecules may serve as markers for the construction of a genomic map in related bacteria, such as Brevibacterium lactofermentum.
The MP nucleic acid molecules of the invention are also useful for evolutionary and protein structural studies. The metabolic processes in which the molecules of the invention participate are utilized by a wide variety of prokaryotic and eukaryotic cells;
by comparing the sequences of the nucleic acid molecules of the present invention to those encoding similar enzymes from other organisms, the evolutionary relatedness of the organisms can be assessed. Similarly, such a comparison permits an assessment of which regions of the sequence are conserved and which are not, which may aid in determining those regions of the protein which are essential for the functioning of the enzyme. This type of determination is of value for protein engineering studies and may give an indication of what the protein can tolerate in terms of mutagenesis without losing function.
Manipulation of the MP nucleic acid molecules of the invention may result in the production of MP proteins having functional differences from the wild-type MP
proteins. These proteins may be improved in efficiency or activity, may be present in greater numbers in the cell than is usual, or may be decreased in efficiency or activity.

The invention also provides methods for screening molecules which modulate the activity of an MP protein, either by interacting with the protein itself or a substrate or binding partner of the MP protein, or by modulating the transcription or translation of an MP nucleic acid molecule of the invention. In such methods, a microorganism expressing one or more MP proteins of the invention is contacted with one or more test compounds, and the effect of each test compound on the activity or level of expression of the MP protein is assessed.
When the desired fine chemical to be isolated from large-scale fermentative culture of C. glutamicum is an amino acid, a vitamin, a cofactor, a nutraceutical, a nucleotide, a nucleoside, or trehalose, modulation of the activity or efficiency of activity of one or more of the proteins of the invention by recombinant genetic mechanisms may directly impact the production of one of these fine chemicals. For example, in the case of an enzyme in a biosynthetic pathway for a desired amino acid, improvement in efficiency or activity of the enzyme (including the presence of multiple copies of the gene) should lead to an increased production or efficiency of production of that desired amino acid. In the case of an enzyme in a biosynthetic pathway for an amino acid whose synthesis is in competition with the synthesis of a desired amino acid, any decrease in the efficiency or activity of this enzyme (including deletion of the gene) should result in an increase in production or efficiency of production of the desired amino acid, due to decreased competition for intermediate compounds andlor energy. In the case of an enzyme in a degradation pathway for a desired amino acid, any decrease in efficiency or activity of the enzyme should result in a greater yield or efficiency of production of the desired product due to a decrease in its degradation. Lastly, mutagenesis of an enzyme involved in the biosynthesis of a desired amino acid such that this enzyme is no longer is capable of feedback inhibition should result in increased yields or efficiency of production of the desired amino acid. The same should apply to the biosynthetic and degradative enzymes of the invention involved in the metabolism of vitamins, cofactors, nutraceuticals, nucleotides, nucleosides and trehalose.
Similarly, when the desired fine chemical is not one of the aforementioned compounds, the modulation of activity of one of the proteins of the invention may still impact the yield and/or efficiency of production of the compound from large-scale culture of C. glutamicum. The metabolic pathways of any organism are closely interconnected; the intermediate used by one pathway is often supplied by a different pathway. Enzyme expression and function may be regulated based on the cellular levels of a compound from a different metabolic process, and the cellular levels of molecules necessary for basic growth, such as amino acids and nucleotides, may critically affect the viability of the microorganism in large-scale culture. Thus, modulation of an amino acid biosynthesis enzyme, for example, such that it is no longer responsive to feedback inhibition or such that it is improved in efficiency or tumover may result in increased cellular levels of one or more amino acids. In turn, this increased pool of amino acids provides not only an increased supply of molecules necessary for protein synthesis, but also of molecules which are utilized as intermediates and precursors in a number of other biosynthetic pathways. If a particular amino acid had been limiting in the cell, its increased production might increase the ability of the cell to perform numerous other metabolic reactions, as well as enabling the cell to more efficiently produce proteins of all kinds, possibly increasing the overall growth rate or survival ability of the cell in large scale culture. Increased viability improves the number of cells capable of producing the desired fine chemical in fermentative culture, thereby increasing the yield of this compound. Similar processes are possible by the modulation of activity of a degradative enzyme of the invention such that the enzyme no longer catalyzes, or catalyzes less efficiently, the degradation of a cellular compound which is important for the biosynthesis of a desired compound, or which will enable the cell to grow and reproduce more efficiently in large-scale culture. It should be emphasized that optimizing the degradative activity or decreasing the biosynthetic activity of certain molecules of the invention may also have a beneficial effect on the production of certain fine chemicals from C. glutamicum. For example, by decreasing the efficiency of activity of a biosynthetic enzyme in a pathway which competes with the biosynthetic pathway of a desired compound for one or more intermediates, more of those intermediates should be available for conversion to the desired product. A
similar situation may call for the improvement of degradative ability or efficiency of one or more proteins of the invention.
This aforementioned list of mutagenesis strategies for MP proteins to result in increased yields of a desired compound is not meant to be limiting; variations on these mutagenesis strategies will be readily apparent to one of ordinary skill in the art. By these mechanisms, the nucleic acid and protein molecules of the invention may be utilized to generate C. glutamicum or related strains of bacteria expressing mutated MP
nucleic acid and protein molecules such that the yield, production, and/or efficiency of production of a desired compound is improved. This desired compound may be any natural product of C. glutamicum, which includes the final products of biosynthesis pathways and intermediates of naturally-occurring metabolic pathways, as well as molecules which do not naturally occur in the metabolism of C. glutamicum, but which are produced by a C. glutamicum strain of the invention.
This invention is further illustrated by the following examples which should not be construed as limiting. The contents of all references, patent applications, patents, published patent applications, Tables, and the sequence listing cited throughout this application are hereby incorporated by reference.

TABLE 1: Included Genes Lysine biosynthesis Nucleic Acid Amino Acid Identification Code Conti . NT Start NT St p Function SEQ ID NO SEQ ID NO
1 2 RXA02229 GR00653 2793 3617 DIAMINOPIMELATE EPIMERASE (EC 5.1.1.7) 3 4 RXS02970 ACETYLORNITHINE AMINOTRANSFERASE (EC 2.6.1.11) 6 F RXA01009 GR00287 4714 5943 ACETYLORNITHINE AMINOTRANSFERASE (EC 2.6.1.11) THREONINE

Trehalose Nucleic Acid Amino Acid ldentification Code Conti . NT Start NT Stop Function SEQ ID NO SEQ ID NO 0) 17 18 RXN00351 W0135 37078 38532 ALPHA,ALPHA-TREHALOSE-PHOSPHATE SYNTHASE (UDP-FORMING) 56 KD N
SUBUNIT (EC 2.4.1.15) 19 20 F RXA00351 GR0o066 1486 2931 ALPHA,ALPHA-TREHALOSE-PHOSPHATE SYNTHASE
(UDP-FORMING) 56 KD ' o SUBUNIT (EC 2.4.1.15) tA 21 22 RXA00873 GR00241 3 758 trehalose synthase (EC 2.4.1.-) 23 24 RXA00891 GR00243 1005 4 trehalose synthase (EC 2.4.1.-) rn Lysine biosynthesis Nucleic Acid Amino Acid Identification Code Contig. NT Start NT Stop Function SEQ ID NO SEQ ID NO
26 RXA00534 GR00137 4758 3496 ASPARTOKINASE ALPHA AND BETA SUBUNITS (EC
2.7.2.4) 27 28 RXA00533 GR00137 3469 2438 ASPARTATE-SEMIALDEHYDE DEHYDROGENASE (EC
1.2.1.11) 29 30 RXA02843 GR00842 543 4 2,3,4,5-TETRAHYDROPYRIDINE-2-CARBOXYLATE N-SUCCINYLTRANSFERASE
(EC 2.3.1.117) 31 32 RXA02022 GR00613 2063 3169 SUCCINYL-DIAMINOPIMELATE DESUCCINYLASE (EC
3.5.1.18) 33 34 RXA00044 GR0o007 3458 4393 DIHYDRODIPICOLINATE SYNTHASE (EC 4.2.1.52) 36 RXA00863 GR00236 896 1639 DIHYDRODIPICOLINATE REDUCTASE (EC 1.3.1.26) 37 38 RXA00864 GR00236 1694 2443 probable 2,3-dihydrodipicolinate N-C6-lyase (cyclizing) (EC 4.3.3.-) -Corynebacterium glutamicum 39 40 RXA02843 GR00842 543 4 2,3,4,5-TETRAHYDROPYRIDINE-2-CARBOXYLATE N-SUCCINYLTRANSFERASE
(EC 2.3.1.117) 43 44 F RXA00352 GR00068 861 4 MESO-DIAMINOPIMELATE D-DEHYDROGENASE (EC
1.4.1_16) Table 1 (continued) Nucleic Acid Amino Acid Identification Code Conti9. NT Start NT Stop Function SEQ ID NO SEQ ID NO
45 46 RXA00972 GR00274 3 1379 DIAMINOPIMELATE DECARBOXYLASE (EC 4.1.1.20) 47 48 RXA02653 GR00752 5237 7234 DIAMINOPIMELATE DECARBOXYLASE (EC 4.1.1.20) 55 56 RXA00865 GR00236 2647 3549 DIHYDRODIPICOLINATE SYNTHASE (EC 4.2.1.52) 57 58 RXS02021 2,3,4,5-TETRAHYDROPYRIDINE-2-CARBOXYLATE N-SUCCINYLTRANSFERASE
(EC 2.3.1.117) 59 60 RXS02157 ACETYLORNITHINE AMINOTRANSFERASE (EC 2.6.1.11) METABOLISM

METABOLISM

Glutamate and glutamine metabolism o 0) 0, Nucleic Acid Amino Acid Identification Code Conti9. NT Start NT Stop Function SEQ ID NO SEQ ID NO
71 72 RXN00367 - W0196 9744 14273 GLUTAMATE SYNTHASE [NADH] PRECURSOR (EC
1.4.1.14) 73 74 F RXA00007 GR00001 7107 8912 GLUTAMATE SYNTHASE (NADPH) LARGE CHAIN
PRECURSOR (EC 1.4.1.13) ~
75 76 F RXA00364 GR00074 1296 4 GLUTAMATE SYNTHASE (NADPH) LARGE CHAIN
PRECURSOR (EC 1.4.1.13) o 77 78 F RXA00367 GR0o075 1806 964 GLUTAMATE SYNTHASE (NADPH) LARGE CHAIN
PRECURSOR (EC 1.4.1.13) rn 79 80 RXN00076 W0154 2752 4122 GLUTAMATE SYNTHASE (NADPH) SMALL CHAIN (EC
1.4.1.13) 81 82 F RXA00075 GR00012 2757 3419 GLUTAMATE SYNTHASE (NADPH) SMALL CHAIN (EC
1.4.1.13) 83 84 RXN00198 W0181 7916 7368 GLUTAMATE SYNTHASE (NADPH) SMALL CHAIN (EC
1.4.1.13) 85 86 F RXA00198 GR00031 2 283 GLUTAMATE SYNTHASE (NADPH) SMALL CHAIN (EC
1.4.1.13) 87 88 RXN00365 W0196 14607 15233 GLUTAMATE SYNTHASE [NADPH] SMALL CHAIN (EC
1.4.1.13) 89 90 F RXA00365 GR0o075 630 4 GLUTAMATE SYNTHASE (NADPH) SMALL CHAIN (EC
1.4.1.13) 91 92 RXA00366 GR00075 961 605 GLUTAMATE SYNTHASE (NADPH) SMALL CHAIN (EC
1.4.1.13) 93 94 RXA02072 GR00628 1259 2599 NADP-SPECIFIC GLUTAMATE DEHYDROGENASE (EC
1.4.1.4) 95 96 RXA00323 GR00057 3855 5192 GLUTAMINE SYNTHETASE (EC 6.3.1.2) 97 98 RXA00335 GR00057 19180 17750 GLUTAMINE SYNTHETASE (EC 6.3.1.2) (EC 2.7.7.42) 101 102 RXN03176 W0332 2 862 GLUTAMINASE (EC 3.5.1.2) 103 104 F RXA02879 GR10017 2 862 GLUTAMINASE (EC 3.5.1.2) 105 106 RXA00278 GR0o043 2612 1581 GLUTAMINE-BINDING PROTEIN PRECURSOR

PRECURSOR

Table I (continued) Alanine and Aspartate and Asparagine metabolism Nucleic Acid Amino Acid Identification Code Conti . NT Start NT Stop Function SEQ ID NO SEQ ID NO
109 110 RXA02139 GR00639 6739 4901 ASPARAGINE SYNTHETASE (GLUTAMINE-HYDROLYZING) (EC 6.3.5.4) 111 112 RXN00116 W0100 26974 25814 ASPARTATE AMINOTRANSFERASE (EC 2.6.1.1) 113 114 F RXA00116 GR00018 510 4 ASPARTATE AMINOTRANSFERASE (EC 2.6.1.1) 115 116 RXN00618 W0135 10288 9182 ASPARTATE AMINOTRANSFERASE (EC 2.6.1.1) 117 118 F RXA00618 GR00163 213 746 ASPARTATE AMINOTRANSFERASE (EC 2.6.1.1) 119 120 F RXA00627 GR00164 854 1138 ASPARTATE AMINOTRANSFERASE (EC 2.6.1.1) 121 122 RXA02550 GR00729 1585 275 ASPARTATE AMINOTRANSFERASE (EC 2.6.1.1) 123 124 RXA02193 GR00645 1942 365 ASPARTATE AMMONIA-LYASE (EC 4.3.1.1) 125 126 RXA02432 GR00708 2669 1695 L-ASPARAGINASE (EC 3.5.1.1) 127 128 RXN03003 W0138 680 6 ASPARTATE AMINOTRANSFERASE (EC 2.6.1.1) 129 130 RXN00508 W0086 4701 5783 ALANINE RACEMASE (EC 5.1.1.1) 131 132 RXN00636 W0135 20972 19944 ALANINE RACEMASE, BIOSYNTHETIC (EC 5.1.1.1) Ln beta-Alanine metabolism 0) 0) Nucleic Acid Amino Acid Identification Code Conti . NT Start NT Stop Function SEQ ID NO SEQ ID NO
133 134 RXA02536 GR00726 8581 7826 BETA-UREIDOPROPIONASE (EC 3.5.1.6) 135 136 RXS00870 METHYLMALONATE-SEMIALDEHYDE DEHYDROGENASE (ACYLATING) (EC
1.2.1.27) v i 137 138 RXS02299 ASPARTATE 1-DECARBOXYLASE PRECURSOR (EC 4.1.1.11) rn N
Glycine and serine metabolism Nucleic Acid Amino Acid Identification Code Conti9. NT Start NT Stop Function SEQ ID NO SEQ ID NO
139 140 RXA01561 GR00435 1113 2042 L-SERINE DEHYDRATASE (EC 4.2.1.13) 141 142 RXA01850 GR00525 481 1827 L-SERINE DEHYDRATASE (EC 4.2.1.13) 143 144 RXA00580 GR00156 7343 6042 SERINE HYDROXYMETHYLTRANSFERASE (EC
2.1.2.1) 145 146 RXA01821 GR00515 10253 9876 SARCOSINE OXIDASE (EC 1.5.3.1) 147 148 RXN02263 W0202 11783 12160 SARCOSINE OXIDASE (EC 1.5.3.1) 149 150 F RXA02263 GR00654 33454 33813 SARCOSINE OXIDASE (EC 1.5.3.1) 151 152 RXA02176 GR00641 11454 12581 PHOSPHOSERINE AMINOTRANSFERASE (EC
2.6.1.52) 153 154 RXN02758 GR00766 5082 4648 PHOSPHOSERINE PHOSPHATASE (EC 3.1.3.3) 155 156 F RXA02479 GR00717 393 4 PHOSPHOSERINE PHOSPHATASE (EC 3.1.3.3) 157 158 F RXA02758 GR00766 5082 4648 PHOSPHOSERINE PHOSPHATASE (EC 3.1.3.3) 159 160 F RXA02759 GR00766 5330 5220 PHOSPHOSERINE PHOSPHATASE (EC 3.1.3.3) 161 162 RXA02501 GR00720 15041 13977 PHOSPHOSERINE PHOSPHATASE (EC 3.1.3.3) 163 164 RXN03105 W0074 15857 15423 SARCOSINE OXIDASE (EC 1.5.3.1) 165 166 RXS01130 D-3-PHOSPHOGLYCERATE DEHYDROGENASE (EC 1.1.1.95) 167 168 RXS03112 D-3-PHOSPHOGLYCERATE DEHYDROGENASE (EC 1.1.1.95) Table I (continued) Threonine metabolism Nucleic Acid Amino Acid Identification Code Conti9. NT Start NT Stop Function SEQ ID NO SEQ ID NO
169 170 RXN00969 W0149 12053 13387 HOMOSERINE DEHYDROGENASE (EC 1.1.1.3) 171 172 F RXA00974 GR00274 2623 3015 HOMOSERINE DEHYDROGENASE (EC 1.1.1.3) 173 174 RXA00970 GR00273 161 1087 HOMOSERINE KINASE (EC 2.7.1.39) 175 176 RXA00330 GR00057 12968 14410 THREONINE SYNTHASE (EC 4.2.99.2) 179 180 F RXA00403 GR00088 723 1832 HOMOSERINE O-ACETYLTRANSFERASE (EC
2.3.1.11) THREONINE

Metabolism of methionine and S-adenosyl methionine Nucleic Acid Amino Acid Identification Code Conti . NT Start NT Stop Function Ln SEQ ID NO SEQ ID NO o 185 186 RXA00115 GR00017 5359 4313 HOMOSERINE O-ACETYLTRANSFERASE (EC
2.3.1.31) ~

189 190 F RXA00403 GR00088 723 1832 HOMOSERINE O-ACETYLTRANSFERASE (EC
2.3.1.11) 191 192 RXS03158 CYSTATHIONINE GAMMA-SYNTHASE (EC 4.2.99.9) 193 194 F RXA00254 GR00038 2404 1811 CYSTATHIONINE GAMMA-SYNTHASE (EC
4.2.99.9) oo -.3 195 196 RXA02532 GR00726 3085 2039 CYSTATHIONINE GAMMA-SYNTHASE (EC 4.2.99.9) 197 198 RXS03159 CYSTATHIONINE GAMMA-SYNTHASE (EC 4.2.99.9) 0) 199 200 F RXA02768 GR00770 1919 2521 CYSTATHIONINE GAMMA-SYNTHASE (EC
4.2.99.9) 201 202 RXA00216 GR00032 16286 15297 5-methyttetrahydrofolate-homocysteine methyltransferase (methionine synthetase) 203 204 RXN00402 W0086 70787 70188 O-ACETYLHOMOSERINE SULFHYDRYLASE (EC
4.2.99.10)/ O-ACETYLSERINE
SULFHYDRYLASE (EC 4.2.99.8) 205 206 F RXA00402 GR00088 1 576 O-ACETYLHOMOSERINE SULFHYDRYLASE (EC
4.2.99.10) / O-ACETYLSERINE
SULFHYDRYLASE (EC 4.2.99.8) 207 208 RXA00405 GR00089 3289 3801 O-ACETYLHOMOSERINE SULFHYDRYLASE (EC
4.2.99.10) 1 O-ACETYLSERINE
SULFHYDRYLASE (EC 4.2.99.8) METHYLTRANSFERASE
(EC 2.1.1.13) METHYLTRANSFERASE
(EC 2.1.1.13) METHYLTRANSFERASE
(EC 2.1.1.13) 215 216 RXN03074 W0042 2238 1741 S-ADENOSYLMETHlONINE:2-DEMETHYLMENAQUINONE
METHYLTRANSFERASE (EC 2.
217 218 F RXA02906 GR10044 1142 645 S-ADENOSYLMETHIONINE:2-DEMETHYLMENAQUINONE
METHYLTRANSFERASE (EC 2.1.-.-) 219 220 RXN00132 W0124 3612 5045 ADENOSYLHOMOCYSTEINASE (EC 3.3.1.1) 221 222 F RXA00132 GR00020 7728 7624 ADENOSYLHOMOCYSTEINASE (EC 3.3.1.1) Table 1 (continued) Nucleic Acid Amino Acid Identification Code Conti . NT Start NT Stop Function SEQ ID NO SEQ ID NO
223 224 F RXA01371 GR00398 2339 3634 ADENOSYLHOMOCYSTEINASE (EC 3.3.1.1) METHYLTRANSFERASE (EC 2.1.1.14) HOMOCYSTEINE
METHYLTRANSFERASE (EC 2.1.1.14) HOMOCYSTEINE
METHYLTRANSFERASE (EC 2.1.1.14) METHYLTRANSFERASE (EC 2.1.1.14) HOMOCYSTEINE
METHYLTRANSFERASE (EC 2.1.1.14) HOMOCYSTEINE
METHYLTRANSFERASE (EC 2.1.1.14) 237 238 RXC02238 PROTEIN INVOLVED IN METABOLISM OF S-ADENOSYLMETHIONINE, PURINES
AND PANTOTHENATE

ADENOSYLHOMOCYSTEINE

S-adenosyl methionine (SAM) Biosynthesis 0) 0) Nucleic Acid Amino Acid Identification Code Contig. NT Start NT Stop Function SEQ ID NO SEQ ID NO
241 242 RXA02240 GR00654 7160 8380 S-ADENOSYLMETHIONiNE SYNTHETASE (EC
2.5.1.6) Cysteine metabolism N
Nucleic Acid Amino Acid Identification Code Cont . NT Start NT Stop Function SEQ ID NO SEQ ID NO
243 244 RXA00780 GR00206 1689 2234 SERINE ACETYLTRANSFERASE (EC 2.3.1.30) 245 246 RXA00779 GR00206 550 1482 CYSTEINE SYNTHASE (EC 4.2.99.8) 247 248 RXN00402 W0086 70787 70188 O-ACETYLHOMOSERINE SULFHYDRYLASE (EC
4.2.99.10) / O-ACETYLSERINE
SULFHYDRYLASE (EC 4.2.99.8) 249 250 F RXA00402 GR00088 1 576 O-ACETYLHOMOSERINE SULFHYDRYLASE (EC
4.2.99.10) / O/1CETYLSERINE
SULFHYDRYLASE (EC 4.2.99.8) 251 252 RXS00405 O-ACETYLHOMOSERINE SULFHYDRYLASE (EC 4.2.99.10) / O-ACETYLSERINE
SULFHYDRYLASE (EC 4.2.99.8) METABOLISM

METABOLISM

Table I (continued) Valine, leucine and isoleucine Nucleic Acid Amino Acid Identification Code Contig= NT Start NT Stop Function SEQ ID NO SEQ ID NO
257 258 RXA02646 GR00751 3856 2588 THREONINE DEHYDRATASE BIOSYNTHETIC (EC
4.2.1.16) (EC 2.6.1.42) 261 262 RXN01690 W0246 1296 196 BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE (EC
2.6.1.42) (EC 2.6.1.42) (EC 4.2.1.33) (EC 4.2.1.33) 269 270 RXN01127 W0157 4491 3472 3-ISOPROPYLMALATE DEHYDROGENASE (EC 1.1.1.85) 271 272 F RXA01132 GR00315 1349 1651 3-ISOPROPYLMALATE DEHYDROGENASE (EC
1.1.1.85) 273 274 RXN00536 W0219 6128 7498 2-ISOPROPYLMALATE SYNTHASE (EC 4.1.3.12) 275 276 F RXA00536 GR00137 6128 7360 2-ISOPROPYLMALATE SYNTHASE (EC 4.1.3.1) (EC 4.2.1.33) HYDROXYMETHYLTRANSFERASE (EC 2.1.2.11) / DECARBOXYLASE (EC 4.1.1.44) HYDROXYMETHYLTRANSFERASE (EC 2.1.2.11) o 283 284 RXN01420 W0122 15584 14643 4"-MYCAROSYL ISOVALERYL-COA TRANSFERASE (EC
2.-.-.-) 285 286 RXS01 145 KETOL-ACID REDUCTOISOMERASE (EC 1.1.1.86) Ln 287 288 F RXA01145 GR00321 1075 1530 KETOL-ACID REDUCTOISOMERASE (EC 1.1.1.86) rn N
Arginine and proline metabolism o .3 Enzymes of proline biosynthesis:
N
Nucleic Acid Amino Acid Identification Code Contig. NT Start NT Stop Function SEQ ID NO SEQ ID NO
289 290 RXA02375 GR00689 1449 223 GLUTAMATE 5-KINASE (EC 2.7.2.11) 291 292 RXN02382 W0213 5162 3867 GAMMA-GLUTAMYL PHOSPHATE REDUCTASE (GPR) (EC
1.2.1.41) 293 294 F RXA02378 GR00690 624 16 GAMMA-GLUTAMYL PHOSPHATE REDUCTASE (GPR) (EC
1.2.1.41) 295 296 F RXA02382 GR00691 2493 1894 GAMMA-GLUTAMYL PHOSPHATE REDUCTASE (GPR) (EC 1.2.1.41) 297 298 RXA02499 GR00720 11883 12692 PYRROLINE-5-CARBOXYLATE REDUCTASE (EC
1.5.1.2) 299 300 RXS02157 ACETYLORNITHINE AMINOTRANSFERASE (EC 2.6.1.11) 301 302 RXS02262 ORNITHINE CYCLODEAMINASE (EC 4.3.1.12) 303 304 RXS02970 ACETYLORNITHINE AMINOTRANSFERASE (EC 2.6.1.11) 305 306 F RXA01009 GR00287 4714 5943 ACETYLORNITHINE AMINOTRANSFERASE (EC
2.6.1.11) Table I (continued) Enzymes of proline degradation:

Nudeic Acid Amino Acid Identification Code Conti . NT Start NT Stop Function SEQ ID NO SEQ ID NO
307 308 RXN00023 W0127 68158 64703 PROLINE DEHYDROGENASE (EC 1.5.99.8) / DELTA-CARBOXYLATE DEHYDROGENASE (EC 1.5.1.12) 309 310 F RXA00023 GR00003 2 454 PROLINE DEHYDROGENASE (EC 1.5.99.8) / DELTA-1-CARBOXYLATE DEHYDROGENASE (EC 1.5.1.12) 311 312 F RXA02284 GR00660 3028 5 PROLINE DEHYDROGENASE (EC 1.5.99.8) / DELTA-CARBOXYLATE DEHYDROGENASE (EC 1.5.1.12) Synthesis of 3-Hydoxy-proline:

Nucleic Acid Amino Acid Identification Code Contig. NT Start NT Stop Function SEQ ID NO SEQ ID NO Ln 315 316 RXA01491 GR00423 5337 4687 DNA FOR L-PROLINE 3-HYDROXYLASE, COMPLETE
CDS
rn rn Enzymes of ornithine, arginine and spermidine metabolism:
Nucleic Acid Amino Acid Identification Code Cont. NT Start NT Stop Function ~
SEQ ID NO SEQ ID NO
317 318 RXA02155 GR00640 1913 3076 GLUTAMATE N-ACETYLTRANSFERASE (EC 2.3.1.35) / AMINO-ACID
ACETYLTRANSFERASE (EC 2.3.1.1) 319 320 RXA02156 GR00640 3125 4075 ACETYLGLUTAMATE KINASE (EC 2.7.2.8) (EC 1.2.1.38) DEHYDROGENASE

DEHYDROGENASE
327 328 RXA02157 GR00640 4079 5251 ACETYLORNITHINE AMINOTRANSFERASE (EC
2.6.1.11) 329 330 RXS02970 ACETYLORNITHINE AMINOTRANSFERASE (EC 2.6.1.11) 331 332 F RXA01009 GR00287 4714 5943 ACETYLORNITHINE AMINOTRANSFERASE (EC
2.6.1.11) 333 334 RXA02158 GR00640 5268 6224 ORNITHINE CARBAMOYLTRANSFERASE (EC 2.1.3.3) 335 336 RXA02160 GR00640 6914 8116 ARGININOSUCCINATE SYNTHASE (EC 6.3.4.5) 337 338 RXN02162 W0122 6683 5253 ARGININOSUCCINATE LYASE (EC 4.3.2.1) 339 340 F RXA02161 GR00640 8180 8962 ARGININOSUCCINATE LYASE (EC 4.3.2.1) 341 342 F RXA02162 GR00640 8949 9611 ARGININOSUCCINATE LYASE (EC 4.3.2.1) 343 344 RXA02262 GR00654 32291 33436 ORNITHINE CYCLODEAMINASE (EC 4.3.1.12) 345 346 RXA00219 GR00032 19289 20230 SPERMIDINE SYNTHASE (EC 2.5.1.16) 347 348 RXA01508 GR00424 12652 14190 SPERMIDINE SYNTHASE (EC 2.5.1.16) 349 350 RXA01757 GR00498 2942 2142 PUTRESCINE OXIDASE (EC 1.4.3.10) (EC 1.2.1.38) 355 356 RXS00147 CARBAMOYL-PHOSPHATE SYNTHASE SMALL CHAIN (EC 6.3.5.5) 357 358 RXS00905 N-ACYL-L-AMINO ACID AMIDOHYDROLASE (EC 3.5.1.14) 359 360 RXS00906 N-ACYL-L-AMINO ACID AMIDOHYDROLASE (EC 3.5.1.14) Table I (continued) Nucleic Acid Amino Acid Identification Code Conti9. NT Start NT Stop Function SEQ ID NO SEQ ID NO
361 362 RXS00907 N-ACYL-L-AMINO ACID AMIDOHYDROLASE (EC 3.5.1.14) 363 364 RXS02001 N-ACYL-L-AMINO ACID AMIDOHYDROLASE (EC 3.5.1.14) 365 366 RXS02101 N-ACYL-L-AMINO ACID AMIDOHYDROLASE (EC 3.5.1.14) 367 368 RXS02234 CARBAMOYL-PHOSPHATE SYNTHASE LARGE CHAIN (EC 6.3.5.5) 369 370 F RXA02234 GR00654 1 3198 CARBAMOYL-PHOSPHATE SYNTHASE LARGE CHAIN (EC
6.3.5.5) 371 372 RXS02565 N-ACYL-L-AMINO ACID AMIDOHYDROLASE (EC 3.5.1.14) 373 374 RXS02937 N-ACYL-L-AMINO ACID AMIDOHYDROLASE (EC 3.5.1.14) Histidine metabolism Nucleic Acid Amino Acid Identification Code 2onti9. NT Start NT StoP Function SEQ ID NO SEQ ID NO
375 376 RXA02194 GR00645 2897 2055 ATP PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.17) 377 378 RXA02195 GR00645 3186 2917 PHOSPHORIBOSYL-ATP PYROPHOSPHOHYDROLASE (EC
3.6.1.31) 379 380 RXA01097 GR00306 4726 4373 PHOSPHORIBOSYL-AMP CYCLOHYDROLASE (EC
3.5.4.19) L"

CARBOXAMIDE
RIBOTIDE ISOMERASE (EC 5.3.1.16) 01 383 384 RXA01101 GR00306 7726 7094 AMIDOTRANSFERASE HISH (EC 2.4.2.-) 0) 385 386 RXN01657 W0010 39950 39351 AMIDOTRANSFERASE HISH (EC 2.4.2.-) 387 388 F RXA01657 GR00460 2444 2944 AMIDOTRANSFERASE HISH (EC 2.4.2.-) o 391 392 RXN01104 W0059 7037 6432 IMIDAZOLEGLYCEROL-PHOSPHATE DEHYDRATASE (EC
4.2.1.19) (EC 4.2.1.19)/
rn HISTIOINOL-PHOSPHATASE (EC 3.1.3.15) N
395 396 RXN00446 W0112 24181 23318 HISTIDINOL-PHOSPHATE AMINOTRANSFERASE (EC
2.6.1.9) 397 398 F RXA00446 GR00108 4 525 HISTIDINOL-PHOSPHATE AMINOTRANSFERASE (EC
2.6.1.9) 399 400 RXA01105 GR00306 12044 10947 HISTIDINOL-PHOSPHATE AMINOTRANSFERASE (EC
2.6.1.9) 401 402 RXA01106 GR00306 13378 12053 HISTIDINOL DEHYDROGENASE (EC 1.1.1.23) Metabolism of aromatic amino acids Nucleic Acid Amino Acid Identification Code C2nti9. NT Start NT Stop Function SEQ ID NO SEO ID NO

CARBOXYVINYLTRANSFERASE (EC 2.5.1.19) 413 414 RXA02790 GR00777 5806 6948 4-AMINO-4-DEOXYCHORISMATE LYASE (EC 4.-.-.-) 415 416 RXN00954 W0247 3197 2577 ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE (EC
2.4.2.18) 417 418 F RXA00954 GR00263 3 590 ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE (EC
2.4.2.18) 419 420 RXN00957 W0208 1211 2764 ANTHRANILATE SYNTHASE COMPONENT I (EC
4.1.3.27) 421 422 F RXA00957 GR00264 3 1130 ANTHRANILATE SYNTHASE COMPONENT 1(EC
4.1.3.27) Table I (continued) Nucleic Acid Amino Acid Identification Code C2nti9. NT Start NT Stop Function SEQ ID NO SEQ ID NO
423 424 RXA02687 GR00754 11306 12250 CHORISMATE MUTASE (EC 5.4.99.5) /
PREPHENATE DEHYDRATASE (EC
4.2.1.51) 425 426 RXN01698 W0134 11507 12736 CHORISMATE SYNTHASE (EC 4.6.1.4) 427 428 F RXA01698 GR00477 2 991 CHORISMATE SYNTHASE (EC 4.6.1.4) 429 430 RXA01095 GR00306 3603 2821 INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE (EC
4.1.1.48) 431 432 RXA00955 GR00263 586 2007 INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE (EC
4.1.1.48) / N-(5'-PHOSPHO-RIBOSYL)ANTHRANILATE ISOMERASE (EC 5.3.1.24) 435 436 RXA00229 GR00033 1715 936 SHIKIMATE 5-DEHYDROGENASE (EC 1.1.1.25) 437 438 RXA02093 GR00629 12444 13247 SHIKIMATE 5-DEHYDROGENASE (EC 1.1.1.25) 439 440 RXA02791 GR00777 6968 7795 SHIKIMATE 5-DEHYDROGENASE (EC 1.1.1.25) 441 442 RXA01699 GR00477 984 1553 SHIKIMATE KINASE (EC 2.7.1.71) 443 444 RXA00952 GR00262 97 936 TRYPTOPHAN SYNTHASE ALPHA CHAIN (EC 4.2.1.20) 445 446 RXN00956 W0247 1140 4 TRYPTOPHAN SYNTHASE BETA CHAIN (EC 4.2.1.20) 447 448 F RXA00956 GR00263 2027 3157 TRYPTOPHAN SYNTHASE BETA CHAIN (EC
4.2.1.20) 449 450 RXA00064 GR00010 2499 3776 TYROSINE AMINOTRANSFERASE (EC 2.6.1.5) 451 452 RXN00448 W0112 33959 32940 PREPHENATE DEHYDROGENASE (EC 1.3.1.12) 453 454 F RXA00448 GR00109 3 668 PREPHENATE DEHYDROGENASE (EC 1.3.1.12) Ln 455 456 F RXA00452 GR00110 854 1099 PREPHENATE DEHYDROGENASE (EC 1.3.1.12) ALDOLASE (EC 4.1.2.15) 00)i 459 460 RXA00579 GR00156 5946 4087 PARA-AMINOBENZOATE SYNTHASE COMPONENT I (EC
4.1.3.-) AMIDOTRANSFERASE tv COMPONENT II (EC 4.1.3.-) ! ANTHRANILATE SYNTHASE COMPONENT II (EC
4.1.3.27) CN
-.3 463 464 RXN03007 W0208 3410 3778 ANTHRANILATE SYNTHASE COMPONENT II (EC
4.1.3.27) 1 o 465 466 RXN02918 W0086 25447 25887 TRYPTOPHAN SYNTHASE BETA CHAIN (EC
4.2.1.20) orn 467 468 RXN01116 W0182 7497 6886 3-OXOADIPATE COA-TRANSFERASE SUBUNIT B (EC
2.8.3.6) 469 470 RXN01115 W0182 10347 11099 3-OXOADIPATE ENOL-LACTONE HYDROLASE (EC
3.1.1.24) / 4-CARBOXYMUCONOLACTONE
471 472 RXS00116 ASPARTATE AMINOTRANSFERASE (EC 2.6.1.1) 473 474 F RXA00116 GR00018 510 4 ASPARTATE AMINOTRANSFERASE (EC 2.6.1.1) 475 476 RXS00391 O-SUCCINYLBENZOIC ACID-COA LIGASE (EC 6.2.1.26) 477 478 RXS00393 1,4-DIHYDROXY-2-NAPHTHOATE OCTAPRENYLTRANSFERASE (EC 2.5.-.-) 479 480 F RXA00393 GR00086 4030 4911 1,4-DIHYDROXY-2-NAPHTHOATE
OCTAPRENYLTRANSFERASE (EC 2.5.-.-) 481 482 RXS00446 HISTIOINOL-PHOSPHATE AMINOTRANSFERASE (EC 2.6.1.9) 483 484 F RXA00446 GR00108 4 525 HISTIDINOL-PHOSPHATE AMINOTRANSFERASE (EC
2.6.1.9) 485 486 RXS00618 ASPARTATE AMINOTRANSFERASE (EC 2.6.1.1) 487 488 F RXA00618 GR00163 213 746 ASPARTATE AMINOTRANSFERASE (EC 2.6.1.1) 489 490 F RXA00627 GR00164 854 1138 ASPARTATE AMINOTRANSFERASE (EC 2.6.1.1) 491 492 RXS01105 HISTIDINOL-PHOSPHATE AMINOTRANSFERASE (EC 2.6.1.9) 493 494 RXS02315 2-SUCCINYL-6-HYDROXY-2,4-CYCLOHEXADIENE-1-CARBOXYLATE
SYNTHASE / 2-OXOGLUTARATE DECARBOXYLASE (EC 4.1.1.71) 495 496 RXS02550 ASPARTATE AMINOTRANSFERASE (EC 2.6.1.1) 497 498 RXS02319 NAPHTHOATE SYNTHASE (EC 4.1.3.36) 499 500 RXS02908 O-SUCCINYLBENZOIC ACID--COA LIGASE (EC 6.2.1.26) 501 502 RXS03003 ASPARTATE AMINOTRANSFERASE (EC 2.6.1.1) 503 504 RXS03026 3-DEHYDROQUINATE DEHYDRATASE (EC 4.2.1.10) Table I (continued) Nucleic Acid Amino Acid Identification Code Conti . NT Start NT Stop Function SEQ ID NO SEQ ID NO
505 506 RXS03074 S-ADENOSYLMETHIONINE:2-DEMETHYLMENAQUINONE
METHYLTRANSFERASE (EC 2 1.-.-) AMINO ACIDS AND RIBOFLAVIN

AMINO ACIDS

ACIDS

AMINO ACIDS
Aminobutyrate metabolism Nucleic Acid Amino Acid Identification Code Contig. NT Start NT StoP Function o SEQ ID NO SEQ ID NO
515 516 RXN03063 W0035 666 1697 4-aminobutyrate aminotransferase (EC 2.6.1.19) Ln 517 518 RXN02970 W0021 4714 6081 ACETYLORNITHINE AMINOTRANSFERASE (EC
2.6.1.11) o 519 520 F RXA01009 GR00287 4714 5943 ACETYLORNITHINE AMINOTRANSFERASE (EC
2.6.1.11) Vitamins, vitamin-like substances (cofactors), nutraceuticals Thiamine metabolism 0' F-' Nucleic Acid Amino Acid Identification Code Conti . NT Start NT StoP Function SEQ ID NO SEQ ID NO

523 524 RXA01019 GR00291 6 995 THIAMIN-MONOPHOSPHATE KINASE (EC 2.7.4.16) 525 526 RXA01352 GR00393 609 4 THIAMIN-PHOSPHATE PYROPHOSPHORYLASE (EC
2.5.1.3) 533 534 RXA01208 GR00348 229 1032 HYDROXYETHYLTHIAZOLE KINASE (EC 2.7.1.50) 539 540 RXN01209 W0270 1019 2446 PHOSPHOMETHYLPYRIMIDINE KINASE (EC 2.7.4.7) 541 542 F RXA01209 GR00348 1019 2446 PHOSPHOMETHYLPYRIMIDINE KINASE (EC
2.7.4.7) 543 544 RXN01413 W0050 27306 27905 PHOSPHOMETHYLPYRIMIDINE KINASE (EC 2.7.4.7) 545 546 RXN01617 W0050 22187 22858 PHOSPHOMETHYLPYRIMIDINE KINASE (EC 2.7.4.7) 547 548 F RXA01617 GR00451 2 616 PHOSPHOMETHYLPYRIMIDINE KINASE (EC 2.7.4.7) 549 550 RXS01807 PYRIDOXINE KINASE (EC 2.7.1.35) Table I (continued) Riboflavin metabolism Nucleic Acid Amino Acid Identification Code Contig. NT Start NT Stop Function SEQ ID NO SEQ ID NO
553 554 RXN02246 W0130 4388 5371 diaminohydroxyphosphoribosylaminopyrimidine deaminase (EC 3.5.4.26) / 5-amino-6-(5-phosphoribosylamino)uracil reductase (EC 1.1.1.193) 555 556 F RXA02246 GR00654 14299 15282 RIBG PROTEIN riboflavin-specific deaminase [EC:3.5.4.-]
557 558 RXA02247 GR00654 15286 15918 RIBOFLAVIN SYNTHASE ALPHA CHAIN (EC
2.5.1.9) 559 560 RXN02248 W0130 6021 7286 GTP CYCLOHYDROLASE II (EC 3.5.4.25) / 3,4-PHOSPHATE SYNTHASE
561 562 F RXA02248 GR00654 15932 17197 RIBA PROTEIN - GTP cyclohydrolase II
[EC:3.5.4.25]
563 564 RXN02249 W0130 7301 7777 6,7-DIMETHYL-B-RIBITYLLUMAZINE SYNTHASE (EC
2.5.1.9) 565 566 F RXA02249 GR00654 17212 17688 RIBH PROTEIN - 6,7-dimethyl-8-ribityllumazine synthase (dmri synthase, lumazine synthase, riboflavin synthase beta chain) [EC:2.5.1.9]

569 570 RXA01489 GR00423 3410 2388 RIBOFLAVIN KINASE (EC 2.7.1.26) / FMN
ADENYLYLTRANSFERASE (EC
2.7.7.2) o 571 572 RXA02135 GR0o639 2809 1736 NICOTINATE-NUCLEOTIDE--DIMETHYLBENZIMIDAZOLE
Ln PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.21) 573 574 RXA01489 GR00423 3410 2388 RIBOFLAVIN KINASE (EC 2.7.1.26) / FMN
ADENYLYLTRANSFERASE (EC 0) 2.7.7.2) tv 575 576 RXN01712 W0191 8993 8298 RIBOFLAVIN-SPECIFIC DEAMINASE (EC 3.5.4.-) 577 578 F RXA01712 GR00484 2652 2152 RIBOFLAVIN-SPECIFIC DEAMINASE (EC 3.5.4.-) 579 580 RXN02384 W0213 1386 679 ALPHA-RIBAZOLE-5'-PHOSPHATE PHOSPHATASE (EC
3.1.3.-) 581 582 RXN01560 W0319 767 438 RIBOFLAVIN-SPECIFIC DEAMINASE (EC 3.5.4.-) ON -.3 0) 589 590 F RXA02380 GR00691 709 56 Predicted nucleotidyltransferases ~

LIPIDS

AMINO ACIDS AND RIBOFLAVIN
Vitamin B6 metabolism Nucleic Acid Amino Acid Identification Code Contig. NT Start NT Stop Function SEQ ID NO SEQ ID NO
595 596 RXA01807 GR00509 7868 7077 PYRIDOXINE KINASE (EC 2.7.1.35), pyridoxal/pyridoxine/pyridoxamine kinase Table 1(continued) Nicotinate (nicotinic acid), nicotinamide, NAD and NADP

Nucleic Acid Amino Acid Identification Code Conti . NT Start NT StoP Function SEQ ID NO SEQ ID NO
597 598 RXN02754 W0084 22564 23901 NICOTINATE PHOSPHORIBOSYLTRANSFERASE (EC
2.4.2.11) 599 600 F RXA02405 GR00701 774 4 NICOTINATE PHOSPHORIBOSYLTRANSFERASE (EC
2.4.2.11) 601 602 F RXA02754 GR00766 3 488 NICOTINATE PHOSPHORIBOSYLTRANSFERASE (EC
2.4.2.11) (CARBOXYLATING) (EC
2.4.2.19) NAD Biosynthesis Nucleic Acid Amino Acid Identification Code Conti9. NT Start NT Stop Function N
SEQ ID NO SEQ ID NO Ln 607 608 RXA01073 GR00300 1274 2104 NH(3)-DEPENDENT NAD(+) SYNTHETASE (EC
6.3.5.1) 609 610 RXN02754 W0084 22564 23901 NICOTINATE PHOSPHORIBOSYLTRANSFERASE (EC
2.4.2.11) rn Pantothenate and Coenzyme A(CoA) biosynthesis -.3 Nucleic Acid Amino Acid Identification Code Conti9' NT Start NT Stop Function 611 612 RXA02299 GR00662 10452 10859 ASPARTATE 1-DECARBOXYLASE PRECURSOR (EC
4.1.1.11) 613 614 RXA01928 GR00555 1957 1121 PANTOATE--BETA-ALANINE LIGASE (EC 6.3.2.1) HYDROXYMETHYLTRANSFERASE (EC 2.1.2.11) / DECARBOXYLASE (EC 4.1.1.44) HYDROXYMETHYLTRANSFERASE (EC 2.1.2.11) 619 620 RXA01521 GR00424 25167 25964 PANTOATE-BETA-ALANINE LIGASE (EC 6.3.2.1) 621 622 RXS01145 KETOL-ACID REDUCTOISOMERASE (EC 1.1.1.86) 623 624 F RXA01145 GR00321 1075 1530 KETOL-ACID REDUCTOISOMERASE (EC 1.1.1.86) 627 628 RXA00581 GR00156 7572 8540 PANTOTHENATE KINASE (EC 2.7.1.33) 629 630 RXS00838 2-DEHYDROPANTOATE 2-REDUCTASE (EC 1.1.1.169) 631 632 RXC02238 PROTEIN INVOLVED IN METABOLISM OF S-ADENOSYLMETHIONINE, PURINES
AND PANTOTHENATE

Biotin metabolism Nucleic Acid Amino Acid Identification Code Conti . NT Start NT Stop Function SEQ ID NO SEQ ID NO

Table I (continued?
Nucleic Acid Amino Acid Identification Code Conti9= NT Start NT Stop Function SEQ ID NO SEQ ID NO

637 638 RXA00166 GR0o025 3650 4309 BIOTIN SYNTHESIS PROTEIN BIOC

AMINOTRANSFERASE
(EC 2.6.1.62) 641 642 RXA00632 GR00166 2281 1610 DETHIOBIOTIN SYNTHETASE (EC 6.3.3.3) 643 644 RXA00295 GR00047 3407 4408 BIOTIN SYNTHASE (EC 2.8.1.6) Lipoic Acid Ln Nucleic Acid Amino Acid Identification Code Contig. NT Start NT Stop Function m SEQ ID NO SEQ ID NO N

663 664 RXA01746 GR00495 1614 2366 LIPOATE-PROTEIN LIGASE B (EC 6.-.-.-) ~ o 665 666 RXA02106 GR00632 472 1527 LIPOATE-PROTEIN LIGASE A(EC
667 668 RXS01 183 DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE COMPONENT (E2) OF 2- o OXOGLUTARATE DEHYDROGENASE COMPLEX (EC 2.3.1.61) 0) 669 670 RXS01260 LIPOAMIDE DEHYDROGENASE COMPONENT (E3) OF BRANCHED-CHAIN
ALPHA-KETO ACID DEHYDROGENASE COMPLEX (EC 1.8.1.4) 671 672 RXS01261 LIPOAMIDE DEHYDROGENASE COMPONENT (E3) OF BRANCHED-CHAIN
ALPHA-KETO ACID DEHYDROGENASE COMPLEX (EC 1.8.1.4) Folate biosynthesis Nucleic Acid Amino Acid Identification Code Conti . NT Start NT Stop Function SEQ ID NO SEQ ID NO
673 674 RXA02717 GR00758 18281 17400 5,10-METHYLENETETRAHYDROFOLATE REDUCTASE
(EC 1.7.99.5) 675 676 RXN02027 W0296 503 1003 5-FORMYLTETRAHYDROFOLATE CYCLO-LIGASE (EC
6.3.3.2) 677 678 F RXA02027 GR00616 500 6 5-FORMYLTETRAHYDROFOLATE CYCLO-LIGASE (EC
6.3.3.2) 679 680 RXA00106 GR00014 17469 17924 DIHYDROFOLATE REDUCTASE (EC 1.5.1.3) 681 682 RXN01321 W0082 8868 9788 FORMYLTETRAHYDROFOLATE DEFORMYLASE (EC
3.5.1.10) 683 684 F RXA01321 GR00384 23 559 FORMYLTETRAHYOROFOLATE DEFORMYLASE (EC
3.5.1.10) 685 686 RXA00461 GR00116 428 1279 METHYLENETETRAHYDROFOLATE DEHYDROGENASE (EC
1.5.1.5) /
METHENYLTETRAHYDROFOLATE CYCLOHYDROLASE (EC 3.5.4.9) 687 688 RXA01514 GR00424 20922 21509 GTP CYCLOHYDROLASE I (EC 3.5.4.16) 689 690 RXA01516 GR00424 22360 22749 DIHYDRONEOPTERIN ALDOLASE (EC 4.1.2.25) Table 1 (continued) Nucleic Acid Amino Acid Identification Code Conti9. NT Start NT Stop Function SEQ ID NO SEQ ID NO
691 692 RXA01515 GR00424 21513 22364 DIHYDROPTEROATE SYNTHASE (EC 2.5.1.15) 693 694 RXA02024 GR00613 4026 4784 DIHYDROPTEROATE SYNTHASE (EC 2.5.1.15) 695 696 RXA00106 GR00014 17469 17924 DIHYDROFOLATE REDUCTASE (EC 1.5.1.3) 697 698 RXA00989 GR00280 2903 1371 FOLYLPOLYGLUTAMATE SYNTHASE (EC 6.3.2.17) HYDROXYMETHYLDIHYDROPTERIDINE
PYROPHOSPHOKINASE (EC 2.7.6.3) 701 702 RXA00579 GR00156 5946 4087 PARA-AMINOBENZOATE SYNTHASE COMPONENT I (EC
4.1.3.-) AMIDOTRANSFERASE
COMPONENT II (EC 4.1.3.-) ! ANTHRANILATE SYNTHASE COMPONENT II (EC
4.1.3.27) 705 706 RXA02790 GR00777 5806 6948 4-AMINO-4-DEOXYCHORISMATE LYASE (EC 4.-.- -) 707 708 RXA00106 GR00014 17469 17924 DIHYDROFOLATE REDUCTASE (EC 1.5.1.3) METHYLTRANSFERASE
(EC 2.1.1.13) METHYLTRANSFERASE ryy (EC 2.1.1.13) HOMOCYSTEINE t~v METHYLTRANSFERASE L"

HOMOCYSTEINE o METHYLTRANSFERASE (EC 2.1.1.14) 01 717 718 F RXA02086 GR0o629 5252 5731 5-METHYLTETRAHYDROPTEROYLTRIGLUTAMATE-HOMOCYSTEINE 0) METHYLTRANSFERASE (EC 2.1.1.14) METHYLTRANSFERASE (EC 2.1.1.14) HOMOCYSTEINE O i METHYLTRANSFERASE (EC 2.1.1.14) ~

HOMOCYSTEINE i METHYLTRANSFERASE (EC 2.1.1.14) (EC 2.1.1.13) Molybdopterin Metabolism Nucleic Acid Amino Acid Identification Code Co2ti9. NT Start NT Stop Function SEQ ID NO SEQ ID NO

739 740 RXN00437 W0112 17824 17369 MOLYBDOPTERIN (MPT) CONVERTING FACTOR, 741 742 F RXA00437 GR00103 3 362 MOLYBDOPTERIN (MPT) CONVERTING FACTOR, Table I (continued) Nucleic Acid Amino Acid Identification Code Contlg. NT Start NT Stop Function SEQ ID NO SEQ ID NO

METHYLTRANSFERASE (EC 2.1.1.14) HOMOCYSTEINE
METHYLTRANSFERASE (EC 2.1.1.14) HOMOCYSTEINE
METHYLTRANSFERASE (EC 2.1.1.14) METHYLTRANSFERASE (EC 2.1.1.14) HOMOCYSTEINE
METHYLTRANSFERASE (EC 2.1.1.14) HOMOCYSTEINE
METHYLTRANSFERASE (EC 2.1.1.14) 767 768 RXA01516 GR00424 22360 22749 DIHYDRONEOPTERIN ALDOLASE (EC 4.1.2.25) ro 769 770 RXA01515 GR00424 21513 22364 DIHYDROPTEROATE SYNTHASE (EC 2.5.1.15) Ln 771 772 RXA02024 GR00613 4026 4784 DIHYDROPTEROATE SYNTHASE (EC 2.5.1.15) BIOSYNTHESIS PROTEIN A 0) 783 784 RXA02318 GR00665 9684 9962 (090909) pterin4a-carbinolamine dehydratase [Synechocystis sp.] .3 HYDROXYMETHYLDIHYDROPTERIDINE
PYROPHOSPHOKINASE (EC 2.7.6.3) m 789 790 RXS02556 FLAVOHEMOPROTEIN / DIHYDROPTERIDINE REDUCTASE (EC 1.6.99.7) ~
791 792 RXS02560 OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE (EC 1.-.-.-) I
DIHYDROPTERIDINE REDUCTASE (EC1.6.99.7) Vitamin B12, porphyrins and heme metabolism Nucleic Acid Amino Acid Identification Code Conti9. NT Start NT Stop Function SEQ ID NO SEQ ID NO
793 794 RXA00382 GR0o082 2752 1451 GLUTAMATE-1-SEMIALDEHYDE 2,1-AMINOMUTASE
(EC 5.4.3.8) 795 796 RXA00156 GR00023 10509 9400 FERROCHELATASE (EC 4.99.1.1) 797 798 RXA00624 GR00163 7910 8596 FERROCHELATASE (EC 4.99.1.1) OXIDASE (EC 1.-.-.-) 803 804 RXN02503 W0007 22456 22854 PORPHOBILINOGEN DEAMINASE (EC 4.3.1.8) 805 806 F RXA02503 GR00720 16906 17340 PORPHOBILINOGEN DEAMINASE (EC 4.3.1.8) 807 808 RXA00377 GR00081 1427 306 UROPORPHYRINOGEN DECARBOXYLASE (EC 4.1.1.37) 809 810 RXN02504 W0007 22805 23362 PORPHOBILINOGEN DEAMINASE (EC 4.3.1.8) 811 812 F RXA02504 GR00720 17379 17816 PORPHOBILINOGEN DEAMINASE (EC 4.3.1.8) Table 1 (continued) Nucleic Acid Amino Acid Identification Code Contig. NT Start NT StoP Function SEQ ID NO SEQ ID NO
813 814 RXN01162 W0088 1849 524 PRECORRIN-6Y METHYLASE (EC 2.1.1.-) 815 816 F RXA01162 GR00330 1248 4 PRECORRIN-6Y METHYLASE (EC 2.1.1.-) 817 818 RXA01692 GR00474 1498 749 UROPORPHYRIN-111 C-METHYLTRANSFERASE (EC
2.1.1.107) 819 820 RXN00371 W0226 4180 5973 UROPORPHYRIN-111 C-METHYLTRANSFERASE (EC
2.1.1.107) /
UROPORPHYRINOGEN-Ili SYNTHASE (EC 4.2.1.75) 821 822 F RXA00371 GR00078 929 6 UROPORPHYRIN-111 C-METHYLTRANSFERASE (EC
2.1.1.107) /
UROPORPHYRINOGEN-III SYNTHASE (EC 4.2.1.75) 823 824 F RXA00374 GR00079 1102 371 UROPORPHYRIN-lil C-METHYLTRANSFERASE (EC
2.1.1.107) /
UROPORPHYRINOGEN-III SYNTHASE (EC 4.2.1.75) 825 826 RXN00383 VV0223 4206 2863 PROTOPORPHYRINOGEN OXIDASE (EC 1.3.3.4) 827 828 F RXA00376 GR00081 287 6 PROTOPORPHYRINOGEN OXIDASE (EC 1.3.3.4) 829 830 F RXA00383 GR00082 3876 2863 PROTOPORPHYRINOGEN OXIDASE (EC 1.3.3.4) 833 834 RXA02134 GR00639 1721 801 COBALAMIN (5'-PHOSPHATE) SYNTHASE

DIMETHYLBENZIMIDAZOLE
PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.21) GUANYLYLTRANSFERASE N
839 840 RXN03114 VV0088 1 552 COBG PROTEIN (EC 1.-.-.-) Ln PRECURSOR
843 844 RXS03205 HEMK PROTEIN 0) 845 846 F RXA00306 HEMK PROTEIN 0) O ~
Vitamin C precursors 0) Nucleic Acid Amino Acid Identification Code Contig. NT Start NT StoP Function SEQ ID NO SEQ ID NO
849 850 RXN00420 W0112 2511 1048 L-GULONOLACTONE OXIDASE (EC 1.1.3.8) 851 852 F RXA00420 GR00096 2 541 L-GULONOLACTONE OXIDASE (EC 1.1.3.8) 853 854 F RXA00426 GR00097 1737 2258 L-GULONOLACTONE OXIDASE (EC 1.1.3.8) 855 856 RXN00708 W0005 4678 3872 2,5-DIKETO-D-GLUCONIC ACID REDUCTASE (EC
1.1.1.-) 857 858 F RXA00708 GR00185 2030 1359 2,5-DIKETO-D-GLUCONIC ACID REDUCTASE (EC
1.1.1.-) 859 860 RXA02373 GR00688 1540 626 2,5-DIKETO-D-GLUCONIC ACID REDUCTASE (EC
1.1.1 -) 861 862 RXS00389 oxoglutarate semialdehyde dehydrogenase (EC 1.2.1.-) 863 864 RXS00419 ACETOACETYL-COA REDUCTASE (EC 1.1.1.36) PRECURSORS

Vitamin K2 Nucleic Acid Amino Acid Identification Code Contig. NT Start NT Stop Function SEQ ID NO SEQ ID NO
869 870 RXS03074 S-ADENOSYLMETHIONINE:2-DEMETHYLMENAQUINONE
METHYLTRANSFERASE (EC 2.1.-.-) Table I (continued) Nucleic Acid Amino Acid Identification Code Contig. NT Start NT Stop Function SEQ ID NO SEQ ID NO
871 872 F RXA02906 GR10044 1142 645 S-ADENOSYLMETHIONINE:2-DEMETHYLMENAQUINONE
METHYLTRANSFERASE (EC 2.1.-.-) 873 874 RXA02315 GR00665 8011 6383 2-SUCCINYL-6-HYDROXY-2,4-CYCLOHEXADIENE-1-CARBOXYLATE
SYNTHASE /2-OXOGLUTARATE DECARBOXYLASE (EC 4.1.1.71) 875 876 RXA02319 GR00665 9977 10933 NAPHTHOATE SYNTHASE (EC 4.1.3.36) 877 878 RXS00393 1,4-DIHYDROXY-2-NAPHTHOATE OCTAPRENYLTRANSFERASE (EC 2.5.-.-) 879 880 F RXA00393 GR00086 4030 4911 1,4-DIHYDROXY-2-NAPHTHOATE
OCTAPRENYLTRANSFERASE (EC 2.5.-.-) 881 882 RXA00391 GR00086 2031 2750 O-SUCCINYLBENZOIC ACID-COA LIGASE (EC
6.2.1,26) 883 884 RXS02908 O-SUCCINYLBENZOIC ACID-COA LIGASE (EC 6-2.1.26) Ubiquinone biosynthesis Nucleic Acid Amino Acid Identification Code Contig= NT Start NT Stop Function SEQ 10 NO SEQ 1D NO 1y (EC 2.1.1.64) (EC 2.1.1.64) tv (EC 2.1.1.64) Ln METHLYTRANSFERASE UBIE
(EC 2.1.1.-) m 893 894 RXS00998 COMA OPERON PROTEIN 2 0) J O
Purines and Pyrimidines and other Nucleotides o Regulation of purine and pyrimidine biosynthesis pathways Purine metabolism Purine Biosynthesis Nucleic Acid Amino Acid Identification Code Contig. NT Start NT Stop Function SEQ ID NO SEQ ID NO
895 896 RXA01215 GR00352 1187 213 RIBOSE-PHOSPHATE PYROPHOSPHOKINASE, PRPP
synthetase (EC 2.7.6.1) 897 898 RXN00558 W0103 8235 9581 AMIDOPHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.14) 899 900 F RXA00558 GR00148 61 501 AMIDOPHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.14) 901 902 RXN00626 W0135 11624 10362 PHOSPHORIBOSYLAMINE-GLYCINE LIGASE (EC
6.3.4.13) 903 904 F RXA00629 GR00165 1450 1713 PHOSPHORIBOSYLAMINE-GLYCINE LIGASE (EC
6.3.4.13) 905 906 F RXA00626 GR00164 1 780 PHOSPHORIBOSYLAMINE--GLYCINE LIGASE, GARS (EC
6.3.4.13) 907 908 RXA02623 GR00746 4875 4285 PHOSPHORIBOSYLAMINE-GLYCINE LIGASE (EC
6.3.4.13) /
PHOSPHORIBOSYLFORMYLGLYCINAMIDINE CYCLO-LIGASE (EC 6.3.3.1)/
PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE (EC 2.1.2.2) FORMYLTRANSFERASE 2 (EC 2_1.2.-) Table I (continued) Nucleic Acid Amino Acid Identification Code C2nti9. NT Start NT Stop Function SEQ ID NO SEQ ID NO

(EC 6.3.5.3) (EC 6.3.5.3) (EC 6.3.5.3) (EC 6.3.5.3) (EC 6.3.5.3) SUCCINOCARBOXAMIDE SYNTHASE
(EC 6.3.2.6) LIGASE (EC 6.3.3.1) LIGASE (EC 6.3.3.1) LIGASE (EC 6.3.3.1) ATPASE SUBUNIT (EC
4.1.1.21) ATPASE SUBUNIT (EC
4.1.1.21) CATALYTIC SUBUNIT
(EC 4.1.1.21) CATALYTIC SUBUNIT
(EC 4.1.1.21) Ln 937 938 F RXA02350 GR00678 1120 911 PHOSPHORIBOSYLAMINOiMIDAZOLE CARBOXYLASE
CATALYTIC SUBUNIT
(EC 4.1.1.21) ~
939 940 RXA01087 GR00304 498 1373 PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE (EC
4.1.1.21) 941 942 RXA00619 GR00163 793 2220 ADENYLOSUCCINATE LYASE (EC 4.3.2.2) FORMYLTRANSFERASE i N
(EC 2.1.2.3) / IMP CYCLOHYDROLASE (EC 3.5.4.10) N o GMP, GDP, AMP and ADP synthesis, from inosine-5'-monophosphate (IMP) 0) Nucleic Acid Amino Acid Identification Code Conii9. NT Start NT Stop Function SEQ ID NO SEQ ID NO
945 946 RXN00488 W0086 19066 20583 INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE (EC
1.1.1.205) 947 948 F RXA00492 GR00122 1171 1644 INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
(EC 1.1.1.205) 949 950 F RXA00488 GR00121 1 534 INOSINE-5'-MONOPHOSPHATE.DEHYDROGENASE (EC
1.1.1.205) 951 952 RXA02469 GR00715 1927 497 INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE (EC
1.1.1.205) 953 954 RXN00487 W0086 23734 25302 GMP SYNTHASE [GLUTAMINE-HYDROLYZING] (EC
6.3.5.2) 955 956 F RXA00487 GR00120 712 2097 GMP SYNTHASE (EC 6.3.4.1) 957 958 RXA02237 GR00654 4577 5146 GUANYLATE KINASE (EC 2.7.4.8) 959 960 RXA01446 GR00418 17765 16476 ADENYLOSUCCINATE SYNTHETASE (EC 6.3.4.4) 961 962 RXA00619 GR00163 793 2220 ADENYLOSUCCINATE LYASE (EC 4.3.2.2) 963 964 RXA00688 GR00179 10443 10985 ADENYLATE KINASE (EC 2.7.4.3) 965 966 RXA00266 GR00040 3769 3362 NUCLEOSIDE DIPHOSPHATE KINASE (EC 2.7.4.6) Table I (continued) GMP/AMP degrading activities NuGeic Acid Amino Acid Identification Code Conti9' NT Start NT Stop Function 967 968 RXA00489 GR00121 654 1775 GMP REDUCTASE (EC 1.6.6.8) 969 970 RXN02281 W0152 1893 3323 AMP NUCLEOSIDASE (EC 3.2.2.4) 971 972 F RXA02281 GR00659 1101 34 AMP NUCLEOSIDASE (EC 3.2.2.4) Pyrimidine metabolism Pyrimidine biosynthesis de novo:

Nucleic Acid Amino Acid Identification Code Contig. NT Start NT Stop Function SEQ ID NO SEQ ID NO

(EC 6.3.5.5) CHAIN (EC 2.1.3.2) tv 977 978 RXA00146 GR0o022 8249 9589 DIHYDROOROTASE (EC 3.5.2.3) L"
979 980 RXA02208 GR00647 2 1003 DIHYDROOROTATE DEHYDROGENASE (EC 1.3.3.1) o 981 982 RXA01660 GR00462 591 1142 OROTATE PHOSPHORIBOSYLTRANSFERASE (EC
2.4.2.10) 983 984 RXA02235 GR00654 3207 4040 OROTIDINE 5'-PHOSPHATE DECARBOXYLASE (EC
4.1.1.23) 985 986 RXN01892 W0150 3020 3748 URIDYLATE KINASE (EC 2.7.4.-) 987 988 F RXA01892 GR00542 47 775 URIDYLATE KINASE (EC 2.7.4.-) J o 989 990 RXA00105 GR0o014 16672 17346 THYMIOYLATE SYNTHASE (EC 2.1.1.45) -.3 991 992 RXA00131 GR00020 7621 7013 THYMIDYLATE KINASE (EC 2.7.4.9) 993 994 RXA00266 GR0o040 3769 3362 NUCLEOSIDE DIPHOSPHATE KINASE (EC 2.7.4.6) 0) 995 996 RXA00718 GR00188 4576 5283 CYTIDYLATE KINASE (EC 2.7.4.14) 997 998 RXA01599 GR00447 8780 10441 CTP SYNTHASE (EC 6.3.4.2) (EC 6.3.5.5) (EC 6.3.5.5) 1003 1004 RXN00450 W0112 34491 34814 CYTOSINE DEAMINASE (EC 3.5.4.1) 1005 1006 F RXA00450 GR00110 322 5 CYTOSINE DEAMINASE (EC 3.5.4.1) 1007 1008 RXN02272 W0020 15566 16810 CYTOSINE DEAMINASE (EC 3.5.4.1) 1009 1010 F RXA02272 GR00655 6691 7935 CREATININE DEAMINASE (EC 3.5.4.21) 1011 1012 RXN03004 W0237 1862 2341 DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE (EC
3.5.4.13) 1013 1014 RXN03137 W0129 9680 9579 THYMIDYLATE SYNTHASE (EC 2.1.1.45) 1015 1016 RXN03171 W0328 568 1080 URACIL PHOSPHORIBOSYLTRANSFERASE (EC
2.4.2.9) 1017 1018 F RXA02857 GR10003 570 1082 URACIL PHOSPHORIBOSYLTRANSFERASE (EC
2.4.2.9) Table I (continued) Purine and pyrimidine base, nucleoside and nucleotide salvage, interconversion, reduction and degradation:
Purines:

Nucleic Acid Amino Acid Identification Code Contig= NT Start NT Stop Function SEQ ID NO SEQ ID NO
1019 1020 RXA02771 GR00772 1329 1883 ADENINE PHOSPHORIBOSYLTRANSFERASE (EC
2.4.2.7) PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.8) PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.22) 1025 1026 RXA00981 GR00276 3388 4017 GTP PYROPHOSPHOKINASE (EC 2.7.6.5) 1027 1028 RXN02772 W0171 2045 1011 GUANOSINE-3',5'-BIS(DIPHOSPHATE) 3'-PYROPHOSPHOHYDROLASE (EC
3.1.7.2) 1029 1030 F RXA02772 GR00772 1962 2741 GUANOSINE-3',5'-BIS(DIPHOSPHATE) 3'-PYROPHOSPHOHYDROLASE (EC
3.1.7.2) 1031 1032 F RXA02773 GR00772 2741 2902 GUANOSINE-3',5'-BIS(DIPHOSPHATE) 3'-PYROPHOSPHOHYDROLASE (EC
3.1.7.2) 1033 1034 RXA01835 GR00517 3147 3677 GUANOSINE-3',5'-BIS(DIPHOSPHATE) 3'-PYROPHOSPHOHYDROLASE (EC
3.1.7.2) TRIPHOSPHOHYDROLASE (EC 3.1.5.1) L"
1037 1038 RXN01027 W0143 5761 6768 DIADENOSINE 5',5"'-P1,P4-TETRAPHOSPHATE
HYDROLASE (EC 3.6.1.17) o 1039 1040 F RXA01024 GR00293 661 5 DIADENOSINE 5',5"'-P1,P4-TETRAPHOSPHATE
HYDROLASE (EC 3.6.1.17) m m 1041 1042 F RXA01027 GR00294 2580 2347 DIADENOSINE 5',5"'-P1,P4-TETRAPHOSPHATE
HYDROLASE (EC 3.6.1.17) tv 1043 1044 RXA01528 GR00425 5653 5126 DIADENOSINE 5',5"'-P1,P4-TETRAPHOSPHATE
HYDROLASE (EC 3.6.1.17) 1045 1046 RXA00072 GR00012 446 6 PHOSPHOADENOSINE PHOSPHOSULFATE REDUCTASE (EC
1.8.99.4) 1047 1048 RXA01878 GR00537 1239 2117 DIMETHYLADENOSINE TRANSFERASE (EC 2.1.1.-) p o 1049 1050 RXN02281 W0152 1893 3323 AMP NUCLEOSIDASE (EC 3.2.2.4) ~ .3 1051 1052 F RXA02281 GR00659 1101 34 AMP NUCLEOSIDASE (EC 3.2.2.4) 1053 1054 RXN01240 W0090 30442 29420 GTP PYROPHOSPHOKINASE (EC 2.7.6.5) 1055 1056 RXN02008 W0171 1138 5 GUANOSINE-3',5'-BIS(DIPHOSPHATE) 3'-PYROPHOSPHOHYDROLASE (EC
3.1.7.2) Pyrimdine and purine metabolism:

Nucleic Acid Amino Acid Identification Code Contig. NT Start NT Stop Function SEQ ID NO SEQ ID NO

HYDROLASE (EC 3.2.2.1) HYDROLASE (EC 3.2.2.1) HYDROLASE (EC 3.2.2.1) 1063 1064 RXA02497 GR00720 10059 10985 EXOPOLYPHOSPHATASE (EC 3.6.1.11) ALPHA CHAIN (EC 1.17.4.1) CHAIN (EC 1.17.4.1) ALPHA CHAIN (EC 1.17.4.1) BETA CHAIN (EC 1.17.4.1) 1077 1078 RXA00867 GR00237 1 627 POLYRiBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE (EC
2.7.7.8) 1079 1080 RXA01416 GR00413 2 631 POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE (EC
2.7.7.8) 1081 1082 RXA01486 GR00423 660 4 POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE (EC
2.7.7.8) Table I (continued) NuGeic Acid Amino Acid Identification Code Conti9. NT Start NT Stop Function SEQ tD NO SEQ ID NO
1083 1084 RXA01678 GR00467 7162 7689 2',3'-CYCLIC-NUCLEOTIDE 2'-PHOSPHODIESTERASE (EC 3.1.4.16) 1085 1086 RXA01679 GR00467 7729 8964 2',3'-CYCLIC-NUCLEOTIDE 2'-PHOSPHODIESTERASE (EC 3.1.4.16) HYDROLASE (EC 3.2.2.1) 1101 1102 RXC02238 PROTEIN INVOLVED IN METABOLISM OF S-ADENOSYLMETHIONINE, PURINES
AND PANTOTHENATE

METABOLISM
Pyrimdines:

Nucleic Acid Amino Acid Identification Code Conti . NT Start NT Stop Function Ln SEQ ID NO SEQ ID NO
1105 1106 RXN03171 W0328 568 1080 URACII PHOSPHORIBOSYLTRANSFERASE (EC
2.4.2.9) 0) 1107 1108 F RXA02857 GR10003 570 1082 URACIL PHOSPHORIBOSYLTRANSFERASE (EC
2.4.2.9) N
1109 1110 RXN00450 W0112 34491 34814 CYTOSINE DEAMINASE (EC 3.5.4.1) 1111 1112 F RXA00450 GR00110 322 5 CYTOSINE DEAMINASE (EC 3.5.4.1) ~ N
1113 1114 RXA00465 GR00117 337 828 CYTOSINE DEAMINASE (EC 3.5.4.1) ~ o0 SYNTHASE B(EC 4.2.1.70) 1117 1118 RXA01894 GR00542 1622 2476 PHOSPHATIDATE CYTIDYLYLTRANSFERASE (EC
2.7.7.41) o 1119 1120 RXA02536 GR00726 8581 7826 BETA-UREIDOPROPIONASE (EC 3.5.1.6) o) 1121 1122 RXN01209 W0270 1019 2446 PHOSPHOMETHYLPYRIMIDINE KINASE (EC 2.7.4.7) tv 1123 1124 F RXA01209 GR00348 1019 2446 PHOSPHOMETHYLPYRIMIDINE KINASE (EC
2.7.4.7) 1125 1126 RXN01617 W0050 22187 22858 PHOSPHOMETHYLPYRIMIDINE KINASE (EC
2.7.4.7) 1127 1128 F RXA01617 GR00451 2 616 PHOSPHOMETHYLPYRIMIDINE KINASE (EC 2.7.4.7) ADENOSYLHOMOCYSTEINE

Sugars Table I (continued) Trehalose Nucleic Acid Amino Acid Identfication Code Contig= NT Start NT Stop Function SEQ ID NO SEQ ID NO
1139 1140 RXA00347 GR00065 246 1013 TREHALOSE-PHOSPHATASE (EC 3.1.3.12) tov 1141 1142 RXN01239 W0090 32921 30489 maltooligosyltrehalose synthase L'' 1143 1144 F RXA01239 GR00358 5147 7579 maltooligosyltrehalose synthase 1145 1146 RXA02645 GR00751 714 2543 maltooligosyltrehalose trehalohydrolase o) 1147 1148 RXN02355 W0051 735 4 TREHALOSE/MALTOSE BINDING PROTEIN 0) 1149 1150 RXN02909 W0135 38532 39017 Hypothetical Trehalose-Binding Protein 1151 1152 RXS00349 Hypothetical Trehalose Transport Protein 1153 1154 RXS03183 TREHALOSE/MALTOSE BINDING PROTEIN ~

rn F-' TABLE 2 - Excluded Genes GenBankTM' Gene Name Gene Function Reference Accession No.
A09073 ppg Phosphoenol pyruvate carboxylase Bachmann, B. et al. "DNA fragment coding for phosphoenolpyruvat corboxylase, recombinant DNA carrying said fragment, strains carrying the recombinant DNA and method for producing L-aminino acids using said strains," Patent: EP 0358940-A 3 03/21/90 A45579, Threonine dehydratase Moeckel, B. et al. "Production of L-isoleucine by means of recombinant A45581, micro-organisms with deregulated threonine dehydratase," Patent: WO
A45583, 9519442-A 5 07/20/95 AB003 t32 murC; ftsQ; ftsZ Kobayashi, M. et al. "Cloning, sequencing, and characterization of the ftsZ
gene from coryneform bacteria," Biochem. Biophys. Res. Commun., 236(2):383-388 (1997) AB015023 murC; ftsQ Wachi, M. et al. "A murC gene from Coryneform bacteria,"
Appl. Microbiol. Ln Biotechnol., 51(2):223-228 (1999) AB018530 dtsR Kimura, E. et al. "Molecular cloning of a novel gene, dtsR, which rescues the O1 rn detergent sensitivity of a mutant derived from Brevibacterium lactofermentum," Biosci. Biotechnol. Biochem., 60(10):1565-1570 (1996) AB018531 dtsRl; dtsR2 AB020624 murl D-glutamate racemase o AB023377 tkt transketolase rn AB024708 gltB; gltD Glutamine 2-oxoglutarate aminotransferase large and small subunits AB025424 acn aconitase AB027714 rep Replication protein AB027715 rep; aad Replication protein; aminoglycoside adenyltransferase AF005242 argC N-acetylglutamate-5-semialdehyde dehydrogenase AF005635 ginA Glutamine synthetase AF030405 hisF cyclase AF030520 argG Argininosuccinate synthetase AF031518 argF Omithine carbamolytransferase AF036932 aroD 3-dehydroquinate dehydratase AF038548 pyc Pyruvate carboxylase Table 2 continued AF038651 dciAE; apt; rel Dipeptide-binding protein; adenine Wehmeier, L. et al. "The role of the Corynebacterium glutamicum rel gene in phosphoribosyltransferase; GTP (p)ppGpp metabolism," Microbiology, 144:1853-1862 (1998) pyrophosphokinase AF041436 argR Arginine repressor AF045998 impA Inositol monophosphate phosphatase AF048764 argH Argininosuccinate lyase AF049897 argC; argJ; argB; N-acetylglutamylphosphate reductase;
argD; argF; argR; ornithine acetyltransferase; N-argG; argH acetylglutamate kinase; acetylornithine transminase; ornithine carbamoyltransferase; arginine repressor;
argininosuccinate synthase;
argininosuccinate lyase AF050109 inhA Enoyl-acyl carrier protein reductase AF050166 hisG ATP phosphoribosyltransferase AF051846 hisA Phosphoribosylformimino-5-amino-l- Ln phosphoribosyi-4-im idazolecarboxam ide m isomerase m AF052652 metA Homoserine 0-acetyltransferase Park, S. et al. "Isolation and analysis of metA, a methionine biosynthetic gene encoding homoserine acetyltransferase in Corynebacterium glutamicum," Mol.
Cells., 8(3):286-294 (1998) O
AF053071 aroB Dehydroquinate synthetase AF060558 hisH Glutamine amidotransferase AF086704 hisE Phosphoribosyl-ATP- ~
pyrophosphohydrolase AF114233 aroA 5-enqipyruvylshikimate 3-phosphate synthase AF 116184 panD L-aspartate-alpha-decarboxylase precursor Dusch, N. et al.
"Expression of the Corynebacterium glutamicum panD gene encoding L-aspartate-alpha-decarboxylase leads to pantothenate overproduction in Escherichia coli," Appl. Environ. Microbiol., 65(4)1530-1539(1999) AF124518 aroD; aroE 3-dehydroquinase; shikimate dehydrogenase AF124600 aroC; aroK; aroB; Chorismate synthase; shikimate kinase; 3-pepQ dehydroquinate synthase; putative cytoplasmic peptidase AF145897 inhA
AF145898 inhA

Table 2 (continued) AJ001436 ectP Transport of ectoine, glycine betaine, Peter, H. et al.
"Corynebacterium glutamicum is equipped with four secondary proline carriers for compatible solutes: Identification, sequencing, and characterization of the proline/ectoine uptake system, ProP, and the ectoine/proline/glycine betaine carrier, EctP," J Bacteriol., 180(22):6005-6012 (1998) AJ004934 dapD Tetrahydrodipicolinate succinylase Wehrmann, A. et al.
"Different modes of diaminopimelate synthesis and their (incomplete') role in cell wall integrity: A study with Corynebacterium glutamicum," J.
Bacteriol., 180(12):3159-3165 (1998) AJ007732 ppc; secG; amt; ocd; Phosphoenolpynuvate-carboxylase; ?; high soxA affinity ammonium uptake protein; putative ornithine-cyclodecarboxylase; sarcosine oxidase AJ010319 ftsY, glnB, g1nD; srp; Involved in cell division; PII protein;
Jakoby, M. et al. "Nitrogen regulation in Corynebacterium glutamicum;
amtP uridylyltransferase (uridylyl-removing Isolation of genes involved in biochemical characterization of corresponding enzmye); signal recognition particle; low proteins," FEMS Microbiol., 173(2):303-310 (1999) affinity ammonium uptake protein <,, AJ132968 cat Chloramphenicol aceteyl transferase AJ224946 mqo L-malate: quinone oxidoreductase Molenaar, D. et al. "Biochemical and genetic characterization of the O1 rn membrane-associated malate dehydrogenase (acceptor) from Corynebacterium glutamicum," Eur. J. Biochem., 254(2):395-403 (1998) AJ238250 ndh NADH dehydrogenase AJ238703 porA Porin Lichtinger, T. et al. "Biochemical and biophysical characterization of the cell 1 wall porin of Corynebacterium glutamicum: The channel is formed by a low rn molecular mass polypeptide," Biochemistry, 37(43):15024-15032 (1998) rv D17429 Transposable element IS31831 Vertes et al."Isolation and characterization of IS31831, a transposable element from Corynebacterium glutamicum," Mol. Microbiol., 11(4):739-746 (1994) D84102 odhA 2-oxoglutarate dehydrogenase Usuda, Y. et al. "Molecular cloning of the Corynebacterium glutamicum (Brevibacterium lactofermentum AJ 12036) odhA gene encoding a novel type of 2-oxoglutarate dehydrogenase," Microbiology, 142:3347-3354 (1996) E01358 hdh; hk Homoserine dehydrogenase; homoserine Katsumata, R. et al.
"Production of L-thereonine and L-isoleucine," Patent: JP
kinase 1987232392-A 1 10/12/87 E01359 Upstream of the start codon of homoserine Katsumata, R. et al.
"Production of L-thereonine and L-isoleucine," Patent: JP
kinase gene 1987232392-A 2 10/12/87 E01375 Tryptophan operon E01376 trpL; trpE Leader peptide; anthranilate synthase Matsui, K. et al.
"Tryptophan operon, peptide and protein coded thereby, utilization of tryptophan operon gene expression and production of tryptophan," Patent: JP 1987244382-A 1 10/24/87 Table 2 (continued) E01377 Promoter and operator regions of Matsui, K. et al. "Tryptophan operon, peptide and protein coded thereby, tryptophan operon utilization of tryptophan operon gene expression and production of tryptophan," Patent: JP 1987244382-A 1 10/24/87 E03937 Biotin-synthase atakeyama, K. et al. "DNA fragment containing gene capable of coding biotin synthetase and its utilization," Patent: JP 1992278088-A 1 10/02/92 E04040 Diamino pelargonic acid aminotransferase Kohama, K. et al. "Gene coding diaminopelargonic acid aminotransferase and desthiobiotin synthetase and its utilization," Patent: JP 1992330284-A 1 E04041 Desthiobiotinsynthetase Kohama, K. et al. "Gene coding diaminopelargonic acid aminotransferase and desthiobiotin synthetase and its utilization," Patent: JP 1992330284-A 1 E04307 Flavum aspartase Kurusu, Y. et al. "Gene DNA coding aspartase and utilization thereof," Patent:

E04376 Isocitric acid lyase Katsumata, R. et al. "Gene manifestation controlling DNA," Patent: JP

E04377 Isocitric acid lyase N-terminal fragment Katsumata, R. et al. "Gene manifestation controlling DNA," Patent: JP Ln 1993056782-A 3 03/09/93 rn E04484 Prephenate dehydratase Sotouchi, N. et al. "Production of L-phenylalanine by fermentation," Patent: JP

E05108 Aspartokinase Fugono, N. et al. "Gene DNA coding Aspartokinase and its use," Patent: JP 00 E05112 Dihydro-dipichorinate synthetase Hatakeyama, K. et al. "Gene DNA coding dihydrodipicolinic acid synthetase rn and its use," Patent: JP 1 993 1 843 7 1-A 1 07/27/93 rv E05776 Diaminopimelic acid dehydrogenase Kobayashi, M. et al. "Gene DNA coding Diaminopimelic acid dehydrogenase ~
and its use," Patent: JP 1993284970-A 1 11/02/93 E05779 Threonine synthase Kohama, K. et al. "Gene DNA coding threonine synthase and its use," Patent:

E061 10 Prephenate dehydratase Kikuchi, T. et a1. "Production of L-phenylalanine by fermentation method,"
Patent: JP 1993344881-A I 12/27/93 E061 I 1 Mutated Prephenate dehydratase Kikuchi, T. et al. "Production of L-phenylalanine by fermentation method,"
Patent: JP 1993344881-A 1 12/27/93 E06146 Acetohydroxy acid synthetase Inui, M. et al. "Gene capable of coding Acetohydroxy acid synthetase and its use," Patent: JP 1993344893-A 1 12/27/93 E06825 Aspartokinase Sugimoto, M. et al. "Mutant aspartokinase gene," patent:

E06826 Mutated aspartokinase alpha subunit Sugimoto, M. et al. "Mutant aspartokinase gene," patent: JP 1994062866-A 1 Table 2 continued E06827 Mutated aspartokinase alpha subunit Sugimoto, M. et al. "Mutant aspartokinase gene," patent: JP 1994062866-A I

E07701 secY Honno, N. et al. "Gene DNA participating in integration of membraneous protein to membrane," Patent: JP 1994169780-A 1 06/21/94 E08177 Aspartokinase Sato, Y. et al. "Genetic DNA capable of coding Aspartokinase released from feedback inhibition and its utilization," Patent: JP 1994261766-A I 09/20/94 E08178, Feedback inhibition-released Aspartokinase Sato, Y. et al. "Genetic DNA capable of coding Aspartokinase released from E08179, feedback inhibition and its utilization," Patent: JP 1994261766-A 1 E08180, E08181, E08232 Acetohydroxy-acid isomeroreductase lnui, M. et al. "Gene DNA coding acetohydroxy acid isomeroreductase,"
Patent: JP 1994277067-A 1 10/04/94 ct E08234 secE
Asai, Y. et al. "Gene DNA coding for translocation machinery of protein,"
Patent: JP 1994277073-A 1 10/04/94 E08643 FT aminotransferase and desthiobiotin Hatakeyama, K. et al. "DNA
fragment having promoter function in Ln synthetase promoter region coryneform bacterium," Patent: JP 1 99503 1 476-A 1 02/03/95 rn E08646 Biotin synthetase Hatakeyama, K. et al. "DNA fragment having promoter function in nO1i coryneform bacterium," Patent: JP 1995031476-A 1 02/03/95 E08649 Aspartase Kohama, K. et al "DNA fragment having promoter function in coryneform ~ o bacterium," Patent: JP 1995031478-A 1 02/03/95 '-E08900 Dihydrodipicolinate reductase Madori, M. et al. "DNA fragment containing gene coding Dihydrodipicolinate acid reductase and utilization thereof," Patent: JP 1995075578-A 1 03/20/95 E08901 Diaminopimelic acid decarboxylase Madori, M. et al. "DNA fragment containing gene coding Diaminopimelic acid decarboxylase and utilization thereof," Patent: JP 1995075579-A 1 03/20/95 E12594 Serine hydroxymethyltransferase Hatakeyama, K. et al. "Production of L-trypophan," Patent: JP 1997028391-A

E 12760, transposase Moriya, M. et al. "Amplification of gene using artificial transposon," Patent:
E12759, JP 1997070291-A 03/18/97 E12764 Arginyl-tRNA synthetase; diaminopimelic Moriya, M. et al.
"Amplification of gene using artificial transposon," Patent:
acid decarboxylase JP 1997070291-A 03/18/97 E12767 Dihydrodipicolinic acid synthetase Moriya, M. et al. "Amplification of gene using artificial transposon," Patent:

E12770 aspartokinase Moriya, M. et al. "Amplification of gene using artificial transposon," Patent:

E12773 Dihydrodipicolinic acid reductase Moriya, M. et al. "Amplification of gene using artificial transposon," Patent:

Table 2 continued E13655 Glucose-6-phosphate dehydrogenase Hatakeyama, K. et al. "Glucose-6-phosphate dehydrogenase and DNA capable of coding the same," Patent: JP 1997224661-A 1 09/02/97 L01508 11vA Threonine dehydratase Moeckel, B. et al. "Functional and structural analysis of the threonine dehydratase of Corynebacterium glutamicum," J. Bacteriol., 174:8065-8072 (1992) L07603 EC 4.2.1.15 3-deoxy-D-arabinoheptulosonate-7- Chen, C. et al. "The cloning and nucleotide sequence of Corynebacterium phosphate synthase glutamicum 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase gene,"
FEMS Microbiol. Lett., 107:223-230 (1993) L09232 llvB; ilvN; ilvC Acetohydroxy acid synthase large subunit; Keilhauer, C. et al. "Isoleucine synthesis in Corynebacterium glutamicum:
Acetohydroxy acid synthase small subunit; molecular analysis of the i1vB-ilvN-ilvC operon," J. Bacteriol., 175(17):5595-Acetohydroxy acid isomeroreductase 5603 (1993) L18874 PtsM Phosphoenolpyruvate sugar Fouet, A et al. "Bacillus subtilis sucrose-specific enzyme 11 of the phosphotransferase phosphotransferase system: expression in Escherichia coli and homology to enzymes II from enteric bacteria," PNAS USA, 84(24):8773-8777 (1987); Lee, I.K. et al. "Nucleotide sequence of the gene encoding the Corynebacterium glutamicum mannose enzyme Il and analyses of the deduced protein Ln to sequence," FEMS Microbiol. Lett., 119(1-2):137-145 (1994) o L27123 aceB Malate synthase Lee, H-S. et al. "Molecular characterization of aceB, a gene encoding malate N
synthase in Corynebacterium glutamicum," J. MicrobioL Biotechnol., 4(4):256-263 (1994) 00 L27126 Pyruvate kinase Jetten, M. S. et al. "Structural and functional analysis of pyruvate kinase from N o Corynebacterium glutamicum," Appl. Environ. Microbiol., 60(7):2501-2507 (1994) L28760 aceA Isocitrate lyase F, L35906 dtxr Diphtheria toxin repressor Oguiza, J.A. et al. "Molecular cloning, DNA sequence analysis, and characterization of the Corynebacterium diphtheriae dtxR from Brevibacterium lactofermentum," J. Bacteriol., 177(2):465-467 (1995) M13774 Prephenate dehydratase Follettie, M.T. et al. "Molecular cloning and nucleotide sequence of the Corynebacterium glutamicum pheA gene," J. Bacteriol., 167:695-702 (1986) M 16175 5S rRNA Park, Y-H. et al. "Phylogenetic analysis of the coryneform bacteria by 56 rRNA sequences," J. Bacteriol., 169:1801-1806 (1987) M 16663 trpE Anthranilate synthase, 5' end Sano, K. et al. "Structure and function of the trp operon control regions of Brevibacterium lactofermentum, a glutamic-acid-producing bacterium," Gene, 52:191-200 (1987) M 16664 trpA Tryptophan synthase, 3'end Sano, K. et al. "Structure and function of the trp operon control regions of Brevibacterium lactofermentum, a glutamic-acid-producing bacterium," Gene, 52:191-200(1987) Table 2 continued M25819 Phosphoenolpyruvate carboxylase O'Regan, M. et al. "Cloning and nucleotide sequence of the Phosphoenolpyruvate carboxylase-coding gene of Corynebacterium glutamicum ATCC 13032," Gene, 77(2):237-251 (1989) M85106 23S rRNA gene insertion sequence Roller, C. et al. "Gram-positive bacteria with a high DNA G+C content are characterized by a common insertion within their 23S rRNA genes," J. Gen.
Microbiol., 138:1167-1175 (1992) M85107, 23S rRNA gene insertion sequence Roller, C. et al. "Gram-positive bacteria with a high DNA G+C content are M85108 characterized by a common insertion within their 23S rRNA genes," J.
Gen.
Microbiol., 138:1167-1175 (1992) M89931 aecD; brnQ; yhbw Beta C-S lyase; branched-chain amino acid Rossol, I.
et al. "The Corynebacterium glutamicum aecD gene encodes a C-S
uptake carrier; hypothetical protein yhbw lyase with alpha, beta-elimination activity that degrades aminoethylcysteine,"
J. BacterioJ., 174(9):2968-2977 (1992); Tauch, A. et al. "Isoleucine uptake in Corynebacterium glutamicum ATCC 13032 is directed by the bmQ gene product," Arch. Microbiol., 169(4):303-312 (1998) S59299 trp Leader gene (promoter) Herry, D.M. et al. "Cloning of the trp gene cluster from a tryptophan- r v hyperproducing strain of Corynebacterium glutamicum: identification of a Ln mutation in the trp leader sequence," Appl. Environ. Microbiol., 59(3):791-799 (1993) U11545 trpD Anthranilate phosphoribosyltransferase O'Gara, J.P. and Dunican, L.K. (1994) Complete nucleotide sequence of the Corynebacterium glutamicum ATCC 21850 tpD gene." Thesis, Microbiology Department, University College Galway, Ireland. 1 .3 U13922 cgllM; cgllR; clgllR Putative type lI 5-cytosoine Schafer, A. et al.
"Cloning and characterization of a DNA region encoding a methyltransferase; putative type II stress-sensitive restriction system from Corynebacterium glutamicum ATCC
restriction endonuclease; putative type I or 13032 and analysis of its role in intergeneric conjugation with Escherichia type III restriction endonuclease coli," J. Bacteriol., 176(23):7309-7319 (1994); Schafer, A. et al. "The Corynebacterium glutamicum cgllM gene encoding a 5-cytosine in an McrBC-deficient Escherichia coli strain," Gene, 203(2):95-101 (1997) U 14965 recA
U31224 ppx Ankri, S. et al. "Mutations in the Corynebacterium glutamicumproline biosynthetic pathway: A natural bypass of the proA step," J Bacteriol., 178(15):4412-4419 (1996) U31225 proC L-proline: NADP+ 5-oxidoreductase Ankri, S. et al. "Mutations in the Corynebacterium glutamicumproline biosynthetic pathway: A natural bypass of the proA step," J. Bacteriol., 178(15):4412-4419 (1996) U31230 obg; proB; unkdh ?;gamma glutamyl kinase;similar to D- Ankri, S. et al.
"Mutations in the Corynebacterium glutamicumproline isomer specific 2-hydroxyacid biosynthetic pathway: A natural bypass of the proA step," J. Bacteriol., dehydrogenases 178(15):4412-4419(1996) Table 2 continued U31281 bioB Biotin synthase Serebriiskii, I.G., "Two new members of the bio B
superfamily: Cloning, sequencing and expression of bio B genes of Methylobacillus flagellatum and Corynebacterium glutamicum," Gene, 175:15-22 (1996) U35023 thtR; accBC Thiosulfate sulfurt ransferase; acyl CoA Jager, W. et al.
"A Corynebacterium giutamicum gene encoding a two-domain carboxylase protein similar to biotin carboxylases and biotin-carboxyl-carrier proteins,"
Arch. Microbiol., 166(2);76-82 (1996) U43535 cmr Multidrug resistance protein Jager, W. et al. "A Corynebacterium glutamicum gene conferring multidrug resistance in the heterologous host Escherichia coli," J. Bacteriol., 179(7):2449-2451(1997) U43536 cipB Heat shock ATP-binding protein U53587 aphA-3 3'5"-aminoglycoside phosphotransferase U89648 Corynebacterium glutamicum unidentified sequence involved in histidine biosynthesis, partial sequence X04960 trpA; trpB; trpC; trpD; Tryptophan operon Matsui, K. et al. "Complete nucleotide and deduced amino acid sequences of trpE; trpG; trpL the Brevibacterium lactofermentum tryptophan operon," Nucleic Acids Res., o 14(24):10113-10114(1986) rn X07563 lys A DAP decarboxylase (meso-diaminopimelate Yeh, P. et al. "Nucleic sequence of the lysA gene of Corynebacterium decarboxylase, EC 4.1.1.20) glutamicum and possible mechanisms for modulation of its expression," Mol. rv Gen. Genet., 212(1):112-1 19 (1988) X 14234 EC 4.1.1.31 Phosphoenolpyruvate carboxylase Eikmanns, B.J. et al. "The Phosphoenolpyruvate carboxylase gene of - 1 .3 Corynebacterium glutamicum: Molecular cloning, nucleotide sequence, and expression," Mol. Gen. Genet., 218(2):330-339 (1989); Lepiniec, L. et al.
"Sorghum Phosphoenolpyruvate carboxylase gene family: structure, function and molecular evolution," Plant. Mol. Biol., 21 (3):487-502 (1993) X17313 fda Fructose-bisphosphate aldolase Von der Osten, C.H. et al.
"Molecular cloning, nucleotide sequence and fine-structural analysis of the Corynebacterium glutamicum fda gene: structural comparison of C. glutamicum fructose-I, 6-biphosphate aldolase to class I and class II aldolases," Mol. Microbiol., X53993 dapA L-2, 3-dihydrodipicolinate synthetase (EC Bonnassie, S. et al.
"Nucleic sequence of the dapA gene from 4.2.1.52) Corynebacterium glutamicum," Nucleic Acids Res., 18(21):6421 (1990) X54223 AttB-related site Cianciotto, N. et al. "DNA sequence homology between att B-related sites of Corynebacterium diphtheriae, Corynebacterium ulcerans, Corynebacterium glutamicum , and the attP site of lambdacorynephage," FEMS. Microbiol, Lett., 66:299-302 (1990) X54740 argS; lysA Arginyl-tRNA synthetase; Diaminopimelate Marcel, T. et al.
"Nucleotide sequence and organization of the upstream region decarboxylase of the Corynebacterium glutamicum lysA gene," Mol. Microbiol., 4(l I):1819-1830 (1990) Table 2 (continued) X55994 trpL; trpE Putative leader peptide; anthranilate Heery, D.M. et al.
"Nucleotide sequence of the Corynebacterium glutamicum synthase component I trpE gene," Nucleic Acids Res., 18(23):7138 (1990) X56037 thrC Threonine synthase Han, K.S. et al. "The molecular structure of the Corynebacterium glutamicum threonine synthase gene," Mol. Microbiol., 4(10):1693-1702 (1990) X56075 attB-related site Attachment site Cianciotto, N. et al. "DNA sequence homology between att B-related sites of Corynebacterium diphtheriae, Corynebacterium ulcerans, Corynebacterium glutamicum , and the attP site of lambdacorynephage," FEMS. Microbiol, Lett., 66:299-302 (1990) X57226 lysC-alpha; lysC-beta; Aspartokinase-alpha subunit; Kalinowski, J. et al. "Genetic and biochemical analysis of the Aspartokinase asd Aspartokinase-beta subunit; aspartate beta from Corynebacterium glutamicum," Mol. Microbiol., 5(5):1197-1204 (1991);
semialdehyde dehydrogenase Kalinowski, J. et al. "Aspartokinase genes lysC
alpha and lysC beta overlap and are adjacent to the aspertate beta-semialdehyde dehydrogenase gene asd in Corynebacterium glutamicum," Mol. Gen. Genet., 224(3):317-324 (1990) X59403 gap;pgk; tpi Glyceraldehyde-3-phosphate; Eikmanns, B.J.
"Identification, sequence analysis, and expression of a o phosphoglycerate kinase; triosephosphate Corynebacterium glutamicum gene cluster encoding the three glycolytic Lõ
isomerase enzymes glyceraldehyde-3-ph osph ate dehydrogenase, 3-phosphoglycerate kinase, and triosephosphate isomeras," J. Bacteriol., 174(19):6076-6086 O1 rn (1992) X59404 gdh Glutamate dehydrogenase Bormann, E.R. et al. "Molecular analysis of the Corynebacterium glutamicum gdh gene encoding glutamate dehydrogenase," Mol. Microbiol., 6(3):317-326 o (1992) 1 X60312 lysl L-lysine permease Seep-Feldhaus, A.H. et al. "Molecular analysis of the Corynebacterium rn glutamicum lysi gene involved in lysine uptake," Mol. Microbiol., 5(12):2995-rv 3005(1991) X66078 copl Psl protein Joliff, G. et al. "Cloning and nucleotide sequence of the cspl gene encoding PSI, one of the two major secreted proteins of Corynebacterium glutamicum:
The deduced N-terminal region of PSI is similar to the Mycobacterium antigen 85 complex," Mol. Microbiol., 6(16):2349-2362 (1992) X66112 glt Citrate synthase Eikmanns, B.J. et al. "Cloning sequence, expression and transcriptional analysis of the Corynebacterium glutamicum gltA gene encoding citrate synthase," Microbiol., 140:1817-1828 (1994) X67737 dapB Dihydrodipicolinate reductase X69103 csp2 Surface layer protein PS2 Peyret, J.L. et al. "Characterization of the cspB gene encoding PS2, an ordered surface-layer protein in Corynebacterium glutamicum," Mol. Microbiol., 9(1):97-109 (1993) X69104 1S3 related insertion element Bonamy, C. et al. "Identification of 1S1206, a Corynebacterium glutamicum 1S3-related insertion sequence and phylogenetic analysis," Mol. Microbiol., 14(3):571-581(1994) Table 2 continued X70959 leuA lsopropylmalate synthase Patek, M. et al. "Leucine synthesis in Corynebacterium glutamicum: enzyme activities, structure of leuA, and effect of leuA inactivation on lysine synthesis," Appl. Environ. Microbiol., 60(1):133-140 (1994) X71489 icd Isocitrate dehydrogenase (NADP+) Eikmanns, B.J. et al. "Cloning sequence analysis, expression, and inactivation of the Corynebacterium glutamicum icd gene encoding isocitrate dehydrogenase and biochemical characterization of the enzyme," J. Bacteriol., 177(3):774-782(1995) X72855 GDHA Glutamate dehydrogenase (NADP+) X75083, mtrA 5-methyltryptophan resistance Heery, D.M. et al. "A sequence from a tryptophan-hyperproducing strain of X70584 Corynebacterium glutamicum encoding resistance to 5-methyltryptophan,"
Biochem. Biophys. Res. Commun., 201(3):1255-1262 (1994) X75085 recA Fitzpatrick, R. et al. "Construction and characterization of recA
mutant strains of Corynebacterium glutamicum and Brevibacterium lactofermentum," Appl.
Microbiol. BiotechnoL, 42(4):575-580 (1994) X75504 aceA; thiX Partial Isocitrate lyase; ? Reinscheid, D1. et al.
"Characterization of the isocitrate lyase gene from Corynebacterium glutamicum and biochemical analysis of the enzyme," J. Ln Bacteriol., 176(12):3474-3483 (1994) o X76875 ATPase beta-subunit Ludwig, W. et al. "Phylogenetic relationships of bacteria based on comparative sequence analysis of elongation factor Tu and ATP-synthase beta-subunit genes," Antonie Van Leeuwenhoek, 64:285-305 (1993) 00 o X77034 tuf Elongation factor Tu Ludwig, W. et al. "Phylogenetic relationships of bacteria based on comparative i sequence analysis of elongation factor Tu and ATP-synthase beta-subunit o genes," Antonie Van Leeuwenhoek, 64:285-305 (1993) O1 X77384 recA Billman-Jacobe, H. "Nucleotide sequence of a recA gene from r Corynebacterium glutamicum," DNA Seq., 4(6):403-404 (1994) X78491 aceB Malate synthase Reinscheid, D.J. et al. "Malate synthase from Corynebacterium glutamicum pta-ack operon encoding phosphotransacetylase: sequence analysis,"
Microbiology, 140:3099-3108 (1994) X80629 16S rDNA 16S ribosomal RNA Rainey, F.A. et al. "Phylogenetic analysis of the genera Rhodococcus and Norcardia and evidence for the evolutionary origin of the genus Norcardia from within the radiation of Rhodococcus species," Microbiol., 141:523-528 (1995) X81191 gluA; gluB; gluC; Glutamate uptake system Kronemeyer, W. et al.
"Structure of the gIuABCD cluster encoding the gluD glutamate uptake system of Corynebacterium glutamicum," J. Bacteriol., 177(5):1152-1 158 (1995) X81379 dapE Succinyldiaminopimelate desuccinylase Wehrmann, A. et al.
"Analysis of different DNA fragments of Corynebacterium glutamicum complementing dapE of Escherichia coli,"
Microbiology, 40:3349-56 (1994) Table 2 (continued) X82061 16S rDNA 16S ribosomal RNA Ruimy, R. et al. "Phylogeny of the genus Corynebacterium deduced from analyses of small-subunit ribosomal DNA sequences," Int. J. Syst. Bacteriol., 45(4):740-746 (1995) X82928 asd; lysC Aspartate-semialdehyde dehydrogenase; ? Serebrijski, 1. et al. "Multicopy suppression by asd gene and osmotic stress-dependent complementation by heterologous proA in proA mutants," J.
Bacteriol., 177(24):7255-7260 (1995) X82929 proA Gamma-glutamyl phosphate reductase Serebrijski, I. et al.
"Multicopy suppression by asd gene and osmotic stress-dependent complementation by heterologous proA in proA mutants," J.
Bacteriol., 177(24):7255-7260 (1995) X84257 16S rDNA 16S ribosomal RNA Pascual, C. et al. "Phylogenetic analysis of the genus Corynebacterium based on 16S rRNA gene sequences," Int. J. Syst. Bacteriol., 45(4):724-728 (1995) X85965 aroP; dapE Aromatic amino acid perrnease; ? Wehrmann et al. "Functional analysis of sequences adjacent to dapE of C.
glutamicum proline reveals the presence of aroP, which encodes the aromatic amino acid transporter," J. Bacteriol., 177(20):5991-5993 (1995) X86157 argB; argC; argD; Acetylglutamate kinase; N-acetyl-gamma- Sakanyan, V.
et al. "Genes and enzymes of the acetyl cycle of arginine argF; argJ glutamyl-phosphate reductase; biosynthesis in Corynebacterium glutamicum: enzyme evolution in the early Ln acetylomithine aminotransferase; ornithine steps of the arginine pathway,"
Microbiology, 142:99-108 (1996) carbamoyltransferase; glutamate N-acetyltransferase X89084 pta; ackA Phosphate acety ltransferase; acetate kinase Reinscheid, D.J.
et al. "Cloning, sequence analysis, expression and inactivation o of the Corynebacterium glutamicum pta-ack operon encoding o phosphotransacetylase and acetate kinase," Microbiology, 145:503-513 (1999) X89850 attB Attachment site Le Marrec, C. et al. "Genetic characterization of site-specific integration O1 functions of phi AAU2 infecting "Arthrobacter aureus C70," J. Bacteriol., 178(7):1996-2004(1996) X90356 Promoter fragment F1 Patek, M. et al. "Promoters from Corynebacterium glutamicum: cloning, molecular analysis and search for a consensus motif," Microbiology, 142:1297-1309 (1996) X90357 Promoter fragment F2 Patek, M. et al. "Promoters from Corynebacterium glutamicum: cloning, molecular analysis and search for a consensus motif," Microbiology, 142:1297-1309(1996) X90358 Promoter fragment Fl0 Patek, M. et al. "Promoters from Corynebacterium glutamicum: cloning, molecular analysis and search for a consensus motif," Microbiology, 142:1297-1309(1996) X90359 Promoter fragment F13 Patek, M. et al. "Promoters from Corynebacterium glutamicum: cloning, molecular analysis and search for a consensus motif," Microbiology, 142:1297-1309(1996) Table 2 continued X90360 Promoter fragment F22 Patek, M. et at. "Promoters from Corynebacterium glutamicum: cloning, molecular analysis and search for a consensus motif," Microbiology, 142:1297-1309 (1996) X90361 Promoter fragment F34 Patek, M. et al. "Promoters from Corynebacterium glutamicum: cloning, molecular analysis and search for a consensus motif," Microbiology, 142:1297-1309(1996) X90362 Promoter fragment F37 Patek, M. et al. "Promoters from C. glutamicum:
cloning, molecular analysis and search for a consensus motif," Microbiology, 142:1297-1309 (1996) X90363 Promoter fragment F45 Patek, M. et al. "Promoters from Corynebacterium glutamicum: cloning, molecular analysis and search for a consensus motif," Microbiology, 142:1297-1309(1996) X90364 Promoter fragment F64 Patek, M. et al. "Promoters from Corynebacterium glutamicum: cloning, molecular analysis and search for a consensus motif," Microbiology, 142:1297-1309 (1996) X90365 Promoter fragment F75 Patek, M. et al. "Promoters from Corynebacterium glutamicum: cloning, Ln molecular analysis and search for a consensus motif," Microbiology, 142:1297-1309(1996) rn X90366 Promoter fragment PF101 Patek, M. et al. "Promoters from Corynebacterium glutamicum: cloning, . nO1i molecular analysis and search for a consensus motif," Microbiology, ~ rv 142:1297-1309 (1996) 00 0 X90367 Promoter fragment PF104 Patek, M. et al. "Promoters from Corynebacterium glutamicum: cloning, O - 1 .3 molecular analysis and search for a consensus motif," Microbiology, 142:1297-1309(1996) X90368 Promoter fragment PF109 Patek, M. et al. "Promoters from Corynebacterium glutamicum: cloning, molecular analysis and search for a consensus motif," Microbiology, 142:1297-1309 (1996) X93513 amt Ammonium transport system Siewe, R.M. et al. "Functional and genetic characterization of the (methyl) ammonium uptake carrier of Corynebacterium glutamicum," J Biol. Chem., 271(10):5398-5403(1996) X93514 betP Glycine betaine transport system Peter, H. et al. "Isolation, characterization, and expression of the Corynebacterium glutamicum betP gene, encoding the transport system for the compatible solute glycine betaine," J. Bacteriol., 178(17):5229-5234 (1996) X95649 orf4 Patek, M. et al. "Identification and transcriptional analysis of the dapB-ORF2-dapA-ORF4 operon of Corynebacterium glutamicum, encoding two enzymes involved in L-lysine synthesis," Biotechnol. Leit., 19:1113-1117 (1997) X96471 lysE; lysG Lysine exporter protein; Lysine export Vrljic, M. et al. "A
new type of transporter with a new type of cellular regulator protein function: L-lysine export from Corynebacterium glutamicum,"
Mol.
Microbiol., 22(5):815-826 (1996) Table 2 (continued) X96580 panB; panC; xylB 3-methyl-2-oxobutanoate Sahm, H. et al. "D-pantothenate synthesis in Corynebacterium glutamicum and hydroxymethyltransferase; pantoate-beta- use of panBC and genes encoding L-valine synthesis for D-pantothenate alanine ligase; xylulokinase overproduction," Appl. Environ. Microbiol., 65(5):1973-1979 (1999) X96962 Insertion sequence 1S1207 and transposase X99289 Elongation factor P Ramos, A. et al. "Cloning, sequencing and expression of the gene encoding elongation factor P in the amino-acid producer Brevibacterium lactofermentum (Corynebacterium glutamicum ATCC 13869)," Gene, 198:217-222 (1997) Y00140 thrB Homoserine kinase Mateos, L.M. et al. "Nucleotide sequence of the homoserine kinase (thrB) gene of the Brevibacterium lactofermentum," Nucleic Acids Res., 15(9):3922 (1987) Y00151 ddh Meso-diaminopimelate D-dehydrogenase lshino, S. et al. "Nucleotide sequence of the meso-diaminopimelate D-(EC 1.4.1.16) dehydrogenase gene from Corynebacterium glutamicum," Nucleic Acids Res., ro 15(9):3917 (1987) cn Y00476 thrA Homoserine dehydrogenase Mateos, L.M. et al. "Nucleotide sequence of the homoserine dehydrogenase o (thrA) gene of the Brevibacterium lactofermentum," Nucleic Acids Res., rn 15(24):10598 (1987) Y00546 hom; thrB Homoserine dehydrogenase; homoserine Peoples, O.P. et al.
"Nucleotide sequence and fine structural analysis of the kinase Corynebacterium glutamicum hom-thrB operon," Mol. Microbiol., 2(1):63-(1988) Y08964 murC; ftsQ/divD; ftsZ UPD-N-acetylmuramate-alanine ligase; Honrubia, M.P. et al. "Identification, characterization, and chromosomal O1 division initiation protein or cell division organization of the ftsZ gene from Brevibacterium lactofermentum," Mol. Gen.
protein; cell division protein Genet., 259(l):97-104 (1998) Y09163 putP High affinity proline transport system Peter, H. et al. "Isolation of the putP gene of Corynebacterium glutamicumproline and characterization of a low-affinity uptake system for compatible solutes," Arch. Microbiol., 168(2):143-151 (1997) Y09548 pyc Pyruvate carboxylase Peters-Wendisch, P.G. et al. "Pyruvate carboxylase from Corynebacterium glutamicum: characterization, expression and inactivation of the pyc gene,"
Microbiology, 144:915-927 (1998) Y09578 leuB 3-isopropylmalate dehydrogenase Patek, M. et al. "Analysis of the leuB gene from Corynebacterium glutamicum," Appl. Microbiol. Biotechnol., 50(1):42-47 (1998) Y12472 Attachment site bacteriophage Phi-16 Moreau, S. et al. "Site-specific integration of corynephage Phi-16: The construction of an integration vector," Microbiol., 145:539-548 (1999) Y 12537 proP Proline/ectoine uptake system protein Peter, H. et al.
"Corynebacterium glutamicum is equipped with four secondary carriers for compatible solutes: Identification, sequencing, and characterization of the proline/ectoine uptake system, ProP, and the ectoine/proline/glycine betaine carrier, EctP," J. Bacteriol., 180(22):6005-6012 (1998) Table 2 continued Y13221 ginA Glutamine synthetase I Jakoby, M. et al. "Isolation of Corynebacterium glutamicum ginA gene encoding glutamine synthetase I," FEMS Microbiol. Lett., 154(l):81-88 (1997) Y 16642 lpd Dihydrolipoamide dehydrogenase Y 18059 Attachment site Corynephage 304L Moreau, S. et al. "Analysis of the integration functions of φ304L: An integrase module among corynephages," Virology, 255(i):150-159 (1999) Z21501 argS; IysA Arginyl-tRNA synthetase; diaminopimelate Oguiza, J.A. et al.
"A gene encoding arginyl-tRNA synthetase is located in the decarboxylase (partial) upstream region of the lysA gene in Brevibacterium lactofermentum:
Regulation of argS-lysA cluster expression by arginine," J.
Bacteriol.,175(22):7356-7362 (1993) Z21502 dapA; dapB Dihydrodipicolinate synthase; Pisabarro, A. et al. "A
cluster of three genes (dapA, orf2, and dapB) of dihydrodipicolinate reductase Brevibacterium lactofermentum encodes dihydrodipicolinate reductase, and a third polypeptide of unknown function," J. Bacteriol., 175(9):2743-2749 (1993) Z29563 thrC Threonine synthase Malumbres, M. et al. "Analysis and expression of the thrC gene of the encoded o threonine synthase," Appi. Environ. Microbiol., 60(7)2209-2219 (1994) ci, Z46753 16S rDNA Gene for 16S ribosomal RNA 1O
Z49822 sigA SigA sigma factor Oguiza, J.A. et al "Multiple sigma factor genes in Brevibacterium lactofermentum: Characterization of sigA and sigB," J. Bacterrol., 178(2):550-= n' 553 (1996) Z49823 galE; dtxR Catalytic activity UDP-galactose 4- Oguiza, J.A. et al "The galE gene encoding the UDP-galactose 4-epimerase of o epimerase; diphtheria toxin regulatory Brevibacterium lactofermentum is coupled transcriptionally to the dmdR 1 protein gene," Gene, 177:103-107 (1996) Z49824 orfl; sigB ?; SigB sigma factor Oguiza, J.A. et al "Multiple sigma factor genes in Brevibacterium lactofermentum: Characterization of sigA and sigB," J. Bacieriol., 178(2):550-553 (1996) Z66534 Transposase Correia, A. et al. "Cloning and characterization of an IS-like element present in the genome of Brevibacterium lactofermentum ATCC 13869," Gene, 170(1):91-94 (1996) A sequence for this gene was published in the indicated reference. However, the sequence obtained by the inventors of the present application is significantly longer than the published version. It is believed that the published version relied on an incorrect start codon, and thus represents only a fragment of the actual coding region.

TABLE 3: Corynebacterium and Brevibacterium Strains Which May be Used in the Practice of the Invention AM~ 1~ERM ~ RRL~ ;C~,,.~F~,~C~-T ~CIMB CBS 'D$iFIZ
Brevibacterium ammoniagenes 21054 Brevibacterium ammoniagenes 19350 Brevibacterium ammoniagenes 19351 Brevibacterium ammoniagenes 19352 Brevibacterium ammoniagenes 19353 Brevibacterium ammoniagenes 19354 Brevibacterium ammoniagenes 19355 Brevibacterium ammoniagenes 19356 Brevibacterium ammoniagenes 21055 Brevibacterium ammoniagenes 21077 Brevibacterium ammoniagenes 21553 Brevibacterium ammoniagenes 21580 Brevibacterium ammoniagenes 39101 Brevibacterium butanicum 21196 Brevibacterium divaricatum 21792 P928 Brevibacterium flavum 21474 Brevibacterium flavum 21129 Brevibacterium flavum 21518 Brevibacterium flavum B11474 Brevibacterium flavum B 11472 Brevibacterium flavum 21127 Brevibacterium flavum 21128 Brevibacterium flavum 21427 Brevibacterium flavum 21475 Brevibacterium flavum 21517 Brevibacterium flavum 21528 Brevibacterium flavum 21529 Brevibacterium flavum B11477, Brevibacterium flavum B 1 1478 Brevibacterium flavum 21127 Brevibacterium flavum B 11474 Brevibacterium healii 15527 Brevibacterium ketoglutamicum 21004 Brevibacterium ketoglutamicum 21089 Brevibacterium ketosoreductum 21914 Brevibacterium lactofermentum 70 Brevibacterium lactofermentum 74 Brevibacterium lactofermentum 77 Brevibacterium lactofermentum 21798 Brevibacterium lactofermentum 21799 Brevibacterium lactofermentum 21800 Brevibacterium lactoferrnentum 21801 Brevibacterium lactofermentum B11470 Brevibacterium lactofermentum B11471 Genus~: species 'ATC~ERi~' ' '_, G :CEC'~T 1VCIMB' rCBS~= N.C-TC,1' DSMZ' Brevibacterium lactofermentum 21086 Brevibacterium lactofermentum 21420 Brevibacterium lactofermentum 21086 Brevibacterium lactofermentum 31269 Brevibacterium linens 9174 Brevibacterium linens 19391 Brevibacterium linens 8377 Brevibacterium paraff inolyticum 11160 Brevibacterium spec. 717.73 Brevibacterium spec. 717.73 Brevibacterium spec. 14604 Brevibacterium spec. 21860 Brevibacterium spec. 21864 Brevibacterium spec. 21865 Brevibacterium spec. 21866 Brevibacterium spec. 19240 Corynebacterium acetoacidophilum 21476 Corynebacterium acetoacidophilum 13870 Corynebacterium acetoglutamicum B11473 Corynebacterium acetoglutamicum 1311475 Corynebacterium acetoglutamicum 15806 Corynebacterium acetoglutamicum 21491 Corynebacterium acetoglutamicum 31270 Corynebacterium acetophilum B3671 Corynebacterium ammoniagenes 6872 2399 Corynebacterium ammoniagenes 15511 Corynebacterium fujiokense 21496 Corynebacterium glutamicum 14067 Corynebacterium glutamicum 39137 Corynebacterium glutamicum 21254 Corynebacterium glutamicum 21255 Corynebacterium glutamicum 31830 Corynebacterium glutamicum 13032 Corynebacterium glutamicum 14305 Corynebacterium glutamicum 15455 Corynebacterium glutamicum 13058 Corynebacterium glutamicum 13059 Corynebacterium glutamicum 13060 Corynebacterium glutamicum 21492 Corynebacterium glutamicum 21513 Corynebacterium glutamicum 21526 Corynebacterium glutamicum 21543 Corynebacterium glutamicum 13287 Corynebacterium glutamicum 21851 Corynebacterium glutamicum 21253 Corynebacterium glutamicum 21514 Corynebacterium glutamicum 21516 Corynebacterium glutamicum 21299 Cenuys ArTCC ~9 -' TERM ~N.RRI~lF; CECT' NCIMB CBS~ NCTG~ !DSM:Z
Corynebacterium glutamicum 21300 Corynebacterium glutamicum 39684 Corynebacterium glutamicum 21488 Corynebacterium glutamicum 21649 Corynebacterium glutamicum 21650 Corynebacterium glutamicum 19223 Corynebacterium glutamicum 13869 Corynebacterium glutamicum 21157 Corynebacterium glutamicum 21158 Corynebacterium glutamicum 21159 Corynebacterium glutamicum 21355 Corynebacterium glutamicum 31808 Corynebacterium glutamicum 21674 Corynebacterium glutamicum 21562 Corynebacterium glutamicum 21563 Corynebacterium glutamicum 21564 Corynebacterium glutamicum 21565 Corynebacterium glutamicum 21566 Corynebacterium glutamicum 21567 Corynebacterium glutamicum 21568 Corynebacterium glutamicum 21569 Corynebacterium glutamicum 21570 Corynebacterium glutamicum 21571 Corynebacterium glutamicum 21572 Corynebacterium glutamicum 21573 Corynebacterium glutamicum 21579 Corynebacterium glutamicum 19049 Corynebacterium glutamicum 19050 Corynebacterium glutamicum 19051 Corynebacterium glutamicum 19052 Corynebacterium glutamicum 19053 Corynebacterium glutamicum 19054 Corynebacterium glutamicum 19055 Corynebacterium glutamicum 19056 Corynebacterium glutamicum 19057 Corynebacterium glutamicum 19058 Corynebacterium glutamicum 19059 Corynebacterium glutamicum 19060 Corynebacterium glutamicum 19185 Corynebacterium glutamicum 13286 Corynebacterium glutamicum 21515 Corynebacterium glutamicum 21527 Corynebacterium glutamicum 21544 Corynebacterium glutamicum 21492 Corynebacterium glutamicum B8183 Corynebacterium glutamicum B8182 Corynebacterium glutamicum B 12416 Corynebacterium glutamicum B12417 A z-. ~.. ~;CW ,W rnTS tcss ~vcTC nsM4 t~ E
~, ~.~~.~ .[-~~ . ~ -~ :g Corynebacterium glutamicum B124I8 Corynebacterium glutamicum B11476 Corynebacterium glutamicum 21608 Corynebacterium lilium P973 Corynebacterium nitrilophilus 21419 11594 Corynebacterium spec. P4445 Corynebacterium spec. P4446 Corynebacterium spec. 31088 Corynebacterium spec. 31089 Corynebacterium spec. 31090 Corynebacterium spec. 31090 Corynebacterium spec. 31090 Corynebacterium spec. 15954 20145 Corynebacterium spec. 21857 Corynebacterium spec. 21862 Corynebacterium spec. 21863 ATCC: American Type Culture Collection, Rockville, MD, USA
FERM: Fermentation Research Institute, Chiba, Japan NRRL: ARS Culture Collection, Northern Regional Research Laboratory, Peoria, IL, USA
CECT: Coleccion Espanola de Cultivos Tipo, Valencia, Spain NCIMB: National Collection of Industrial and Marine Bacteria Ltd., Aberdeen, UK
CBS: Centraalbureau voor Schimmelcultures, Baam, NL
NCTC: National Collection of Type Cultures, London, UK
DSMZ: Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany For reference see Sugawara, H. et al. (1993) World directory of collections of cultures of microorganisms: Bacteria, fungi and yeasts (4th edn), World federation for culture collections world data center on microorganisms, Saimata, Japen.

Table 4: Alignment Results ID# len h Genbank Hit Len h Accession Name of Genbank Hit Source of Genbank Hit k homoloav Date of (NT) (GAP) De it rxa00023 3579 GB_EST33:AI776129 483 A1776129 EST257217 tomato resistant, Cornell Lycopersicon esculentum cDNA clone Lycopersicon esculentum 40,956 29-Jun-99 cLER17D3, mRNA sequence.
GB_EST33:AI776129 483 A1776129 EST257217 tomato resistant, Cornell Lycopersicon esculentum cDNA clone Lycopersicon esculentum 40,956 29-Jun-99 cLER1 703, mRNA sequence.

rxa00044 1059 EM_PAT:E11760 6911 E11760 Base sequence of sucrase gene.
Corynebacterium 42,979 08-OCT-glutamicum 1997 (Rel.
52, Created) GB_PAT:126124 6911 126124 Sequence 4 from patent US 5556776. Unknown. 42,979 GB_BA2:ECOUW89 176195 U00006 E. coli chromosomal region from 89.2 to 92.8 minutes. Escherichia coli 39,097 17-DEC-rxa00064 1401 GB_PAT:E16763 2517 E16763 gDNA encoding aspartate transferase (AAT). Corynebacterium 95,429 28-Jul-99 L'' glutamicum 0 GB_HTG2:AC007892 134257 AC007892 Drosophila melanogaster chromosome 3 clone BACR02003 (D797) RPCI-98 Drosophila melanogaster 31,111 2-Aug-99 02Ø3 map 99B-99B strain y; cn bw sp, "' SEQUENCING IN PROGRESS W
113 unordered pieces.
GB_HTG2:AC007892 134257 AC007892 Drosophila melanogaster chromosome 3 clone BACR02003 (D797) RPCI-98 Drosophila melanogaster 31,111 2-Aug-99 0 02Ø3 map 99B-99B strain y; cn bw sp, "' SEQUENCING IN i .3 PROGRESS"', 113 unordered pieces.
0) rxa00072 F-' rxa00105 798 GB_BA1:MTV002 56414 AL008967 Mycobacterium tuberculosis H37Rv complete genome; segment 122/162. Mycobacterium 37,753 17-Jun-98 tuberculosis GB_BA1:ECU29581 71128 U29581 Escherichia coli K-12 genome; approximately 63 to 64 minutes. Escherichia coli 35,669 14-Jan-97 GB_BA2:AE000366 10405 AE000366 Escherichia coli K-12 MG1655 section 256 of 400 of the complete genome. Escherichia coli 35,669 12-Nov-98 rxa00106 579 GB_EST15:AA494237 367 AA494237 ng83f04.s1 NCI_CGAP_Pr6 Homo sapiens cDNA clone IMAGE:941407 Homo sapiens 42.896 20-Aug-97 similar to SW:DYR_LACCA P00381 DIHYDROFOLATE REDUCTASE ;, mRNA sequence.
GB_BA2:AF161327 2021 AF161327 Corynebacterium diphtheriae histidine kinase ChrS (chrS) and response Corynebacterium 40,210 9-Sep-99 regulator ChrA (chrA) genes, complete cds. diphtheriae GB_PAT:AR041189 654 AR041189 Sequence 4 from patent US 5811286. Unknown.
41,176 29-Sep-99 rxa00115 1170 GB_PR4:AC007110 148336 AC007110 Homo sapiens chromosome 17, clone hRPK.472_J_18, complete sequence. Homo sapiens 36,783 30-MAR-GB_HTG3:AC008537 170030 AC008537 Homo sapiens chromosome 19 clone CIT-HSPC_490E21, SEQUENCING Homo sapiens 40,296 2-Sep-99 IN PROGRESS "', 93 unordered pieces.
GB_HTG3:AC008537 170030 AC008537 Homo sapiens chromosome 19 clone CIT-HSPC_490E21, '"= SEQUENCING Homo sapiens 40,296 2-Sep-99 IN PROGRESS "', 93 unordered pieces.

Table 4 (continued) nca00116 1284 GB_BA2:AF062345 16458 AF062345 Caulobacter crescentus Sstl (sstl), S-layer protein subunft (rsaA), ABC Caulobacter crescentus 36,235 19-OCT-transporter (rsaD), membrane forming unit (rsaE), putative GDP-mannose-4,6-dehydratase (IpsA), putative acetyftransferase (IpsB), putative perosamine synthetase (IpsC), putative mannosyltransferase (IpsD), putative mannosyltransferase (IpsE), outer membrane protein (rsaF), and putative perosamine transferase (IpsE) genes, complete cds.
GB_PAT:118647 3300 118647 Sequence 6 from patent US 5500353. Unknown. 36,821 GB_GSS13:AQ44619 751 AQ446197 nbxb0062D16r CUGI Rice BAC Library Oryza sativa genomic clone Oryza sativa 38,124 8-Apr-99 7 nbxb0062D16r, genomic survey sequence.
rxaO0131 732 GB_BA1:MTY20B11 36330 Z95121 Mycobacterium tuberculosis H37Rv complete genome; segment 139/162. Mycobacterium 43,571 17-Jun-98 tuberculosis GB_BA1:SAR7932 15176 AJ007932 Streptomyces argillaceus mithramycin biosynthetic genes. Streptomyces argillaceus 41,116 15-Jun-99 GB_BA1:MTY20B11 36330 Z95121 Mycobacterium tuberculosis H37Rv complete genome;
segment 139/162. Mycobacterium 39,726 17-Jun-98 tuberculosis rxa00132 1557 GB_BAI:MTY20B11 36330 Z95121 Mycobacterium tuberculosis H37Rv complete genome; segment 139/162. Mycobacterium 36,788 17-Jun-98 tuberculosis Ln GB_IN2:TVU40872 1882 U40872 Trichomonas vaginalis S-adenosyl-L-homocysteine hydrolase gene, complete Trichomonas vaginalis 61,914 31-OCT- o cds. 1996 ~
GB HTG6:AC010706 169265 AC010706 Drosophila melanogaster chromosome X clone BACR36D15 (D887) RPCI-98 Drosophila melanogaster 51,325 22-Nov-99 36.D.15 map 13C-13E strain y; cn bw sp, "' SEQUENCING IN PROGRESS N
74 unordered pieces.
rxa00145 1059 GB_BAI:MTCY2B12 20431 Z81011 Mycobacterium tuberculosis H37Rv complete genome; segment 61/162. Mycobacterium 63,365 18-Jun-98 1 .3 tuberculosis GB_BAI:PSEPYRBX 2273 L19649 Pseudomonas aeruginosa aspartate transcarbamoylase (pyrB) and Pseudomonas aeruginosa 56,080 26-Jul-93 N
dihydroorotase-like (pyrX) genes, complete cds's.
GB BA1:LLPYRBDNA 1468 X84262 L.leichmannii pyr8 gene. Lactobacillus leichmannii 47,514 29-Apr-97 nca00146 1464 GB_BAI:MTCY2B12 20431 Z81011 Mycobacterium tuberculosis H37Rv complete genome; segment 61/162. Mycobacterium 60,714 18-Jun-98 tuberculosis GB_BA1:MTCY154 13935 Z98209 Mycobacterium tuberculosis H37Rv complete genome;
segment 121/162. Mycobacterium 39,229 17-Jun-98 tuberculosis GB_BAI:MSGY154 40221 AD000002 Mycobacterium tuberculosis sequence from clone y154. Mycobacterium 36,618 03-DEC-tuberculosis 1996 nca00147 1302 GB_BAI:MTCY2B12 20431 Z81011 Mycobacterium tuberculosis H37Rv complete genome; segment 61/162. Mycobacterium 61,527 18-Jun-98 tuberculosis GB_BAI:MSGB937C 38914 L78820 Mycobacterium leprae cosmid B937 DNA sequence.
Mycobacterium leprae 59,538 15-Jun-96 S
G8_BAI:PAU81259 7285 U81259 Pseudomonas aeruginosa dihydrodipicolinate reductase (dapB) gene, partial Pseudomonas aeruginosa 55,396 23-DEC-cds, carbamoylphosphate synthetase small subunit (carA) and 1996 carbamoylphosphate synthetase large subunit (carB) genes, complete cds, and FtsJ homolog (ftsJ) gene, partial cds.
rxa00156 1233 GB_BA1:SC9B10 33320 AL009204 Streptomyces coelicolor cosmid 9B10. Streptomyces coelicolor 52,666 10-Feb-99 Table 4 (continued) GB_BA2:AF002133 15437 AF002133 Mycobacterium avium strain GIR10 transcriptional regulator (mav81) gene, Mycobacterium avium 54,191 26-MAR-partial cds, aconitase (acn), invasin 1 (invl), invasin 2 (inv2), transcriptional 1998 regulator (moxR), ketoacyl-reductase (fabG), enoyl-reductase (inhA) and ferrochelatase (mav272) genes, complete cds.
GB_BA1:D85417 7984 D85417 Propionibacterium freudenreichii hemY, hemH, hemB, hemX, hemR and Propionibacterium 46,667 6-Feb-99 hemL genes, complete cds. freudenreichii rxa00166 783 GB HTG3:AC008167 174223 AC008167 Homo sapiens clone NH0172013, SEQUENCING IN PROGRESS 7 Homo sapiens 37,451 21-Aug-99 unordered pieces.
GB_HTG3:AC008167 174223 AC008167 Homo sapiens clone NH0172013, SEQUENCING IN
PROGRESS 7 Homo sapiens 37,451 21-Aug-99 unordered pieces.
GB_HTG4:AC010118 80605 AC010118 Drosophila melanogaster chromosome 3L/62B1 clone RPCI98-10D15, Drosophila melanogaster 38,627 16-OCT-SEQUENCING IN PROGRESS "', 51 unordered pieces. 1999 nca00198 672 GB_BA1:AB024708 8734 AB024708 Corynebacterium glutamicum gltB and gltD genes for glutamine 2- Corynebacterium 92,113 13-MAR-oxoglutarate aminotransferase large and small subunits, complete cds.
glutamicum 1999 GB_BA1:AB024708 8734 AB024708 Corynebacterium glutamicum gltB and gltD genes for glutamine 2- Corynebacterium 93,702 13-MAR-aminotransferase large and small subunits, complete cds. glutamicum 1999 N
oxoglutarate GB_EST24:AI232702 528 A1232702 EST229390 Normalized rat kidney, Bento Soares Rattus sp. cDNA clone Rattus sp. 34,221 31-Jan-99 cn RKICF35 3' end, mRNA sequence.
rxa00216 1113 GB_HTG2:HSDJ850E 117353 AL121758 Homo sapiens chromosome 20 clone RP5-850E9, SEQUENCING IN Homo sapiens 37,965 03-DEC- ~ 0) 9 PROGRESS "', in unordered pieces. 1999 r GB_HTG2:HSDJ850E 117353 AL121758 Homo sapiens chromosome 20 clone RP5-850E9, SEQUENCING IN Homo sapiens 37,965 03-DEC-9 9 PROGRESS "', in unordered pieces. 1999 GB_PR2:CNS01DSA 159400 AL121766 Human chromosome 14 DNA sequence'"= IN
PROGRESS "' BAC R-412H8 Homo sapiens 38,796 11-Nov-99 i ~
of RPCI-1 1 library from chromosome 14 of Homo sapiens (Human), complete o rn sequence.
nca00219 1065 GB_HTG2:AC005079 110000 AC005079 Homo sapiens clone RG252P22, "=
SEQUENCING IN PROGRESS 3 Homo sapiens 38,227 22-Nov-98 _0 unordered pieces.
GB_HTG2:AC005079 110000 AC005079 Homo sapiens clone RG252P22, SEQUENCING IN
PROGRESS 3 Homo sapiens 38,227 22-Nov-98 _1 unordered pieces.
GB_HTG2:AC005079 110000 AC005079 Homo sapiens clone RG252P22, SEQUENCING IN
PROGRESS 3 Homo sapiens 38,227 22-Nov-98 _1 unordered pieces.
rxa00223 1212 GB_BA1:PPEA3NIF 19771 X99694 Plasmid pEA3 nitrogen fixation genes. Enterobacter agglomerans 48,826 2-Aug-96 GB_BA2:AF128444 2477 AF128444 Rhodobacter capsulatus molybdenum cofactor biosynthetic gene cluster, Rhodobacter capsulatus 40,135 22-MAR-partial sequence. 1999 GB_HTG4:AC010111 138938 AC010111 Drosophla melanogaster chromosome 3LI70C1 clone RPCI98-9B18, Drosophila melanogaster 39,527 16-OCT-SEQUENCING IN PROGRESS "', 64 unordered pieces. 1999 rxa00229 803 GB_BA2:AF124518 1758 AF124518 Corynebacterium glutamicum 3-dehydroquinase (aroD) and shikimate Corynebacterium 98,237 18-MAY-dehydrogenase (aroE) genes, complete cds. glutamicum 1999 GB_PR3:AC004593 150221 AC004593 Homo sapiens PAC clone DJ0964C1 1 from 7p14-p15, complete sequence. Homo sapiens 36,616 18-Apr-98 GB_HTG2:AC006907 188972 AC006907 Caenorhabditis elegans clone Y76B12, "' SEQUENCING IN PROGRESS Caenorhabditis elegans 37,095 26-Feb-99 25 unordered pieces.
rxa00241 1626 GB BA1:CGLYSI 4232 X60312 C.glutamicum lysl gene for L-lysine permease. Corynebacterium 100,000 30-Jan-92 glutamicum Table 4 (continued) GB_HTG1:PFMAL13P 192581 AL049180 Plasmodium falciparum chromosome 13 strain 3D7, '=' SEQUENCING IN Plasmodium falciparum 34,947 11-Aug-99 1 PROGRESS "', in unordered pieces.
GB_HTG1:PFMAL13P 192581 AL049180 Plasmodium falciparum chromosome 13 strain 3D7, SEQUENCING IN Plasmodium falciparum 34,947 11-Aug-99 1 PROGRESS "" in unordered pieces.
rxa00262 1197 GB_IN2:EHU89655 3219 U89655 Entamoeba histolytica unconventional myosin IB mRNA, complete cds. Entamoeba histolytica 36,496 23-MAY-GB_IN2:EHU89655 3219 U89655 Entamoeba histolytica unconventional myosin IB
mRNA, complete cds. Entamoeba histotytica 37,544 23-MAY-rxa00266 531 GB_RO:AF016190 2939 AF016190 Mus musculus connexin-36 (Cx36) gene, complete cds. Mus musculus 41,856 9-Feb-99 EM_PAT:E09719 3505 E09719 DNA encoding precursor protein of alkaline cellulase. Bacillus sp. 34,741 08-OCT-1997 (Rel.
52, Created) GB_PAT:E02133 3494 E02133 gDNA encoding alkaline cellulase. Bacillus sp.
34,741 29-Sep-97 rxa00278 1155 G8_INI:CELK05F6 36912 AF040653 Caenorhabditis elegans cosmid K05F6. Caenorhabditis elegans 36,943 6-Jan-98 GB_BA1:CGU43535 2531 U43535 Corynebacterium glutamicum multidrug resistance protein (cmr) gene, Corynebacterium 36,658 9-Apr-97 complete cds. glutamicum Ln GB_RO:RNU30789 3510 U30789 Rattus norvegicus clone N27 mRNA, Rattus norvegicus 38,190 20-Aug-96 0 rxa00295 1125 GB_BA2:CGU31281 1614 U31281 Corynebacterium glutamicum biotin synthase (bioB) gene, complete cds. Corynebacterium 99,111 21-Nov-96 ~
glutamicum co n' GBBA1:BRLBIOBA 1647 D14084 Brevibacterium flavum gene for biotin synthetase, complete cds. Corynebacterium 98,489 3-Feb-99 glutamicum 0 G8_PAT:E03937 1005 E03937 DNA sequence encoding Brevibacterium flavum biotin-synthase. Corynebacterium 98,207 29-Sep-97 1 .3 gtutamicum o rn rxa00323 1461 GB_BAI:MTCY427 38110 Z70692 Mycobacterium tuberculosis H37Rv complete genome; segrnent 991162. Mycobacterium 35,615 24-Jun-99 tuberculosis F-GB_BA1:MSG832CS 36404 L78818 Mycobacterium leprae cosmid 832 DNA sequence.
Mycobacterium leprae 60,917 15-Jun-96 GB BA1:MTCY427 38110 Z70692 Mycobacterium tuberculosis H37Rv complete genome;
segment 99/162. Mycobacterium 44,606 24-Jun-99 tuberculosis rxa00324 3258 GB_BA1:MSGB32CS 36404 L78818 Mycobacterium leprae cosmid B32 DNA
sequence. Mycobacterium leprae 52,516 15-Jun-96 GB_BAI:MTCY427 38110 Z70692 Mycobacterium tuberculosis H37Rv complete genome;
segment 99/162. Mycobacterium 38,079 24-Jun-99 tuberculosis GB_OM:BOVELA 3242 J02717 Bovine elastin a mRNA, complete cds. Bos taurus 39,351 27-Apr-93 rxa00330 1566 GB_BA1:CGTHRC 3120 X56037 Corynebacterium glutamicum thrC gene for threonine synthase (EC 4.2.99.2). Corynebacterium 99,808 17-Jun-97 glutamicum GB_PAT:I09078 3146 109078 Sequence 4 from Patent WO 8809819. Unknown. 99,617 GB_BA1:BLTHRESY 1892 Z29563 Brevibacterium lactofermentum; ATCC 13869;; DNA
(genomic);. Corynebacterium 99,170 20-Sep-95 N glutamicum rxa00335 1554 GB_BAI:CGGLNA 3686 Y13221 Corynebacterium glutamicum gInA gene.
Corynebacterium 100,000 28-Aug-97 glutamicum Table 4 (continued) GB_BA2:AF005635 1690 AF005635 Corynebacterium glutamicum glutamine synthetase (glnA) gene, complete Corynebacterium 98,906 14-Jun-99 cds= glutamicum GB_BAI:MSGB27CS 38793 L78817 Mycobacterium leprae cosmid B27 DNA sequence.
Mycobacterium leprae 66,345 15-Jun-96 rxa00347 891 GB_EST27:AI455217 624 A1455217 LD21828.3prime LD Drosophila melanogaster embryo pOT2 Drosophila Drosophila melanogaster 34,510 09-MAR-melanogaster cDNA clone LD21828 3prime, mRNA sequence. 1999 GB_BA2:SSU30252 2891 U30252 Synechococcus PCC7942 nucleoside diphosphate kinase and ORF2 protein Synechococcus PCC7942 37,084 29-OCT-genes, complete cds, ORFt protein gene, partial cds, and neutral site I for vector use.
GB_EST21:AA911262 581 AA911262 oe75a02.s1 NCI_CGAP_Lu5 Homo sapiens cDNA clone IMAGE: 1417418 3' Homo sapiens 37,500 21-Apr-98 similar to gb:A18757 UROKINASE PLASMINOGEN ACTIVATOR SURFACE
RECEPTOR, GPI-ANCHORED (HUMAN);, mRNA sequence.
nca00351 1578 GB_BA1:MLU15187 36138 U15187 Mycobacterium leprae cosmid L296.
Mycobacterium Ieprae 52,972 09-MAR-GB_IN2:AC004373 72722 AC004373 Drosophila melanogaster DNA sequence (P1 DS05273 (D80)), complete Drosophila melanogaster 46,341 17-Jul-98 sequence. o GB_IN2:AF145653 3197 AF145653 Drosophila melanogaster clone GH08860 BcDNA.GH08860 Drosophila melanogaster 49,471 14-Jun-99 (BcDNA.GH08860) mRNA, complete cds. Ln rxa00365 727 GB_BA1:AB024708 8734 AB024708 Corynebacterium glutamicum gttB and gltD genes for glutamine 2- Corynebacterium 96,556 13-MAR- rn oxoglutarate aminotransferase large and small subunits, complete cds.
glutamicum 1999 N
GB_BA1:MTCYIA6 37751 Z83864 Mycobacterium tuberculosis H37Rv complete genome;
segment 159/162. Mycobacterium 39,496 17-Jun-98 tuberculosis o GB BA1:SC3A3 15901 AL109849 Streptomyces coelicolor cosmid 3A3. Streptomyces coelicolor 37,946 16-Aug-99 A3(2) o rxa00366 480 GB_BA1:A8024708 8734 AB024708 Corynebacterium glutamicum gltB and gltD genes for glutamine 2- Corynebacterium 99,374 13-MAR- o) oxoglutarate aminotransferase large and small subunits, complete cds.
glutamicum 1999 GB_BA1:MTCYIA6 37751 Z83864 Mycobacterium tuberculosis H37Rv complete genome;
segment 159/162. Mycobacterium 41,333 17-Jun-98 tuberculosis GB_BA1:SC3A3 15901 AL109849 Streptomyces coelicolor cosmid 3A3. Streptomyces coelicolor 37,554 16-Aug-99 A3(2) nca00367 4653 GB_BA1:AB024708 8734 AB024708 Corynebacterium glutamicum gltB
and gltD genes for glutamine 2- Corynebacterium 99,312 13-MAR-oxoglutarate aminotransferase large and small subunits, complete cds.
glutamicum 1999 GB BA1:MTCYIA6 37751 Z83864 Mycobacterium tuberculosis H37Rv complete genome;
segment 159/162. Mycobacterium 36,971 17-Jun-98 tuberculosis GB_BA1:SC3A3 15901 AL109849 Streptomyces coelicolor cosmid 3A3. Streptomyces coelicolor 37,905 16-Aug-99 A3(2) nca00371 1917 GB_VI:SBVORFS 7568 M89923 Sugarcane bacilliform virus ORF
1,2,and 3 DNA, complete cds. Sugarcane bacilliform virus 35,843 12-Jun-93 GB EST37:AI967505 380 A1967505 Ljirnpest03-215-c10 Ljirnp Lambda HybriZap two-hybrid library Lotus Lotus japonicus 42,593 24-Aug-99 japonicus cDNA clone LP215-03-c10 5' similar to 60S ribosomal protein L39, mRNA sequence.
GB_INI:CELK09H9 37881 AF043700 Caenorhabditis elegans cosmid K09H9.
Caenorhabdftis elegans 34,295 22-Jan-98 Table 4lcontinued-nca00377 1245 GB BAI:CCU13664 1678 U13664 Caulobacter crescentus uroporphyrinogen decarboxylase homolog (hemE) Caulobacter crescentus 36,832 24-MAR-gene, partial cds. 1995 GB_PL1:ANSDGENE 1299 Y08866 A.nidulans sD gene. Emericella nidulans 39,603 17-OCT-GB_GSS4:AQ730303 483 AQ730303 HS_5505_B1_C04_T7A RPCI-11 Human Male BAC
Library Homo sapiens Homo sapiens 36,728 15-Jul-99 genomic clone Plate=1081 Col=7 Row=F, genomic survey sequence.
rxa00382 1425 GB_BA1:PAHEML 4444 X82072 P.aeruginosa hemL gene. Pseudomonas aeruginosa 54,175 18-DEC-GB_BAI:MTY25D10 40838 Z95558 Mycobacterium tuberculosis H37Rv complete genome;
segment 28/162. Mycobacterium 61,143 17-Jun-98 tuberculosis GB_BA1:MSGY224 40051 AD000004 Mycobacterium tuberculosis sequence from clone y224. Mycobacterium 61,143 03-DEC-tuberculosis 1996 rxa00383 1467 GB_BAI:MLCB1222 34714 AL049491 Mycobacterium leprae cosmid B1222. Mycobacterium leprae 43,981 27-Aug-99 GB_HTG2:AC006269 167171 AC006269 Homo sapiens chromosome 17 clone hRPK.515_E_23 map 17, Homo sapiens 35,444 10Jun-99 SEQUENCING IN PROGRESS "", 2 ordered pieces.
GB_HTG2:AC007638 178053 AC007638 Homo sapiens chromosome 17 clone hRPK.515_O_17 map 17, Homo sapiens 34,821 22-MAY- o SEQUENCING IN PROGRESS "', 8 unordered pieces. 1999 Ln rxa00391 843 G8_EST38:AW01705 613 AW017053 EST272398 Schistosoma mansoni male, Phil LoVerde/Joe Merrick Schistosoma mansoni 40,472 10-Sep-99 3 Schistosoma mansoni cDNA clone SMMAS14 5' end, mRNA sequence. 0) GB_PAT:AR065852 32207 AR065852 Sequence 20 from patent US 5849564. Unknown.
38,586 29-Sep-99 0) GB_VI:AF148805 28559 AF148805 Kaposi's sarcoma-associated herpesvirus ORF 68 gene, partial cds; and ORF Kaposi's sarcoma- 38,509 2-Aug-99 69, kaposin, v-FLIP, v-cyclin, latent nuclear antigen, ORF K14, v-GPCR, associated herpesvirus putative phosphoribosytformylglycinamidine synthase, and LAMP
(LAMP) genes, complete cds. ~
rxa00393 1017 GB_BA1:MTY25D10 40838 Z95558 Mycobacterium tuberculosis H37Rv complete genome; segment 28/162. Mycobacterium 36,308 17-Jun-98 O1 tuberculosis GB_BA1:MSGY224 40051 AD0G0004 Mycobacterium tuberculosis sequence from clone y224. Mycobacterium 39,282 03-DEC-tuberculosis GB BAI:MLB1306 7762 Y13803 Mycobacterium teprae cosmid B1306 DNA.
Mycobacterium leprae 39,228 24-Jun-97 nca00402 623 GB_BA2:AF052652 2096 AF052652 Corynebacterium glutamicum homoserine O-acetyltransferase (metA) gene, Corynebacterium 99,672 19-MAR-complete cds. glutamicum 1998 GB_BA2:AF109162 4514 AF109162 Corynebacterium diphtheriae heme uptake locus, complete sequence. Corynebacterium 40,830 8-Jun-99 diphtheriae GB_BA2:AF092918 20758 AF092918 Pseudomonas alcaligenes outer membrane Xcp-secretion system gene Pseudomonas alcaligenes 50,161 06-DEC-cluster, 1998 rxa00403 1254 GB_BA2:AF052652 2096 AF052652 Corynebacterium glutamicum homoserine 0-acetyltransferase (metA) gene, Corynebacterium 99,920 19-MAR-complete cds glutamicum 1998 GB_BA1:MTV016 53662 AL021841 Mycobacterium tuberculosis H37Rv complete genome;
segment 143/162. Mycobacterium 52,898 23-Jun-99 tuberculosis GB EST23:AI111288 750 AI111288 SWOvAMCAQO2A05SK Onchocerca volvulus adult male cDNA (SAW98MLW-Onchocerca volvulus 37,565 31 -Aug-98 OvAM) Onchocerca volvulus cDNA clone SWOvAMCAQ02A05 5', mRNA
sequence.

Table 4 (continued) rxa00405 613 GB_BAI:MTV016 53662 AL021841 Mycobacterium tuberculosis H37Rv complete genome; segment 143/162. Mycobacterium 57,259 23-Jun-99 tuberculosis GB PR4:AC005145 143678 AC005145 Homo sapiens Xp22-166-169 GSHB-523A23 (Genome Systems Human BAC Homo sapiens 34,179 08-DEC-library) complete sequence. 1998 GB_BA1:MTV016 53662 AL021841 Mycobacterium tuberculosis H37Rv complete genome;
segment 143/162. Mycobacterium 40,169 23-Jun-99 tuberculosis rxa00420 1587 GB_BAI:MTY13D12 37085 Z80343 Mycobacterium tuberculosis H37Rv complete genome; segment 156/162. Mycobacterium 62,031 17-Jun-98 tuberculosis GB_BA1:MSGY126 37164 AD000012 Mycobacterium tuberculosis sequence from clone y126. Mycobacterium 61,902 10-DEC-tuberculosis 1996 GB_BA1:MSGB971C 37566 L78821 Mycobacterium leprae cosmid B971 DNA sequence.
Mycobacterium leprae 39,651 15-Jun-96 S
rxa00435 1296 GB_BA1:AFACBBTZ 2760 M68904 Alcaligenes eutrophus chromsomal transketolase (cbbTc) and Ralstonia eutropha 38,677 27-Jul-94 phosphoglycolate phosphatase (cbbZc) genes, complete cds.
GB_HTG4:AC009541 169583 AC009541 Homo sapiens chromosome 7, SEQUENCING IN
PROGRESS 25 Homo sapiens 36,335 12-OCT-unordered pieces. 1999 GBHTG4:AC009541 169583 AC009541 Homo sapiens chromosome 7, SEQUENCING IN
PROGRESS 25 Homo sapiens 36,335 12-OCT-tn unordered pieces. 1999 to rxa00437 579 GB_PR4:AC005951 155450 AC005951 Homo sapiens chromosome 17, 41onB
hRPK.372_K_20, complete sequence. Homo sapiens 31,738 18-Nov-98 0 0) ~. oi GB_BA1:SC2A11 22789 AL031184 Streptomyces coelicolor cosmid 2A11. Streptomyces coelicolor 43,262 5-Aug-98 ~
GB_PR4:AC005951 155450 AC005951 Homo sapiens chromosome 17, clone hRPK.372_K_20, complete sequence. Homo sapiens 37,647 18-Nov-98 0 -.3 rxa00439 591 GB_BAI:MTV016 53662 AL021841 Mycobacterium tuberculosis H37Rv complete genome; segment 143l162. Mycobacterium 37,088 23-Jun-99 tuberculosis oi GB PL2:AF167358 1022 AF167358 Rumex acetosa expansin (EXP3) gene, partial cds.
Rumex acetosa 46,538 17-Aug-99 rv GB_HTG3:AC009120 269445 AC009120 Homo sapiens chromosome 16 clone RPCI-1 1484E3, "' SEQUENCING IN Homo sapiens 43,276 3-Aug-99 PROGRESS "", 34 unordered pieces.
rxa00440 582 GB_BA2:SKZ86111 7860 Z861 11 Streptomyces lividans rpsP, trmD, rplS, sipW, sipX, sipY, sipZ, mutT genes Streptomyces lividans 43,080 27-OCT-and 4 open reading frames. 1999 GB_BA1:SC2E1 38962 AL023797 Streptomyces coelicolor cosmid 2E1. Streptomyces coelicolor 42,931 4-Jun-98 GB BA1:SC2E1 38962 AL023797 Streptomyces coelicolor cosmid 2E1. Streptomyces coelicolor 36,702 4-Jun-98 rxa00441 1287 GB_PR2:HS173D1 117338 AL031984 Human DNA sequence from clone 173D1 on chromosome 1p36.21- Homo sapiens 38,027 23-Nov-99 36.33.Contains ESTs, STSs and GSSs, complete sequence.
GB_HTG2:HSDJ719K 267114 AL109931 Homo sapiens chromcsome X clone RP4-719K3 map q21.1-21.31, Homo sapiens 34,521 03-DEC-3 SEQUENCING IN PROGRESS "", in unordered pieces. 1999 GB_HTG2:HSDJ719K 267114 AL109931 Homo sapiens chromosome X done RP4-719K3 map q21.1-21.31, Homo sapiens 34,521 03-DEC-3 SEQUENCING IN PROGRESS "', in unordered pieces. 1999 rxa00446 987 GB_BA1:SCD78 36224 AL034355 Streptomyces coelicolor cosmid D78.
Streptomyces coelicolor 56,410 26-Nov-98 GB_HTG4:AC009367 226055 AC009367 Drosophila melanogaster chromosome 3L/76A2 clone RPCI98-48B15, Drosophila melanogaster 34,959 16-OCT-SEQUENCING IN PROGRESS "', 44 unordered pieces. 1999 GB_HTG4:AC009367 226055 AC009367 Drosophila melanogaster chromosome 3L/76A2 clone RPCI98-48B1 5, Drosophila melanogaster 34,959 16-OCT-SEQUENCING IN PROGRESS "', 44 unordered pieces. 1999 Table 4 (continued) rxa00448 1143 GB PR3:AC003670 88945 AC003670 Homo sapiens 12q13.1 PAC RPCI1-130F5 (Roswell Park Cancer Institute Homo sapiens 35,682 9Jun-98 Human PAC library) complete sequence.
GB HTG2:AF029367 148676 AF029367 Homo sapiens chromosome 12 clone RPCI-1 130F5 map 12q13.1, =" Homo sapiens 31,373 18-OCT-SEQUENCING IN PROGRESS "', 156 unordered pieces. 1997 GB_HTG2:AF029367 148676 AF029367 Homo sapiens chromosome 12 clone RPCI-1 130F5 map 12q13.1, Homo sapiens 31,373 18-OCT-SEQUENCING IN PROGRESS "", 156 unordered pieces. 1997 rxa00450 424 GB_HTG2:AC007824 133361 AC007824 Drosophila melanogaster chromosome 3 clone BACR02L16 (D715) RPCI-98 Drosophila melanogaster 40,000 2-Aug-99 02.L.16 map 89E-90A strain y: cn bw sp, "' SEQUENCING IN PROGRESS
' , 91 unordered pieces.
GB_HTG2:AC007824 133361 AC007824 Drosophila melanogaster chromosome 3 clone BACR02L16 (D715) RPCI-98 Drosophila melanogaster 40,000 2-Aug-99 02.L.16 map 89E-90A strain y, cn bw sp, "' SEQUENCING IN PROGRESS
"', 91 unordered pieces.
GB_EST35:A1818057 412 A1818057 wkl4aO8.xl NCI_CGAP_Lyml2 Homo sapiens cDNA
clone IMAGE:2412278 Homo sapiens 35,714 24-Aug-99 3' similar to gb:Y00764 UBIQUINOL-CYTOCHROME C REDUCTASE 11 KD
PROTEIN (HUMAN);, mRNA sequence.
rxa00461 975 GB_BA1:MLCB1779 43254 Z98271 Mycobacterium leprae cosmid 81779.
Mycobacterium leprae 39,308 8-Aug-97 GB_INI:DMC86E4 29352 AL021086 Drosophila melanogaster cosmid clone 86E4.
Drosophila melanogaster 37.487 27-Apr-99 r v GB_GSS15:AQ64032 467 AQ640325 927P1-2H3.TP 927P1 Trypanosoma brucei genomic clone 927P1-21i3, Trypanosoma brucei 38,116 8-Jul-99 L"
genomic survey sequence. o rxa00465 rn r N

rxa00487 1692 GB BAI:BAGUAA 3866 Y10499 B.ammoniagenes guaA gene.
Corynebacterium 74,259 8-Jan-98 N o ammoniagenes GB_BA2:U00015 42325 U00015 Mycobacterium leprae cosmid B1620. Mycobacterium leprae 37,248 01-MAR- 0) GB_BA1:MTCY78 33818 Z77165 Mycobacterium tuberculosis H37Rv complete genome;
segment 145/162. Mycobacterium 39,725 17-Jun-98 tuberculosis rxa00488 1641 GB_BA1:MTCY78 33818 Z77165 Mycobacterium tuberculosis H37Rv complete genome; segment 145/162. Mycobacterium 39,451 17-Jun-98 tuberculosis GB_BA2:U00015 42325 U00015 Mycobacterium leprae cosmid B1620. Mycobacterium leprae 39,178 01-MAR-GB_BA1:SCAJ10601 4692 AJ010601 Streptomyces coelicolor A3(2) DNA for whiD and whiK loci. Streptomyces coelicolor 60,835 17-Sep-98 rna00489 1245 GB_BA2:U00015 42325 U00015 Mycobacterium leprae cosmid B1620.
Mycobacterium leprae 38,041 01-MAR-GB HTG2:HS225E12 126464 AL031772 Homo sapiens chromosome 6 clone RP1-225E12 map q24, Homo sapiens 36,756 03-DEC-SEQUENCING IN PROGRESS "', in unordered pieces. 1999 GB_HTG2:HS225E12 126464 AL031772 Homo sapiens chromosome 6 clone RPI-225E12 map q24, =" Homo sapiens 36,756 03-DEC-SEQUENCING IN PROGRESS "', in unordered pieces. 1999 rxa00533 1155 GB_BAI:CGLYS 2803 X57226 C. glutamicum lysC-alpha, IysC-beta and asd genes for aspartokinase-alpha Corynebacterlum 99,913 17-Feb-97 and -beta subunits, and aspartate beta semialdehyde dehydrogenase, glutamicum respectively (EC 2.7.2.4; EC 1.2.1.11).

Table 4 (continued) GB_BAI:CGCYSCAS 1591 X82928 C.glutamicum aspartate-semialdehyde dehydrogenase gene. Corynebacterium 99,221 17-Feb-97 0 glutamicum GB PAT:A07546 2112 A07546 Recombinant DNA fragment (Pstl-Xhol). synthetic construct 99,391 30-Jul-93 rxa00534 1386 GB BA1:CGLYS 2803 X57226 C. glutamicum lysC-alpha, lysC-beta and asd genes for aspartokinase-alpha Corynebacterlum 99,856 17-Feb-97 and -beta subunits, and aspartate beta semialdehyde dehydrogenase, glutamicum respectively (EC 2.7.2.4; EC 1.2.1.11).
GB_BA1:CORASKD 2957 L16848 Corynebacterium flavum aspartokinase (ask), and aspartate-semialdehyde Corynebacterium 98,701 11-Jun-93 dehydrogenase (asd) genes, complete cds. flavescens GB_PAT:E14514 1643 E14514 DNA encoding Brevibacterium aspartokinase.
Corynebacterium 98,773 28-Jul-99 glutamicum rxa00536 1494 GB_BAI:CGLEUA 3492 X70959 C.glutamicum gene leuA for isopropylmalate synthase. Corynebacterium 100,000 10-Feb-99 glutamicum GB_BA1:MTV025 121125 AL022121 Mycobacterium tuberculosis H37Rv complete genome; segment 155/162. Mycobacterium 68,003 24-Jun-99 tuberculosis GB_BA1:MTU88526 2412 U88526 Mycobacterium tuberculosis putative alpha-isopropyl malate synthase (IeuA) Mycobacterium 68,185 26-Feb-97 gene, complete cds. tuberculosis rxa00537 2409 GB_BA2:SCD25 41622 AL118514 Streptomyces coelicolor cosmid D25.
Streptomyces coelicolor 63,187 21-Sep-99 A3(2) GB_BA1:MTCY7H7A 10451 Z95618 Mycobacterium tuberculosis H37Rv complete genome;
segment 39/162. Mycobacterium 62,401 17-Jun-98 Ln tuberculosis GB_BA1:MTU34956 2462 U34956 Mycobacterium tuberculosis phosphoribosylformyfglycinamidine synthase Mycobacterium 62,205 28-Jan-97 N
(purL) gene, complete cds. tuberculosis W N
rxa00541 792 GB_PAT:192052 2115 192052 Sequence 19 from patent US 5726299.
Unknown. 98,359 01-DEC- =

GB_BA1:MLCB5 38109 Z95151 Mycobacterium leprae cosmid B5. Mycobacterium leprae 62,468 24-Jun-97 .3 GB_BAI:MTCY369 36850 Z80226 Mycobacterium tuberculosis H37Rv complete genome;
segment 36/162. Mycobacterium 60,814 17-Jun-98 rn tuberculosis rxa00558 1470 GB_BA1:BAPURF 1885 X91252 B.ammoniagenes purF gene.
Corynebacterium 66,095 5-Jun-97 ammoniagenes GB_BA1:MLU15182 40123 U15182 Mycobacterium leprae cosmid B2266. Mycobacterium leprae 64,315 09-MAR-GB_BA1:MTCY7H7A 10451 Z95618 Mycobacterium tuberculosis H37Rv complete genome:
segment 39/162. Mycobacterium 64,863 17-Jun-98 tuberculosis rxa00579 1983 GB_PAT:AR016483 2104 AR016483 Sequence 1 from patent US 5776740.
Unknown. 98,810 05-DEC-EM_PAT:E11273 2104 E11273 DNA encoding serine hydroxymethyl transferase.
Corynebacterium 98,810 08-OCT-glutamicum 1997 (Rel.
52, Created) GB_PAT:E12594 2104 E12594 DNA encoding serine hydroxymethyltransferase from Brevibacterium flavum. Corynebacterium 98,810 24-Jun-98 glutamicum rxa00580 1425 GB_PAT:E12594 2104 E12594 DNA encoding serine hydroxymethyltransferase from Brevibacterium flavum. Corynebaderium 99,368 24-Jun-98 glutamicum Table 4 (continued) GB_PAT:AR016483 2104 AR016483 Sequence 1 from patent US 5776740. Unknown.
99,368 05-DEC-EM_PAT:E11273 2104 E11273 DNA encoding serine hydroxymethyl transferase.
Corynebacterium 99,368 08-OCT-glutamicum 1997 (Rel.
52, Created) nca00581 1092 GB_PAT:E12594 2104 E12594 DNA encoding serine hydroxymethyttransferase from Brevibacterium flavum. Corynebacterium 37,071 24-Jun-98 glutamicum EM_PAT:E11273 2104 E11273 DNA encoding serine hydroxymethyl transferase.
Corynebacterium 37,071 08-OCT-glutamicum 1997 (Rel.
52, Created) GB_PAT:AR016483 2104 AR016483 Sequence 1 from patent US 5776740. Unknown.
37,071 05-DEC-rxa00584 1248 GB_BA1:CORAHPS 2570 L07603 Corynebacterium glutamicum 3-deoxy-D-arabinoheptulosonate-7-phosphate Corynebacterium 98,236 26-Apr-93 synthase gene, complete cds. glutamicum GB_BAIAOPCZA361 37941 AJ223998 Amycolatopsis orientalis cosmid PCZA361.
Amycolatopsis orientalis 54,553 29-MAR-GB_BA1:D90714 14358 D90714 Escherichia coli genomic DNA. (16.8 - 17.1 min).
Escherichia coli 53,312 7-Feb-99 rxa00618 1230 GB_EST19:AA802737 280 AA802737 GM06236.5prime GM Drosophila melanogaster ovary BlueScript Drosophila Drosophila melanogaster 39,928 25-Nov-melanogaster cDNA clone GM06236 5prime, mRNA sequence.
GB_EST28:A1534381 581 AI534381 SD07186.5prime SD Drosophila melanogaster Schneider L2 cell culture pOT2 Drosophila melanogaster 41,136 18-MAR-o Drosophila melanogaster cDNA clone SD07186 5prime similar to X89858: Ani 1999 4- 0) FBgn0011558 PID:g927407 SPTREMBL:Q24240, mRNA sequence.

GB_IN1:DMANILLIN 4029 X89858 D.melanogaster mRNA for anillin protein.
Drosophila melanogaster 34,398 8-Nov-95 nea00619 1551 GB_BA1:MTCY369 36850 Z80226 Mycobacterium tuberculosis H37Rv complete genome; segment 361162. Mycobacterium 62,776 17-Jun-98 tuberculosis 0) GB_BA1:MLCB5 38109 Z95151 Mycobacterium leprae cosmid B5. Mycobacterium leprae 61,831 24-Jun-97 rv GB_PAT:A60305 1845 A60305 Sequence 5 from Patent W09708323. unidentified 61,785 06-MAR-1998 rxa00620 1014 GB PL2:AF063247 1450 AF063247 Pneumocystis carinii f. sp.
ratti enolase mRNA, complete cds. Pneumocystis carinii f. sp. 41,060 5-Jan-99 ratti GB_BA1:STMAPP 2069 M91546 Streptomyces lividans aminopeptidase P (PepP) gene, complete cds. Streptomyces lividans 37,126 12-Jun-93 GB_HTG3:AC008763 214575 AC008763 Homo sapiens chromosome 19 clone CITB-E1_3214H19, '=' SEQUENCING Homo sapiens 40,020 3-Aug-99 IN PROGRESS "', 21 unordered pieces.
rxa00624 810 GB_IN1:CEY41E3 150641 Z95559 Caenorhabditis elegans cosmid Y41E3, complete sequence. Caenorhabditis elegans 36,986 2-Sep-99 GB_EST13:AA362167 372 AA362167 EST71561 Macrophage I Homo sapiens cDNA 5' end, mRNA sequence. Homo sapiens 38,378 21-Apr-97 GB_IN1:CEY41 E3 150641 Z95559 Caenorhabditis elegans cosmid Y41 E3, complete sequence. Caenorhabditis elegans 37,694 2-Sep-99 rxa00626 1386 Gt3_BAI:MTCY369 36850 Z80226 Mycobacterium tuberculosis H37Rv complete genome; segment 36/162. Mycobacterium 57,971 17-Jun-98 tuberculosis GB BAI:MLCB5 38109 Z95151 Mycobacterium leprae cosmid B5. Mycobacterium leprae 58,806 24-Jun-97 GB_BA1:MLU15187 36138 U15187 Mycobacterium leprae cosmid L296. Mycobacterium leprae 38,007 09-MAR-Table 4 (continued) rxa00632 795 GB_BA1:BRLBIOAD 2272 014083 Brevibacterium flavum genes for 7,8-diaminopelargonic acid aminotransferase Corynebacterium 97,358 3-Feb-99 and dethiobiotin synthetase, complete cds. glutamicum GB PAT:E04041 675 E04041 DNA sequence coding for desthiobiotinsynthetase.
Corynebacterium 98,074 29-Sep-97 glutamicum GB_PAT:E04040 1272 E04040 DNA sequence coding for diamino pelargonic acid aminotransferase. Corynebacterium 93,814 29-Sep-97 glutamicum rxa00633 1392 GB_BA1:BRLBIOAD 2272 D14083 Brevibacterium flavum genes for 7,8-diaminopelargonic acid aminotransferase Corynebacterium 95,690 3-Feb-99 and dethiobiotin synthetase, complete cds. glutamicum GB_PAT:E04040 1272 E04040 DNA sequence coding for diamino pelargonic acid aminotransferase. Corynebacterium 95,755 29-Sep-97 glutamicum GB_BA2:EHU38519 1290 U38519 Erwinia herbicola adenosylmethionine-8-amino-7-oxononanoate transaminase Erwinia herbicola 55,564 4-Nov-96 (bioA) gene, complete cds.
rxa00688 666 GB_BA1:MTV041 28826 AL021958 Mycobacterium tuberculosis H37Rv complete genome; segment 35/162. Mycobacterium 60,030 17-Jun-98 tuberculosis GB_BAI:BRLSECY 1516 D14162 Brevibacterium flavum gene for SecY protein (complete cds) and gene or Corynebacterium 99,563 3-Feb-99 adenylate kinase (partial cds). glutamicum o GB_BA2:MBU77912 7163 U77912 Mycobacterium bovis MBE50a gene, partial cds; and MBE50b, MBE50c, Mycobacterium bovis 60,030 27-Jan-99 preprotein translocase SecY subunit (secY), adenylate kinase (adk), Ln methionine aminopeptidase (map), RNA polymerase ECF sigma factor 0) (sigE50), MBE50d, and MBE50e genes, complete cds. o) r N
rxa00708 930 GB_BA2:AF157493 25454 AF157493 Zymomonas mobilis ZM4 fosmid clone 42D7, complete sequence. Zymomonas mobilis 39,116 5-Jul-99 ln ~ N
GB_PAT:100836 1853 100836 Sequence 1 from Patent US 4758514. Unknown. 47,419 1993 1993 -.3 GB_PAT:E00311 1853 E00311 DNA coding of 2,5-diketogluconic acid reductase.
unidentified 47,419 29-Sep-97 0 rxa00717 1083 G8_PAT:178753 1187 178753 Sequence 9 from patent US 5693781.
Unknown. 37,814 3-Apr-98 0) GB_PAT:192042 1187 192042 Sequence 9 from patent US 5726299. Unknown. 37,814 GB_BA1:MTCI125 37432 Z98268 Mycobacterium tuberculosis H37Rv complete genome;
segment 76/162. Mycobacterium 50,647 17-Jun-98 tuberculosis rxa00718 831 GB_BA1:MTCI125 37432 Z98268 Mycobacterium tuberculosis H37Rv complete genome; segment 76/162. Mycobacterium 55,228 17-Jun-98 tuberculosis GB BAI:MTCI125 37432 Z98268 Mycobacterium tuberculosis H37Rv complete genome;
segment 76/162. Mycobacterium 40,300 17-Jun-98 tuberculosis G8_GSSI2:AQ42075 671 AQ420755 RPCI-11-168G18.TJ RPCI-1 1 Homo sapiens genomic clone RPCI-1 1- Homo sapiens 35,750 23-MAR-168G18, genomic survey sequence. 1999 rxa00727 1035 GB_HTG3:AC008332 118545 AC008332 Drosophila melanogaster chromosome 2 clone BACR48D10 (D867) RPCI-98 Drosophila melanogaster 40,634 6-Aug-99 48.D.10 map 34A-34A strain y; cn bw sp, "' SEQUENCING IN PROGRESS
"", 78 unordered pieces.
GB_HTG3:AC008332 118545 AC008332 Drosophila melanogaster chromosome 2 clone BACR48D10 (D867) RPCI-98 Drosophila melanogaster 40,634 6-Aug-99 48.D.10 map 34A-34A strain y; cn bw sp, "" SEQUENCING IN
PROGRESS"', 78 unordered pieces.

Table 4 (continued) GB_HTG3:AC008332 118545 AC008332 Drosophila melanogaster chromosome 2 clone BACR48D10 (D867) RPCI-98 Drosophila melanogaster 33,888 6-Aug-99 48Ø10 map 34A-34A strain y; cn bw sp, "' SEQUENCING IN
PROGRESS"', 78 unordered pieces.
rxa00766 966 GB_HTG2:AC006789 83823 AC006789 Caenorhabditis elegans clone Y49F6, SEQUENCING IN PROGRESS Caenorhabditis elegans 36,737 25-Feb-99 2 unordered pieces.
GB_HTG2:AC006789 83823 AC006789 Caenorhabditis elegans clone Y49F6, SEQUENCING
IN PROGRESS Caenorhabditis elegans 36,737 25-Feb-99 2 unordered pieces.
GB_BA1:D90810 20476 D90810 E.coli genomic DNA, Kohara clone #319(37.4-37.8 min.). Escherichia coli 36,526 29-MAY-rxa00770 1293 GB_BA1:MTV043 68848 AL022004 Mycobacterium tuberculosis H37Rv complete genome; segment 40/162. Mycobacterium 66,193 24-Jun-99 tuberculosis GB_BAt:MLU15182 40123 U15182 Mycobacterium leprae cosmid B2266. Mycobacterium leprae 61,443 09-MAR-GB_BA2:SCD25 41622 AL118514 Streptomyces coelicolor cosmid D25. Streptomyces coslicolor 59,938 21-Sep-99 A3(2) rxa00779 1056 GB_HTGI:CER08A5 51920 Z82281 Caenorhabditis elegans chromosome V
clone R08A5, SEQUENCING IN Caenorhabditis elegans 64,896 14-OCT-"', in unordered pieces. 1998 PROGRESS
GB HTG1:CER08A5 51920 Z82281 Caenorhabditis elegans chromosome V clone R08A5, SEQUENCING IN Caenorhabditis elegans 64,896 14-OCT-Ln PROGRESS "', in unordered pieces. 1998 to GB_PL2:AF078693 1492 AF078693 Chlamydomonas reinhardtii putative O-acetylserine(thiol)lyase precursor Chlamydomonas reinhardtii 57,970 3-Nov-99 0 0) (Crcys-1A) mRNA, nuclear gene encoding organellar protein, complete cds. o) rxa00780 669 GB_BA1:MTCY98 31225 Z83860 Mycobacterium tuberculosis H37Rv complete genome: segment 103/162. Mycobacterium 54,410 17-Jun-98 tuberculosis o GB_BA1:AVINIFREG 7099 M60090 Azotobacter chroococcum nifU, nifS, nifV, nifP, nifW, nifZ and nifM genes, Azotobacter chroococcum 51,729 26-Apr-93 complete cds.
GB_BA2:AF001780 6701 AF001780 Cyanothece PCC 8801 NifP (nifP), nitrogenase (nifB), FdxN (fdxN), NifS (nifS) Cyanothece PCC8801 36,309 08-MAR- 0) and NifU (n'rfU) genes, complete cds, and NifH (nifH) gene, partial cds. 1999 rv rxa00838 1023 GB_EST1:Z30506 329 Z30506 ATTS2430 AC16H Arabidopsis thaliana cDNA clone TAI306 3', mRNA Arabidopsis thaliana 44,308 11-MAR-sequence. 1994 GB_PL2:AC006258 110469 AC006258 Arabidopsis thaliana BAC F18G18 from chromosome V near 60.5 cM, Arabidopsis thaliana 35,571 28-DEC-complete sequence. 1998 GB EST37:AI998439 455 A1998439 701545695 A. thaliana, Columbia Col-0, rosette-2 Arabidopsis thaliana cDNA Arabidopsis thaliana 36,044 8-Sep-99 clone 701545695, mRNA sequence.
nca00863 867 GB_BAI:BLDAPAB 3572 Z21502 B.lactofemientum dapA and dapB genes for dihydrodipicolinate synthase and Corynebacterium 99,539 16-Aug-93 dihydrodipicolinate reductase. glutamicum GB_PAT:E16749 2001 E16749 gDNA encoding dihydrodipicolinate synthase (DDPS).
Corynebacterium 99,539 28-Jul-99 glutamicum GB PAT:E14520 2001 E14520 DNA encoding Brevibacterium dihydrodipicolinic acid synthase. Corynebacterium 99,539 28-Jul-99 glutamicum rxa00864 873 GB BA1:BLDAPAB 3572 Z21502 B.lactofermentum dapA and dapB genes for dihydrodipicolinate synthase and Corynebacterium 99,885 16-Aug-93 dihydrodipicolinate reductase. glutamicum GB_BAI:CGDAPB 1902 X67737 C.gfutamicum dapB gene for dihydrodipicolinate reductase Corynebacterium 100,000 1-Apr-93 glutamicum Table 4 (continued) GB_PAT:E14520 2001 E14520 DNA encoding Brevibacterium dihydrodipicolinic acid synthase. Corynebacterium 100,000 28-Jul-99 glutamicum rxa00865 1026 GB_BA1:BLDAPAB 3572 Z21502 B.lactofermentum dapA and dapB genes for dihydrodipicolinate synthase and Corynebacterium 100,000 16-Aug-93 dihydrodipicolinate reductase. glutamicum GB_PAT:E16752 1411 E16752 gONA encoding dihydrodipicolinate reductase (DDPR).
Corynebacterium 99,805 28-Jul-99 glutamicum GB_PAT:AR038113 1411 AR038113 Sequence 18 from patent US 5804414. Unknown.
99,805 29-Sep-99 rxa00867 650 GB_BA1:MTV002 56414 AL008967 Mycobacterium tuberculosis H37Rv complete genome; segment 122/162. Mycobacterium 39,179 17-Jun-98 tuberculosis G8_BA1:MLCB22 40281 Z98741 Mycobacterium leprae cosmid 822. Mycobacterium leprae 39,482 22-Aug-97 GB_BA1:SAU19858 2838 U19858 Streptomyces antibioticus guanosine pentaphosphate synthetase (gpsl) gene, Streptomyces antibioticus 69,706 25-OCT-complete cds. 1996 rxa00873 779 GB_BA1:SC0001206 9184 AJ001206 Streptomyces coelicolor A3(2), glycogen metabolism cluster H. Streptomyces coelicolor 63,415 29-MAR-GB_BA1:SC0001205 9589 AJ001205 Streptomyces coelicolor A3(2) glycogen metabolism clusterl. Streptomyces coelicolor 61,617 29-MAR-GB_BA1:D78198 2304 D78198 Pimelobacter sp. DNA for trehalose synthase, complete cds. Pimelobacter sp. 60,594 5-Feb-99 rxa00884 1263 GB_BAI:MTCY253 41230 Z81368 Mycobacterium tuberculosis H37Rv complete genome; segment 106/162. Mycobacterium 37,785 17-Jun-98 noi tuberculosis u' GBBAI:MSGY222 41156 AD00001 0 Mycobacterium tuberculosis sequence from clone y222. Mycobacterium 38.006 03-DEC-tuberculosis 1996 rn GB_GSS15:AQ65460 468 AQ654600 Sheared DNA-1014.TF Sheared DNA Trypanosoma brucei genomic clone Trypanosoma brucei 33,974 22-Jun-99 p N
0 Sheared DNA-1014, genomic survey sequence.
rxa00891 1102 GB_BAI:MTCI418B 11700 Z96071 Mycobacterium tuberculosis H37Rv complete genome; segment 7/162. Mycobacterium 63,297 18-Jun-98 tuberculosis .3 GB BA1:SC0001206 9184 AJ001206 Streptomyces coelicolor A3(2), glycogen metabolism cluster II. Streptomyces coelicolor 61,965 29-MAR- 0) GB_BA1:SC0001205 9589 AJ001205 Streptomyces coelicolor A3(2) glycogen metabolism clusterl. Streptomyces coelicolor 61,727 29-MAR- ~

nca00952 963 EM_PAT:E10963 3118 E10963 gDNA encoding tryptophan synthase.
Corynebacterium 99,688 08-OCT-glutamicum 1997 (Rel.
52, Created) GB_BA1:BLTRP 7725 X04960 Brevibacterium lactofermentum tryptophan operon.
Corynebacterium 98,847 10-Feb-99 glutamicum GB_PAT:E01688 7725 E01688 Genomic DNA of trp operon of prepibacterium latophelmentamn. unidentified 98,428 29-Sep-97 rxa00954 644 GB_PAT:E01375 7726 E01375 DNA sequence of tryptophan operon.
Corynebacterium 98,758 29-Sep-97 glutamicum GB_PAT:E01688 7725 E01688 Genomic DNA of trp operon of prepibacterium latophelmentamn. unidentified 98,758 29-Sep-97 GB_BA1:BLTRP 7725 X04960 Brevibacterium lactofermentum tryptophan operon.
Corynebacterium 98,758 10-Feb-99 glutamicum rxa00955 1545 GB_PAT:E01375 7726 E01375 DNA sequence of tryptophan operon.
Corynebacterium 98,372 29-Sep-97 glutamicum Table 4 (continued) GB_BAI:BLTRP 7725 X04960 Brevibacterium lactofermentum tryptophan operon.
Corynebacterium 98,372 10-Feb-99 glutamicum GB_PAT:E01688 7725 E01688 Genomic DNA of trp operon of prepibacterium latophelmentamn. unidentified 98,242 29-Sep-97 rxa00956 1237 EM_PAT:E10963 3118 E10963 gDNA encoding tryptophan synthase.
Corynebacterium 98,949 08-OCT-glutamicum 1997 (Rel.
52, Created) GB_BAI:BLTRP 7725 X04960 Brevibacterium lactofermentum tryptophan operon.
Corynebacterium 99,107 10-Feb-99 glutamicum G8_PAT:E01375 7726 E01375 DNA sequence of tryptophan operon. Corynebacterium 98,945 29-Sep-97 glutamicum rxa00957 1677 GB BAI:BLTRP 7725 X04960 Brevibacterium lactofermentum tryptophan operon. Corynebacterium 99,165 10-Feb-99 glutamicum GB_PAT:E01375 7726 E01375 DNA sequence of tryptophan operon. Corynebacterium 98.927 29-Sep-97 glutamicum GB PAT:E01688 7725 E01688 Genomic DNA of trp operon of prepibacterium tatophelmentamn. unidentified 98,867 29-Sep-97 rxa00958 747 GB_BA1:BLTRP 7725 X04960 Brevibacterium lactofermentum tryptophan operon. Corynebacterium 98.792 10-Feb-99 glutamicum GB_PAT:E01375 7726 E01375 DNA sequence of tryptophan operon. Corynebacterium 98,792 29-Sep-97 c.i, glutamicum o GB_PAT:E01688 7725 E01688 Genomic DNA of trp operon of prepibacterium latophelmentamn. unidentified 98,658 29-Sep-97 ,--, 01 rn rxaO0970 1050 GB_BA1:CGHOMTHR 3685 Y00546 Corynebacterium glutamicum hom-thrB
genes for homoserine dehydrogenase Corynebacterium 99,905 12-Sep-93 N
~
and homoserine kinase. glutamicum rv GB_PAT:109077 3685 109077 Sequence 1 from Patent WO 8809819. Unknown. 99,810 1994 1994 -.3 GB_PAT:E01358 2615 E01358 DNA encoding for homoserine dehydrogenase(HDH)and homoserine Corynebacterium 97,524 29-Sep-97 ~
kinase(HK). glutamicum rxa00972 1458 GBPAT:E16755 3579 E16755 gDNA encoding diaminopimelate decarboxylase (DDC) and arginyl-tRNA Corynebacterium 99,931 28-Jul-99 synthase. glutamicum GB PAT:AR038110 3579 AR038110 Sequence 15 from patent US 5804414. Unknown.
99,931 29-Sep-99 GB_PAT:E14508 3579 E14508 DNA encoding Brevibacterium diaminopimelic acid decarboxylase and arginyl-Corynebacterium 99,931 28-Jul-99 tRNA synthase. glutamicum nca0O981 753 GB_OV:GGA245664 512 AJ245664 Gallus gallus partial mRNA for ATP-citrate lyase (ACL gene). Gallus gallus 37,538 28-Sep-99 GB_PL2:AC007887 159434 AC007887 Genomic sequence for Arabidopsis thaliana BAC
F1504 from chromosome I, Arabidopsis thaliana 37,600 04-OCT-complete sequence. 1999 GB_GSS1:CNSOORN 542 AL087338 Arabidopsis thaliana genome survey sequence T7 end of BAC F14D7 of IGF Arabidopsis thaliana 41,264 28-Jun-99 w library from strain Columbia of Arabidopsis thaliana, genomic survey sequence.
rxa00989 1644 GB_BAI:MTV008 63033 AL021246 Mycobacterium tuberculosis H37Rv complete genome; segment 108/162. Mycobacterium 40,773 17-Jun-98 tuberculosis GB_BA1:SCVALSFP 3619 Y13070 S.coelicolor valS, fpgs, ndk genes. Streptomyces coelicolor 58,119 03-MAR-GB_BAI:MTV008 63033 AL021246 Mycobacterium tuberculosis H37Rv complete genome;
segment 108l162. Mycobacterium 38,167 17-Jun-98 tuberculosis Table 4 (continued) rxa00997 705 GB_BA2:CGU31225 1817 U31225 Corynebacterium glutamicum L-proline:NADP+ 5-oxidoreductase (proC) gene, Corynebacterium 40,841 2-Aug-96 complete cds. glutamicum GB HTG1:CEY39C12 282838 AL009026 Caenorhabditis elegans chromosome IV clone Y39C12, "' SEQUENCING IN Caenorhabditis elegans 36,416 26-OCT-PROGRESS ~', in unordered pieces. 1999 GB_IN1:CEB0001 39416 Z69634 Caenorhabditis elegans cosmid B0001, complete sequence. Caenorhabditis elegans 36,416 2-Sep-99 rxa01019 1110 GB_HTG2:AC005052 144734 AC005052 Homo sapiens clone RG038K21, SEQUENCING IN PROGRESS 3 Homo sapiens 39,172 12-Jun-98 unordered pieces.
GB HTG2AC005052 144734 AC005052 Homo sapiens clone RG038K21, SEQUENCING IN
PROGRESS 3 Homo sapiens 39,172 12-Jun-98 unordered pieces.
GB_GSS9:AQ171808 512 AQ171808 HS 3179 A1_G03_T7 CIT Approved Human Genomic Sperm Library D Homo sapiens 34,661 17-OCT-Homo sapiens genomic done Plate=3179 Col=5 Row=M, genomic survey 1998 sequence.
nca01026 1782 GB_BA1:SC1C2 42210 AL031124 Streptomyces coelicolor cosmid 1C2.
Streptomyces coelicolor 68,275 15-Jan-99 GB_BA1:ATLEUCD 2982 X84647 A.teichomyceticus leuC and leuD genes. Actinoplanes 65.935 04OCT-teichomyceticus 1995 GB BA1:MTV012 70287 AL021287 Mycobacterium tuberculosis H37Rv complete genome;
segment 132/162. Mycobacterium 40,454 23-Jun-99 tuberculosis rxa01027 1131 GB_BA1:MLCB637 44882 Z99263 Mycobacterium leprae cosmid B637.
Mycobacterium leprae 38,636 17-Sep-97 GB_BA1:MTCY349 43523 Z83018 Mycobacterium tuberculosis H37Rv complete genome;
segment 131/162. Mycobacterium 51,989 17-Jun-98 Ln tuberculosis r..
GB BAI:SPUNGMUT 1172 Z21702 S.pneumoniae ung gene and mutX genes encoding uracil-DNA glycosylase Streptococcus pneumoniae 38,088 15-Jun-94 rn X and 8-oxodGTP nucleoside triphosphatase. N
nca01073 954 GB_BA1:BACOUTB 1004 M15811 Bacillus subtilis outB gene encoding a sporulation protein, complete cds. Bacillus subtilis 53,723 26-Apr-93 GB PR4:AC007938 167237 AC007938 Homo sapiens clone UWGC:djs201 from 7q31, complete sequence. Homo sapiens 34,322 1-Jul-99 GB PL2:ATAC006282 92577 AC006282 Arabidopsis thaliana chromosome II BAC F13K3 genomic sequence, Arabidopsis thaliana 36,181 13-MAR- -.3 complete sequence. 1999 0 nca01079 2226 GB_BA2:AF112535 4363 AF112535 Corynebacterium glutamicum putative glutaredoxin NrdH (nrdH), Nrdl (nrdl), Corynebacterium 99,820 5-Aug-and ribonucleotide reductase alpha-chain (nrdE) genes, complete cds.
glutamicum N
GB_BAI:CANRDFGE 6054 Y09572 Corynebacterium ammoniagenes nrdH, nrdl, nrdE, nrdF genes. Corynebacterium 75,966 18-Apr-98 N ammoniagenes GB_BA1:MTV012 70287 AL021287 Mycobacterium tuberculosis H37Rv complete genome;
segment 132/162. Mycobacterium 38,296 23-Jun-99 tuberculosis nca01080 567 GB_BA2:AF112535 4363 AF112535 Corynebacterium glutamicum putative glutaredoxin NrdH (nrdH), Nrdl (nrdl), Corynebacterium 100,000 5-Aug-99 and ribonucleotide reductase alpha-chain (nrdE) genes, complete cds.
glutamicum GB BA1:CANRDFGE 6054 Y09572 Corynebacterium ammoniagenes nrdH, nrdl, nrdE, nrdF genes. Corynebacterium 65,511 18-Apr-98 N ammoniagenes GB_BA1:STNRD 4894 X73226 S.typhimurium nrdEF operon. Salmonella typhimurium 52,477 03-MAR-nca01087 999 GB 1N2:AF063412 1093 AF063412 Limnadia lenticularis elongation factor 1-alpha mRNA, partial cds. Limnadia lenticularis 43,750 29-MAR-GB_PR3:HS24M15 134539 Z94055 Human DNA sequence from PAC 24M15 on chromosome 1. Contains Homo sapiens 37,475 23-Nov-99 tenascin-R (restrictin), EST.
GB_IN2:ARU85702 1240 U85702 Anathix ralla elongation factor-1 alpha (EF-1a) gene, partial cds. Anathix ralla 37,319 16-Jul-97 Table 4 (continued) rza01095 857 GB_BA1:MTCY01 B2 35938 Z95554 Mycobacterium tuberculosis H37Rv complete genome; segment 72/162. Mycobacterium 43,243 17-Jun-98 tuberculosis GB_HTG5:AC011632 175917 AC011632 Homo sapiens clone RP11-3N13, WORKING DRAFT
SEQUENCE, 9 Homo sapiens 36,471 19-Nov-99 unordered pieces.
GB_HTG5:AC011632 175917 AC011632 Homo sapiens clone RP11-3N13, WORKING DRAFT
SEQUENCE, 9 Homo sapiens 36,836 19-Nov-99 unordered pieces.
rxa01097 477 GB_BA2:AF030405 774 AF030405 Corynebacterium glutamicum cyclase (hisF) gene, complete cds. Corynebacterium 100,000 13-Nov-97 glutamicum GB BA2:AF030405 774 AF030405 Corynebacterium glutamicum cyclase (hisF) gene, complete cds. Corynebacterium 41,206 13-Nov-97 glutamicum rxa01098 897 GB_BA2:AF030405 774 AF030405 Corynebacterium glutamicum cyclase (hisF) gene, complete cds. Corynebacterium 97,933 13-Nov-97 glutamicum GB_BA1:MSGY223 42061 AD000019 Mycobacterium tuberculosis sequence from clone y223. Mycobacterium 40,972 10-DEC-tuberculosis 1996 GB_BAI:MLCB7610 40055 AL049913 Mycobacterium leprae cosmid B1610.
Mycobacterium leprae 61,366 27-Aug-99 rxa01100 861 GB_BA2:AF051846 738 AF051846 Corynebacterium glutamicum phosphoribosylformimino-5-amino-l- Corynebacterium 97,154 12-MAR-phosphoribosyl-4-imidazolecarboxamide isomerase (hisA) gene, glutamicum 1998 c.n complete cds.
GB_BA2:AF060558 636 AF060558 Corynebacterium glutamicum glutamine amidotransferase (hisH) gene, Corynebacterium 95,455 29-Apr-98 01 complete cds. glutamicum N
GB_HTGI:HSDJ140A 221755 AL109917 Homo sapiens chromosome 1 clone RP1-140A9, "' SEQUENCING IN Homo sapiens 30,523 23-Nov-99 o rv 9 PROGRESS "', in unordered pieces.
rxa01101 756 GB_BA2:AF060558 636 AF060558 Corynebacterium glutamicum glutamine amidotransferase (hisH) gene. Corynebacterium 94,462 29-Apr-98 com lete cds.
p glutamicum 0 GB_BA1:SC4G6 36917 AL096884 Streptomyces coelicolor cosmid 4G6. Streptomyces coelicolor 38,378 23-Ju1-99 O1 A3(2) GB_BAI:STMHISOPA 3981 M31628 S.coelicolor histidine biosynthesis operon encoding hisD, partial cds., and Streptomyces coelicolor 60,053 26-Apr-93 hisC, hisB, hisH, and hisA genes, complete cds.
rxa01104 729 GB_BAI:STMHISOPA 3981 M31628 S.coelicolor histidine biosynthesis operon encoding hisD, partial cds., and Streptomyces coelicolor 58,333 26-Apr-hisC, hisB, hisH, and hisA genes, complete cds.
GB_BA1:SC4G6 36917 AL096884 Streptomyces coelicolor cosmid 4G6. Streptomyces coelicolor 39,045 23-Jul-99 A3(2) GB BA1:MTCY336 32437 Z95586 Mycobacterium tuberculosis H37Rv complete genome;
segment 701162. Mycobacterium 60,364 24-Jun-99 tuberculosis rxa01105 1221 GB_BA1:MTCY336 32437 Z95586 Mycobacterium tuberculosis H37Rv complete genome; segment 70/162. Mycobacterium 60,931 24-Jun-99 tuberculosis GB_BAI:MSGY223 42061 AD000019 Mycobacterium tuberculosis sequence from clone y223. Mycobacterium 36,851 10-DEC-tuberculosis 1996 GB_BA1:MLCB1610 40055 AL049913 Mycobacterium leprae cosmid B1610.
Mycobacterium leprae 60,902 27-Aug-99 rxa01106 1449 GB_BA1:MSGY223 42061 AD000019 Mycobacterium tuberculosis sequence from clone y223. Mycobacterium 37,233 10-DEC-tuberculosis 1996 Table 4 (continued) GB_BA1:MSHISCD 2298 X65542 M.smegmatis genes hisD and hisC for histidinof dehydrogenase and histidinol-Mycobacterium smegmatis 60,111 30-Jun-93 phosphate aminotransferase, respectivety.
GB BAI:MTCY336 32437 Z95586 Mycobacterium tuberculosis H37Rv complete genome;
segment 70/162. Mycobacterium 58,420 24-Jun-99 tuberculosis nca01145 1137 GB_BAI:CORAIA 4705 L09232 Corynebacterium glutamicum acetohydroxy acid synthase (ifvB) and (ilvN) Corynebacterium 100,000 23-Feb-95 genes, and acetohydroxy acid isomeroreductase (itvC) gene, complete cds.
glutamicum GB_BAI:BRLILVCA 1364 D14551 Brevibacterium flavum ifvC gene for acetohydroxy acid isomeroreductase, Corynebacterium 99,560 3-Feb-99 complete cds. glutamicum GB PAT:E08232 1017 E08232 DNA encoding acetohydroxy-acid isomeroreductase.
Corynebacterium 99,803 29-Sep-97 glutamicum rxa01162 1449 G13_PAT:A60299 2869 A60299 Sequence 18 from Patent WO9706261.
Aspergillus niger 38,675 06-MAR-GB PR3:HS24E5 35506 Z82185 Human DNA sequence from Fosmid 24E5 on chromosome 22q11.2-qter Homo sapiens 36,204 23-Nov-99 contains parvalbumin, ESTs, STS.
GB_PR3:AC005265 43900 AC005265 Homo sapiens chromosome 19, cosmid F19750, complete sequence. Homo sapiens 38,363 6-Jul-98 rxa01208 846 GB_HTG2:AC004965 323792 AC004965 Homo sapiens clone DJ1106H14, "= SEQUENCING IN PROGRESS 42 Homo sapiens 36,058 12-Jun-98 unordered pieces. LNn GB_HTG2:AC004965 323792 AC004965 Homo sapiens clone DJ1106H14, === SEQUENCING
IN PROGRESS 42 Homo sapiens 36,058 12-Jun-98 0 rn unordered pieces. 0) GB PL2:TAU55859 2397 U55859 Tritfcum aestivum heat shock protein 80 mRNA, complete cds.. Triticum aestivum 37,269 1-Feb-99 r-= N
rxa01209 1528 GB HTG3:AC011469 113436 AC011469 Homo sapiens chromosome 19 clone CIT-HSPC_475D23, "' SEQUENCING Homo sapiens 40,000 07-OCT-IN
PROGRESS "', 31 unordered pieces. 1999 0 GB_HTG3:AC011469 113436 AC011469 Homo sapiens chromosome 19 clone CIT-HSPC_475D23, '"' SEQUENCING Homo sapiens 40,000 07-OCT- .3 IN PROGRESS "", 31 unordered pieces. 1999 0) GB_PL1:AB010077 77380 AB010077 Arabidopsis thaliana genomic DNA, chromosome 5, P1 clone: MYH19, Arabidopsis thaliana 36,803 20-Nov-99 complete sequence.
N
rxa01215 1098 GB BA1:MTCY10G2 38970 Z92539 Mycobacterium tuberculosis H37Rv complete genome; segment 47/162. Mycobacterium 37,047 17-Jun-98 tuberculosis GB_INI:LEIPRPP 1887 M76553 Leishmania donovani phosphoribosylpyrophosphate synthetase gene, Leishmania donovani 50,738 7-Jun-93 complete cds.
GB_HTG2:HSJ799D1 130149 AL050344 Homo sapiens chromosome 1 clone RP4799D16 map p34.3-36.1, Homo sapiens 38,135 29-Nov-99 6 SEQUENCING IN PROGRESS "', in unordered pieces.
rxa01239 2556 GB_BA1:MTCY48 35377 Z74020 Mycobacterium tuberculosis H37Rv complete genome; segment 69/162. Mycobacterium 38,139 17-Jun-98 tuberculosis GB PR2AB029032 6377 AB029032 Homo sapiens mRNA for KIAA1109 protein, partial cds. Homo sapiens 39,394 4-Aug-99 GB_GSS9:AQ107201 355 AQ107201 HS 3098_A1 C03_T7 CIT Approved Human Genomic Sperm Library D Homo sapiens 41,408 28-Aug-98 Homo sapiens genomic clone Plate=3098 Col=5 Row=E, genomic survey sequence.
rxa01253 873 GB_PL2:F508 99923 AC005990 Arabidopsis thaliana chromosome 1 BAC
F508 sequence, complete Arabidopsis thaliana 36,118 23-DEC-sequence. 1998 GB_PL2:F508 99923 AC005990 Arabidopsis thaliana chromosome 1 BAC F508 sequence, complete Arabidopsis thaliana 35,574 23-DEC-sequence. 1998 ,; "
GB_INI:CELC06G1 31205 U41014 Caenorhabditis elegans cosmid CO6G1.
Caenorhabditis elegans 38,560 30-Nov-95 Table 4 (continued) rxa01321 1044 GB_GSSI4:AQ51884 441 AQ518843 HS 5106_A1_D10_SP6E RPCI-11 Human Male BAC Library Homo sapiens Homo sapiens 41,121 05-MAY-3 genomic clone Plate=682 Co1=19 Row=G, genomic survey sequence. 1999 GB HTG2:AC007473 194859 AC007473 Drosophila melanogaster chromosome 2 clone BACR38D12 (D590) RPCI-98 Drosophila melanogaster 40,634 2-Aug-99 38.D.12 map 48A-48B strain y, cn bw sp, "' SEQUENCING IN PROGRESS
"', 60 unordered pieces.
GB_HTG4:AC011696 115847 AC011696 Drosophila melanogaster chromosome 2 clone BACR35F01 (D1156) RPCI-98 Drosophila melanogaster 38,290 26-OCT-35.F.1 map 48A-48C strain y; cn bw sp, "' SEQUENCING IN PROGRESS 1999 '==, 108 unordered pieces.
rxa01352 706 GB PL2:ATAC005167 83260 AC005167 Arabidopsis thaliana chromosome II BAC F12A24 genomic sequence, Arabidopsis thaliana 34,311 15-OCT-complete sequence. 1998 GB_PL2:ATAC005825 97380 AC005825 Arabidopsis thaliana chromosome 11 BAC T24121 genomic sequence, Arabidopsis thaliana 34,311 12-Apr-99 complete sequence.
GB HTG3:AC011150 127222 AC011150 Homo sapiens clone 4_K_17, LOW-PASS SEQUENCE
SAMPLING. Homo sapiens 37,722 01-OCT-rxa01360 259 GB EST32:AI725583 728 A1725583 BNLGHi12371 Six-day Cotton fiber Gossypium hirsutum cDNA 5' similar to Gossypium hirsutum 38,492 11-Jun-99 (U86081) root hair defective 3(Arabidopsis thaliana], mRNA sequence.
GB PR2:HS227P17 82951 Z81007 Human DNA sequence from PAC 227P17, between markers DXS6791 Homo sapiens 39,738 23-Nov-99 0 andDXS8038 on chromosome X contains CpG island, EST. Ln GB_EST34:AV171099 173 AV171099 AV171099 Mus musculus head C57BU6J 14, 17 day embryo Mus musculus Mus musculus 46,237 6-Jul-99 1O
cDNA clone 3200002M1 1, mRNA sequence. rn rxa01361 629 GB RO:AB008915S1 530 AB008915 Mus musculus mGpil gene, exon 1.
Mus musculus 45,574 28-Sep-99 N
GB EST22:A1050532 293 A1050532 uc83dlO.yl Sugano mouse kidney mkia Mus musculus cDNA clone Mus musculus 44,097 9-Jul-98 IMAGE:1432243 5' similar to TR:035120 035120 MGPI1 P. ;, mRNA
sequence. ~
GB_RO:AB008895 3062 AB008895 Mus musculus mRNA for mGpi1 p, complete cds. Mus musculus 41,316 23-Nov-97 0 rxa01381 944 GB_PL1:AB005237 87835 AB005237 Arabidopsis thaliana genomic DNA, chromosome 5, P1 clone: MJJ3,complete Arabidopsis thaliana 36.606 20-Nov-99 O1 sequence.
GB GSS5:AQ766840 491 AQ766840 HS_2026_A2_C09_T7C CIT Approved Human Genomic Sperm Library D Homo sapiens 37,916 28-Jul-99 Homo sapiens genomic clone Plate=2026 Co1=18 Row=E, genomic survey sequence.
GB BAI:MTV043 68848 AL022004 Mycobacterium tuberculosis H37Rv complete genome:
segment 40/162. Mycobacterium 37,419 24-Jun-99 tuberculosis nca01393 993 GB_BAI:CGLYSEG 2374 X96471 C.glutamicum lysE and lysG genes.
Corynebacterium 34,831 24-Feb-97 glutamicum GB_BA1:SC5A7 40337 AL031107 Streptomyces coelicolor cosmid 5A7. Streptomyces coelicolor 35,138 27-Jul-98 GB_PR3:AC004054 112184 AC004054 Homo sapiens chromosome 4 clone B220G8 map 4q21, complete sequence. Homo sapiens 37,277 9-Jul-98 rxa01394 822 GB_BA1:CGLYSEG 2374 X96471 C.glutamicum lysE and lysG genes.
Corynebacterium 100,000 24-Feb-97 glutamicum GB_GSS5:AQ769223 500 AQ769223 HS_3155 B2_G10_T7C CIT Approved Human Genomic Sperm Library D Homo sapiens 38,400 28-Jul-99 Homo sapiens genomic clone Plate=3155 Co1=20 Row=N, genomic survey sequence.

Table 4 (continued) GB BAI:CGLYSEG 2374 X96471 C.glutamicum lysE and lysG genes. Corynebacterium 33,665 24-Feb-97 glutamicum rxa01416 630 GB BA1:SC3C3 31382 AL031231 Streptomyces coelicolor cosmid 3C3.
Streptomyces coelicolor 62,726 10-Aug-98 GBBAI:MLCB22 40281 Z98741 Myoobacterium leprae cosmid B22. Mycobacterium leprae 39,159 22-Aug-97 GB_BA1:M'N002 56414 AL008967 Mycobacterium tuberculosis H37Rv complete genome;
segment 1221162. Mycobacterium 37,340 17-Jun-98 tuberculosis rxa01442 1347 GB_BA1:D90827 18886 D90827 E.coli genomic DNA, Kohara clone #336(41.2-41.6 min.). Escherichia coli 58,517 21-MAR-GB_BA1:D90828 14590 D90828 E.coli genomic DNA, Kohara clone #336gap(41.6-41.9 min.). Escherichia coli 56,151 21-MAR-GB BA2:AE000279 10855 AE000279 Escherichia coli K-12 MG1655 section 169 of 400 of the complete genome. Escherichia coli 56,021 12-Nov-98 rxa01446 1413 GB BAI:SCH10 39524 AL049754 Streptomyces coelicolor cosmid H10.
Streptomyces coelicolor 39,037 04-MAY-GB BAI:MTY13E10 35019 Z95324 Mycobacterium tuberculosis H37Rv complete genome;
segment 18/162. Mycobacterium 40,130 17-Jun-98 tuberculosis GBBA1:MLCB4 36310 AL023514 Mycobacterium leprae cosmid B4. Mycobacterium leprae 37,752 27-Aug-99 rxa01483 1395 GB_BAI:MTCY98 31225 Z83860 Mycobacterium tuberculosis H37Rv complete genome; segment 103/162. Mycobacterium 39,057 17-Jun-98 Ln tuberculosis rn GB_BA1:MSGB1229C 30670 L78812 Mycobacterium leprae cosmid 81229 DNA sequence.
Mycobacterium leprae 54,382 15-Jun-96 0) s GB_BA2:AF027507 5168 AF027507 Mycobacterium smegmatis dGTPase (dgt), and primase (dnaG) genes, Mycobacterium smegmatis 52,941 16-Jan-98 complete cds; tRNA-Asn gene, complete sequence.
rxa01486 757 GB_BA1:MTV002 56414 AL008967 Mycobacterium tuberculosis H37Rv complete genome; segment 122/162. Mycobacterium 40,941 17-Jun-98 w tuberculosis oi GB_BA1:MLCB22 40281 Z98741 Mycobacterium leprae cosmid B22. Mycobacterium leprae 38,451 22-Aug-97 rv GB_BA1:SC3C3 31382 AL031231 Streptomyces coelicolor cosmid 3C3. Streptomyces coelicolor 61,194 10-Aug-98 rxa01489 1146 GB_BAI:CORFADS 1547 D37967 Corynebacterium ammoniagenes gene for FAD synthetase, complete cds. Corynebacterium 58,021 8-Feb-99 ammoniagenes GB_BA1:MLCB22 40281 Z98741 Mycobacterium leprae cosmid 822. Mycobacterium leprae 38,414 22-Aug-97 GB BA1:SC10A7 39739 AL078618 Streptomyces coelicolor cosmid 10A7. Streptomyces coelicolor 36,930 9-Jun-99 rxaO1491 774 GB BAI:MTV002 56414 AL008967 Mycobacterium tuberculosis H37Rv complete genome; segment 122/162. Mycobacterium 37,062 17-Jun-98 tuberculosis GB_EST13:AA356956 255 AA356956 EST65614 Jurkat T-cells III Homo sapiens cDNA
5' end, mRNA sequence. Homo sapiens 37,647 21-Apr-97 GB_OV:OMDNAPROI 7327 X92380 O.mossambicus prolactin I gene. Tilapia mossambica 38,289 19-OCT-rxa01508 1662 GB_INI:CEF28C12 14653 Z93380 Caenorhabditis elegans cosmid F28C12, complete sequence. Caenorhabditis elegans 37,984 23-Nov-98 GB_IN1:CEF28C12 14653 Z93380 Caenorhabditis elegans cosmid F28C12, complete sequence. Caenorhabditis elegans 38,469 23-Nov-98 nca01512 723 GB BAI:SCE9 37730 AL049841 Streptomyces coelicolor cosmid E9.
Streptomyces coelicolor 39,021 19-MAY-~ 1999 GB BAI:MAU88875 840 U88875 Mycobacterium avium hypoxanthine-guanine phosphoribosyl transferase Mycobacterium avium 57,521 05-MAR-gene, complete cds. 1997 Table 4 (continued) GB_BA1:MTY15C10 33050 Z95436 Mycobacterium tuberculosis H37Rv complete genome;
segment 154/162. Mycobacterium 40,086 17-Jun-98 tuberculosis rxa01514 711 GB_BAI:MTCY7H76 24244 Z95557 Mycobacterium tuberculosis H37Rv complete genome; segment 153/162. Mycobacterium 43,343 18-Jun-98 tuberculosis GB BA1:MLCB2548 38916 AL023093 Mycobacterium leprae cosmid B2548.
Mycobacterium leprae 38,177 27-Aug-99 GB_PL1:EGGTPCHI 242 Z49757 E.gracilis mRNA for GTP cyclohydrolase I (core region). Euglena gracilis 64,876 20-OCT-rxa01515 975 GB_BA1:ECOUW93 338534 U14003 Escherichia coli K-12 chromosomal region from 92.8 to 00.1 minutes. Escherichia coli 38,943 17-Apr-96 GB BA1:ECOUW93 338534 U14003 Escherichia coli K-12 chromosomal region from 92.8 to 00.1 minutes. Escherichia coli 37,500 17-Apr-96 GB BA1:MTCY49 39430 Z73966 Mycobacterium tuberculosis H37Rv complete genome;
segment 93/162. Mycobacterium 38,010 24-Jun-99 tuberculosis rxa01516 513 GB IN1:DME238847 5419 AJ238847 Drosophila melanogaster mRNA for drosophila dodeca-satellite protein 1 Drosophila melanogaster 36,346 13-Aug-99 (DDP-1).
GB HTG3AC009210 103814 AC009210 Drosophila melanogaster chromosome 2 clone BACR01106 (D1054) RPCI-98 Drosophila melanogaster 37,897 20-Aug-99 01.1.6 map 550-55D strain y: cn bw sp, "' SEQUENCING IN PROGRESS c1 86 unordered pieces.
GB_IN2:AF132179 4842 AF132179 Drosophila melanogaster clone LD21677 unknown mRNA. Drosophila melanogaster 36,149 3-Jun-99 rxa01517 600 GB_PL2:F6H8 82596 AF178045 Arabidopsis thaliana BAC F6H8.
Arabidopsis thaliana 35,846 19-Aug-99 Ln GB PL2:AF038831 647 AF038831 Sorosporium saponariae intemal transcribed spacer 1, 5.8S ribosomal RNA Sorosporium saponariae 40,566 13-Apr-99 -- o gene; and internal transcribed spacer 2, complete sequence. 41 o) rn GB_PL2:ATAC005957 108355 AC005957 Arabidopsis thaliana chromosome II BAC
T15J14 genomic sequence, Arabidopsis thaliana 38,095 7-Jan-99 complete sequence. rv rxa01521 921 GB_BAI:ANANIFBH 5936 J05111 Anabaena sp. (clone AnH2O.1) nitrogen fixation operon nif6, fdxN, nifS, nifU, Anabaena sp. 38.206 26-Apr-93 and n1fH genes, complete cds. .3 GB_PR2:AC002461 197273 AC002461 Human BAC clone RG204116 from 7q31, complete sequence. Homo sapiens 36,623 20-Aug-97 0) GB PR2:AC002461 197273 AC002461 Human BAC clone RG204116 from 7q31, complete sequence. Homo sapiens 34,719 20-Aug-97 rxa01528 651 GB_RO:MM437P9 165901 AL049866 Mus musculus chromosome X, clone 437P9. Mus musculus 37,500 29-Jun-99 N
GB_PR3:AC005740 186780 AC005740 Homo sapiens chromosome 5p, BAC clone 50g21 (LBNL H154), complete Homo sapiens 37,031 01-OCT-sequence. 1998 GB_PR3:AC005740 186780 AC005740 Homo sapiens chromosome 5p, BAC clone 50g21 (LBNL H154), complete Homo sapiens 38,035 01-OCT-sequence. 1998 rxa01551 1998 GB BAI:MTCY22G10 35420 Z84724 Mycobacterium tuberculosis H37Rv complete genome; segment 21/162. Mycobacterium 38,371 17-Jun-98 tuberculosis GB_BA2:ECOUW89 176195 U00006 E. coli chromosomal region from 89.2 to 92.8 minutes. Escherichia coli 38,064 17-DEC-GB_BAI:SCQ11 15441 AL096823 Streptomyces coelicolor cosmid Q11. Streptomyces coelicolor 60,775 8-Jul-99 rxa01561 1053 GB_INI:CEY62H9A 47396 AL032630 Caenorhabditis elegans cosmid Y62H9A, complete sequence. Caenorhabditis elegans 38,514 2-Sep-99 GB_PR4:HSU51003 3202 U51003 Homo sapiens DLX-2 (DLX-2) gene, complete cds.
Homo sapiens 37,730 07-DEC-GB_OM:PIGDAO1 395 M18444 Pig D-amino acid oxidase (DAO) gene, exon 1. Sus scrofa 39,340 27-Apr-93 rxa01599 1785 GB BAI:MTC1125 37432 Z98268 Mycobacterium tuberculosis H37Rv complete genome; segment 76/162. Mycobacterium 63,300 17-Jun48 tuberculosis GB_BA1:U00021 39193 U00021 Mycobacterium leprae cosmid L247. Mycobacterium leprae 36,756 29-Sep-94 Table 4 (continued) GB BA1:MLCB1351 38936 Z95117 Mycobacterium leprae cosmid B1351. Mycobacterium leprae 36,756 24-Jun-97 nca01617 795 GB PR2:HSMTMO 217657 AL034384 Human chromosome Xq28, cosmid clones 7H3, 14D7, C1230, 11 E7, F1096, Homo sapiens 40,811 5-Jul-99 A12197, 12G8, A09100; complete sequence bases 1. .217657.
GB_PR2:HS13D10 153147 AL021407 Homo sapiens DNA sequence from PAC 13D10 on chromosome 6p22.3-23. Homo sapiens 38,768 23-Nov-99 Contains CpG island.
GB_PR2:HSMTMO 217657 AL034384 Human chromosome Xq28, cosmid clones 7H3, 14D7, C1230, 11 E7, F1096, Homo sapiens 39,018 5-Jul-99 A12197, 12G8, A09100; complete sequence bases 1. .217657.
rxa01657 723 GB_BA1:MTCY1A10 25949 Z95387 Mycobacterium tuberculosis H37Rv complete genome: segment 117/162. Mycobacterium 40,656 17-Jun-98 tuberculosis GB_EST6:D79278 392 D79278 HUM213D06B Human aorta polyA+ (TFujiwara) Homo sapiens cDNA clone Homo sapiens 44,262 9-Feb-96 GEN-213D06 5', mRNA sequence.
GB BA2:AF129925 10243 AF129925 Thiobacillus ferrooxidans carboxysome operon, complete cds. Thiobacillus ferrooxidans 40,709 17-MAY-rxa01660 675 GB_BAI:MTV013 11364 AL021309 Mycobacterfum tuberculosis H37Rv complete genome; segment 134/162. Mycobacterium 40,986 17-Jun-98 tuberculosis GB_RO:MMFV1 6480 X97719 M.musculus retrovirus restriction gene Fv1. Mus musculus 35.364 29-Aug-96 GB PAT:A67508 6480 A67508 Sequence 1 from Patent W0974341 0. Mus musculus 35,364 05-MAY-Ln rxa01678 651 GB_VI:TVU95309 600 U95309 Tula virus 064 nucleocapsid protein gene, partial cds. Tula virus 41,894 28-OCT- .~ 0 1997 u"
GB_VI:TVU95303 600 U95303 Tula virus 052 nucleocapsid protein gene, partial cds. Tula virus 41,712 28-OCT-GB_VI:TVU95302 600 U95302 Tula virus 024 nucleocapsid protein gene, partial cds. Tula virus 39,576 28-OCT-1997 1997 .3 rxa01679 1359 GB EST5:H91843 362 H91843 ys81e01.s1 Soares retina N2b4HR Homo sapiens cDNA clone Homo sapiens 39,157 29-Nov-95 IMAGE:221208 3' similar to gb:X63749_mai GUANINE NUCLEOTIDE- 0) BINDING PROTEIN G(T), ALPHA-1 (HUMAN);, mRNA sequence. N
GB_STS:G26925 362 G26925 human STS SHGC-30023, sequence tagged site. Homo sapiens 39,157 14-Jun-96 GB_PL2:AF139451 1202 AF139451 Gossypium robinsonii CelA2 pseudogene, partial sequence. Gossypium robinsonii 38,910 1-Jun-99 rxa01690 1224 GB BA1:SC1C2 42210 AL031124 Streptomycescoelicolorcosmid1C2.
Streptomyces coelicolor 60,644 15-Jan-99 GB EST22:A1064232 493 AI064232 GH04563.5prime GH Drosophila melanogaster head pOT2 Drosophila Drosophila melanogaster 38,037 24-Nov-98 melanogaster cONA clone GH04563 5prime, mRNA sequence.
GB_IN2:AF117896 1020 AF117896 Drosophila melanogaster neuropeptide F (npf) gene, complete cds. Drosophila melanogaster 36,122 2-Jul-99 rxa01692 873 GB_BA2:AF067123 1034 AF067123 Lactobaciltus reuteri cobalamin biosynthesis protein J (cbiJ) gene, partial ods; Lactobacillus reuteri 48,079 3-Jun-98 and uroporphyrin-III C-methyltransferase (sumT) gene, complete cds.
GB_RO:RATNFHPEP 3085 M37227 Rat heavy neurofilament (NF-H) polypeptide, partial cds. Rattus norvegicus 37,093 27-Apr-93 GB RO:RSNFH 3085 X13804 Rat mRNA for heavy neurofilarnent polypeptide NF-H C-terminus. Rattus sp. 37,093 14-Jul-95 nca01698 1353 GB BA2AF124600 4115 AF124600 Corynebacterium glutamicum chorismate synthase (aroC), shikimate kinase Corynebacterium 100,000 04-MAY-(aroK), and 3-dehydroquinate synthase (aroB) genes, complete cds; and glutamicum 1999.
.
putative cytoplasmic peptidase (pepQ) gene, partial cds.
GB_BA1:MTCY159 33818 Z83863 Mycobacterium tuberculosis H37Rv complete genome;
segment 111/162. Mycobacterium 36,323 17-Jun-98 tuberculosis Table 4 (continued) GB_BA1:MSGB937C 38914 L78820 Mycobacterium leprae cosmid B937 DNA sequence.
Mycobacterium leprae 62.780 15-Jun-96 S
rx201699 693 GB_BA2:AF124600 4115 AF124600 Corynebacterium glutamicum chorismate synthase (aroC), shikimate kinase Corynebacterium 100,000 04-MAY-(aroK), and 3-dehydroquinate synthase (aroB) genes, complete cds; and glutamicum 1999 putative cytoplasmic peptidase (pepQ) gene, partial cds.
GB_BA2:AF016585 41097 AF016585 Streptomyces caelestis cytochrome P-450 hydroxylase homolog (nidi) gene, Streptomyces caelestis 40,260 07-DEC-partial cds; polyketide synthase modules 1 through 7 (nidA) genes, complete cds; and N-methyltransferase homolog gene, partial cds.
GB EST9:C19712 399 C19712 C19712 Rice panicle at ripening stage Oryza sativa cONA clone E10821_1A, Oryza sativa 45,425 24-OCT-mRNA sequence. 1996 rxa01712 805 GB EST21:AA952466 278 AA952466 TENS1404 T. cruzi epimastigote normalized cDNA Library Trypanosoma cruzi Trypanosoma cruzi 40,876 29-OCT-cDNA clone 1404 5', mRNA sequence. 1998 GB_EST21:AA952466 278 AA952466 TENS1404 T. cruzi epimastigote normalized cDNA
Library Trypanosoma cruzi Trypanosoma cruzi 41,367 29-OCT-cDNA clone 1404 5', mRNA sequence. 1998 nca01719 684 GB_HTG1:HSDJ534K 154416 AL109925 Homo sapiens chromosome 1 clone RP4-534K7, SEQUENCING IN Homo sapiens 35,651 23-Nov-99 7 PROGRESS "', in unordered pieces.
GB HTGI:HSDJ534K 154416 AL109925 Homo sapiens chromosome 1 clone RP4-534K7, SEQUENCING IN Homo sapiens 35,651 23-Nov-99 Ln 7 PROGRESS "', in unordered pieces. 0) GB EST27:A1447108 431 A1447108 mq9leO8.xl Stratagene mouse heart (#937316) Mus musculus.cDNA clone Mus musculus 39,671 09-MAR- 01 - N
IMAGE:586118 3', mRNA sequence. 1999 nca01720 1332 GB_PR4:AC006322 179640 AC006322 Homo sapiens PAC clone DJ1060B11 from 7q11.23-q21.1, complete Homo sapiens 35,817 18-MAR- ~ o sequence. 1999 GB_PL2:TM018A10 106184 AF013294 Arabidopsis thaliana BAC TM018A10. Arabidopsis thaliana 35.698 12-Jul-97 GB_PR4:AC006322 179640 AC006322 Homo sapiens PAC clone DJ1060B11 from 7q11.23-q21.1, complete Homo sapiens 37,243 18-MAR- 0) sequence. 1999 rxa01746 876 GB_EST3:R46227 443 R46227 yg52a03.s1 Soares infant brain 1NIB
Homo sapiens cDNA clone Homo sapiens 42,812 22-MAY-3', mRNA sequence. 1995 IMAGE:36000 GB_EST3:R46227 443 R46227 yg52a03.s1 Soares infant brain 1NIB Homo sapiens cDNA clone Homo sapiens 42,655 22-MAY-IMAGE:36000 3', mRNA sequence. 1995 rxa01747 1167 GB BAI:MTCY190 34150 Z70283 Mycobacterium tuberculosis H37Rv complete genome; segment 98062. Mycobacterium 59,294 17-Jun-98 tuberculosis GB_BAI:MLC822 40281 Z98741 Mycobacterium leprae cosmid B22. Mycobacterium leprae 57,584 22-Aug-97 GB 8A1:SC5F7 40024 AL096872 Streptomyces coelicolor cosmid 5F7_ Streptomyces coelicolor 61,810 22-Jul-99 A3(2) rxa01757 924 GB EST21:AA918454 416 AA918454 om38c02.s1 Soares_NFL_T_GBC-S1 Homo sapiens cDNA clone Homo sapiens 39,655 23-Jun-98 IMAGE:1543298 3' similar to WP:F28F8.3 CE09757 SMALL NUCLEAR
RIBONUCLEOPROTEIN E ;, mRNA sequence.
GB_EST4:H34042 345 H34042 EST110563 Rat PC-12 cells, NGF-treated (9 days) Rattus sp, cDNA clone Rattus sp. 35,942 2-Apr,98 RPNB181 5' end, mRNA sequence.
GB_EST20:AA899038 450 AA899038 NCP6G8T7 Perithecial Neurospora crassa cDNA
clone NP6G8 3' end, mRNA Neurospora crassa 40,000 12-Apr-'98 sequenoe.

Table 4 (continued) nca01807 915 GB BA1:AP000063 185300 AP000063 Aeropyrum pemix genomic DNA, section 6/7. Aeropyrum pemix 40,067 22-Jun-99 GB_HTG4:AC010694 115857 AC010694 Drosophila melanogaster clone RPCI98-6H2, SEQUENCING IN Drosophila melanogaster 35,450 16-OCT-PROGRESS "=', 75 unordered pieces. 1999 GB_HTG4:AC010694 115857 AC010694 Drosophila melanogaster clone RPCI98-6H2, "'=
SEQUENCING IN Drosophila melanogaster 35,450 16-OCT-PROGRESS "=, 75 unordered pieces. 1999 rxa01821 401 GB_BA1:CGL007732 4460 AJ007732 Corynebacterium glutamicum 3' ppc gene, secG gene, amt gene, ocd gene Corynebacterium 100,000 7Jan-99 and 5' soxA gene. glutamicum GB_RO:RATALGL 7601 M24108 Rattus norvegicus (clone A2U42) alpha2u globulin gene, exons 1-7. Rattus norvegicus 38,692 15-DEC-GB_OV:APIGY2 1381 X78272 Anas platyrhynchos (Super M) IgY upsilon heavy chain gene, exon 2. Anas platyrhynchos 36,962 15-Feb-99 nca01835 654 GB_EST30:AI629479 353 AI629479 486101 D10.x1 486 - leaf primordia cDNA library from Hake lab Zea mays Zea mays 38,109 26-Apr-99 cDNA, mRNA sequence.
GB_STS:G48245 515 G48245 SHGC-62915 Human Homo sapiens STS genomic, sequence tagged site. Homo sapiens 37,021 26-MAR-GB GSS3:B49052 515 B49052 RPCI11-4112.TV RPCI-1 1 Homo sapiens genomic clone RPCI-1 1-4112, Homo sapiens 37,021 8-Apr-99 genomic survey sequence.
nca01850 1470 GB_BA2:ECOtJW67_ 110000 U18997 Escherichia coli K-12 chromosomal region from 67.4 to 76.0 minutes. Escherichia coli 37,196 U18997 Ui 0 ~
GB_BA2:AE000392 10345 AE000392 Escherichia coli K-12 MG1655 section 282 of 400 of the complete genome. Escherichia coli 38,021 12-Nov-98 0i GB_BA2:U32715 13136 U32715 Haemophilus influenzae Rd section 30 of 163 of the complete genome. Haemophilus influenzae 39,860 29-MAY- ~ N
Rd 1998 rxa01878 1002 GB HTGI:CEY64Fi 1 177748 Z99776 Caenorhabditis elegans chromosome IV clone Y64F11, "=' SEQUENCING IN Caenorhabditis elegans 37,564 14-OCT- o PROGRESS "=, in unordered pieces. 1998 GB_HTG1:CEY64F11 177748 Z99776 Caenorhabditis elegans chromosome IV clone Y64F11, "= SEQUENCING IN Caenorhabditis elegans 37,564 14-OCT-PROGRESS ***, in unordered pieces. 1998 0) GB_HTGI:CEY64F11 177748 Z99776 Caenorhabditis elegans chromosome IV clone Y64F11, ="' SEQUENCING IN Caenorhabditis elegans 37,576 14OCT- rv PROGRESS =", in unordered pieces. 1998 nca01892 852 GB_BA1:MTCY274 39991 Z74024 Mycobacterium tuberculosis H37Rv complete genome; segment 126/162. Mycobacterium 35,910 19-Jun-98 tuberculosis GB_BA1:MLCB250 40603 Z97369 Mycobacterium leprae cosmid 8250. Mycobacterium leprae 64,260 27-Aug-99 GB_BA1:MSGB1529C 36985 L78824 Mycobacterium Ieprae cosmid B1529 DNA sequence.
Mycobacterium leprae 64,260 15-Jun-96 S
rxa01894 978 GB_BA1:MTCY274 39991 Z74024 Mycobacterium tuberculosis H37Rv complete genome; segment 126/162. Mycobacterium 37,229 19-Jun-98 tuberculosis GB_IN1:CELF46H5 38886 U41543 Caenorhabditis elegans cosmid F46H5.
Caenorhabditis elegans 38,525 29-Nov-96 GB_HTG3:AC009204 115633 AC009204 Drosophila melanogaster chromosome 2 clone BACR03E19 (D1033) RPCI-98 Drosophila melanogaster 31,579 18-Aug-99 03.E.19 map 36E-37C strain y; cn bw sp, =" SEQUENCING IN PROGRESS
===, 94 unordered pieces, rxa01920 1125 GB_BA2:AF112536 1798 AF112536 Corynebacterium glutamicum ribonucleotide reductase beta-chain (nrdF) Corynebacterium 99,733 5-Aug-99 gene, complete cds. glutamicum GB_BA1:CANRDFGE 6054 Y09572 Corynebacterium ammoniagenes nrdH, nrdl, nrdE, nrdF genes. Corynebacterium 70,321 18-Apr-98 N ammoniagenes Table 4 (continued) GB_BA2:AF050168 1228 AF050168 Corynebacterium ammoniagenes ribonucleoside diphosphate reductase small Corynebacterium 72,082 23-Apr-98 subunit (nrdF) gene, complete cds. ammoniagenes rxa01928 960 GB_BAI:CGPAN 2164 X96580 C.glutamicum panB, panC & xylB genes.
Corynebacterium 100,000 11-MAY-glutamicum 1999 GB PL1:AP000423 154478 AP000423 Arabidopsis thaliana chloroplast genomic DNA, complete sequence, Chloroplast Arabidopsis 35,917 15-Sep-99 strain:Columbia. thaliana GB_PL1:AP000423 154478 AP000423 Arabidopsis thaliana chloroplast genomic DNA, complete sequence, Chloroplast Arabidopsis 33,925 15-Sep-99 strain:Columbia. thaliana rxa01929 936 GB_BAI:CGPAN 2164 X96580 C.glutamicum panB, panC & xylB genes.
Corynebacterium 100,000 11-MAY-glutamicum 1999 GB_BAI:XCU33548 8429 U33548 Xanthomonas campestris hrpB pathogenicity locus proteins HrpBl, HrpB2, Xanthomonas campestris 38,749 19-Sep-96 HrpB3, HrpB4, HrpB5, HrpB6, HrpB7, HrpB8, HrpAl, and ORF62 pv. vesicatoria genes, complete cds.
GB_BA1:XANHRPB6 1329 M99174 Xanthomonas campestris hrpB6 gene, complete cds.
Xanthomonas campestris 39,305 14-Sep-93 A
nca01940 1059 GB_IN2:CFU43371 1060 U43371 Crithidia fasciculata inosine-uridine preferring nucleoside hydrolase (IUNH) Crithidia fasciculata 61,417 18-Jun-96 gene, complete cds.
GB_BA2:AE001467 11601 AE001467 Helicobacter pylori, strain J99 section 28 of 132 of the complete genome. Helicobacter pylori J99 38,560 20-Jan-99 GB
RO:AF175967 3492 AF175967 Homo sapiens Leman coiled-coil protein (LCCP) mRNA, complete cds. Mus musculus 40,275 26-Sep-99 Ln rxa02022 1230 GB BA1:CGDAPE 1966 X81379 C.glutamicum dapE gene and orf2.
Corynebacterfum 100,000 8-Aug-95 r o glutamicum '-" ~
~
GB BAI:CGDNAARO 2612 X85965 C.glutamicum ORF3 and aroP gene. Corynebacterium 38,889 30-Nov-97 P glutamicum N
GB_BAI:APU47055 6469 U47055 Anabaena PCC7120 nitrogen fixation proteins (nifE, nifN, n'rfX, niNV) genes, Anabaena PCC7120 36,647 17-Feb-96 0 complete cds, and nitrogenase (nifK) and hesA genes, partial cds. 1 .3 rxa02024 859 G8_BA1:MTCI364 29540 Z93777 Mycobacterium tuberculosis H37Rv complete genome; segment 52/162 Mycobacterium 59,415 17-Jun-98 rn tuberculosis GB_BA1:MSGB1912C 38503 L01536 M. leprae genomic dna sequence, cosmid b1912.
Mycobacterium leprae 57,093 14-Jun-96 S
GB BA1:MLU15180 38675 U15180 Mycobacterium leprae cosmid B1756. Mycobacterium leprae 57,210 09-MAR-nca02027 rxa02031 rxa02072 1464 GB_BA1:CGGDHA 2037 X72855 C.glutamicum GDHA gene.
Corynebacterium 99,317 24-MAY-glutamicum 1993 GS BA1:CGGDH 2037 X59404 Corynebacterium glutamicum, gdh gen for glutamate dehydrogenase. Corynebacterium 94,387 30-Jul-99 glutamicum GB_BA1:PAE18494 1628 Y18494 Pseudomonas aeruginosa gdhA gene, strain PAC1.
Pseudomonas aeruginosa 62,247 6-Feb-99' Table 4 (continued) rxa02085 2358 GB_BAI:MTCY22G8 22550 Z95585 Mycobacterium tuberculosis H37Rv complete genome, segment 49/162. Mycobacterium 38,442 17-Jun-98 tuberculosis GB BA1:MLCB33 42224 Z94723 Mycobacterium leprae cosmid B33. Mycobacterium leprae 56,486 24-Jun-97 GB BAI:ECOUW85 91414 M87049 E. coli genomic sequence of the region from 84.5 to 86.5 minutes. Escherichia coli 52,127 29-MAY-rxa02093 927 GB_EST14:AA448146 452 AA448146 zw82h01.r1 Soares_testis_NHT Homo sapiens cONA clone IMAGE:782737 Homo sapiens 34,163 4-Jun-97 5', mRNA sequence.
GB_EST17:AA641937 444 AA641937 nsl8blO.rl NCI_CGAP_GCB1 Homo sapiens cDNA
clone IMAGE:1 183963 Homo sapiens 35,586 27-OCT-5', mRNA sequence. 1997 GB_PR3:AC003074 143029 AC003074 Human PAC clone DJ0596009 from 7p15, complete sequence. Homo sapiens 31,917 6-Nov-97 nca02106 1179 GB_BA1:SC1A6 37620 AL023496 Streptomyces coelicolor cosmid 1A6.
Streptomyces coelicolor 35,818 13-Jan-99 GB PR4:AC005553 179651 AC005553 Homo sapiens chromosome 17, clone hRPK.112_J_9, complete sequence. Homo sapiens 34,274 31-DEC-GB EST3:R49746 397 R49746 yg71g10.r1 Soares infant brain 1NIB Homo sapiens cDNA clone Homo sapiens 41,162 18-MAY-IMAGE:38768 5' similar to gb:V00567 BETA-2-MICROGLOBULIN 1995 PRECURSOR (HUMAN);, mRNA sequence.
nca02111 1407 GB_BA1:SC6G10 36734 AL049497 Streptomyces coelicolor cosmid 6G10. Streptomyces coelicolor 50,791 24-MAR-GB_BA1:U00010 41171 U00010 Mycobacterium leprae cosmid B1170. Mycobacterium leprae 37,563 01-MAR- Ln 1994 '- o 0) GB_BA1:MTCY336 32437 Z95586 Mycobacterium tuberculosis H37Rv complete genome;
segment 701162. Mycobacterium 39,504 24-Jun-99 01 tuberculosis nca02112 960 GB_HTG3:AC010579 157658 AC010579 Drosophila melanogaster chromosome 3 clone BACR09D08 (D1101) RPCI-98 Drosophila melanogaster 37,909 24-Sep-99 ' o 09.D.8 map 96F-96F strain y; cn bw sp, "' SEQUENCING IN PROGRESS
.3 121 unordered pieces.
GB_GSS3:B09839 1191 B09839 T12A12-Sp6 TAMU Arabidopsis thaliana genomic clone T12A12, genomic Arabidopsis thaliana 37,843 14-MAY- 0) survey sequence. 1997 rv GB HTG3:AC010579 157658 AC010579 Drosophila melanogaster chromosome 3 clone BACR09D08 (D1101) RPCI-98 Drosophila melanogaster 37,909 24-Sep-99 09.D.8 map 96F-96F strain y; cn bw sp, "' SEQUENCING IN PROGRESS
"', 121 unordered pieces.
rxa02134 1044 GB_BA1:SCSECYDN 6154 X83011 S.coelicolor secY locus DNA.
Streptomyces coelicolor 36,533 02-MAR-GB_EST32:AI731596 568 AI731596 BNLGHi10185 Six-day Cotton fiber Gossypium hirsutum cDNA 5' sirnilar to Gossypium hirsutum 33,451 11-Jun-99 (AC004005) putative ribosomal protein L7 (Arabidopsis thalianaj, mRNA
sequence.
GB_BA1:SCSECYDN 6154 X83011 S.coelicolor secY locus DNA. Streptomyces coelicolor 36,756 02-MAR-rxa02135 1197 GB_PR3:HS525L6 168111 AL023807 Human DNA sequence from clone RP3-525L6 on chromosome 6p22.3-23 Homo sapiens 34,365 23-Nov-99 Contains CA repeat, STSs, GSSs and a CpG Island, complete sequence.
GB_PL2:ATF21 P8 85785 AL022347 Arabidopsis thaliana DNA chromosome 4, BAC
clone F21P8 (ESSA project). Arabidopsis thaliana 34,325 9-Jun-99 GB_PL2:U89959 106973 U89959 Arabidopsis thaliana BAC T7123, complete sequence.
Arabidopsis thaliana 33,874 26Juri-98 Table 4 (continued) rxa02136 645 GB PL.2:ATAC005819 57752 AC005819 Arabidopsis thaliana chromosome II BAC T3A4 genomic sequence, complete Arabidopsis thaliana 34,123 3-Nov-98 sequence.
GB_PL2:F75K9 71097 AC005278 Arabidopsis thaliana chromosome 1 BAC F15K9 sequence, complete Arabidopsis thaliana 31,260 7-Nov-98 sequence.
GB PL2:U89959 106973 U89959 Arabidopsis thaliana BAC T7123, complete sequence.
Arabidopsis thaliana 34,281 26-Jun-98 rxa02139 1962 GB BAI:MTCY190 34150 Z70283 Mycobacterium tuberculosis H37Rv complete genome; segment 98/162. Mycobacterium 62,904 17Jun-98 tuberculosis GB_BAI:MSGB1554C 36548 L78814 Mycobacterium leprae cosmid B1554 DNA sequence.
Mycobacterium leprae 36,648 15-Jun-96 S
GB BAI:MSGB1551C 36548 L78813 Mycobacterium leprae cosmid B1551 DNA sequence.
Mycobacterium teprae 36,648 15-Jun-96 S
rxa02153 903 GB_BA2:AF049897 9196 AF049897 Corynebacterium glutamicum N-acetylglutamylphosphate reductase (argC), Corynebacterium 99,104 1-Jul-98 ornithine acetyltransferase (argJ), N-acetylglutamate kinase (argB), glutamicum acetylomithine transaminase (argD), ornithine carbamoyltransferase (argF), arginine repressor (argR), argininosuccinate synthase (argG), and argininosuccinate lyase (argH) genes, complete cds.
GB_BA1:AF005242 1044 AF005242 Corynebacterium glutamicum N-acetylglutamate-5-semialdehyde Corynebacterium 99,224 2-Jul-97 dehydrogenase (argC) gene, complete cds. glutamicum GB_BAI:CGARGCJB 4355 X86157 C.glutamicum argC, argJ, arg6, argD, and argF
genes. Corynebacterium 100,000 25-Jul-96 Ln D glutamicum 0) rxa02154 414 GB_BA2:AF049897 9196 AF049897 Corynebacterium glutamicum N-acetylglutamylphosphate reductase (argC), Corynebacterium 98,551 1-Jul-98 01 Q N
omithine acetyltransferase (argJ), N-acetylglutamate kinase (argB), glutamicum acetylornithine transaminase (argD), ornithine carbamoyltransferase (argF), o arginine repressor (argR), argininosuccinate synthase (argG), and argininosuccinate lyase (argH) genes, complete cds.
GB_BA1:AF005242 1044 AF005242 Corynebacterium glutamicum N-acetylglutamate-5-semialdehyde Corynebacterium 98,477 2-Jul-97 0) dehydrogenase (argC) gene, complete cds. glutamicum rv GB_BA1:CGARGCJB 4355 X86157 C.glutamicum argC, argJ, argB, argD, and argF
genes. Corynebacterium 100,000 25-Jul-96 D glutamicum rxa02155 1287 GB BA1:CGARGCJB 4355 X86157 C.glutamicum argC, argJ, argB, argD, and argF genes. Corynebacterium 99,767 25-Jul-96 D glutamicum GB BA2:AF049897 9196 AF049897 Corynebacterium glutamicum N-acetylglutamylphosphate reductase (argC), Corynebacterium 99,378 1-Jul-98 ornithine acetyltransferase (argJ), N-acetylglutamate kinase (argB), glutamicum acetylornithine transaminase (argD), ornithine carbamoyltransferase (argF), arginine repressor (argR), argininosuccinate synthase (argG), and argininosuccinate lyase (argH) genes, complete cds.
GB BAI:MSGB1133C 42106 L78811 Mycobacterium leprae cosmid B1133 DNA sequence.
Mycobacterium leprae 55,504 15-Jun-96 S
rxa02156 1074 G8_BA2:AF049897 9196 AF049897 Corynebacterium glutamicum N-acetylglutamylphosphate reductase (argC), Corynebacterium 100,000 1-Jul-98 ornithine acetyltransferase (argJ), N-acetylglutamate kinase (argB), glutamicum acetylornithine transaminase (argD), ornithine carbamoyttransferase (argF), arginine repressor (argR), argininosuccinate synthase (argG), and argininosuccinate lyase (argH) genes, complete cds.

Table 4 (continued) GB BA1:CGARGCJB 4355 X86157 C.glutamicum argC, argJ, argB, argD, and argF
genes. Corynebacterium 100,000 25-Jul-96 D glutamicum GB_BA2:AE001816 10007 AE001816 Thermotoga maritima section 128 of 136 of the complete genome. Thermotoga maritima 50,238 2-Jun-99 rxa02157 1296 GB BA2:AF049897 9196 AF049897 Corynebacterium glutamicum N-acetylglutamylphosphate reductase (argC), Corynebacterium 99,612 1-Jul-98 omithine acetyltransferase (argJ), N-acetylglutamate kinase (argB), glutamicum acetylornithine transaminase (argD), omithine carbamoyltransferase (argF), arginine repressor (argR), argininosuccinate synthase (argG), and argininosuccinate lyase (argH) genes, complete cds.
GB_BAI:CGARGCJB 4355 X86157 C.glutamicum argC, argJ, argB, argD, and argF
genes. Corynebacterium 99,612 25-Jul-96 D glutamicum GB_BA1:MTCYO6H11 38000 Z85982 Mycobacterium tuberculosis H37Rv complete genome: segment 731162. Mycobacterium 57,278 17-Jun-98 tuberculosis rxa02158 1080 GB_BA2:AF049897 9196 AF049897 Corynebacterium glutamicum N-acetylgiutamylphosphate reductase (argC), Corynebacterium 100,000 1-Jul-98 ornithine acetyltransferase (argJ), N-acetylglutamate kinase (argB), glutamicum acetylornithine transaminase (argD), omithine carbamoyltransferase (argF), arginine repressor (argR), argininosuccinate synthase (argG), and argininosuccinate lyase (argH) genes, complete cds.
GB_BA2:AF031518 2045 AF031518 Corynebacterium glutamicum ornithine carbamolytransferase (argF) gene. Corynebacterium 99,898 5-Jan-99 complete cds. glutamicum L'' GB BA1:CGARGCJB 4355 X86157 C.glutamicum argC, argJ, argB, argD, and argF
genes. Corynebacter9um 100,000 25-Jul-96 0 D glutamicum N
rxa02159 636 GB_BA2:AF049897 9196 AF049897 Corynebacterium glutamicum N-acetylglutamylphosphate reductase (argC), Corynebacterium 99,843 1-Jul-98 ornithine acetyltransferase (argJ), N-acetylglutamate kinase (argB), glutamicum acetylornithine transaminase (argD), ornithine carbamoyftransferase (argF), o arginine repressor (argR), argininosuccinate synthase (argG), and .3 argininosuccinate lyase (argH) genes, complete cds.
rn GB_BA2:AF031518 2045 AF031518 Corynebacterium glutamicum ornithine carbamolytransferase (argF) gene, Corynebacterium 88,679 5-Jan-99 complete cds. glutamicum GB_BA2:AF041436 516 AF041436 Corynebacterium glutamicum arginine repressor (argR) gene, complete cds. Corynebacterium 100,000 5-Jan-99 glutamicum nca02160 1326 GB_BA2:AF049897 9196 AF049897 Corynebacterium glutamicum N-acetylglutamylphosphate reductase (argC), Corynebacterium 99,774 1-Jul-98 ornithine acetykransferase (argJ), N-acetylglutamate kinase (argB), glutamicum acetylomithine transaminase (argD), omithine carbamoyltransferase (argF), arginine repressor (argR), argininosuccinate synthase (argG), and argininosuccinate Iyase (argH) genes, complete cds.
GB BA2:AF030520 1206 AF030520 Corynebacterium glutamicum argininosuccinate synthetase (argG) gene, Corynebacterium 99,834 19-Nov-97 complete cds. glutamicum GB_BA1:SCARGGH 1909 Z49111 S.clavuligerus argG gene and argH gene (partial).
Streptomyces clavuligerus 65,913 22-Apr-96 rxa02162 1554 GB_BA2AF049897 9196 AF049897 Corynebacterium glutamicum N-acetylglutamylphosphate reductase (argC), Corynebacterium 88,524 1-Jul-98 omithine acetyltransferase (argJ), N-acetylglutamate kinase (argB), glutamicum acetylornithine transaminase (argD), ornithine carbamoyltransferase (argF), arginine repressor (argR), argininosuccinate synthase (argG), and argininosuccinate lyase (argH) genes, complete cds.

Table 4 (continued) GB_BA2:AF048764 1437 AF048764 Corynebacterium glutamicum argininosuccinate lyase (argH) gene,complete Corynebacterium 87,561 1 -Jul-98 cds. glutamicum GB_BAI:MTCY06H11 38000 Z85982 Mycobacterium tuberculosis H37Rv complete genome; segment 73/162. Mycobacterium 64,732 17-Jun-98 tuberculosis rxa02176 1251 GB_BA1:MTCY31 37630 Z73101 Mycobacterium tuberculosis H37Rv complete genome; segment 41/162. Mycobacterium 36,998 17-Jun-98 tuberculosis GB_BA1:CGGLTG 3013 X66112 C.glutamicum glt gene for citrate synthase and ORF.
Corynebacterium 39,910 17-Feb-95 glutamicum GB PL2:PGU65399 2700 U65399 Basidiomycete CECT 20197 phenoloxidase (poxl) gene, complete cds. basidiomycete CECT 38,474 19-Jul-97 rxa02189 861 GB_PR3:AC002468 115888 AC002468 Human Chromosome 15q26.1 PAC Gone pDJ417d7, complete sequence. Homo sapiens 35,941 16-Sep-98 GB_BAI:MSG81970C 39399 L78815 Mycobacterium leprae cosmid B1970 DNA sequence.
Mycobacterium leprae 40,286 15-Jun-96 S
G8_PR3AC002468 115888 AC002468 Human Chromosome 15q26.1 PAC clone pDJ417d7, complete sequence. Homo sapiens 33,689 16-Sep-98 rxa02193 1701 GB_BAI:BRLASPA 1987 D25316 Brevibacterium flavum aspA gene for aspartase, complete cds. Corynebacterium 99,353 6-Feb-99 glutamicum o GB_PAT:E04307 1581 E04307 DNA encoding Brevibacterium flavum aspartase.
Corynebacterium 99,367 29-Sep-97 Ln glutamicum GB_BAI:ECOUW93 338534 U14003 Escherichia coli K-12 chromosomal region from 92.8 to 00.1 minutes. Escherichia coli 37,651 17-Apr-96 0) rxa02194 966 GB_BA2:AF050166 840 AF050166 Corynebacterium glutamicum ATP
phosphoribosyltransferase (hisG) gene, Corynebacterium 98,214 5-Jan-99 N 0) complete cds. glutamicum GB_BA1:BRLASPA 1987 D25316 Brevibacterium flavum aspA gene for aspartase, complete cds. Corynebacterium 93,805 6-Feb-99 glutamicum GB_PAT:E08649 188 E08649 DNA encoding part of aspartase from coryneform bacteria. Corynebacterium 100,000 29-Sep-97 ' o glutamicum O1 rxa02195 393 GBBA2:AF086704 264 AF086704 Corynebacterium glutamicum phosphoribosyl-ATP-pyrophosphohydrolase Corynebacterium 100,000 8-Feb-99 (hisE) gene, complete cds. glutamicum GB_BA1:EAY17145 6019 Y17145 Eubacterium acidaminophilum grdR, grdl, grdH genes and partial Idc, grdT Eubacterium 39,075 5-Aug-98 genes. acidaminophilum GB STS:G01195 332 G01195 fruit fly STS Om1930 clone OS06959 T7. Drosophila melanogaster 35,542 28-Feb-95 rxa02197 551 GB BAI:MTCY261 27322 Z97559 Mycobacterium tuberculosis H37Rv complete genome; segment 95/162. Mycobacterium 33,938 17-Jun-98 tuberculosis GB BAI:MLCB2533 40245 AL035310 Mycobacterium leprae cosmid B2533.
Mycobacterium leprae 65,517 27-Aug-99 GB BA1:U00017 42157 U00017 Mycobacterium leprae cosmid 82126. Mycobacterium leprae 36,770 01-MAR-rxa02198 2599 GB_BA1:U00017 42157 U00017 Mycobacterium leprae cosmid B2126.
Mycobacterium leprae 38,674 01-MAR-GB_BA1:MLCB2533 40245 AL035310 Mycobacterium leprae cosmid B2533.
Mycobacterium leprae 65,465 27-Aug-99 G8_BAI:MTCY261 27322 Z97559 Mycobacterium tuberculosis H37Rv complete genome;
segment 951162. Mycobacterium 37,577 17-Jun-98 tuberculosis rxa02208 1025 GB_BA1:U00017 42157 U00017 Mycobacterium leprae cosmid 82126.
Mycobacterium leprae 59,823 01-MAR-GB_BA1:AP000063 185300 AP000063 Aeropyrum pernix genomic DNA, section 6/7.
Aeropyrum pernix 39,442 22-Jun-99 Table 4 (continued) GB_PR4:AC006236 127593 AC006236 Homo sapiens chromosome 17, clone hCIT.162_E_12, complete sequence. Homo sapiens 37,191 29-DEC-rxa02229 948 GB_BA1:MSGY154 40221 AD000002 Mycobacterium tuberculosis sequence from clone y154. Mycobacterium 53,541 03-DEC-tuberculosis 1996 GB_BA1:MTCY154 13935 Z98209 Mycobacterium tuberculosis H37Rv complete genome;
segment 121/162. Mycobacterium 40,407 17-Jun-98 tuberculosis GB_BA1:U00019 36033 U00019 Mycobacterium leprae cosmid 82235. Mycobacterium leprae 40,541 01-MAR-rxa02234 3462 GB_BA1:MSGB937C 38914 L78820 Mycobacterium leprae cosmid B937 DNA sequence. Mycobacterium leprae 66,027 15-Jun-96 S
GB_BA1:MTCY2812 20431 Z81011 Mycobacterium tuberculosis H37Rv complete genome;
segment 61/162. Mycobacterium 71,723 18-Jun-98 tuberculosis GB_BA2:U01072 4393 U01072 Mycobacterium bovis BCG orotidine-5'-monophosphate decarboxylase (uraA) Mycobacterium bovis 67,101 22-DEC-gene. 1993 rxa02235 727 GB_BAI:MSU91572 960 U91572 Mycobacterium smegmatis carbamoyl phosphate synthetase (pyrAB) gene, Mycobacterium smegmatis 60,870 22-MAR-partial cds and orotidine 5'-monophosphate decarboxylase (pyrF) gene, 1997 complete cds. Lõ
GB_HTG3:AC0093(>4 192791 AC009364 Homo sapiens chromosome 7, SEQUENCING IN
PROGRESS 57 Homo sapiens 37,994 1-Sep-99 unordered pieces, o) GB_HTG3:AC009364 192791 AC009364 Homo sapiens chromosome 7, SEQUENCING IN
PROGRESS57 Homo sapiens 37,994 1-Sep-99 tNa unordered pieces.
rxa02237 693 GB BAI:MTCY21 B4 39150 Z80108 Mycobacterium tuberculosis H37Rv complete genome; segment 62/162. Mycobacterium 55,844 23-Jun-98 tuberculosis GB BA2:AF077324 5228 AF077324 Rhodococcus equi strain 103 plasmid RE-VPI
fragment f. Rhodococcus equi 41,185 5-Nov-98 GB EST22:AU017763 586 AU017763 AU017763 Mouse two-cell stage embryo cDNA Mus musculus cDNA clone Mus musculus 38,616 19-OCT- 0' J0744A04 3', mRNA sequence. 1998 rxa02239 1389 GB_BA1:MTCY21 B4 39150 Z80108 Mycobacterium tuberculosis H37Rv complete genome: segment 62/162.
Mycobacterium 56,282 23-Jun-98 tuberculosis GB_HTG3:AC010745 193862 AC010745 Homo sapiens clone NH0549D18, SEQUENCING IN
PROGRESS 30 Homo sapiens 36,772 21-Sep-99 unordered pieces.
GB_HTG3:AC010745 193862 AC010745 Homo sapiens clone NH0549D18, SEQUENCING IN
PROGRESS 30 Homo sapiens 36,772 21-Sep-99 unordered pieces.
rxa02240 1344 EM PAT:E09855 1239 E09855 gDNA encoding S-adenosylmethionine synthetase. Corynebacterium 99,515 07-OCT-glutamicum 1997 (Rel.
52, Created) GB_PAT:A37831 5392 A37831 Sequence 1 from Patent W09408014. Streptomyces 63,568 05-MAR-pristinaespiralis 1997 GB_BA2:AF117274 2303 AF117274 Streptomyces spectabilis flavoprotein homolog Dfp (dfp) gene, partial cds; and Streptomyces spectabilis 65,000 31-MAR-S-adenosylmethionine synthetase (metK) gene, complete cds. 1999 rxa02246 1107 EM_BA1:AB003693 5589 AB003693 Corynebacterium ammoniagenes DNA
for rib operon, complete cds. Corynebacterium 52,909 03-OCT-ammoniagenes 1997 (Rel.
52, Created) Table 4 (continued) GB_PAT:E07957 5589 E07957 gDNA encoding at least guanosine triphosphate cyclohydrolase and riboflavin Corynebacterium 52,909 29-Sep-97 synthase. ammoniagenes GB_PAT:132742 5589 132742 Sequence 1 from patent US 5589355. Unknown. 52,909 6-Feb-97 rxa02247 756 GB_PAT:132743 2689 132743 Sequence 2 from patent US 5589355.
Unknown. 57,937 6-Feb-97 EM_BA1:AB003693 5589 AB003693 Corynebacterium ammoniagenes DNA for rib operon, complete cds. Corynebacterium 57,937 03-OCT-ammoniagenes 1997 (Rel.
52, Created) GB_PAT:132742 5589 132742 Sequence 1 from patent US 5589355. Unknown. 57,937 6-Feb-97 rxa02248 1389 GB_PAT:132742 5589 132742 Sequence 1 from patent US 5589355.
Unknown. 61,843 6-Feb-97 EM_BA1:AB003693 5589 AB003693 Corynebacterium ammoniagenes DNA for rib operon, complete cds. Corynebacterium 61,843 03-OCT-ammoniagenes 1997 (Rel.
52, Created) GB PAT:E07957 5589 E07957 gDNA encoding at least guanosine triphosphate cyclohydrolase and riboflavin Corynebacterium 61,843 29-Sep-97 synthase. ammoniagenes rxa02249 =600 GB_PAT:E07957 5589 E07957 gDNA encoding at least guanosine triphosphate cyclohydrolase and riboflavin Corynebacterium 64,346 29-Sep-97 synthase. ammoniagenes GB_PAT:132742 5589 132742 Sequence 1 from patent US 5589355. Unknown. 64,346 6-Feb-97 GB_PAT:132743 2689 132743 Sequence 2 from patent US 5589355. Unknown. 64,346 6-Feb-97 ci, rxa02250 643 GB_PAT:E07957 5589 E07957 gDNA encoding at least guanosine triphosphate cyclohydrolase and riboflavin Corynebacterium 56,318 29-Sep-97 0 synthase. ammoniagenes o) rn GBPAT:132742 5589 132742 Sequence 1 from patent US 5589355. Unknown. 56,318 6-Feb-97 ~ N
EM_BA1:AB003693 5589 AB003693 Corynebacterium ammoniagenes DNA for rib operon, complete cds. Corynebacterium 56,318 03-OCT- 41 ammoniagenes 1997 (Rel. o 52, Created) .3 rxa02262 1269 GB_BA1:CGL007732 4460 AJ007732 Corynebacterium glutamicum 3' ppc gene, secG gene, amt gene, ocd gene Corynebacterium 100,000 7-Jan-99 and 5' soxA gene. glutamicum O1 GB BA1:CGAMTGEN 2028 X93513 C.glutamicum amt gene. Corynebacterium 100,000 29-MAY-E
glutamicum 1996 GB VI:HEHCMVCG 229354 X17403 Human cytomegalovirus strain AD169 complete genome. human herpesvirus 5 38,651 10-Feb-99 rxa02263 488 GB_BAI:CGL007732 4460 AJ007732 Corynebacterium glutamicum 3' ppc gene, secG gene, amt gene, ocd gene Corynebacterium 100,000 7-Jan-99 and 5' soxA gene. glutamicum GB_BAI:CGL007732 4460 AJ007732 Corynebacterium glutamicum 3' ppc gene, secG
gene, amt gene, ocd gene Corynebacterium 37,526 7-Jan-99 and 5' soxA gene, glutamicum rxa02272 1368 EM_PAT:E09373 1591 E09373 Creatinine deiminase gene. Bacillus sp. 96,928 08-OCT-1997 (Rel.
52, Created) GB_BA1:D38505 1591 D38505 Bacillus sp. gene for creatinine deaminase, complete cds. Bacillus sp. 96,781 7-Aug-98 GB_HTG2:AC006595 146070 AC006595 Homo sapiens, =" SEQUENCING IN PROGRESS '"', 4 unordered pieces. Homo sapiens 36,264 20-Feb-99 rxa02281 1545 GB_GSS12:AQ41101 551 AQ411010 HS 2257_B1 H02_MR CIT Approved Human Genomic Sperm Library D Homo sapiens 36,197 , 17-MAR-0 Homo sapiens genomic clone Plate=2257 Col=3 Row=P, genomic survey lggg _;
sequence.

Table 4 (continued) GB_EST23:AI128623 363 A1128623 qa62c01.s1 Soares_fetal_heart_NbHH19W Homo sapiens cDNA clone Homo sapiens 37,017 05-OCT-IMAGE:1691328 3', mRNA sequence. 1998 GB PL2:ATAC007019 102335 AC007019 Arabidopsis thaliana chromosome II BAC F7D8 genomic sequence, complete Arabidopsis thaliana 33,988 16-MAR-sequence. 1999 rxa02299 531 GB_BA2:AF116184 540 AF116184 Corynebacterium glutamicum L-aspartate-alpha-decarboxylase precursor Corynebacterium 100,000 02-MAY-(panD) gene, complete cds. glutamicum 1999 GB GSS9:AQ164310 507 AQ164310 HS_2171_A2_E01_MR CIT Approved Human Genomic Sperm Library D Homo sapiens 37,278 16-OCT-Homo sapiens genomic clone Plate=2171 Col=2 Row=I, genomic survey 1998 sequence.
GB_VI:MH68TKH 4557 X93468 Murine herpesvirus type 68 thymidine kinase and glycoprotein H genes. murine herpesvirus 68 40,288 3-Sep-96 nca02311 813 GB_HTG4:AC006091 176878 AC006091 Drosophila melanogaster chromosome 3 clone BACR48G05 (D475) RPCI-98 Drosophila melanogaster 36,454 27-OCT-48.G.5 map 91 F1-91 F13 strain y; cn bw sp, "' SEQUENCING IN 1999 PROGRESS "=, 4 unordered pieces.
GB_HTG4:AC006091 176878 AC006091 Drosophila melanogaster chromosome 3 clone BACR48GO5 (0475) RPCi-98 Drosophila melanogaster 36,454 27-OCT-48.G.5 map 91 F1-91 F13 strain y, cn bw sp, "' SEQUENCING IN 1999 PROGRESS "', 4 unordered pieces.
GB_BA2:RRU65510 16259 U65510 Rhodospirillum rubrum CO-induced hydrogenase operon (cooM, cooK, cooL, Rhodospirillum rubrum 37,828 9-Apr-97 cooX, cooU, cooH) genes, iron sulfur protein (cooF) gene, carbon monoxide Lr' dehydrogenase (cooS) gene, carbon monoxide dehydrogenase N o accessory proteins (cooC, cooT, cooJ) genes, putative transcriptional activator (cooA) gene, nicotinate-nucleotide pyrophosphorylase (nadC) gene, complete N
cds, L-aspartate oxidase (nadB) gene, and alkyl hydroperoxide reductase (ahpC) gene, partial cds. o -.3 i rxa02315 1752 GB_BA1:MSGY224 40051 AD000004 Mycobacte(um tuberculosis sequence from clone y224. Mycobacterium 49,418 03-DEC- 0) tuberculosis 1996 GB_BAI:MTY25D10 40838 Z95558 Mycobacterium tuberculosis H37Rv complete genome;
segment 28/162. Mycobacterium 49,360 17-Jun-98 r tuberculosis GB_BAI:MSGY224 40051 AD000004 Mycobacterium tuberculosis sequence from clone y224. Mycobacterium 38,150 03-DEC-tuberculosis 1996 rxa02318 402 GB HTG3:AC011348 111083 AC011348 Homo sapiens chromosome 5 clone CIT-HSPC_303E13, SEQUENCING Homo sapiens 35,821 06-OCT-IN PROGRESS "", 3 ordered pieces. 1999 GB HTG3:AC011348 111083 AC011348 Homo sapiens chromosome 5 clone CIT-HSPC_303E13, SEQUENCING Homo sapiens 35,821 06-OCT-IN PROGRESS "', 3 ordered pieces. 1999 GB_HTG3:AC011412 89234 AC011412 Homo sapiens chromosome 5 clone CIT978SKB_81K21, ==' SEQUENCING Homo sapiens 36,181 06-OCT-IN PROGRESS "', 3 ordered pieces. 1999 rxa02319 1080 GB_BAI:MSGY224 40051 A0000004 Mycobacterium tuberculosis sequence from clone y224. Mycobacterium 37,792 03-DEC-tuberculosis 1996 G8_BAI:MTY25D10 40838 Z95558 Mycobacterium tuberculosis H37Rv complete genome;
segment 28/162. Mycobacterium 37,792 17-Jun-98 tuberculosis GB_EST23:AI117213 476 AI117213 ub83h02.r1 Soares 2NbMT Mus musculus cDNA clone IMAGE:1395123 Mus musculus 35,084 2-Sep-98 5',mRNA sequence.

Table 4 (continued) rxa02345 1320 GB 8A1:BAPURKE 2582 X91189 B.ammoniagenes purK and purE genes.
Corynebacterium 61,731 14-Jan-97 ammoniagenes GB_8A1:MTCY71 42729 Z92771 Mycobacterium tuberculosis H37Rv complete genome;
segment 141/162. Mycobacterium 39,624 10-Feb-99 tuberculosis GB_BAI:MTCY71 42729 Z92771 Mycobacterium tuberculosis H37Rv complete genome;
segment 141/162. Mycobacterium 39,847 10-Feb-99 tuberculosis rxa02350 618 GB BAI:BAPURKE 2582 X91189 B.ammoniagenes purK and purE genes.
Corynebacterium 64,286 14-Jan-97 ammoniagenes GS_PL1:SC130KBXV 129528 X94335 S.cerevisiae 130kb DNA fragment from chromosome XV. Saccharomyces cerevisiae 36,617 15-Jul-97 GB PLI:SCXVORFS 50984 X90518 S.cerevisiae DNA of 51 Kb from chromosome XV
right arm. Saccharomyces cerevisiae 36,617 1-Nov-95 rxa02373 1038 GB_PAT:E00311 1853 E00311 DNA coding of 2,5-diketogluconic acid reductase. unidentified 56,123 29-Sep-97 GB_PAT:106030 1853 106030 Sequence 4 from Patent EP 0305608. Unknown. 56,220 GB_PAT:100836 1853 100836 Sequence 1 from Patent US 4758514. Unknown. 56,220 Ln rxa02375 1350 GBBA2:CGU31230 3005 U31230 Corynebacterium glutamicum Obg protein homolog gene, partial cds, gamma Corynebacterium 99,332 2-Aug-96 glutamyl kinase (proB) gene, complete cds, and (unkdh) gene, complete cds.
glutamicum 0) r 0) N N
GB_HTG3:AC009946 169072 AC009946 Homo sapiens clone NH0012C17, =" SEQUENCING
IN PROGRESS 1 Homo sapiens 36,115 8-Sep-99 v, - N
unordered pieces. o GB_HTG3:AC009946 169072 AC009946 Homo sapiens clone NH0012C17, SEQUENCING IN
PROGRESS 1 Homo sapiens 36,115 8-Sep-99 .3 unordered pieces.
rxa02380 777 GB BA1:MTCY253 41230 Z81368 Mycobacterium tuberculosis H37Rv complete genome; segment 106/162. Mycobacterium 38,088 17-Jun-98 0) tuberculosis GB_HTG4:AC010658 120754 AC010658 Drosophila melanogaster chromosome 3L175C1 clone RPCI98-3820, "" Drosophila melanogaster 35,817 16-OCT-IN PROGRESS "', 78 unordered pieces. 1999 SEQUENCING
GB_HTG4:AC010658 120754 AC010658 Drosophila melanogaster chromosome 3L175C1 clone RPCI98-3B20, Drosophila melanogaster 35,817 16-OCT-SEQUENCING IN PROGRESS "', 78 unordered pieces. 1999 rxa02382 1419 GB_BA1:CGPROAGE 1783 X82929 C.glutamicum proA gene.
Corynebacterium 98,802 23Jan-97 N glutamicum GB_BAI:MTCY428 26914 Z81451 Mycobacterium tuberculosis H37Rv complete genome;
segment 107/162. Mycobacterium 38,054 17-Jun-98 tuberculosis GB_8A2:CGU31230 3005 U31230 Corynebacterium glutamicum Obg protein homolog gene, partial cds, gamma Corynebacterium 98,529 2-Aug-96 glutamyl kinase (proB) gene, complete cds, and (unkdh) gene, complete cds.
glutamicum rxa02400 693 GB_BAI:CGACEA 2427 X75504 C.glutamicum aceA gene and thiX genes (partial). Corynebacterium 100,000 9-Sep-94 glutamicum GB_PAT:186191 2135 186191 Sequence 3 from patent US 5700661. Unknown. 100,000 10-Jun-98 GB_PAT:113693 2135 113693 Sequence 3 from patent US 5439822. Unknown. 100.000 26-Sep-95 rxa02432 1098 GB_GSS15:AQ60684 574 AQ606842 HS 5404_B2_E07_T7A RPCI-1 1 Human Male BAC Library Homo sapiens Homo sapiens 39,716 10-Juri=99 2 genomic clone Plate=980 Co1=14 Row=J, genomic survey sequence.

Table 4 (continued) GB_EST1:T05804 406 T05804 EST03693 Fetal brain, Stratagene (cat#936206) Homo sapiens cDNA clone Homo sapiens 37,915 30-Jun-93 HFBDG63 similar to EST containing Alu repeat, mRNA sequence.
GB_PL1:AB006699 77363 AB006699 Arabidopsis thaliana genomic DNA, chromosome 5, P1 clone: MDJ22, Arabidopsis thaliana 35,526 20-Nov-99 complete sequence.
rna02458 1413 GB_BA2:AF114233 1852 AF114233 Corynebacterium glutamicum 5-enolpyruvylshikimate 3-phosphate synthase Corynebacterium 100,000 7-Feb-99 (aroA) gene, complete cds, glutamicum GB_EST37:AW01306 578 AW013061 ODT-0033 Winter flounder ovary Pleuronectes americanus cDNA clone ODT- Pleuronecies americanus 39,175 10-Sep-99 1 0033 5' similar to FRUCTOSE-BISPHOSPHATE ALDOLASE 8(LIVER), mRNA sequence.
GB_GSS15:AQ65002 728 A0650027 Sheared DNA-5L2.TF Sheared DNA Trypanosoma brucei genomic clone Trypanosoma brucei 39,281 22-Jun-99 7 Sheared DNA-5L2, genomic survey sequence.
rxa02469 1554 GB_BA1:MTCY359 36021 Z83859 Mycobacterium tuberculosis H37Rv complete genome; segment 84/162. Mycobacterium 39,634 17-Jun-98 tuberculosis GB_BA1:MLCB1788 39228 AL008609 Mycobacterium leprae cosmid B1788.
Mycobacterium leprae 59,343 27-Aug-99 GB_BAI:SCAJ10601 4692 AJ010601 Streptomyces coelicolor A3(2) DNA for whiD and whiK loci. Streptomyces coelicolor 48,899 17-Sep-98 rxa02497 1050 GB_BA2:CGU31224 422 U31224 Corynebacter9um glutamicum (ppx) gene, partial cds. Corynebacterium 96,445 2-Aug-96 glutamicum GB_BA1:MTCY20G9 37218 Z77162 Mycobacterium tuberculosis H37Rv complete genome;
segment 25/162. Mycobacterium 59,429 17-Jun-98 Ln tuberculosis 1O
GB_BA1:SCE7 16911 AL049819 Streptomyces coelicolor cosmid E7. Streptomyces coelicolor 39,510 10-MAY- 01 r rn rxa02499 933 GB_BA2:CGU31225 1817 U31225 Corynebacterium glutamicum L-proline;NADP+ 5-oxidoreductase (proC) gene, Corynebacterium 97,749 2-Aug-96 v N
complete cds. glutamicum GB_BA1:NG17PILA 1920 X13965 Neisseria gonorrhoeae pilA gene. Neisseria gonorrhoeae 43,249 30-Sep-93 - 1 .3 GB_HTG2:AC007984 129715 AC007984 Drosophila melanogaster chromosome 3 clone BACR05C10 (D781) RPCI-98 Drosophila melanogaster 33,406 2-Aug-99 - 0) 05.C.10 map 97D-97E strain y; cn bw sp, "' SEQUENCING IN PROGRESS
87 unordered pieces.
rxa02501 1188 GB_BAI:MTCY20G9 37218 Z77162 Mycobacterium tuberculosis H37Rv complete genome; segment 25/162. Mycobacterium 39,357 17-Jun-98 tuberculosis GB BA1:U00018 42991 U00018 Mycobacterium leprae cosmid B2168. Mycobacterium leprae 51,768 01-MAR-GB_VI:HEICG 152261 X14112 Herpes simplex virus (HSV) type 1 complete genome.
human herpesvirus 1 39,378 17-Apr-97 rxa02503 522 GB_PR3:AC005328 35414 AC005328 Homo sapiens chromosome 19, cosmid R26660, complete sequence. Homo sapiens 39,922 28-Jul-98 GB_PR3:AC005545 43514 AC005545 Homo sapiens chromosome 19, cosmid R26634, complete sequence. Homo sapiens 39,922 3-Sep-98 GB PR3:AC005328 35414 AC005328 Homo sapiens chromosome 19, cosmid R26660, complete sequence. Homo sapiens 34,911 28-Jul-98 rxa02504 681 GB BA1:MTCY20G9 37218 Z77162 Mycobacterium tuberculosis H37Rv complete genome; segment 25l162. Mycobacterium 54,940 17-Jun-98 tuberculosis GB_PR3:AC005328 35414 AC005328 Homo sapiens chromosome 19, cosmid R26660, complete sequence. Homo sapiens 41,265 28-Jul-98 GB_PR3:AC005545 43514 AC005545 Homo sapiens chromosome 19, cosmid R26634, complete sequence. Homo sapiens 41,265 3-Sep-98 rxa02516 1386 GB_BAI:MLCL536 36224 Z99125 Mycobacterium leprae cosmid L536.
Mycobacterium leprae 37,723 04-DEC-GB_BA1:U00013 35881 U00013 Mycobacterium leprae cosmid B1496. Mycobacterium leprae 37,723 01-MAR-Table 4 (continued) GB BA1:MTV007 32806 AL021184 Mycobacterium tuberculosis H37Rv complete genome;
segment 64/162. Mycobacterium 61,335 17-Jun-98 tuberculosis rxa02517 570 GB_SAI:MLCL536 36224 Z99125 Mycobacterium leprae cosmid L536.
Mycobacterium Ieprae 37,018 04-DEC-GB_BA1:U00013 35881 U00013 Mycobacterium leprae cosmid B1496. Mycobacterium leprae 37,018 01-MAR-GB_BAI:SCC22 22115 AL096839 Streptomyces coelicolor cosmid C22. Streptomyces coelicolor 37,071 12-Jul-99 nca02532 1170 GB_OV:AF137219 831 AF137219 Amia calva mixed lineage leukemia-like protein (MII) gene, partial cds. Amia calva 36,853 7-Sep-99 GB_EST30:A1645057 301 A1645057 vs52a10.y1 Stratagene mouse Tcell 937311 Mus musculus cDNA clone Mus musculus 41,860 29-Apr-99 IMAGE:1149882 5', mRNA sequence.
GB_EST20:AA822595 429 AA822595 vs52a10.r1 Stratagene mouse Tcell 937311 Mus musculus cDNA clone Mus musculus 42,353 17-Feb-98 IMAGE:1149882 5', mRNA sequence.
rxa02536 879 GB_HTG2:AF130866 118874 AF130866 Homo sapiens chromosome 8 clone PAC 172N13 map 8q24, "= Homo sapiens 40,754 21-MAR-SEQUENCING IN PROGRESS "', in unordered pieces. 1999 GB_HTG2:AF130866 118874 AF130866 Homo sapiens chromosome 8 clone PAC 172N13 map 8q24, Homo sapiens 40,754 21-MAR-SEQUENCING IN PROGRESS =", in unordered pieces. 1999 GB_PL1:ATT12J5 84499 AL035522 Arabidopsis thaliana DNA chromosome 4, BAC clone T12J5 (ESSAII project). Arabidopsis thaliana 35,063 24-Feb-99 0 rxa02550 1434 GB_BA1:MTCY279 9150 Z97991 Mycobacterium tuberculosis H37Rv complete genome; segment 17/162. Mycobacterium 37,773 17-Jun-98 Ln tuberculosis GB_BAI:MSG81970C 39399 L78815 Mycobacterium leprae cosmid 81970 DNA sequence.
Mycobacterium leprae 39,024 15-Jun-96 ~ 0) S o) GB_BA2:SC2H4 25970 AL031514 Streptomyces coelicolor cosmid 2H4. Streptomyces coelicolor 37,906 19-OCT-A3(2) 1999 " - o rxa02559 1026 GB_BAI:MTV004 69350 AL009198 Mycobacterium tuberculosis H37Rv complete genome; segment 144/162. Mycobacterium 47,358 18-Jun-98 .3 tuberculosis 10 GB_PAT:128684 5100 128684 Sequence 1 from patent US 5573915. Unknown. 39,138 6-Feb-97 = 0) GB_BAI:MTU27357 5100 U27357 Mycobacterium tuberculosis cyclopropane mycolic acid synthase (cmal) Mycobacterium 39,138 26-Sep-95 gene, complete cds. tuberculosis nca02622 1683 GB_BA2:AE001780 11997 AE001780 Themiotoga maritima section 92 of 136 of the complete genome. Thermotoga maritima 44,914 2-Jun-99 GB_OV:AF064564 49254 AF064564 Fugu rubripes neurofibromatosis type 1(NF1), A-kinase anchor protein Fugu rubripes 39,732 17-Aug-99 (AKAP84), BAW protein (BAW), and WSB1 protein (WSB1) genes, complete cds.
GB_OV:AF064564 49254 AF064564 Fugu rubripes neurofibromatosis type 1(NF1), A-kinase anchor protein Fugu rubripes 36,703 17-Aug-99 (AKAP84), BAW protein (BAW), and WSB1 protein (WSB1) genes, complete cds.
rxa02623 714 GB_GSS5:AQ818728 444 AQ818728 HS_5268_A1_G09_SP6E RPCI-1 1 Human Male BAC Library Homo sapiens Homo sapiens 38,801 26-Aug-99 genomic clone Plate=844 Col=17 Row=M, genomic survey sequence.

GB_HTG5:AC011083 198586 AC011083 Homo sapiens chromosome 9 clone RP11-111M7 map 9, WORKING DRAFT Homo sapiens 35,714 19-Nov-99 SEQUENCE, 51 unordered pieces.
GB GSS6:AQ826948 544 AQ826948 HS 5014_A2_C12_T7A RPCI-11 Human Male BAC
Library Homo sapiens Homo sapiens 39,146 27-Aug=99 genomic clone Plate=590 Co1=24 Row=E, genomic survey sequence.

Table 4 (continued) rxa02629 708 GB VI:BRSMGP 462 M86652 Bovine respiratory syncytial virus membrane glycoprotein mRNA, complete Bovine respiratory syncytial 37,013 28-Apr-93 cds. virus GB_VI:BRSMGP 462 M86652 Bovine respiratory syncytial virus membrane gtycoprotein mRNA, complete Bovine respiratory syncytial 37,013 28-Apr-93 cds. virus rxa02645 1953 GB_PAT:A45577 1925 A45577 Sequence 1 from Patent W09519442.
Corynebacterium 39,130 07-MAR-glutamicum 1997 GB_PAT:A45581 1925 A45581 Sequence 5 from Patent W09519442. Corynebacterium 39,130 07-MAR-glutamicum 1997 GB BAI:CORILVA 1925 L01508 Corynebacterium glutamicum threanine dehydratase (ilvA) gene, complete Corynebacterium 39,130 26-Apr-93 cds. glutamicum rxa02646 1392 GB_BA1:CORILVA 1925 L01508 Corynebacterium glutamicum threonine dehydratase (IIvA) gene, complete Corynebacterium 99,138 26-Apr-93 cds. glutamicum GB_PAT:A45585 1925 A45585 Sequence 9 from Patent W09519442. Corynebacterium 99,066 07-MAR-glutamicum 1997 GB_PAT:A45583 1925 A45583 Sequence 7 from Patent W09519442. Corynebacterium 99,066 07-MAR-glutamicum rxa02648 1326 GBOV:ICTCNC 2049 M83111 Ictalurus punctatus cyclic nucleotide-gated channel RNA sequence. Ictalurus punctatus 38,402 24-MAY-1993 1993 u' GB_EST11:AA265464 345 AA265464 mx91cO6.r1 Soares mouse NML Mus musculus cDNA
clone IMAGE:693706 Mus musculus 38,655 20-MAR- r o 5', mRNA sequence. 1997 %D rn GB_GSS8:AQ006950 480 A0006950 CIT-HSP-2294E14.TR CIT-HSP Homo sapiens genomic clone 2294E14, Homo sapiens 36,074 27-Jun-98 genomic survey sequence.
rxa02653 -.3 rn nca02687 1068 GB_BA1:CORPHEA 108B M13774 C.glutamicum pheA gene encoding prephenate dehydratase, complete cds. Corynebacterium 99,715 26-Apr-93 glutamicum GB_PAT:E04483 948 E04483 DNA encoding prephenate dehydratase. Corynebacterium 98,523 29-Sep-97 glutamicum GB PAT:E06110 948 E06110 DNA encoding prephenate dehydratase. Corynebacterium 98,523 29-Sep-97 glutamicum rxa02717 1005 GB_PLI:HVCH4H 59748 Y14573 Hordeum vulgare DNA for chromosome 4H. Hordeum vulgare 36,593 25-MAR-GB PR2:HS310H5 29718 Z69705 Human DNA sequence from cosmid 310H5 from a contig from the tip of the Homo sapiens 36,089 22-Nov-99 short arm of chromosome 16, spanning 2Mb of 16p13.3. Contains EST and CpG island.
GB_PR3:AC004754 39188 AC004754 Homo sapiens chromosome 16, cosmid clone RT286 (LANL), complete Homo sapiens 36,089 28-MAY-sequence. 1998 rxa02754 1461 GB_HTG2:AC008223 130212 AC008223 Drosophila melanogaster chromosome 3 clone BACR16118 (D815) RPCI-98 Drosophila melanogaster 32,757 2-Aug-99 16.1.18 map 95A-95A strain y; cn bw sp, "' SEQUENCING IN
PROGRESS"', 101 unordered pieces.

Table 4(continued) GB_HTG2:AC008223 130212 AC008223 Drosophila melanogaster chromosome 3 clone BACR16I18 (D815) RPCI-98 Drosophila melanogaster 32,757 2-Aug-99 16.1.18 map 95A-95A strain y; cn bw sp, "' SEQUENCING IN PROGRESS
"=, 101 unordered pieces.
GB_BA1:MTCY71 42729 Z92771 Mycobacterium tuberculosis H37Rv complete genome;
segment 141/162. Mycobacterium 37,838 10-Feb-99 tuberculosis rxa02758 1422 GB_HTG5:AC011678 171967 AC011678 Homo sapiens clone 14_B_7, SEQUENCING IN PROGRESS 20 Homo sapiens 35,331 5-Nov-99 unordered pieces.
GB_HTG5:AC011678 171967 AC011678 Homo sapiens clone 14_B_7, SEQUENCING IN
PROGRESS 20 Homo sapiens 33,807 5-Nov-99 unordered pieces.
GB_BA2:AF064070 23183 AF064070 Burkholderia pseudomallei putative dihydroorotase (pyrC) gene, partial cds; Burkholderia pseudomallei 36,929 20-Jan-99 putative 1-acyl-sn-glycerol-3-phosphate acyftransferase (plsC), putative diadenosine tetraphosphatase (apaH), complete cds; type II 0-antigen biosynthesis gene cluster, complete sequence; putative undecaprenyl rr phosphate N-acetylglucosaminyltransferase, and putative UDP-glucose 4- p epimerase genes, complete cds; and putative galactosyl transferase gene, partial cds.
rxa02771 678 GB_BA2:AF038651 4077 AF038651 Ccrynebacterium glutamicum dipeptide-binding protein (dciAE) gene, partial Corynebacterium 99,852 14-Sep-cds; adenine phosphoribosyltransferase (apt) and GTP pyrophosphokinase glutamicum Ui (ret) genes, complete cds; and unknown gene.
GB_IN1:CELT19B4 37121 U80438 Caenorhabditis elegans cosmid T19B4.
Caenorhabditis elegans 43,836 04-DEC- 0) GB_EST36:AV193572 360 AV193572 AV193572 Yuji Kohara unpublished cDNA:Strain N2 hermaphrodite embryo Caenorhabditis elegans 48,588 22-Jul-99 Caenorhabditis elegans cDNA clone yk618h8 5', mRNA sequence. o rxa02772 1158 GBBA2:AF038651 4077 AF038651 Co nebacterium lutamicum di _ ryg peptide-binding protein (dciAE) gene, partial Corynebacterium 99,914 14-Sep-98 ~
cds; adenine ph osphoribosyftransfe rase (apt) and GTP pyrophosphokinase glutamicum o (rel) genes, complete cds: and unknown gene. o) GB_BA1:MTCY227 35946 Z77724 Mycobacterium tuberculosis H37Rv complete genome;
segment 114/162. Mycobacterium 38,339 17-Jun-98 tuberculosis GB_BA1:U00011 40429 U00011 Mycobacterium leprae cosmid B1177. Mycobacterium leprae 38,996 01-MAR-rxa02790 1266 GB_BAI:MTCY159 33818 Z83863 Mycobacterium tuberculosis H37Rv complete genome; segment 111/162. Mycobacterium 37,640 17-Jun-98 tuberculosis GB_PR4:AC006581 172931 AC006581 Homo sapiens 12p21 BAC RPCI11-259018 (Roswell Park Cancer Institute Homo sapiens 37,906 3-Jun-99 Human BAC Library) complete sequence.
GB_PR4:AC006581 172931 AC006581 Homo sapiens 12p21 BAC RPCI11-259018 (Roswell Park Cancer Institute Homo sapiens 35,280 3-Jun-99 Human BAC Library) complete sequence.
rxa02791 951 GB_BA1:MTCY159 33818 Z83863 Mycobacterium tuberculosis H37Rv complete genome; segment 111/162. Mycobacterium 39,765 17-Jun-98 tuberculosis GB_OV:CHKCEK2 3694 M35195 Chicken tyrosine kinase (cek2) mRNA, complete cds.
Gallus gallus 38,937 28-Apr-93 GB BA1:MSASDASK 5037 Z17372 M.smegmatis asd, ask-alpha, and ask-beta genes.
Mycobacterium smegmatis 38,495 9-Aug-94 nca02802 1194 GB_EST24:AI223401 169 A1223401 qg48g01.x1 Soares_testis_NHT Homo sapiens cDNA clone IMAGE:1838448 Homo sapiens 40,828 27-OCt-3' similar to INP:C25D7.8 CE08394 ;, mRNA sequence. 1998 Table 4 (continued) GB_EST24:AI223401 169 A1223401 qg48gOl.xl Soares testis_NHT Homo sapiens cDNA
clone IMAGE:1838448 Homo sapiens 40,828 27-OCT-3' similar to WP:C25D7.8 CE08394 ;, mRNA sequence. 1998 rxa02814 494 GB_BA1:MTCY7D11 22070 Z95120 Mycobacterium tuberculosis H37Rv complete gename; segment 1381162. Mycobacterium 58,418 17-Jun-98 tuberculosis GB_BAI:MTCY7011 22070 Z95120 Mycobacterium tuberculosis H37Rv complete genome;
segment 138/162. Mycobacterium 40,496 17-Jun-98 tuberculosis GB PRI:HSAJ2962 778 AJ002962 Homo sapiens mRNA for hB-FABP. Homo sapiens 39,826 8-Jan-98 rxa02843 608 GB BA1:CGAJ4934 1160 AJ004934 Corynebacterium glutamicum dapD
gene, complete COS. Corynebacterium 100,000 17-Jun-98 glutamicum GB_BAI:MTCI364 29540 Z93777 Mycobacterium tuberculosis H37Rv complete genome;
segment 52/162. Mycobacterium 37,710 17-Jun-98 tuberculosis GB_BAI:MLU15180 38675 U15180 Mycobacterium leprae cosmid 81756. Mycobacterium leprae 39,626 09-MAR-rxs03205 963 GB BA1:BLSIGBGN 2906 Z49824 B.lactofermentum orfl gene and sigB
gene. Corynebacterium glutamicur@8,854 25-Apr-96 GB EST21:AA980237 377 AA980237 ua32a12.r1 Soares_mammary _gland NbMMG Mus musculus cDNA clone Mus musculus 41,489 27-MAY-Ln IMAGE:1348414 5' similar to TR:Q61025 061025 HYPOTHETICAL 15.2 KD 1998 PROTEIN. ;, mRNA sequence. rn GB_EST23:AI158316 371 A1158316 ud27c05.r1 Soares_thymus_2NbMT Mus musculus cDNA clone Mus musculus 38,005 30-Sep-98 N
IMAGE:1447112 5', mRNA sequence.
rxs03223 1237 GB_IN1:LMFL2743 38368 AL031910 Leishmania major Friedlin chromosome 4 cosmid L2743. Leishmania major 39,869 15-DEC- - o 1999 W o GB PR3:HSDJ61 B2 119666 AL096710 Human DNA sequence from clone RP1-6182 on chromosome 6p11.2-12.3 Homo sapiens 34,930 17-DEC-_ o Contains isoforrns 1 and 3 of BPAG1 (bullous pemphigoid antigen 1 1999 = 0) (230/240kD), an exon of a gene similar to murine MACF cytoskeletal protein, STSs and GSSs, complete sequence.
GB_PR3:HSDJ61B2 119666 AL096710 Human DNA sequence from clone RP1-61B2 on chromosome 6p11.2-12.3 Homo sapiens 34,634 17-DEC-Contains isoforms 1 and 3 of BPAG1 (builous pemphigoid antigen 1 1999 (2301240kD), an exon of a gene similar to murine MACF cytoskeletal protein, STSs and GSSs, complete sequence.

Exemplification Example 1: Preparation of total genomic DNA of Corynebacterium glutamicum A culture of Corynebacterium glutamicum (ATCC 13032) was grown overnight at 30 C with vigorous shaking in BHI medium (Difco). The cells were harvested by centrifugation, the supernatant was discarded and the cells were resuspended in 5 ml buffer-I (5% of the original volume of the culture - all indicated volumes have been calculated for 100 ml of culture volume). Composition of buffer-I: 140.34 g/1 sucrose, 2.46 g/I MgSO4 x 7HZ0, 10 mi/I KHZPO, solution (100 g/l, adjusted to pH 6.7 with KOH), 50 ml/1 M12 concentrate (10 g/1(NH,)2S0,, 1 g/1 NaCl, 2 g/1 MgSO4 x 7H20, 0.2 g/l CaC1Z1 0.5 g/1 yeast extract (Difco), 10 ml/1 trace-elements-mix (200 mg/1 FeSO4 x HZO, 10 mg/1 ZnSO4 x 7 HZO, 3 mg/1 MnCIZ x 4 H20, 30 mg/1 H,BO3 20 mg/1 CoCIZ x 6 H20, I mg/I NiCIZ x 6 HZO, 3 mg/1 Na2MoO4x 2 HZO, 500 mg/1 complexing agent (EDTA or critic acid), 100 ml/1 vitamins-mix (0.2 mg/1 biotin, 0.2 mg/l folic acid, 20 mg/1 p-amino benzoic acid, 20 mg/1 riboflavin, 40 mg/I ca-panthothenate, 140 mg/1 nicotinic acid, 40 mg/1 pyridoxole hydrochloride, 200 mg/1 myo-inositol).
Lysozyme was added to the suspension to a final concentration of 2.5 mg/ml. After an approximately 4 h incubation at 37 C, the cell wall was degraded and the resulting protoplasts are harvested by centrifugation. The pellet was washed once with 5 ml buffer-I and once with 5 ml TE-buffer (10 mM Tris-HCI, l mM EDTA, pH 8). The pellet was resuspended in 4 ml TE-buffer and 0.5 ml SDS solution (10%) and 0.5 ml NaCI solution (5 M) are added. After adding of proteinase K to a final concentration of 200 g/ml, the suspension is incubated for ca. 18 h at 37 C. The DNA was purified by extraction with phenol, phenol-chloroform-isoamylalcohol and chloroform-isoamylalcohol using standard procedures. Then, the DNA was precipitated by adding 1/50 volume of 3 M sodium acetate and 2 volumes of ethanol, followed by a 30 min incubation at -20 C and a 30 min centrifugation at 12,000 rpm in a high speed centrifuge using a SS34 rotor (Sorvall). The DNA was dissolved in I ml TE-buffer containing 20 g/ml RNaseA and dialysed at 4 C against 1000 ml TE-buffer for at least 3 hours.
During this time, the buffer was exchanged 3 times. To aliquots of 0.4 ml of the dialysed DNA solution, 0.4 ml of 2 M LiCI and 0.8 ml of ethanol are added.
After a 30 min incubation at -20 C, the DNA was collected by centrifugation (13,000 rpm, Biofuge Fresco, Heraeus, Hanau, Germany). The DNA pellet was dissolved in TE-buffer.
DNA
prepared by this procedure could be used for all purposes, including southern blotting or construction of genomic libraries.
Example 2: Construction of genomic libraries in Escherichia colt of Corynebacterium glutamicum ATCC13032.
Using DNA prepared as described in Example 1, cosmid and plasmid libraries were constructed according to known and well established methods (see e.g., Sambrook, J. et al.
(1989) "Molecular Cloning : A Laboratory Manual", Cold Spring Harbor Laboratory Press, or Ausubel, F.M. et al. (1994) "Current Protocols in Molecular Biology", John Wiley &
Sons.) Any plasmid or cosmid could be used. Of particular use were the plasmids pBR322 (Sutcliffe, J.G. (1979) Proc. Natl. Acad. Sci. USA, 75:3737-3741); pACYC177 (Change &
Cohen (1978) J. Bacteriol 134:1141-1156), plasmids of the pBS series (pBSSK+, pBSSK- and others; Stratagene, LaJolla, USA), or cosmids as SuperCos 1(Stratagene, LaJolla, USA) or Lorist6 (Gibson, T.J., Rosenthal A. and Waterson, R.H. (1987) Gene 53:283-286.
Gene libraries specifically for use in C. glutamicum may be constructed using plasmid pSL 109 (Lee, H.-S. and A. J. Sinskey (1994) J. Microbiol. Biotechnol. 4: 256-263).
Example 3: DNA Sequencing and Computational Functional Analysis Genomic libraries as described in Example 2 were used for DNA sequencing according to standard methods, in particular by the chain ten=nination method using AB1377 sequencing machines (see e.g., Fleischman, R.D. et al. (1995) "Whole-genome Random Sequencing and Assembly of Haemophilus Influenzae Rd., Science, 269:496-512). Sequencing primers with the following nucleotide sequences were used: 5'-GGAAACAGTATGACCATG-3' or 5'-GTAAAACGACGGCCAGT-3'.

Example 4: In vivo Mutagenesis In vivo mutagenesis of Corynebacterium glutamicum can be performed by passage of plasmid (or other vector) DNA through E. coli or other microorganisms (e.g.
Bacillus spp. or yeasts such as Saccharomyces cerevisiae) which are impaired in their capabilities to maintain the integrity of their genetic information. Typical mutator strains have mutations in the genes for the DNA repair system (e.g., mutHLS, mutD, mutT, etc.; for reference, see Rupp, W.D.
(1996) DNA repair mechanisms, in: Escherichia coli and Salmonella, p. 2277-2294, ASM:
Washington.) Such strains are well known to those of ordinary skill in the art. The use of such strains is illustrated, for example, in Greener, A. and Callahan, M. (1994) Strategies 7: 32-34.
Example 5: DNA Transfer Between Escherichia coli and Corynebacterium glutamicum Several Corynebacterium and Brevibacterium species contain endogenous plasmids (as e.g., pHM1519 or pBL1) which replicate autonomously (for review see, e.g., Martin, J.F. et a!. (1987) Biotechnology, 5:137-146). Shuttle vectors for Escherichia coli and Corynebacterium glutamicum can be readily constructed by using standard vectors for E. coli (Sambrook, J. et al. (1989), "Molecular Cloning: A Laboratory Manual", Cold Spring Harbor Laboratory Press or Ausubel, F.M. et al. (1994) "Current Protocols in Molecular Biology", John Wiley & Sons) to which a origin or replication for and a suitable marker from Corynebacterium glutamicum is added. Such origins of replication are preferably taken from endogenous plasmids isolated from Corynebacterium and Brevibacterium species. Of particular use as transformation markers for these species are genes for kanamycin resistance (such as those derived from the Tn5 or Tn903 transposons) or chloramphenicol (Winnacker, E.L. (1987) "From Genes to Clones -Introduction to Gene Technology, VCH, Weinheim). There are numerous examples in the literature of the construction of a wide variety of shuttle vectors which replicate in both E.
coli and C. glutamicum, and which can be used for several purposes, including gene over-expression (for reference, see e.g., Yoshihama, M. et al. (1985) J. Bacteriol.
162:591-597, Martin J.F. et al. (1987) Biotechnology, 5:137-146 and Eikmanns, B.J. et al.
(1991) Gene, 102:93-98).
Using standard methods, it is possible to clone a gene of interest into one of the shuttle vectors described above and to introduce such a hybrid vectors into strains of Corynebacterium glutamicum. Transformation of C. glutamicum can be achieved by protoplast transformation (Kastsumata, R. et al. (.1984) J. Bacteriol. 1 59306-3 1 1), electroporation (Liebi, E. et al. (1989) FEMSMicrobiol. Letters, 53:399-303) and in cases where special vectors are used, also by conjugation (as described e.g. in Schafer, A et al.

(1990) J. Bacteriol. 172:1663-1666). It is also possible to transfer the shuttle vectors for C. glutamicum to E. coli by preparing plasmid DNA from C. glutamicum (using standard methods well-known in the art) and transforming it into E. coli. This transforrnation step can be performed using standard methods, but it is advantageous to use an Mcr-deficient E. coli strain, such as NM522 (Gough & Murray (1983) J. Mol. Biol. 166:1-19).
Genes may be overexpressed in C. glutamicum strains using plasmids which comprise pCGI (U.S. Patent No. 4,617,267) or fragments thereof, and optionally the gene for kanamycin resistance from TN903 (Grindley, N.D. and Joyce, C.M.
(1980) Proc. Natl. Acad. Sci. USA 77(12): 7176-7180). In addition, genes may be overexpressed in C. glutamicum strains using plasmid pSL 109 (Lee, H.-S. and A. J.
Sinskey (1994) J. Microbiol. Biotechnol. 4: 256-263).
Aside from the use of replicative plasmids, gene overexpression can also be achieved by integration into the genome. Genomic integration in C. glutamicum or other Corynebacterium or Brevibacterium species may be accomplished by well-known methods, such as homologous recombination with genomic region(s), restriction endonuclease mediated integration (REMI) (see, e.g., DE Patent 19823834), or through the use of transposons. It is also possible to modulate the activity of a gene of interest by modifying the regulatory regions (e.g., a promoter, a repressor, and/or an enhancer) by sequence modification, insertion, or deletion using site-directed methods (such as homologous recombination) or methods based on random events (such as transposon mutagenesis or REMI). Nucleic acid sequences which function as transcriptional terminators may also be inserted 3' to the coding region of one or more genes of the invention; such terminators are well-known in the art and are described, for example, in Winnacker, E.L. (1987) From Genes to Clones - Introduction to Gene Technology.
VCH:
Weinheim.

Example 6: Assessment of the Expression of the Mutant Protein Observations of the activity of a mutated protein in a transformed host cell rely on the fact that the mutant protein is expressed in a similar fashion and in a similar quantity to that of the wild-type protein. A useful method to ascertain the level of transcription of the mutant gene (an indicator of the amount of mRNA available for translation to the gene product) is to perform a Northern blot (for reference see, for example, Ausubel et al.

(1988) Current Protocols in Molecular Biology, Wiley: New York), in which a primer designed to bind to the gene of interest is labeled with a detectable tag (usually radioactive or chemiluminescent), such that when the total RNA of a culture of the organism is extracted, run on gel, transferred to a stable matrix and incubated with this probe, the binding and quantity of binding of the probe indicates the presence and also the quantity of mRNA for this gene. This information is evidence of the degree of transcription of the mutant gene. Total cellular RNA can be prepared from Corynebacterium glutamicum by several methods, all well-known in the art, such as that described in Bormann, E.R. et al.
(1992) Mol. Microbiol. 6: 317-326.
To assess the presence or relative quantity of protein translated from this mRNA, standard techniques, such as a Westem blot, may be employed (see, for example, Ausubel et al. (1988) Current Protocols in Molecular Biology, Wiley: New York). In this process, total cellular proteins are extracted, separated by gel electrophoresis, transferred to a matrix such as nitrocellulose, and incubated with a probe, such as an antibody, which specifically binds to the desired protein. This probe is generally tagged with a chemiluminescent or colorimetric label which may be readily detected. The presence and quantity of label observed indicates the presence and quantity of the desired mutant protein present in the cell.

Example 7: Growth of Genetically Modified Corynebacterium glutamicum - Media and Culture Conditions Genetically modified Corynebacteria are cultured in synthetic or natural growth media. A number of different growth media for Corynebacteria are both well-known and readily available (Lieb et al. (1989) Appl. Microbiol. Biotechnol., 32:205-2 10; von der Osten et al. (1998) Biotechnology Letters, 11:11-16; Patent DE 4,120,867;
Liebl (1992) "The Genus Corynebacterium, in: The Procaryotes, Volume II, Balows, A. et al., eds.
Springer-Verlag). These media consist of one or more carbon sources, nitrogen sources, inorganic salts, vitamins and trace elements. Preferred carbon sources are sugars, such as mono-, di-, or polysaccharides. For example, glucose, fructose, mannose, galactose, ribose, sorbose, ribulose, lactose, maltose, sucrose, raffinose, starch or cellulose serve as very good carbon sources. It is also possible to supply sugar to the media via complex compounds such as molasses or other by-products from sugar refinement. It can also be advantageous to supply mixtures of different carbon sources. Other possible carbon sources are alcohols and organic acids, such as methanol, ethanol, acetic acid or lactic acid. Nitrogen sources are usually organic or inorganic nitrogen compounds, or materials which contain these compounds. Exemplary nitrogen sources include ammonia gas or ammonia salts, such as NH4CI or (NH,)ZSO., NH4OH, nitrates, urea, amino acids or complex nitrogen sources like corn steep liquor, soy bean flour, soy bean protein, yeast extract, meat extract and others.
Inorganic salt compounds which may be included in the media include the chloride-, phosphorous- or sulfate- salts of calcium, magnesium, sodium, cobalt, molybdenum, potassium, manganese, zinc, copper and iron. Chelating compounds can be added to the medium to keep the metal ions in solution. Particularly useful chelating compounds include dihydroxyphenols, like catechol or protocatechuate, or organic acids, such as citric acid. It is typical for the media to also contain other growth factors, such as vitamins or growth promoters, examples of which include biotin, riboflavin, thiamin, folic acid, nicotinic acid, pantothenate and pyridoxin. Growth factors and salts frequently originate from complex media components such as yeast extract, molasses, corn steep liquor and others. The exact composition of the media compounds depends strongly on the immediate experiment and is individually decided for each specific case.
Information about media optimization is available in the textbook "Applied Microbiol.
Physiology, A
Practical Approach (eds. P.M. Rhodes, P.F. Stanbury, IRL Press (1997) pp. 53-73, ISBN 0 19 963577 3). It is also possible to select growth media from commercial suppliers, like standard 1(Merck) or BHI (grain heart infusion, DIFCO) or others.
All medium components are sterilized, either by heat (20 minutes at 1.5 bar and 121 C) or by sterile filtration. The components can either be sterilized together or, if necessary, separately. All media components can be present at the beginning of growth, or they can optionally be added continuously or batchwise.
Culture conditions are defined separately for each experiment. The temperature should be in a range between 15 C and 45 C. The temperature can be kept constant or can be altered during the experiment. The pH of the medium should be in the range of 5 to 8.5, preferably around 7.0, and can be maintained by the addition of buffers to the media.
An exemplary buffer for this purpose is a potassium phosphate buffer.
Synthetic buffers such as MOPS, HEPES, ACES and others can alternatively or simultaneously be used. It is also possible to maintain a constant culture pH through the addition of NaOH or NH4OH during growth. If complex medium components such as yeast extract are utilized, the necessity for additional buffers may be reduced, due to the fact that many complex compounds have high buffer capacities. If a fermentor is utilized for culturing the micro-organisms, the pH can also be controlled using gaseous anunonia.
The incubation time is usually in a range from several hours to several days.
This time is selected in order to permit the maximal amount of product to accumulate in the broth. The disclosed growth experiments can be carried out in a variety of vessels, such as microtiter plates, glass tubes, glass flasks or glass or metal fermentors of different sizes.
For screening a large number of clones, the microorganisms should be cultured in microtiter plates, glass tubes or shake flasks, either with or without baffles. Preferably 100 ml shake flasks are used, filled with 10% (by volume) of the required growth medium. The flasks should be shaken on a rotary shaker (amplitude 25 mm) using a speed-range of 100 - 300 rpm. Evaporation losses can be diminished by the maintenance of a humid atmosphere; alternatively, a mathematical correction for evaporation losses should be performed.
If genetically modified clones are tested, an unmodified control clone or a control clone containing the basic plasmid without any insert should also be tested.
The medium is inoculated to an OD600 of 0.5 - 1.5 using cells grown on agar plates, such as CM plates (10 g/I glucose, 2,5 g/1 NaCI, 2 g/1 urea, 10 g/1 polypeptone, 5 g/l yeast extract, 5 g/1 meat extract, 22 g/1 NaCI, 2 g/1 urea, 10 g/1 polypeptone, 5 g/1 yeast extract, 5 g/1 meat extract, 22 g/1 agar, pH 6.8 with 2M NaOH) that had been incubated at 30 C. Inoculation of the media is accomplished by either introduction of a saline suspension of C, glutamicum cells from CM plates or addition of a liquid preculture of this bacterium.
Example 8- In vitro Analysis of the Function of Mutant Proteins The determination of activities and kinetic parameters of enzymes is well established in the art. Experiments to determine the activity of any given altered enzyme must be tailored to the specific activity of the wild-type enzyme, which is well within the ability of one of ordinary skill in the art. Overviews about enzymes in general, as well as specific details concerning structure, kinetics, principles, methods, applications and examples for the determination of many enzyme activities may be found, for example, in the following references: Dixon, M., and Webb, E.C., (1979) Enzymes. Longmans: London; Fersht, (1985) Enzyme Structure and Mechanism.
Freeman: New York; Walsh, (1979) Enzymatic Reaction Mechanisms. Freeman: San Francisco; Price, N.C., Stevens, L. (1982) Fundamentals of Enzymology. Oxford Univ.
Press: Oxford; Boyer, P.D., ed. (1983) The Enzymes, 3'd ed. Academic Press:
New York; Bisswanger, H., (1994) Enzymkinetik, 2"d ed. VCH: Weinheim (ISBN
3527300325); Bergmeyer, H.U., Bergmeyer, J., GraBl, M., eds. (1983-1986) Methods of Enzymatic Analysis, 3rd ed., vol. I-XII, Verlag Chemie: Weinheim; and Ulimann's Encyclopedia of Industrial Chemistry (1987) vol. A9, "Enzymes". VCH: Weinheim, p.
352-363.
The activity of proteins which bind to DNA can be measured by several well-established methods, such as DNA band-shift assays (also called gel retardation assays).
The effect of such proteins on the expression of other molecules can be measured using reporter gene assays (such as that described in Kolmar, H. et al. (1995) EMBO
J. 14:
3895-3904 and references cited therein). Reporter gene test systems are well known and established for applications in both pro- and eukaryotic cells, using enzymes such as beta-galactosidase, green fluorescent protein, and several others.
The determination of activity of membrane-transport proteins can be performed according to techniques such as those described in Gennis, R.B. (1989) "Pores, Channels and Transporters", in Biomembranes, Molecular Structure and Function, Springer: Heidelberg, p. 85-137; 199-234; and 270-322.

Example 9: Analysis of Impact of Mutant Protein on the Production of the Desired Product The effect of the genetic modification in C. glutamicum on production of a desired compound (such as an amino acid) can be assessed by growing the modified microorganism under suitable conditions (such as those described above) and analyzing the medium and/or the cellular component for increased production of the desired product (i.e., an amino acid). Such analysis techniques are well known to one of ordinary skill in the art, and include spectroscopy, thin layer chromatography, staining methods of various kinds, enzymatic and microbiological methods, and analytical chromatography such as high performance liquid chromatography (see, for example, Ullman, Encyclopedia of Industrial Chemistry, vol. A2, p. 89-90 and p. 443-613, VCH:
Weinheim (1985); Fallon, A. et al., (1987) "Applications of HPLC in Biochemistry" in:
Laboratory Techniques in Biochemistry and Molecular Biology, vol. 17; Rehm et al.
(1993) Biotechnology, vol. 3, Chapter III: "Product recovery and purification", page 469-714, VCH: Weinheim; Belter, P.A. et al. (1988) Bioseparations: downstream processing for biotechnology, John Wiley and Sons; Kennedy, J.F. and Cabral, J.M.S.
(1992) Recovery processes for biological materials, John Wiley and Sons;
Shaeiwitz, J.A. and Henry, J.D. (1988) Biochemical separations, in: Ulmann's Encyclopedia of Industrial Chemistry, vol. B3, Chapter 11, page 1-27, VCH: Weinheim; and Dechow, F.J. (1989) Separation and purification techniques in biotechnology, Noyes Publications.) In addition to the measurement of the final product of fennentation, it is also possible to analyze other components of the metabolic pathways utilized for the production of the desired compound, such as intermediates and side-products, to determine the overall efficiency of production of the compound. Analysis methods include measurements of nutrient levels in the medium (e.g., sugars, hydrocarbons, nitrogen sources, phosphate, and other ions), measurements of biomass composition and growth, analysis of the production of common metabolites of biosynthetic pathways, and measurement of gasses produced during fermentation. Standard methods for these measurements are outlined in Applied Microbial Physiology, A Practical Approach, P.M. Rhodes and P.F. Stanbury, eds., IRL Press, p. 103-129; 131-163; and 165-(ISBN: 0199635773) and references cited therein.

Example 10: Purification of the Desired Product from C. glutamicum Culture Recovery of the desired product from the C. glutamicum cells or supematant of the above-described culture can be performed by various methods well known in the art.
If the desired product is not secreted from the cells, the cells can be harvested from the culture by low-speed centrifugation, the cells can be lysed by standard techniques, such as mechanical force or sonication. The cellular debris is removed by centrifugation, and the supernatant fraction containing the soluble proteins is retained for further purification of the desired compound. If the product is secreted from the C.
glutamicum cells, then the cells are removed from the culture by low-speed centrifugation, and the supernate fraction is retained for further purification.
The supernatant fraction from either purification method is subjected to chromatography with a suitable resin, in which the desired molecule is either retained on a chromatography resin while many of the impurities in the sample are not, or where the impurities are retained by the resin while the sample is not. Such chromatography steps may be repeated as necessary, using the same or different chromatography resins. One of ordinary skill in the art would be well-versed in the selection of appropriate chromatography resins and in their most efficacious application for a particular molecule to be purified. The purified product may be concentrated by filtration or ultrafiltration, and stored at a temperature at which the stability of the product is maximized.
There are a wide array of purification methods known to the art and the preceding method of purification is not meant to be limiting. Such purification techniques are described, for example, in Bailey, J.E. & Ollis, D.F.
Biochemical Engineering Fundamentals, McGraw-Hill: New York (1986).
The identity and purity of the isolated compounds may be assessed by techniques standard in the art. These include high-performance liquid chromatography (I-IPLC), spectroscopic methods, staining methods, thin layer chromatography, NIRS, enzymatic assay, or microbiologically. Such analysis methods are reviewed in: Patek et al. (1994) Appl. Environ. Microbiol. 60: 133-140; Malakhova et al. (1996) Biotekhnologiya 11: 27-32; and Schmidt et al. (1998) Bioprocess Engineer. 19: 67-70. Ulmann's Encyclopedia of Industrial Chemistry, (1996) vol. A27, VCH: Weinheim, p. 89-90, p. 521-540, p. 540-547, p. 559-566, 575-581 and p. 581-587; Michal, G. (1999) Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology, John Wiley and Sons; Fallon, A.
et al.
(1987) Applications of HPLC in Biochemistry in: Laboratory Techniques in Biochemistry and Molecular Biology, vol. 17.

Example 11: Analysis of the Gene Sequences of the Invention The comparison of sequences and determination of percent homology between two sequences are art-known techniques, and can be accomplished using a mathematical algorithm, such as the algorithm of Karlin and Altschul (1990) Proc. Natl.
Acad. Sci.
USA 87:2264-68, modified as in Karlin and Altschul (1993) Proc. Natl. Acad.
Sci. USA

90:5873-77. Such an algorithm is incorporated into the NBLAST and XBLAST
programs (version 2.0) of Altschul, et al. (1990) J. Mol. Biol. 215:403-10.
BLAST
nucleotide searches can be performed with the NBLAST program, score = 100, wordlength = 12 to obtain nucleotide sequences homologous to MP nucleic acid molecules of the invention. BLAST protein searches can be performed with the XBLAST program, score = 50, wordlength = 3 to obtain amino acid sequences homologous to MP protein molecules of the invention. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul el al., (1997) Nucleic Acids Res. 25(17):3389-3402. When utilizing BLAST and Gapped BLAST programs, one of ordinary skill in the art will know how to optimize the parameters of the program (e.g., XBLAST and NBLAST) for the specific sequence being analyzed.
Another example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Meyers and Miller ((1988) Comput. Appl. Biosci.
4: 11-17). Such an algorithm is incorporated into the ALIGN program (version 2.0) which is part of the GCG sequence alignment software package. When utilizing the ALIGN
program for comparing amino acid sequences, a PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used. Additional algorithrns for sequence analysis are known in the art, and include ADVANCE and ADAM.
described in Torelli and Robotti (1994) Comput. Appl. Biosci. 10:3-5; and FASTA, described in Pearson and Lipman (1988) P.N.A.S. 85:2444-8.
The percent homology between two amino acid sequences can also be accomplished using the GAP program in the GCG software package (available at http://www.gcg.com), using either a Blosum 62 matrix or a PAM250 matrix, and a gap weight of 12, 10, 8, 6, or 4 and a length weight of 2, 3, or 4. The percent homology between two nucleic acid sequences can be accomplished using the GAP program in the GCG software package, using standard parameters, such as a gap weight of 50 and a length weight of 3.
A comparative analysis of the gene sequences of the invention with those present in Genbank has been performed using techniques known in the art (see, e.g., Bexevanis and Ouellette, eds. (1998) Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins. John Wiley and Sons: New York). The gene sequences of the invention were compared to genes present in Genbank in a three-step process. In a first step, a BLASTN analysis (e.g., a local alignment analysis) was performed for each of the sequences of the invention against the nucleotide sequences present in Genbank, and the top 500 hits were retained for further analysis. A subsequent FASTA search (e.g., a combined local and global alignment analysis, in which limited regions of the sequences are aligned) was performed on these 500 hits. Each gene sequence of the invention was subsequently globally aligned to each of the top three FASTA hits, using the GAP
program in the GCG software package (using standard parameters). In order to obtain correct results, the length of the sequences extracted from Genbank were adjusted to the length of the query sequences by methods well-known in the art. The results of this analysis are set forth in Table 4. The resulting data is identical to that which would have been obtained had a GAP (global) analysis alone been performed on each of the genes of the invention in comparison with each of the references in Genbank, but required significantly reduced computational time as compared to such a database-wide GAP
(global) analysis. Sequences of the invention for which no alignments above the cutoff values were obtained are indicated on Table 4 by the absence of alignment information.
It will further be understood by one of ordinary skill in the art that the GAP
alignment homology percentages set forth in Table 4 under the heading "% homology (GAP)"
are listed in the European numerical format, wherein a',' represents a decimal point. For example, a value of "40,345" in this column represents "40.345%".

Example 12: Construction and Operation of DNA Microarrays The sequences of the invention may additionally be used in the construction and application of DNA microarrays (the design, methodology, and uses of DNA
arrays are well known in the art, and are described, for example, in Schena, M. et al.
(1995) Science 270: 467-470; Wodicka, L. et al. (1997) Nature Biotechnology 15: 1359-1367;
DeSaizieu, A. et al. (1998) Nature Biotechnology 16: 45-48; and DeRisi, J.L.
et al.
(1997) Science 278: 680-686).
DNA microarrays are solid or flexible supports consisting of nitrocellulose, nylon, glass, silicone, or other materials. Nucleic acid molecules may be attached to the surface in an ordered manner. After appropriate labeling, other nucleic acids or nucleic acid mixtures can be hybridized to the immobilized nucleic acid molecules, and the label may be used to monitor and measure the individual signal intensities of the hybridized molecules at defined regions. This methodology allows the simultaneous quantification of the relative or absolute amount of all or selected nucleic acids in the applied nucleic acid sample or mixture. DNA microarrays, therefore, penmit an analysis of the expression of multiple (as many as 6800 or more) nucleic acids in parallel (see, e.g., Schena, M. (1996) BioEssays 18(5): 427-431).
The sequences of the invention may be used to design oligonucleotide primers which are able to amplify defined regions of one or more C. glulamicum genes by a nucleic acid amplification reaction such as the polymerase chain reaction. The choice and design of the 5' or 3' oligonucleotide primers or of appropriate linkers allows the covalent attachment of the resulting PCR products to the surface of a support medium described above (and also described, for example, Schena, M. et al. (1995) Science 270:
467-470).
Nucleic acid microarrays may also be constructed by in situ oligonucleotide synthesis as described by Wodicka, L. et al. (1997) Nature Biotechnology 15:

1367. By photolithographic methods, precisely defined regions of the matrix are exposed to light. Protective groups which are photolabile are thereby activated and undergo nucleotide addition, whereas regions that are masked from light do not undergo any modification. Subsequent cycles of protection and light activation permit the synthesis of different oligonucleotides at defined positions. Small, defined regions of the genes of the invention may be synthesized on microarrays by solid phase oligonucleotide synthesis.
The nucleic acid molecules of the invention present in a sample or mixture of nucleotides may be hybridized to the microarrays. These nucleic acid molecules can be labeled according to standard methods. In brief, nucleic acid molecules (e.g., mRNA
molecules or DNA molecules) are labeled by the incorporation of isotopically or fluorescently labeled nucleotides, e.g., during reverse transcription or DNA
synthesis.
Hybridization of labeled nucleic acids to microarrays is described (e.g., in Schena, M. et al. (1995) supra; Wodicka, L. et al. (1997), supra; and DeSaizieu A. et al.
(1998), supra). The detection and quantification of the hybridized molecule are tailored to the specific incorporated label. Radioactive labels can be detected, for example, as described in Schena, M. et al. (1995) supra) and fluorescent labels may be detected, for example, by the method of Shalon et al. (1996) Genome Research 6: 639-645).
The application of the sequences of the invention to DNA microarray technology, as described above, permits comparative analyses of different strains of C.
glutamicum or other Corynebacteria. For example, studies of inter-strain variations based on individual transcript profiles and the identification of genes that are important for specific and/or desired strain properties such as pathogenicity, productivity and stress tolerance are facilitated by nucleic acid array methodologies. Also, comparisons of the profile of expression of genes of the invention during the course of a fermentation reaction are possible using nucleic acid array technology.

Example 13: Analysis of the Dynamics of Cellular Protein Populations (Proteomics) The genes, compositions, and methods of the invention may be applied to study the interactions and dynamics of populations of proteins, termed 'proteomics'.
Protein populations of interest include, but are not limited to, the total protein population of C.
glutamicum (e.g., in comparison with the protein populations of other organisms), those proteins which are active under specific environmental or metabolic conditions (e.g., during fermentation, at high or low temperature, or at high or low pH), or those proteins which are active during specific phases of growth and development.
Protein populations can be analyzed by various well-known techniques, such as gel electrophoresis. Cellular proteins may be obtained, for example, by lysis or extraction, and may be separated from one another using a variety of electrophoretic techniques. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) separates proteins largely on the basis of their molecular weight. Isoelectric focusing polyacrylamide gel electrophoresis (IEF-PAGE) separates proteins by their isoelectric point (which reflects not only the amino acid sequence but also posttranslational modifications of the protein). Another, more preferred method of protein analysis is the consecutive combination of both IEF-PAGE and SDS-PAGE, known as 2-D-gel electrophoresis (described, for example, in Hermann et al. (1998) Electrophoresis 19:
3217-3221; Fountoulakis et al. (1998) Electrophoresis 19: 1193-1202; Langen et al.
(1997) Electrophoresis 18: 1184-1192; Antelmann et al. (1997) Electrophoresis 18:

1451-1463). Other separation techniques may also be utilized for protein separation, such as capillary gel electrophoresis; such techniques are well known in the art.
Proteins separated by these methodologies can be visualized by standard techniques, such as by staining or labeling. Suitable stains are known in the art, and include Coomassie Bri(liant Blue, silver stain, or fluorescent dyes such as Sypro Ruby (Molecular Probes). The inclusion of radioactively labeled amino acids or other protein precursors (e.g., 35S-methionine, 35S-cysteine,14C-labelled amino acids,15N-amino acids, "N03 or "NH4+ or 13 C-labelled amino acids) in the medium of C.
glutamicum permits the labeling of proteins from these cells prior to their separation.
Similarly, fluorescent labels may be employed. These labeled proteins can be extracted, isolated and separated according to the previously described techniques.
Proteins visualized by these techniques can be further analyzed by measuring the amount of dye or label used. The amount of a given protein can be determined quantitatively using, for example, optical methods and can be compared to the amount of other proteins in the same gel or in other gels. Comparisons of proteins on gels can be made, for example, by optical comparison, by spectroscopy, by image scanning and analysis of gels, or through the use of photographic films and screens. Such techniques are well-known in the art.
To determine the identity of any given protein, direct sequencing or other standard techniques may be employed. For example, N- and/or C-terminal amino acid sequencing (such as Edman degradation) may be used, as may mass spectrometry (in particular MALDI or ESI techniques (see, e.g., Langen et al. (1997) Electrophoresis 18:
1184-1192)). The protein sequences provided herein can be used for the identification of C. glutamicum proteins by these techniques.
The information obtained by these methods can be used to compare patterns of protein presence, activity, or modification between different samples from various biological conditions (e.g., different organisms, time points of fermentation, media conditions, or different biotopes, among others). Data obtained from such experiments alone, or in combination with other techniques, can be used for various applications, such as to compare the behavior of various organisms in a given (e.g., metabolic) situation, to increase the productivity of strains which produce fine chemicals or to increase the efficiency of the production of fine chemicals.

Equivalents Those of ordinary skill in the art will recognize, or will be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following claims.

Claims

1. An isolated nucleic acid molecule comprising the nucleotide sequence of SEQ
ID
NO: 449, or a complement thereof.

2. An isolated nucleic acid molecule which encodes a polypeptide comprising the amino acid sequence of SEQ ID NO:450, or a complement thereof.

3. An isolated nucleic acid molecule which encodes a naturally occurring allelic variant of a polypeptide comprising the amino acid sequence of SEQ ID NO:450, or a complement thereof.

4. An isolated nucleic acid molecule comprising a nucleotide sequence which is at least 50% identical to the entire nucleotide sequence of SEQ ID NO:449, or a complement thereof

5. An isolated nucleic acid molecule comprising a fragment of at least 15 contiguous nucleotides of the nucleotide sequence of SEQ ID NO:449, or a complement thereof.

6. An isolated nucleic acid molecule which encodes a polypeptide comprising an amino acid sequence which is at least 50% identical to the entire amino acid sequence of SEQ ID NO:450, or a complement thereof

7 An isolated nucleic acid molecule comprising the nucleic acid molecule of any one of claims 1-6 and a nucleotide sequence encoding a heterologous polypeptide.

8. A vector comprising the nucleic acid molecule of any one of claims 1-7.

9. The vector of claim 8, which is an expression vector.

10. A host cell transfected with the expression vector of claim 9.

11. The host cell of claim 10, wherein said cell is a microorganism

12. The host cell of claim 11, wherein said cell belongs to the genus Corynebacterium or Brevibacterium.

13 The host cell of claim 10, wherein the expression of said nucleic acid molecule results in the modulation in production of a fine chemical from said cell.

14. The host cell of claim 14, wherein said fine chemical is an organic acid, a proteinogenic or nonproteinogenic amino acid, a purine or pyrimidine base, a nucleoside, a nucleotide, a lipid, a saturated or unsaturated fatty acid, a diol, a carbohydrate, an aromatic compound, a vitamin, a cofactor, a polyketide, or an enzyme.

15. A method of producing a polypeptide comprising culturing the host cell of claim in an appropriate culture medium to, thereby, produce the polypeptide.

16. An isolated polypeptide comprising the amino acid sequence of SEQ ID
NO:450.

17. An isolated polypeptide comprising a naturally occurring allelic variant of a polypeptide comprising the amino acid sequence of SEQ ID NO:450.

18. An isolated polypeptide which is encoded by a nucleic acid molecule comprising a nucleotide sequence which is at least 50% identical to the entire nucleotide sequence of SEQ ID NO:449.

19. An isolated polypeptide comprising an amino acid sequence which is at least 50%
identical to the entire amino acid sequence of SEQ ID NO:450

20. An isolated polypeptide comprising a fragment of a polypeptide comprising the amino acid sequence of SEQ ID NO.450, wherein said polypeptide fragment maintains a biological activity of the polypeptide comprising the amino sequence of SEQ ID NO:450.

21. An isolated polypeptide comprising an amino acid sequence which is encoded by a nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO:449.

22. The isolated polypeptide of any of claims 16-21, further comprising a heterologous amino acid sequence.

23. A method for producing a fine chemical, comprising culturing the cell of claim 10 such that the fine chemical is produced.

24. The method of claim 23, wherein said method further comprises the step of recovering the fine chemical from said culture.

25. The method of claim 23, wherein said cell belongs to the genus Corynebacterium or Brevibacterium.

26. The method of claim 23, wherein said cell is Corynebacterium glutamicum, Corynebacterium herculis, Corynebacterium lilium, Corynebacterium acetoacidophilum, Corynebacterium acetoglutamicum, Corynebacterium acetophilum, Corynebacterium ammoniagenes, Corynebacterium fujiokense, Corynebacterium nitrilophilus, Brevibacterium ammoniagenes, Brevibacterium butanicum, Brevibacterium divaricatum, Brevibacterium flavum, Brevibacterium healii, Brevibacterium ketoglutamicum, Brevibacterium ketosoreductum, Brevibacterium lactofermentum, Brevibacterium linens, Brevibacterium paraffinolyticum, or a strain from Table 3.

27. The method of claim 23, wherein expression of the nucleic acid molecule from said vector results in modulation of production of said fine chemical

28. The method of claim 23, wherein said fine chemical is an organic acid, a proteinogenic or nonproteinogenic amino acid, a purine or pyrimidine base, a nucleoside, a nucleotide, a lipid, a saturated or unsaturated fatty acid, a diol, a carbohydrate, an aromatic compound, a vitamin, a cofactor, a polyketide or an enzyme.

29 The method of claim 23, wherein said fine chemical is an amino acid.

30. The method of claim 29, wherein said amino acid is lysine, glutamate, glutamine, alanine, aspartate, glycine, serine, threonine, methionine, cysteine, valine, leucine, isoleucine, arginine, proline, histidine, tyrosine, phenylalanine, or tryptophan.

31. A method for producing a fine chemical, comprising culturing a cell whose genomic DNA has been altered by the introduction of the nucleic acid molecule of any one of claims 1-6.

32. A method for diagnosing the presence or activity of Corynebacterium diphtheria, comprising detecting the presence of at least one of the nucleic acid molecules of any one of claims 1-6 or the isolated polypeptide molecule of any one of claims 16-21, thereby diagnosing the presence or activity of Corynebacterium daphtheriae.

33. A host cell comprising the nucleic acid molecule of SEQ ID NO:449, wherein the nucleic acid molecule is disrupted.

34. A host cell comprising the nucleic acid molecule of SEQ ID NO:449, wherein the nucleic acid molecule comprises one or more nucleic acid modifications as compared to the sequence of SEQ ID NO:449.

35 A host cell comprising the nucleic acid molecule of SEQ ID NO:449, wherein the regulatory region of the nucleic acid molecule is modified relative to the wild-type regulatory region of the molecule.