WO2013169350A1 - Biosynthetic pathways, recombinant cells, and methods - Google Patents

Abstract

This disclosure describes, generally, recombinant cells modified to exhibit increased biosynthesis of pentanoic acid, methods of making such recombinant cells, and methods of inducing the cells to produce pentanoic acid. This disclosure also describes, generally, recombinant cells modified to exhibit increased biosynthesis of 2-methylbutyric acid, methods of making such recombinant cells, and methods of inducing the cells to produce 2-methylbutyric acid.

Description

BIOSYNTHETIC PATHWAYS, RECOMBINANT CELLS, AND METHODS

CROSS-REFERENCE TO RELATED APPLICATION

This application claims priority to U.S. Provisional Patent Application Serial No. 61/645,900, filed May 11, 2012, which is incorporated herein by reference.

SUMMARY

This disclosure describes, in one aspect, a recombinant cell modified to exhibit increased biosynthesis of pentanoic acid compared to a wild-type control. In another aspect, this disclosure describes a recombinant cell modified to exhibit increased biosynthesis of 2- methylbutyric acid compared to a wild-type control.

In each aspect, the recombinant cell can be a fungal cell or a bacterial cell. In each aspect, the recombinant cell can be photosynthetic. In each aspect, the recombinant cell can be cellulolytic.

In the aspect in which the recombinant cell exhibits increased biosynthesis of pentanoic acid, the increased biosynthesis of pentanoic acid can include an increase in conversion of L-aspartate to L-threonine compared to a wild-type control, an increase in conversion of L-threonine to 2-ketobutyrate compared to a wild-type control, an increase in 2-ketobutyrate elongation activity compared to a wild-type control, an increase in 2- ketovalerate elongation activity compared to a wild-type control, an increase in ketoacid decarboxylase activity compared to a wild-type control, an increase in ketoacid

decarboxylase selectivity toward a predetermined substrate compared to a wild-type control, or an increase in aldehyde dehydrogenase activity compared to a wild-type control.

In the aspect in which the recombinant cell exhibits increased biosynthesis of 2- methylbutyric acid, the increased biosynthesis of 2-methylbutyric acid can include an increase in conversion of L-aspartate to L-threonine compared to a wild-type control, an increase in conversion of L-threonine to 2-ketobutyrate compared to a wild-type control, an increase in conversion of 2-ketobutyrate to 2-keto-3-methylvalerate, an increase in ketoacid decarboxylase activity compared to a wild-type control, an increase in ketoacid decarboxylase selectivity toward a predetermined substrate c

control, or an increase in aldehyde dehydrogenase activity compared to a wiia-xype coniroi.

In another aspect, this disclosure describes a method that generally includes incubating a recombinant cell that exhibits increased biosynthesis of pentanoic acid in medium that includes a carbon source under conditions effective for the recombinant cell to produce pentanoic acid. In some embodiments, the carbon source can include one or more of: glucose, pyruvate, L-aspartate, L-threonine, 2-ketobutyrate, 2-ketovalerate, 2- ketocaproate, valeraldehyde, C0₂, cellulose, xylose, sucrose, arabinose, or glycerol.

In another aspect, this disclosure describes a method that generally includes incubating a recombinant cell that exhibits increased biosynthesis of 2-methylbutyric acid in medium that includes a carbon source under conditions effective for the recombinant cell to produce 2-methylbutyric acid. In some embodiments, the carbon source can include one or more of: glucose, pyruvate, L-aspartate, L-threonine, 2-ketobutyrate, 2-keto-3- methylvalerate, 2-methyl butyraldehyde, C0₂, cellulose, xylose, sucrose, arabinose, or glycerol.

In another aspect, this disclosure describes a method that generally includes introducing into a host cell a heterologous polynucleotide encoding at least one polypeptide that catalyzes conversion of a carbon source to pentanoic acid, wherein the at least one polynucleotide is operably linked to a promoter so that the modified host cell catalyzes conversion of the carbon source to pentanoic acid.

In another aspect, this disclosure describes a method that generally includes introducing into a host cell a heterologous polynucleotide encoding at least one polypeptide that catalyzes conversion of a carbon source to 2-methylbutyric acid, wherein the at least one polynucleotide is operably linked to a promoter so that the modified host cell catalyzes conversion of the carbon source to 2-methylbutyric acid.

The above summary of the present invention is not intended to describe each disclosed embodiment or every implementation of the present invention. The description that follows more particularly exemplifies illustrative embodiments. In several places throughout the application, guidance is provided through lists of examples, which examples can be used in various combinations. In each instance, the recited list serves only as a representative group and should not be interpreted as an exclusive list. BRIEF DESCRIPTION OF THE FIGURES

FIG. 1. Routes for production of 2-methylbutyric acid (2MB) and pentanoic acid

(PA). (A) Chemical process for 2-methylbutyric acid and pentanoic acid from 1-Butene and

2-Butene. (B) Metabolic pathway for synthesis of 2-methylbutyric acid from glucose. (C)

Metabolic pathway for synthesis of pentanoic acid from glucose.

FIG. 2. Synthetic operons for (A) 2-methylbutyric acid (2MB) production. (B)

Pentanoic acid (PA) production. DC, 2-ketoacid decarboxylase; DH, aldehyde

dehydrogenase.

FIG. 3. Results of fermentation experiments with different aldehyde

dehydrogenases. (A) Comparison of aldehyde dehydrogenases for 2-methylbutyric acid production. (B) Comparison of aldehyde dehydrogenases for production of pentanoic acid.

FIG. 4. Results of fermentation experiments with different ketoacid decarboxylases. (A) Comparison of ketoacid decarboxylases for 2-methylbutyric acid production. (B) Comparison of ketoacid decarboxylases for production of pentanoic acid.

FIG. 5. Results of fermentation experiments for combinations of ketoacids decarboxylases and aldehyde dehydrogenases (A) Comparison of various combinations for 2-methylbutyric acid production. (B) Comparison of various combinations for production of pentanoic acid.

DETAILED DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

In the description of exemplary embodiments that follow, certain metabolic enzymes, and the natural source of those enzymes, are specified. These are merely examples of suitable enzymes and suitable sources of the specified enzymes. Alternative enzymes with similar catalytic activities are possible, as are homologs that are obtainable from different microbial species or strains. Accordingly, the exemplary embodiments described herein should not be construed as limiting the scope of the microbes or methods that are reflected in the claims.

Pentanoic acid and 2-methylbutyric acid serve as chemical intermediates for a variety of applications such as, for example, plasticizers, lubricants, and pharmaceuticals. This disclosure describes the construction of synthetic metabolic pathways in Escherichia coli to biosynthesize these two acids: the native leucine biosynthetic pathway was modified to produce pentanoic acid; the native isoleucine biosynthetic pathway was modified to produce 2-methylbutyric acid. Various aldehyde dehydrogenases and 2-ketoacid

decarboxylases were investigated for their activities in the constructed pathways. Highest titers of 2.59 g/L for 2-methylbutyric acid and 2.58 g/L for pentanoic acid were achieved through optimal combinations of enzymes in shake flask fermentation. This work demonstrates the feasibility of renewable production of high volume aliphatic acids.

Crude oil is a major source of energy and industrial organic chemicals. However, crude oil reserves are being actively depleted making the development of sustainable routes to fuels and chemicals more attractive. To address this challenge, one can take a

biosynthetic approach involving engineering microbes to produce non-natural chemical intermediates. Production of non-natural metabolites can involve the engineering and development of synthetic metabolic pathways. In this work, biosynthetic strategies were developed for renewable production of pentanoic acid (PA) and 2-methylbutyric acid (2MB) from glucose or other suitable carbon source.

The total U.S. consumption of pentanoic acid and 2-methylbutyric acid was approximately 14,000 metric tons in 2005 (Dow. Product Safety Assessment: Isopentanoic Acid. The Dow chemical company 2008). These chemicals can serve as intermediates for a variety of applications such as plasticizers, lubricants, and pharmaceuticals. They are also used for extraction of mercaptans from hydrocarbons. Esters of pentanoic acid are gaining increased attention as pentanoic biofuels because they can be used in both gasoline and diesel with very high blend ratios (Lange et al., Angew Chem Int Edit 2010;49:4479-4483). Commercially, these chemicals are typically manufactured by oxidizing valeraldehyde and/or 2-methyl butyraldehyde, each of which may be made through a process in which a petroleum-based compound is reacted with synthesis gas (Dow. Product Safety

Assessment: Isopentanoic Acid. The Dow chemical company 2008). Since the process uses toxic intermediates like synthesis gas and non-renewable petroleum-based feedstock, a sustainable route to these chemicals is needed. Biosynthesis is presented here as a potential alternative route to these chemicals.

One advantage of engineered biosynthetic pathways is the conservation of native biosynthetic pathways between microbes. Thus, once a newly engineered biosynthetic pathway is established in one microbe, it often can be employed in other microbes. In this work, the native leucine and isoleucine biosynthetic pathways in E. coli were modified by introducing into the E. coli host cells heterologous (non-native) enzymes aldehyde dehydrogenase and/or 2-ketoacid decarboxylase. Exemplary synthetic metabolic routes to 2-methylbutyric acid and pentanoic acid are shown in FIG. IB and FIG. 1C, respectively. A common intermediate for both the pathways is 2-ketobutyrate (2KB), which is derived from threonine by biosynthetic deaminase IlvA. Overexpressing thrA, thrB, and thrC can drive the carbon flux towards threonine biosynthesis (Zhang et al., Proc Natl Acad Sci USA 2010;107:6234-6239) and, therefore, into the synthetic metabolic pathways to produce pentanoic acid and/or 2-methylbutyric acid.

For the synthesis of 2-methylbutyric acid, shown in FIG. IB, 2-ketobutyrate is driven into synthesis of 2-keto-3-methylvalerate (KMV), the penultimate precursor to 2- methylbutyric acid. The condensation of 2-ketobutyrate and pyruvate to 2-aceto-2- hydroxybutyrate (AHB) is catalyzed by IlvG and IlvM. Another two enzymes IlvC and IlvD can catalyze conversion of AHB into KMV. KMV is then decarboxylated by a ketoacid decarboxylase (DC) into 2-methyl butyraldehyde, which can be oxidized to 2- methylbutyric acid by an aldehyde dehydrogenase (DH).

For the synthesis of pentanoic acid, 2-ketobutyrate can undergo two cycles of "+1" carbon chain elongation to make 2-ketocaproate (2KC). In the native leucine biosynthetic pathway, 2-ketoiso valerate is converted to 2-ketoisocaproate through a 3 -step chain elongation cycle catalyzed by 2-isopropylmalatesynthase (LeuA), isopropyl malate isomerase complex (LeuC, LeuD) and 3-isopropylmalate dehydrogenase (LeuB). In our synthetic pathways, however, LeuA, LeuB, LeuC, and LeuD are flexible enough to similarly elongate 2-ketobutyrate to 2-ketovalerate, and then to elongate 2-ketovalerate to 2-ketocaproate (4). 2-ketocaproate can then be decarboxylated by a 2-ketoacid

decarboxylase (DC) into valeraldehyde, which can be oxidized to pentanoic acid by a dehydrogenase (DH).

Construction of metabolic pathways for biosynthesis of 2-methylbutyric acid and pentanoic acid

The biosynthetic schemes for the production of 2-methylbutyric acid (2MB) and pentanoic acid (PA) are shown in FIG. IB and FIG. 1C, respectively. All enzymes downstream of aspartate biosynthesis were overexpressed from three synthetic operons. One operon includes coding regions for ThrA, ThrB, and ThrC, each of which is involved in threonine synthesis, under control of the P_LlacOl promoter on a low copy plasmid pIPAl carrying spectinomycin resistance marker. For 2-methylbutyric acid synthesis (FIG. IB), ilvA, ilvG, ilvM, ilvC, and ilvD were cloned on a low copy plasmid with a kanamycin resistance marker to get pIPA2. Similarly, for synthesis of pentanoic acid, ilvA, leuA, leuB, leuC, and leuD were cloned on a low copy plasmid pIPA3 carrying a kanamycin resistance marker. Various aldehyde dehydrogenases and ketoacid decarboxylases were present under PilacOl promoter in the transcriptional order DC-DH (2-ketoacid decarboxylase- dehydrogenase) on high copy plasmids (pIPA4 to pIPA15, Table 2) carrying ampicillin resistance marker.

Since threonine is a common intermediate in both the pathways, a threonine overproducer E, coli strain ATCC98082 was used in the study. The strain had threonine exporter gene rhtA removed to ensure high intracellular level of threonine (Zhang et al., Proc Natl Acad Sci USA 2010;107:6234-6239) as well as the alcohol dehydrogenase yqhD gene deletion to eliminate the side reactions leading to respective alcohols. The resultant strain is referred to hereafter as the PA1 straia

The synthetic pathways shown in FIG. IB and FIG. 1C were designed to include decarboxylation of ketoacids 2-keto-3-methylvalerate (FIG. IB) and 2-ketocaproate (2KC, FIG. 1C) into their respective aldehydes, followed by oxidation of the aldehydes to carboxylic acids. Based on our previous work on producing isobutyric acid (Zhang et al., ChemSusChem 2011;4: 1068-1070), we cloned wild-type 2-ketoisovalerate decarboxylase KIVD from Lactococcus lactis (de la Plaza et al., FEMS Microbiol Lett 2004;238:367-374) and phenylacetaldehyde dehydrogenase PadA (Rodriguez-Zavala et al., Protein Sci 2006;15:1387-1396) from E. coli to check the production of our target chemicals. The PA1 strain was transformed with plasmids pIPAl, pIPA2, and pIPA4 to produce 2- methylbutyric acid. The PA1 strain was transformed with plasmids pIPAl, pIPA3, and pIPA4 to produce pentanoic acid. Shake flask fermentations were carried out using each recombinant strain. Using this approach, we produced 2.26 g/L of 2-methylbutyric acid and 2.12 g/L of pentanoic acid, demonstrating the feasibility of our biosynthetic approach.

Screening of aldehyde dehydrogenases

In order to improve production titers, the effect of choosing different aldehyde dehydrogenases was examined (FIG. 3 A and FIG. 3B). Six aldehyde dehydrogenases were selected as candidate enzymes for this study: acetaldehyde dehydrogenase AldB (Ho and Weiner, J Bacteriol 2005;187:1067-1073), 3-hydroxypropionaldehyde dehydrogenase AldH (Jo et al., Appl Microbiol Biotechnol 2008;81 :51-60), phenylacetaldehyde dehydrogenase PadA (Rodriguez-Zavala et al., Protein Sci 2006;15:1387-1396), succinate semialdehyde dehydrogenase GabD (Bartsch et al., J Bacteriol 1990;172:7035-7042), γ- aminobutyraldehyde dehydrogenase YdcW (Gruez et al., J Mol Biol 2004;343:29-41) from E. coli, and a-ketoglutaric semialdehyde dehydrogenase KDH_ba (Jo et al., Appl Microbiol Biotechnol 2008;81 :51-60) from Burkholderia ambifaria. Bacterial strains were constructed with three synthetic operons as shown in FIG. 2. All heterologous enzymes introduce into the strains were identical across the strain with the exception of the aldehyde

dehydrogenase. Wild-type KIVD was selected as the 2-ketoacid decarboxylase for each strain. Shake flask fermentations were carried out at 30°C and samples were analyzed by HPLC. The fermentations were analyzed to identify the strain— and therefore the aldehyde dehydrogenase— that produced the highest quantity of desired product.

To compare activities of various aldehyde dehydrogenases for producing 2- methylbutyric acid, the PA1 strain was transformed with plasmids pIPAl, pIPA2, and any one of pIPA4 to pIPA9. After fermentation, the highest titer of 2.51 g/L was achieved with AldH, while AldB, PadA, KDH_ba, GabD and YdcW produced 2.31 g/L, 2.26 g/L, 0.67 g/L, 0.14 g/L and 0.23 g/L, respectively (FIG. 3 A).

For production of pentanoic acid, the PA1 strain was transformed with plasmids pIPAl, pIPA3, and any one of pIPA4 to pIPA9. Κϋ¾_& was found to be most active aldehyde dehydrogenase for producing pentanoic acid (2.25 g/L), while AldH, AldB, PadA, GabD and YdcW produced 1.76 g/L, 0.42 g/L, 2.12 g/L, 0.54 g/L, and 0.22 g/L, respectively (FIG. 3B).

Screening of 2-ketoacid decarboxylases

Several metabolic byproducts such as acetate, propionic acid, butyric acid, and 3- methylbutyric acid were observed during fermentation. Wild-type ketoacid decarboxylase KIVD from Lactococcus lactis (de la Plaza et al., FEMS Microbiol Lett 2004;238:367-374) and several of its mutants were investigated for an increase in yield of target C5 acids and a reduction in byproduct formation. The single amino acid substitution mutation V461A was reported to increase the specificity of KIVD towards larger substrates. The effect of three other mutations M538A, F381L, and F542L, each in combination with the V461A mutation, was investigated. These mutations replace a bulky residue in key locations by a smaller hydrophobic residue. The effect of indolepyruvate decarboxylase (IPDC) from Salmonella typhimurium also was studied. Plasmids were constructed with different 2-ketoacid decarboxylases but all possessed the same aldehyde dehydrogenase (PadA) and other enzymes.

To compare the activities of the selected 2-ketoacid decarboxylases for 2- methylbutyric acid synthesis, the PA1 strain was transformed with pIPAl, pIPA2, and any one of the plasmids pIPAlO to pIPA13 for 2-methylbutyric acid. To compare the activities of the selected 2-ketoacid decarboxylases for pentanoic acid synthesis, the PA1 strain was transformed with pIPAl, pIPA3, and any one of the plasmids pIPAlO to pIPA13 for pentanoic acid synthesis. Shake flask fermentations showed that IPDC worked better than KIVD or any of its mutants for producing either 2-methylbutyric acid (2.5 g/L) or pentanoic acid (2.14 g/L). (FIG. 4A and FIG. 4B).

Having established that AldH and IPDC have the highest activity among all of candidate aldehyde dehydrogenases and 2-ketoacid decarboxylases for the production of 2- methylbutyric acid, they were combined together (pIPA14) to investigate if the effects are additive. In combination, 2-methylbutyric acid titer reached 2.59 g/L, only marginally higher than 2.51 g/L for AldH with WT KIVD or 2.5 g/L for PadA with IPDC (FIG. 5 A). Similarly, KDH_ba was cloned together with IPDC (pIPA15) for the production of pentanoic acid. This increased pentanoic acid titer to 2.58 g/L. In comparison, the production titer was 2.25 g/L for KDH_ba with WT KIVD or 2.14 g/L for PadA with IPDC (FIG. 5B).

Purification and characterization of enzymes

The most active ketoacid decarboxylase, IPDC, and most active aldehyde dehydrogenases, AldH and KDH_ba , were characterized for their activity on substrates involved in the constructed pathways. AldH was expressed from a His-tag plasmid and purified. IPDC and KD¾_a were available from earlier study. The kinetic parameters were measured by monitoring the NADH absorbance at 340 nm. The values for kc_at and KM are given in Table 1. Table 1. Kinetic Parameters for Enzymes

Enzyme Substrate K_M (mM) kcat (s^"1) kcat KM

IPDC 2-Keto-3 -methylvalerate 0.85 ± 0.18 4.13 ± 0.21 4.86

AldH 2-Methyl butyraldehyde 1.89 ± 0.24 3.55 ± 0.17 1.88

IPDC 2-Ketocaproate 0.63 ± 0.1 1.89 ± 0.06 3

KDH_ba Valeraldehyde 0.031 ± 8.69 ± 0.26 289.7

0.005

In vitro enzymatic assays were carried out to confirm that these enzymes indeed have good activities towards target substrates. The kinetic parameters were measured by monitoring the NADH absorbance at 340 nm. The activity of IPDC was measured using a coupled enzymatic assay method. The values for the catalytic rate constant (k_cat) and Michaelis-Menten constant (KM) are given in Table 1. The KM and k_cst of IPDC for 2-keto- 3 -methylvalerate were determined to be 0.85 mM and 4.13 s^"1, while the KM and k_cat for 2- ketocaproate were 0.63 mM and 1.89 s^"1 respectively. The specificity constants k_c K_M of IPDC for both the substrates were found to be very close. The KM and k_cat of AldH for 2- methyl butyraldehyde were found to be 1.89 mM and 3.55 s^"1. KD¾a has significantly lower KM towards valeraldehyde (0.031 mM) than smaller or branched substrates like isobutyraldehyde (34.5 mM) and isovaleraldehyde (7.62 mM) but similar A;_cat values (Xiong et al., Sci Rep 2012;2). Therefore, the specificity constant (k_cat/K ) of KDH_ba towards valeraldehyde is 1260-fold and 308-fold higher than those toward isobutyraldehyde and isovaleraldehyde.

Pentanoic acid and 2-methylbutyric acid are two valuable chemical intermediates in chemical industry. The purpose of this study was to investigate feasibility of biosynthetic approach to synthesize these chemicals. We were successful in modifying the native leucine and isoleucine biosynthetic pathways to produce these non-natural chemicals in E. coli. The heterologous enzymes involved in the pathways were overexpressed by cloning

polynucleotides that encode the enzymes into a synthetic operon. The designed pathways exemplified herein include decarboxylation of ketoacids 2-keto-3 -methylvalerate and 2- ketocaproate into respective aldehydes, followed by oxidation to carboxylic acids. In this work, we investigated these last two steps to improve production quantities. We cloned wild-type kivD and padA to investigate production of our target chemicals. We observed production levels of 2.26 g/L for 2-methylbutyric acid and 2.12 g/L for pentanoic acid from 40 g/L glucose after two days of shake flask fermentation. This confirmed the feasibility of our biosynthetic approach.

In order to improve the product titers, we then examined the effect of different aldehyde dehydrogenases on product titers in shake flask fermentation. Κϋ¾₃ was found to be the most effective aldehyde dehydrogenase among those examined for production of pentanoic acid. AldH proved most effective aldehyde dehydrogenase among those examined for 2-methylbutyric acid production.

Several byproducts such as propionic acid, butyric acid, and 3-methylbutyric acid were observed during the fermentation to produce 2-methylbutyric acid or pentanoic acid. We therefore sought to further increase production of our target products by directing biosynthesis away from these byproducts and toward 2-methylbutyric acid or pentanoic acid. Mutants of KivD were shown previously to increase the decarboxylation activity towards larger ketoacid substrates (Bartsch et al., J Bacteriol 1990;172:7035-7042). Thus, we compared KivD to several KivD mutants and IPDC for their ability to increase production of target compounds by reducing the byproducts. IPDC was most effective at directing biosynthesis away from undesired byproducts and toward the desired compounds. Thus, we were able to achieve a production titer of 2.59 g/L for 2-methylbutyric acid with IPDC- AldH and a production titer of 2.58 g/L for pentanoic acid with IPDC-KDH_ba. This production corresponds to yields of 22.1% and 16.6% of theoretical maximum (0.28 g/g of glucose and 0.38 g/g of glucose) for pentanoic acid and 2-methylbutyric acid respectively. Finally, enzymatic assays were carried out to confirm the activities of these enzymes and to find the kinetic parameters.

This work demonstrates the feasibility of renewable production of these chemicals. To the best of our knowledge, this is the earliest report of metabolic engineering for the synthesis of C5 monocarboxylic acids. This work also demonstrates the use of aerobic process for production of acids. The organisms capable of producing acids typically do so in anaerobic conditions, which also results in significant acetate production, thus reducing the yield from glucose. Use of aerobic process will allow better control and reduce the acetate levels in fermentation broths. This can be accomplished in a carefully operated stirred-tank type fermenter where oxygen is provided by passing air through the tank. Such fermenters will also able to achieve high cell densities, which can lead to greater production of the desired product compounds.

The biosynthetic strategy described herein is a promising advance towards sustainable production of such platform chemicals. Moreover, since the biosynthetic pathways described herein are modifications of the host's native amino acid biosynthetic pathways, and those native biosynthetic pathways are highly conserved across species, the biosynthetic modifications described herein may be applied to the native biosynthetic pathways of a variety of additional organisms.

Thus, in one aspect, the invention provides recombinant microbial cell modified to exhibit increased biosynthesis of pentanoic acid compared to a wild-type control. In another aspect, the invention provides a recombinant microbial cell modified to exhibit increased biosynthesis of 2-methylbutyric acid compared to a wild-type control. In some cases, the wild-type control may be unable to produce pentanoic acid or 2-methylbutyric acid and, therefore, an increase in the biosynthesis of a particular product may reflect any measurable biosynthesis of that product. In certain embodiments, an increase in the biosynthesis of pentanoic acid or 2-methylbutyric acid can include biosynthesis sufficient for a culture of the microbial cell to accumulate pentanoic acid or 2-methylbutyric acid to a predetermine concentration.

The predetermined concentration may be any predetermined concentration of the product suitable for a given application. Thus, a predetermined concentration may be, for example, a concentration of at least 0.1 g/L such as, for example, at least 0.5 g/L, at least 1.0 g/L, at least 2.0 g/L, at least 3.0 g/L, at least 4.0 g/L, at least 5.0 g/L, at least 6.0 g/L, at least 7.0 g/L, at least 8.0 g/L, at least 9.0 g/L, at least 10 g/L, at least 20 g/L, at least 50 g/L, at least 100 g/L, or at least 200 g/L.

The recombinant cell can be, or be derived from, any suitable microbe including, for example, a prokaryotic microbe or a eukaryotic microbe. As used herein, the term "or derived from" in connection with a microbe simply allows for the "host cell" to possess one or more genetic modifications before being modified to exhibit the indicated increased biosynthetic activity. Thus, the term "recombinant cell" encompasses a "host cell" that may contain nucleic acid material from more than one species before being modified to exhibit the indicated biosynthetic activity. As noted above, the leucine and isoleucine biosynthetic pathways that are the basis for our engineered biosynthetic pathways are highly conserved across species. This conservation across species means that our pathways, exemplified in an E. coli host, may be introduced into other host cell species, if desired.

In some embodiments, the host cell may be selected to possess one or more natural physiological activities. For example, the host cell may be photosynthetic (e.g.,

cyanobacteria) or may be cellulolytic (e.g., Clostridium cellulolyticum).

In some embodiments, the recombinant cell may be, or be derived from, a eukaryotic microbe such as, for example, a fungal cell. In some of these embodiments, the fungal cell may be, or be derived from, a member of the Saccharomycetaceae family such as, for example, Saccharomyces cerevisiae, Candida rugosa, or Candida albicans.

In other embodiments, the recombinant cell may be, or be derived from, a prokaryotic microbe such as, for example, a bacterium. In some of these embodiments, the bacterium may be a member of the phylum Protobacteria. Exemplary members of the phylum Protobacteria include, for example, members of the Enterobacteriaceae family (e.g., Escherichia coli) and, for example, members of the Pseudomonaceae family (e.g.,

Pseudomonas putida). In other cases, the bacterium may be a member of the phylum Firmicutes. Exemplary members of the phylum Firmicutes include, for example, members of the Bacillaceae family (e.g., Bacillus subtilis), members of the Clostridiaceae family (e.g., Clostridium cellulolyticum) and, for example, members of the Streptococcaceae family (e.g., Lactococcus lactis). In other cases, the bacterium may be a member of the phylum Cyanobacteria.

In some embodiments, the increased biosynthesis of pentanoic acid compared to a wild-type control can include an increase in elongating 2-ketobutyrate to 2-ketovalerate compared to a wild-type control, an increase in elongating 2-ketovalerate to 2-ketocaproate compared to wild-type control, increased ketoacid decarboxylase activity compared to a wild-type control, and/or increased aldehyde dehydrogenase activity compared to a wild- type control. In other embodiments, the increased biosynthesis of 2-methylbutyric acid compared to a wild-type control can include increased conversion of threonine to 2- ketobutyrate compared to a wild-type control, increased conversion of 2-ketobutyrate to 2- keto-3-methylvalerate compared to a wild-type control, increased ketoacid decarboxylase activity compared to a wild-type control, and/or increased aldehyde dehydrogenase activity compared to a wild-type control. In some cases, at least a portion of the increased ketoacid decarboxylase activity can result from modification of the ketoacid decarboxylase enzyme. For example, 2-ketoacid decarboxylase of Lactococcus lactis (or an analog) may be modified to include at least one amino acid substitution selected from: V461A, M538A, or F542L, or an analogous substitution. In some cases, the 2-ketoacid decarboxylase can be modified to include the V461A substitution (or an analogous substitution) in combination with either the M528A substitution (or an analogous substitution) or the V461A substitution (or an analogous substitution).

As used herein, the term "analog" refers to a related enzyme from the same or a different microbial source with similar enzymatic activity. As such, analogs often show significant conservation and it is a trivial matter for a person of ordinary skill in the art to identify a suitable related analog of any given enzyme. Also, it is a trivial matter for a person of ordinary skill in the art to identify an "analogous substitution" by aligning the amino acid sequence of the analog with the amino acid sequence of the reference enzyme. Thus, positional differences and/or amino acid residue differences may exist between the recited substitution and an analogous substitution despite conservation between the analog and the reference enzyme.

In some embodiments, the recombinant cell can exhibit an increase in

indolepyruvate decarboxylase (IPDC) activity. The increase in IPDC activity can result from expression of an IPDC enzyme. Exemplary IPDC enzymes include, for example, any one of the polypeptides reflected in any one of SEQ ID NO: 1-21. Thus, in some

embodiments, the recombinant cell can include a heterologous polynucleotide sequence that encodes an IPDC decarboxylase such as, for example, any one of the polypeptides reflected in any one SEQ ID NO: 1-21.

In some embodiments the recombinant cell can exhibit an increase in aldehyde dehydrogenase activity. The increase in aldehyde dehydrogenase activity can result from expression of an aldehyde dehydrogenase enzyme. Exemplary aldehyde dehydrogenase enzymes include, for example, any one of the polypeptides reflected in any one of SEQ ID NO:22-55. Thus, in some embodiments, the recombinant cell can include a heterologous polynucleotide sequence that encodes an aldehyde dehydrogenase such as, for example, any one of the polypeptides reflected in any one SEQ ID NO:22-55.

As used herein, the term "activity" with regard to particular enzyme refers to the ability of a polypeptide, regardless of its common name or native function, to catalyze the conversion of the enzyme's substrate to a product, regardless of whether the "activity" is less than, equal to, or greater than the native activity of the identified enzyme. Methods for measuring the biosynthetic activities of cells are routine and well known to those of ordinary skill in the art. In the context of a genetically-modified cell, the term "activity" refers to the ability of the genetically-modified cell to synthesize an identified product compound, regardless of whether the "activity" is less than, equal to, or greater than the native activity of a wild-type strain of the cell.

As used herein, an increase in catalytic activity of an enzyme or an increase in the biosynthetic activity of a genetically-modified cell can be quantitatively measured and described as a percentage of the activity of an appropriate wild-type control. The catalytic activity exhibited by a genetically-modified polypeptide or the biosynthetic activity of a genetically-modified cell can be, for example, at least 110%, at least 125%, at least 150%, at least 175%, at least 200% (two-fold), at least 250%, at least 300% (three-fold), at least 400% (four-fold), at least 500% (five-fold), at least 600% (six-fold), at least 700% (sevenfold), at least 800% (eight-fold), at least 900% (nine-fold), at least 1000% (10-fold), at least 2000% (20-fold), at least 3000% (30-fold), at least 4000% (40-fold), at least 5000% (50- fold), at least 6000% (60-fold), at least 7000% (70-fold), at least 8000% (80-fold), at least 9000% (90-fold), at least 10,000% (100-fold), or at least 100,000% (1000-fold) of the activity of an appropriate wild-type control.

Alternatively, an increase in catalytic activity may be expressed as an increase in k_cat such as, for example, at least a two-fold increase, at least a three-fold increase, at least a four-fold increase, at least a five-fold increase, at least a six-fold increase, at least a sevenfold increase, at least an eight-fold increase, at least a nine-fold increase, at least a 10-fold increase, at least a 15 -fold increase, or at least a 20-fold increase in the k_cat value of the enzymatic conversion.

An increase in catalytic activity also may be expressed in terms of a decrease in K_m such as, for example, at least a two-fold decrease, at least a three-fold decrease, at least a four-fold decrease, at least a five-fold decrease, at least a six-fold decrease, at least a sevenfold decrease, at least an eight-fold decrease, at least a nine-fold decrease, at least a 10-fold decrease, at least a 15-fold decrease, or at least a 20-fold decrease in the K_m value of the enzymatic conversion.

A decrease in catalytic activity of an enzyme or an increase in the biosynthetic activity of a genetically-modified cell can be quantitatively measured and described as a percentage of the catalytic activity of an appropriate wild-type control. The catalytic activity exhibited by a genetically-modified polypeptide or the biosynthetic activity of a genetically-modified cell can be, for example, no more than 95%, no more than 90%, no more than 85%, no more than 80%, no more than 75%, no more than 70%, no more than 65%, no more than 60%, no more than 55%, no more than 50%, no more than 45%, no more than 40%, no more than 35%, no more than 30%, no more than 25%, no more than 20%, no more than 15%, no more than 10%, no more than 5%, no more than 4%>, no more than 3%, no more than 2%, no more than 1% of the activity, or 0% of the activity of a suitable wild-type control.

Alternatively, a decrease in catalytic activity can be expressed as a decrease in £_cat such as, for example, at least a two-fold decrease, at least a three-fold decrease, at least a four-fold decrease, at least a five-fold decrease, at least a six-fold decrease, at least a sevenfold decrease, at least an eight-fold decrease, at least a nine-fold decrease, at least a 10-fold decrease, at least a 15-fold decrease, or at least a 20-fold decrease in the k_cst value of the enzymatic conversion.

A decrease in catalytic activity also may be expressed in terms of an increase in K_m such as, for example, an increase in K_m of at least two-fold, at least three-fold, at least fourfold, at least five-fold, at least six-fold, at least seven-fold, at least an eight-fold, at least nine-fold, at least 10-fold, at least 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least 50-fold, at least 75-fold, at least 100-fold, at least 150-fold, at least 200-fold, at least 230-fold, at least 250-fold, at least 300- fold, at least 350-fold, or at least 400-fold.

Thus, in another aspect, we describe herein methods for biosynthesis of pentanoic acid or 2-methylbutyric acid. Generally, the methods includes incubating a recombinant cell as described herein in medium that includes a carbon source under conditions effective for the recombinant cell to produce pentanoic acid or 2-methylbutyric acid. For producing pentanoic acid, the carbon source can include one or more of: glucose, pyruvate, L- aspartate, L-threonine, 2-ketobutyrate, 2-ketovalerate, 2-ketocaproate, or valeraldehyde. For producing 2-methylbutyric acid, the carbon source can include one or more of: glucose, pyruvate, L-aspartate, L-threonine, 2-ketobutyrate, 2-keto-3 -methyl valerate, or 2-methyl butyraldehyde. In addition, the carbon sources for cell growth can be C0₂, cellulose, glucose, xylose, sucrose, arabinose, glycerol, etc. as long as the related carbon assimilation pathways are introduced in the engineered microbe.

In yet another aspect, we describe herein methods for introducing a heterologous polynucleotide into cell so that the host cell exhibits an increased ability to convert a carbon source to pentanoic acid or 2-methylbutyric acid. For cells to produce pentanoic acid, the heterologous polynucleotide can encode a polypeptide operably linked to a promoter so that the modified cell catalyzes conversion of the carbon source to pentanoic acid. In some of these embodiments, the carbon source can include one or more of glucose, pyruvate, L- aspartate, L-threonine, 2-ketobutyrate, 2-ketovalerate, 2-ketocaproate, or valeraldehyde. For cells to produce 2-methyl butyraldehyde, the heterologous polynucleotide can encode a polypeptide operably linked to a promoter so that the modified cell catalyzes conversion of the carbon source to 2-methyl butyraldehyde. In some of these embodiments, the carbon source can include one or more of glucose, pyruvate, L-aspartate, L-threonine, 2- ketobutyrate, 2-keto-3 -methyl valerate, or 2-methyl butyraldehyde. The host cells for such methods can include, for example, any of the microbial species identified above with regard to the recombinant cells described herein.

As used in the preceding description, the term "and/or" means one or all of the listed elements or a combination of any two or more of the listed elements; the term "comprises" and variations thereof do not have a limiting meaning where these terms appear in the description and claims; unless otherwise specified, "a," "an," "the," and "at least one" are used interchangeably and mean one or more than one; and the recitations of numerical ranges by endpoints include all numbers subsumed within that range (e.g., 1 to 5 includes 1, 1.5, 2, 2.75, 3, 3.80, 4, 5, etc.).

In the preceding description, particular embodiments may be described in isolation for clarity. Unless otherwise expressly specified that the features of a particular

embodiment are incompatible with the features of another embodiment, certain

embodiment can include a combination of compatible features described herein in connection with one or more embodiments.

For any method disclosed herein that includes discrete steps, the steps may be conducted in any feasible order. And, as appropriate, any combination of two or more steps may be conducted simultaneously. The present invention is illustrated by the following examples. It is to be understood that the particular examples, materials, amounts, and procedures are to be interpreted broadly in accordance with the scope and spirit of the invention as set forth herein.

EXAMPLES

Example 1

Bacterial strains, reagents, media and cultivation

The E. coli strain used in this study was a threonine overproducer strain

ATCC98082 which had threonine and homoserine exporter gene rhtA knocked out to ensure high intracellular level of threonine (Zhang et al., Proc Natl Acad Sci USA

2010;107:6234-6239). The yqhD gene deletion strain was obtained from the Keio collection (Baba et al., Mol Syst Biol 2006;2:2006.0008). It was transformed with plasmid pCP20 to remove the kanamycin resistance marker. This strain was transformed with plasmids pIPAl, pIPA2 and one of the pIPA4 to pIPA15 for production of 2-methylbutyric acid. For production of pentanoic acid, it was transformed with pIPAl, pIPA3 and any one of the pIPA4 to pIPA15.

XL 1 -Blue and XLIO-Gold competent cells used for propagation of plasmids were from Stratagene (La Jolla, CA) while BL21 competent cells used for protein expression were from New England Biolabs (Ipswich, MA). All the restriction enzymes, QUICK LIGATION kit and PHUSION high-fidelity PCR kit were also from New England Biolabs.

A 2x YT rich medium (16 g/L Bacto-tryptone, 10 g/L yeast extract and 5 g/L NaCl) was used to culture the E. coli strains at 37°C and 250 rpm. Antibiotics were added as needed (100 mg/L ampicillin, 25 mg/L kanamycin and 25 mg/L spectinomycin).

Fermentation procedure and HPLC analysis

Fermentation experiments were carried out in triplicate and the data are presented as the mean values with error bars indicating the standard error. 250 \x of overnight cultures were transferred into 125 mL conical flasks containing 5 mL M9 medium supplemented with 5 g/L yeast extract, 40 g/L glucose, 10 mg/L thiamine, 100 mg/L ampicillin, 25 mg/L kanamycin and 25 mg/L spectinomycin. Protein expression was induced by adding 0.1 mM isopropyl- -D-thiogalactoside (IPTG). 0.2 g CaC0₃ was added into the flask for neutralization of acids produced. After incubation for 48 hours at 30°C and 250 rpm, samples were collected and analyzed using an Agilent 1260 Infinity HPLC containing a Aminex HPX 87H column (Bio-Rad Laboratories, Inc., Hercules, CA) equipped with a refractive-index detector. The mobile phase was 5 mM H₂S0₄ at a flow rate of 0.6 mL/minute. The column temperature was 35°C and detection temperature was 50°C.

Protein expression and purification

AldH was purified by cloning the gene into an expression plasmid encoding an N- terminal 6x His-tag to get pIPA16. This plasmid was then transformed into E. coli strain BL21. Cells were inoculated from an overnight pre-culture at 1/300 dilution and grown at 30°C in 300 ml 2x YT rich medium containing 100 μg/L ampicillin. When the OD reached 0.6, IPTG was added to induce protein expression. Cell pellets were lysed by sonication in a buffer (pH 9.0) containing 250 mM NaCl, 2 mM DTT, 5 mM imidazole and 50 mM Tris. The enzyme was purified from crude cell lysate through Ni-NTA column

chromatographyand buffer-exchanged using Amicon Ultra centrifugal filters (EMD

Millipore Corp., Billerica, MA). Storage buffer (pH 8.0) containing 50 μΜ tris buffer, 1 mM MgS0₄ and 20% glycerol was used for AldH. The 100 μΤ of concentrated protein solutions were aliquoted into PCR tubes and flash frozen at -80°C for long term storage. Protein concentration was determined by measuring UV absorbance at 280 run. Purified KDHba and IPDC were available from an earlier study (Xiong et al., Sci Rep 2012;2).

Enzymatic assay

Enzymatic assay of KDH_ba consisted of 0.5 mM NAD+ and valeraldehyde in the range of 50 μΜ to 400 μΜ in assay buffer (50 mM NaH₂P0₄, pH 8.0, lmM DTT) with a total volume of 78 μΤ. To start the reaction, 2 μΐ, of 1 μΜ KDH_ba was added and generation of NADH was monitored at 340 nm (extinction coefficient, 6.22 mM^"1 cm^"1). A similar protocol was used for AldH with 2-Methyl butyraldehyde concentrations in the range of 1 mM to 6 mM.

The activity of IPDC was measured using a coupled enzymatic assay method.

Excess of an appropriate aldehyde dehydrogenase (AldH for 2-Keto-3-methylvalerate and ΚΟ¾₃ for 2-Ketocaproate) was used to oxidize aldehyde into acid while cofactor NAD+ was reduced to NADH. The assay mixture contained 0.5 mM NAD+, 0.1 μΜ appropriate aldehyde dehydrogenase and corresponding 2-keto acid in the range of 1 mM to 8 mM in assay buffer (50 mM NaH₂P0₄, pH 6.8, 1 mM MgS04, 0.5 mM ThDP) with a total volume of 78 iL. To start the reaction, 2 μΐ, of 1 μΜ IPDC was added and generation of NADH was monitored at 340 nm. Kinetic parameters (k_cat and K ) were determined by fitting initial rate data to the Michaelis-Menten equation.

Table 2. Strains and primers used in the study

a. Zhang et al., Proc Natl Acad Sci USA 2008;105:20653-20658.

b. Zhang et al., ChemSusChem 201 1 ;4: 1068-1070.

c. Xiong et al., Sci Rep 2012;2.

The complete disclosure of all patents, patent applications, and publications, and electronically available material (including, for instance, nucleotide sequence submissions in, e.g., GenBank and RefSeq, and amino acid sequence submissions in, e.g., SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq) cited herein are incorporated by reference in their entirety. In the event that any inconsistency exists between the disclosure of the present application and the disclosure(s) of any document incorporated herein by reference, the disclosure of the present application shall govern. The foregoing detailed description and examples have been given for clarity of understanding only. No unnecessary limitations are to be understood therefrom. The invention is not limited to the exact details shown and described, for variations obvious to one skilled in the art will be included within the invention defined by the claims.

Unless otherwise indicated, all numbers expressing quantities of components, molecular weights, and so forth used in the specification and claims are to be

understood as being modified in all instances by the term "about." Accordingly, unless otherwise indicated to the contrary, the numerical parameters set forth in the

specification and claims are approximations that may vary depending upon the desired properties sought to be obtained by the present invention. At the very least, and not as an attempt to limit the doctrine of equivalents to the scope of the claims, each

numerical parameter should at least be construed in light of the number of reported significant digits and by applying ordinary rounding techniques.

Notwithstanding that the numerical ranges and parameters setting forth the broad scope of the invention are approximations, the numerical values set forth in the specific examples are reported as precisely as possible. All numerical values, however, inherently contain a range necessarily resulting from the standard deviation found in their respective testing measurements.

All headings are for the convenience of the reader and should not be used to limit the meaning of the text that follows the heading, unless so specified.

Sequence Listing Free Text

SEQ ID N0:1

SeqID: YP_004731039.1 GL340000155

Protein name: putative decarboxylase [Salmonella bongori NCTC 12419]

1 mqtpytvady lldrlagcgi dhlfgvpgdy nlqfldhvid hptlr vgca nelnaayaad 61 gyarmsgaga llttfgvgel saingiagsy aeyvpvlhiv gapcsdaqqr gelmhhtlgd 121 gdfrhfyrms qaisaasavl neqnacyeid rvlgemltah rpcyillpad vakkpaippt 181 etlmlpanka qssvetafry harqclmnsr rialladfla rrfglrpllq rwmvetpiah 241 atllmgkglf neqhpnfvgt ysagasskev rqaiedadmv icvgtrf dt ltagftqqlp 301 aertleiqpy asrigdswft lpmelavsil relclecafa psptrssgqs ipvekgaltq 361 enfwqtlqqf ikpgdiilvd qgtaafgaaa Islpdgaevl vqplwgsigy slpaafgaqt 421 acpdrrvili igdgaaqlti qemgsmlrde qapiilllnn egytveraih gaaqryndia 481 s nwtqipqa lsaaqqaecw rvtqaiqlee ilarlarpqr lslievmlpk adlpellrtv 541 tralemrngg

SEQ ID NO:2

SeqID: ZP_03365331.1 GL213583505

Protein name: putative decarboxylase [Salmonella enterica subsp. enterica serovar Typhi str. E98-0664]

1 ldhvidhptl rwvgcaneln aaytadgyar msgagalltt fgvgelsain giagsyaeyv 61 pvlhivgapc saaqqrgelm hhtlgdgdfr hfyrmsqais aasaildeqn acfeidrvlg 121 emlaarrpgy imlpadvakk taippteala Ipvheaqsgv etafryharq clmnsrrial 181 ladflagrfg lrpllqrwma etpiahatll mgkglfdeqh pnfvgtysag asskevrqai 241 edadrvicvg trf dtltag ftqqlpaert leiqpyasri getwfnlpma qavstlrelc 301 lecafapppt rsagqpvrid kgeltqesfw qtlqqclkpg diilvdqgta afgaaalslp 361 dgaevvvqpl wgsigyslpa afgaqtacpd rrviliigdg aaqltiqemg smlrdgqapv 421 illlnndgyt veraihgaaq ryndiaswnw tqippalnaa qqaecwrvtq aiqlaevler 481 larpqrlsfi evmlpkadlp ellrtvtral earngg

SEQ ID NO:3

SeqID: YP 001569550.1 GI:161502438

Protein name: hypothetical protein SARI 00479 [Salmonella enterica subsp. arizonae serovar 62:z4,z23:~ str. RSK2980]

1 mqtpytvady lldrlagcgi ghlfgvpgdy nlqfldhvid hptlrwvgca nelnaayaad

61 gyarmsgaga llttfgvgel saingiagsy aeyvpvlhiv gapcsaaqqr gelmhhtlgd

121 gdfhhfyrms qaisagsail neqnacfeid rvlgemvaar rpgyimlpad vakktaippi

181 ealtlpahet qngvetafry rarqclmnsr rialladfla rrfglrpllq rwmaetsiah

241 atllmgkglf deqhpnfvgt ysagasskav rqaiedadmv icvgtrfvdt Itagftqqlp

301 aertleiqpy asrigetwfn lpmaqavstl relclecafa ppptrpvcqp vqiekgeltq

361 enfwqtlqqy Ikpgdiilvd qgtaafgaaa lslpdgae v vqplwgsigy slpaafgaqt

421 acpdrrvili igdgaaqlti qemgsmlrdg qapiilllnn dgytveraih gaaqryndia

481 swnwtqipqa lnaaqqaecw rvtqaiqlae vlerlarpqr lsfievmlpk adlpellrtv 541 tralearngg SEQ ID NO:4

SeqID: YP_149772.1 GI:56412697

Protein name: decarboxylase [Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150]

1 mqnpytvady lldrlagcgi ghlfgvpgdy nlqfIdhvid hptlrwvgca nelnaayaad 61 gyarmsgaga llttfgvgel saingiagsy aeyvpvlhiv gapcsaaqqr gelmhhtlgd 121 gdfrhfyrms qaisaasail deqnacfeid rvlgemlaar rpgyimlpad vakktaippt 181 qaltlpvhea qsgvetafry harqclmnsr rialladfla grfglrpllq rwmaetpiah 241 atllmekglf deqhpnf gt ysagasskev rqaiedadrv icvgtrfvdt ltagftqqlp 301 aertleiqpy asrigetwfn lpmaqavstl relclecafa ppptrsagqp vridkgeltq 361 esfwqtlqqy lkpgdivlvd qgtaafgaaa lslpdgaevv vqplwgsigy slpaafgaqt 421 acpdrrvili igdgaaqlti qemgsmlrdg qapvilllnn ggytveraih gaaqryndia 481 swnwtqippa Inaaqqvecw rvaqaiqlae vlerlarpqr lsfievmlpk adlpellrtv 541 tralearngg

SEQ ID NO:5

SeqID: ZP_02654846.1 GL168229788

Protein name: indole-3-pyruvate decarboxylase [Salmonella enterica subsp. enterica serovar Kentucky str. CDC 191]

1 mqnpytvady lldrlagcgi ghlfgvpgdy nlqfldhvid hptlrwvgca nelnaayaad 61 gyarmsgaga llttfgvgel saingiagsy aeyvpvlhiv gapcsaaqqr gelmhhtlgd 121 gdfrhfyrms qaisvasail deqnacfeid rvlgemfaar rpgyimlpad vakktaippt 181 qaltlpvhea qsgvetafry harqclmnsr rialladfla grfglrpllq rwmvetpiah 241 atllmgkglf deqhpnfvgt ysagasskev rqaiedadrv icvgtrfvdt ltagftqqlp 301 aertleiqpy asrigetwfn lpmaqavstl relclecafa ppptrsagqp vridkgeltq 361 esfwqtlqqy lkpgdivlvd qgtaafgaaa lslpdgaevv vqplwgsigy slpaafgaqt 421 acpdrrvili igdgaaqlti qemgsmlrdg qapvilllnn dgytveraih gaaqryndia 481 swnwtqippa lnaaqqaecw rvtqaiqlae vlerlvrpqr lsfievmlpk adlpellrtv 541 tralearngg

SEQ ID NO:6

SeqID: ZP_03220347.1 GL204929204

Protein name: indole-3-pyruvate decarboxylase [Salmonella enterica subsp. enterica serovar Javiana str. GAJVIM04042433]

1 mqnpytvady lldrlagcgi ghlfgvpgdy nlqfldhvid hptlrwvgca nelnaayaad

61 gyarmsgaga llttfgvgel saingiagsy aeyvpvlhiv gapcsaaqqr gelmhhtlgd

121 gdfrhfyrms qaisvasail yeqnacfeid rvlgemlaar rpgyimlpad vakktaippt

181 ealalpvhea qsgvetafry harqclmnsr rialladfla grfglrpllq rwmaetpiah

241 atllmgkglf deqhpnfvgt ysagasskev rqaiedadrv icvgtrfvdt ltagftqqlp

301 aertleiqpy asrigetwfn lpmaqavstl relclecafa ppptrstgqp vridkgeltq

361 esfwqtlqqy Ikpgdiilvd qgtaafgaaa lslpdgaevv vqplwgsigy slpaafgaqt

421 acpdrrvili igdgaaqlti qemgsmlrdg qapvilllnn dgytveraih gaaqryndia

481 swnwtqippa lnaaqqaecw rvtqaiqlae vlerlarpqr lsfievmlpk adlpellrtv 541 tralearng SEQ ID NO:7

SeqID: NP_456948.1 GL16761331

Protein name: decarboxylase [Salmonella enterica subsp. enterica serovar Typhi str. CT18]

1 mqnpytvady lldrlagcgi ghlfgvpgdy nlqfldhvid hptlrwvgca nelnaaytad

61 gyarmsgaga llttfgvgel saingiagsy aeyvpvlhiv gapcsaaqqr gelmhhtlgd

121 gdfrhfyrms qaisaasail deqnacfeid rvlgemlaar rpgyimlpad vakktaippt

181 ealalpvhea qsgvetafry harqclmnsr rialladfla grfglrpllq rwmaetpiah

241 atllmgkglf deqhpnfvgt ysagasskev rqaiedadrv icvgtrfvdt ltagftqqlp

301 aertleiqpy asrigetwfn lpmaqavstl relclecafa ppptrsagqp vridkgeltq

361 esfwqtlqqc lkpgdiilvd qgtaafgaaa lslpdgae v vqplwgsigy slpaafgaqt

421 acpdrrvili igdgaaqlti qemgsmlrdg qapvilllnn dgytveraih gaaqryndia

481 swnwtqippa lnaaqqaecw rvtqaiqlae vlerlarpqr lsfievmlpk adlpellrtv

541 tralearngg

SEQ ID NO:8

SeqID: ZP 03215433.1 GL200388821

Protein name: indole-3-pyruvate decarboxylase [Salmonella enterica subsp. enterica serovar Virchow str. SL491]

1 mqnpytvady lldrlagcgi ghlfgvpgdy nlqfldhvid hptlrwvgca nelnaayaad

61 gyarmsgaga llttfgvgel saingiagsy aeyvpvlhiv gapcsaaqqr gelmhhtlgd

121 gdfrhfyrms qaisvasail deqnacfeid rvlgemlvar rpgyimlpad vakktaippt

181 qalalpvhea qsgvetafry harqclmnsr rialladfla grfglrpllq rwmaetpiah

241 atllmgkglf deqhpnfvgt ysagasskev rqaiedadrv icvgtrfvdt ltvgftqqlp

301 tertleiqpy asrigetwfn lpmaqavstl relclecafa ppptrsagqp vridkgeltq

361 esfwqtlqqy lkpgdiilvd qgtaafgaaa lslpdgak v vqplwgsigy slpaafgaqt

421 acpdrrvili igdgaaqlti qemgsmlrdg qapvilllnn dgytveraih gaaqryndia

481 swnwtqippa lnaaqqaecw rvtqaiqlae vlerlarpqr lsfievmlpk adlpellrtv 541 tralearngg

SEQ ID NO:9

SeqID: EFY11092.1 GI:322614157

Protein name: indole-3-pyruvate decarboxylase [Salmonella enterica subsp. enterica serovar Montevideo str. 315996572]

1 mqnpytvady lldrlagcgi ghlfgvpgdy nlqfldhvid hptlrwvgca nelnaayaad 61 gyarmsgtga llttfgvgel saingiagsy aeyvpvlhiv gapcsaaqqr gelmhhtlgd 121 gdfrhfyrms qaisvassil deqnacfeid rvlgemlaar rpgyimlpad vakktaippt 181 ealalpvhea qsgvetafry harqclmnsr rialladfla grfglrpllq rwmaetpiah 241 atllmgkglf deqhpnfvgt ysagasskev rqaiedadrv icvgtrfvdt ltagftqqlp 301 aertleiqpy asrigetwfn lpmaqavstl relclecafa ppptrsagqp vridkgeltq 361 esfwqtlqqy lkpgdiilvd qgtaafgaaa lslpdgaevv vqplwgsigy slpaafgaqt 421 acpdrrvili igdgaaqlti qemgsmlrdg qapvilllnn dgytveraih gaaqryndia 481 swnwtqippa lnaaqqaecw rvtqaiqlae vlerlarpqr lsfievmlpk adlpellrtv 541 tralearngg SEQ ID NO:10

SeqID: ZP_02662493.1 GL168237435

Protein name: indole-3-pyruvate decarboxylase (Indolepyruvatedecarboxylase) [Salmonella enterica subsp. enterica serovar Schwarzengrund str. SL480]

1 mqnpytvady lldrlagcgi ghlfgvpgdy nlqfldhvid hptlrwvgca nelnaayaad 61 gyarmsgtga llttfgvgel saingiagsy aeyvpvlhiv gapcsaaqqr gelmhhtlgd 121 gdfrhfyrms qaisvassil deqnacfeid rvlgemlaar rpgyimlpad vakktaippt 181 ealalpvhea qsgvetafry harqclmnsr rialladfla grfglrpllq rwmaetpiah 241 atllmgkglf deqhpnfvgt ysagasskev rqaiedadrv icvgtrfvdt ltagftqqlp 301 aertleiqpy asrigetwfn lpmaqavstl relclecafa ppptrsagqp vridkgeltq 361 esfwqtlqqy Ikpgdiilvd qgtaafgaaa lslpdgaevv vqplwgsigy slpaafgaqt 421 acpdrrvilv igdgaaqlti qemgsmlrdg qapvilllnn dgytveraih gaaqryndia 481 swnwtqippa Inaaqqaecw rvtqaiqlae vlerlarpqr lsfievmlpk adlpellrtv 541 tralearngg

SEQ ID NO:l l

SeqID: YP_217395.1 GI:62180978

Protein name: putative thiamine pyrophosphate enzyme [Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67]

1 mqnpytvady lldrlagcgi ghlfgvpgdy nlqfldhvid hptlrwvgca nelnaayaad

61 gyarmsgaga llttfgvgel saingiagsy aeyvpvlhiv gapcsaaqqr gelmhhtlgd

121 gdfrhfyrms qaisaasail deqnacfeid rvlgemlaar rpgyimlpad vakktaippt

181 qalalpvhea qsgvetafry harqclmnsr rialladfla grfglrpllq rwmaetpiah

241 atllmgkglf deqhpnfvgt ysagasskev rqaiedadrv icvgtrfvdt ltagftqqlp

301 tertleiqpy alrigetwfn lpmaqavstl relclecafa ppptrsagqp vridkgeltq

361 esfwqtlqqy Ikpgdiilvd qgtaafgaaa lslpdgaevv vqplwgsigy slpaafgaqt

421 acpdrrvili igdgaaqlti qemgsmlrdg qapvilllnn dgytveraih gaaqryndia

481 swnwtqippa Inaaqqaecw rvtqaiqlae vlerlarpqr lsfievmlpk aelpellrtv 541 tralearngg

SEQ ID NO: 12

SeqID: ZP_02829849.1 GI:168817849

Protein name: indoIe-3-pyruvate decarboxylase [Salmonella enterica subsp. enterica serovar Weltevreden str. HI N05-537]

1 mqnpytvady lldrlagcgi ghlfgvpgdy nlqfldhvid hptlrwvgca nelnaaytad

61 gyarmsgaga llttfgvgel saingiagsy aeyvpvlhiv gapcsaaqqr gelmhhtlgd

121 gdfrhfyrms qaisvasail deqnacfeid rvlgemlaar rpgyimlpad vakktaippt

181 qalalpvhea qsgvetafry harqclmnsr rialladfla grfglrpllq rwmaetpiah

241 atllmgkglf deqhpnfvgt ysagasskev rqaiedadrv icvgtrfvdt ltagftqqlp

301 aertleiqpy asrigetwfn lpmaqavstl relclecafa ppptrsagqp vridkgeltq

361 esfwqtlqqy Ikpgdiilvd qgtaafgaaa lslpdgaevv vqplwgsigy slpaafgaqt

421 acpdrrvili igdgaaqlti qemgsmlrdg qapvilllnn dgytveraih gaaqryndia

481 swnwtqippa Inaaqqaecw rvtqgiqlae vlerlarpqr lsfievmlpk adlpellrtv 541 tralearngg SEQ ID NO:13

SeqID: ZP_02683535.1 GL168261562

Protein name: indole-3-pyruvate decarboxylase [Salmonella enterica subsp. enterica serovar Hadar str. RI 05P066]

1 mqnpytvady lldrlagcgi ghlfgvpgdy nlqfldhvid hptlrwvgca nelnaayaad 61 gyarmsgaga llttfgvgel saingiagsy aeyvpvlhiv gapcsaaqqr gelmhhtlgd 121 gdfrhfyrms qaisaasail deqnacfeid rvlgemlaar rpgyimlpad vakktaippt 181 qalalpvhea qsgvetafry harqclmnsr rialladfla grfglrpllq rwmaetpiah 241 atllmgkglf deqhpnfvgt ysagasskev rqaiedadrv icvgtrfvdt Itagftqqlp 301 tertleiqpy asrigetwfn lpmaqavstl relclecafa ppptrsagqp vridkgeltq 361 esfwqtlqqy lkpgdiilvd qgtaafgaaa lslpdgak v vqplwgsigy slpaafgaqt 421 acpdrrvili igdgaaqlti qemgsmlrdg qapvilllnn dgytveraih gaaqryndia 481 swnwtqippa lnaaqqaecw rvtqaiqlae vlerlarpqr lsfievmlpk adlpellrtv 541 tralearngg

SEQ ID NO: 14

SeqID: YP_002227320.1 GI:205353519

Protein name: decarboxylase [Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91]

1 mqnpytvady lldrlagcgi ghlfgvpgdy nlqfldhvid hptlrwvgca nelnaayaad 61 gyarmsgaga llttfgvgel saingiagsy aeyvpvlhiv gapcsaaqqr gelmhhtlgd 121 gdfrhfyrms qaisaasail deqnacfeid rvlgemlaar rpgyimlpad vakktaippt 181 qalalpvhea qsgvetafry harqclmnsr rialladfla grfglrpllq rwmaetpiah 241 atllmgkglf deqhpnfvgt ysagasskev rqaiedadrv icvgtrfvdt Itagftqqlp 301 tertleiqpy asrigetwfn lpmaqavstl relclecafa ppptrsagqp vridkgeltq 361 esfwqtlqqy lkpgdiilvd qgtaafgaaa lslpdgaevv vqplwgsigy slpaafgaqt 421 acpdrrvili igdgaaqlti qemgsmlrdg qapvilllnn dgytveraih gaarryndia 481 swnwtqippa lnaaqqaecw rvtqaiqlae vlerlarpqr lsfievmlpk adlpellrtv 541 tralearngg

SEQ ID NO: 15

SeqID: YP_002636855.1 GL224583057

Protein name: decarboxylase [Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594]

1 mqnpytvady lldrlagcgi ghlfgvpgdy nlqfldhvid hptlrwvgca nelnaayaad 61 gyarmsgaga llttfgvgel saingiagsy aeyvpvlhiv gapcsaaqqr gelmhhtlgd 121 gdfrhfyrms qaisaasail deqnacfeid rvlgemlaar rpgyimlpad vakktaippt 181 qalalpvhea qsgvetafry harqclmnsr rialladfla grfglrpllq rwmaetpiah 241 atllmgkglf deqhpnfvgt ysagasskev rqaiedadrv icvgtrfvdt Itagftqqlp 301 tertleiqpy asrigetwfn lpmaqavstl relclecafa ppptrsagqp vridkgeltq 361 esfwqtlqqy lkpgdiilvd qgtaafgaaa lslpdgaevv vqplwgaigy slpaafgaqt 421 acpdrrvili igdgaaqlti qemgsmlrdg qapvilllnn dgytveraih gaaqryndia 481 swnwtqippa lnaaqqaecw rvtqaiqlae vlerlarpqr lsfievmlpk adlpellrtv 541 tralearngg SEQ ID NO:16

SeqID: ZP_04656662.1 GL238912825

Protein name: indole-3-pyruvate decarboxylase [Salmonella enterica subsp. enterica serovar Tennessee str. CDC07-0191]

1 mqnpytvady lldrlagcgi ghlfgvpgdy nlqfldhvid hptlrwvgca nelnaayaad 61 gyarmsgaga llttfgvgel saingiagsy aeyvpvlhiv gapcsaaqqr gelmhhtlgd 121 gdfrhfyrms qaisaasail deqnacfeid rvlgemfaar rpgyimlpad vakktaippt 181 qaltlpvhea qsgvetafry harqclmnsr rialladfla grfglrpllq rwmaetpiah 241 atllmgkglf deqhpnfvgt ysagasskev rqaiedadrv icvgtrfvdt Itagftqqlp 301 aertleiqpy asrigetwfn lpmaqavstl relclecafa ppptrsagqp vridkgeltq 361 esfwqtlqqy lkpgdivlvd qgtaafgaaa lslpdgaevv vqplwgsigy slpaafgaqt 421 acpdrrvili igdgaaqlti qemgsmlrdg qapvilllnn dgytveraih gaaqryndia 481 swnwtqippa Inaaqqaecw rvtqaiqlae vlerlarpqr lsfievmlpk adlpellrtv 541 tralearngg

SEQ ID NO:17

SeqID: CBW18475.1 01:301158962

Protein name: putative decarboxylase [Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344]

1 mqnpytvady lldrlagcgi ghlfgvpgdy nlqfldhvid hptlrwvgca nelnaayaad

61 gyarmsgaga llttfgvgel saingiagsy aeyvpvlhiv gapcsaaqqr gelmhhtlgd

121 gdfrhfyrms qaisaasail deqnacfeid rvlgemlaar rpgyimlpad vakktaippt

181 qalalpvhea qsgvetafry harqclmnsr rialladfla grfglrpllq rwmaetpiah

241 atllmgkglf deqhpnfvgt ysagasskev rqaiedadrv icvgtrfvdt ltarftqqlp

301 aertleiqpy asrigetwfn lpmaqavstl relclecafa ppptrsagqp vridkgeltq

361 esfwqtlqqy Ikpgdiilvd qgtaafgaaa lslpdgaevv lqplwgsigy slpaafgaqt

421 acpdrrvili igdgaaqlti qemgsmlrdg qapvilllnn dgytveraih gaaqryndia

481 swnwtqippa Inaaqqaecw rvtqaiqlae vlerlarpqr lsfievmlpk adlpellrtv 541 tralearngg

SEQ ID NO: 18

SeqID: YP 002147363.1 GL197247765

Protein name: indole-3-pyruvate decarboxylase [Salmonella enterica subsp. enterica serovar Agona str. SL483]

1 mqnpytvady lldrlagcgi ghlfgvpgdy nlqfldhvid hptlrwvgca nelnaayaad 61 gyarmsgaga llttfgvgel saingiagsy aeyvpvlhiv gapcsaaqqr gelmhhtlgd 121 gdfrhfyrms qaisaasail deqnacfeid rvlgemlaar rpgyimlpad vakktaippt 181 qalalpvhea qsgvetafry harqclmnsr rialladfla grfglrpllq rwmaetpiah 241 atllmgkglf deqhpnfvgt ysagasskev rqaiedadrv icvgtrfvdt Itagftqqlp 301 aertleiqpy asrigetwfn lpmaqavstl relclecafa ppptrsagqp vridkgeltq 361 esfwqtlqqy lkpgdivlvd qgtaafgaaa lslpdgaevv vqplwgsigy slpaafgaqt 421 acpdrrvili igdgaaqlti qemgsmlrdg qapvilllnn dgytveraih gaaqryndia 481 swnwtqippa Inaaqqaecw rvtqaiqlae vlerlarpqr lsfievmlpk adlpellrtv 541 tralearngg SEQ ID NO:19

SeqID: ZP_02667483.1 GI:168242551

Protein name: indole-3-pyruvate decarboxylase [Salmonella enterica subsp. enterica serovar Heidelberg str. SL486]

1 mqnpytvady lldrlagcgi ghlfgvpgdy nlqfldhvid hptlrwvgca nelnaayaad

61 gyarmsgaga llttfgvgel saingiagsy aeyvpvlhiv gapcsaaqqr gelmhhtlgd

121 gdfrhfyrms qaisaasail deqnacfeid rvlgemlaar rpgyimlpad vakktaippt

181 qalalpvhea qsgvetafry harqclmnsr rialladfla grfglrpllq rwmaetpiah

241 atllmgkglf deqhpnfvgt ysagasskev rqaiedadrv icvgtrfvdt ltagftqqlp

301 tertleiqpy asrxgetwfn Ipmaqavstl relclecafa ppptrsagqp vridkgeltq

361 esfwqtlqqy lkpgdiilvd qgtaafgaaa lslpdgaevv vqplwgsigy slpaafgaqt

421 acpdrrvili igdgaaqlti qemgsmlrdg qapvilllnn dgytveraih gaaqryndia

481 swnwtqippa lnaaqqaecw rvtqaiqlae vlerlarpqr lsfievmlpk adlpellrtv 541 tralearngg

SEQ ID NO:20

SeqID: YP_001586815.1 GL161612850

Protein name: hypothetical protein SPAB 00555 [Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7]

1 mqnpytvady lldrlagcgi ghlfgvpgdy nlqfldhvid hptlrwvgca nelnaayaad 61 gyarmsgaga llttfgvgel saingiagsy aeyvpvlhiv gapcsaaqqr gelmhhtlgd 121 gdfrhfyrms qaisaasail deqnacfeid rvlgemlaar rpgyimlpad vakktaippt 181 qalalpvhea qsgvetafry harqclmnsr rialladfla grfglrpllq rwmaetpiah 241 atllmgkglf deqhpnfvgt ysagasskev rqaiedadrv icvgtrfvdt ltagftqqlp 301 aertlexqpy asrxgetwfn Ipmaqavstl relclecafa ppptrsagqp vridkgeltq 361 esfwqtlqqy lkpgdiilvd qgtaafgaaa lslpdgaevv vqplwgsigy slpaafgaqt 421 acpdrrvili igdgaaqlti qemgsmlrdg qapvilllnn dgytveraih gaaqryndia 481 swnwtqippa lnaaqqaecw rvtqaiqlae vlerlarpqr lsfievmlpk adlpellrtv 541 tralearngg

SEQ ID NO:21

SeqID: NP_461346.1 GI: 16765731

Protein name: indolepyruvate decarboxylase [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]

1 mqnpytvady lldrlagcgi ghlfgvpgdy nlqfldhvid hptlrwvgca nelnaayaad

61 gyarmsgaga llttfgvgel saingiagsy aeyvpvlhiv gapcsaaqqr gelmhhtlgd

121 gdfrhfyrms qaisaasail deqnacfeid rvlgemlaar rpgyimlpad vakktaippt

181 qalalpvhea qsgvetafry harqclmnsr rialladfla grfglrpllq rwmaetpiah

241 atllmgkglf deqhpnfvgt ysagasskev rqaiedadrv icvgtrfvdt ltagftqqlp

301 aertlexqpy asrxgetwfn Ipmaqavstl relclecafa ppptrsagqp vridkgeltq

361 esfwqtlqqy lkpgdiilvd qgtaafgaaa lslpdgaevv lqplwgsigy slpaafgaqt

421 acpdrrvili igdgaaqlti qemgsmlrdg qapvilllnn dgytveraih gaaqryndia

481 swnwtqippa lnaaqqaecw rvtqaiqlae vlerlarpqr lsfievmlpk adlpellrtv 541 tralearngg SEQ ID NO:22

SeqID: YP_004156811.1 GI:319795171

Protein name: aldehyde dehydrogenase [Variovorax paradoxus EPS]

1 mtatytdtrl lidnewvdat ggktldvvnp atgkvigkva hasiadldra laaaqrgfdk 61 wrntpanera avmrraagli reragdiakl Itqeqgkpla eakgetlaaa diiewfadeg 121 rrvygrivps rnlaaqqlvl keplgpvaaf tpwnfpinqi vrklgaalat gcsflvkape 181 etpaspaall qafvdagipp gtvglvfgnp aeisnyliah piirkvtftg stpvgkqlaa 241 lagshmkrvt melgghapvi vaedadvala vkaagaakfr nagqvcispt rflvhnslre 301 efartlvkyt eglklgdgla egttigplan arrltamayv ledarkkgat vaaggervgd 361 sgnffaptvl tdvpldadvf nnepfgpiaa irgfdtleea iaeanrlpfg lagyaftksi 421 ksahllsqkl elgmlwinqp atpspempfg gvkdsgygse ggpealeayl ntkavsilgv

SEQ ID NO:23

SeqID: YP_002945800.1 GL239816890

Protein name: aldehyde dehydrogenase (NAD(+)) [Variovorax paradoxus S110]

1 mtatytdtrl lidnewvdat ggktldvvnp atgkaigkva hasiadldra laaaqrgfek 61 wrntpanera avmrraagli rerapeiakl Itqeqgkpla eakgetlaaa diiewfadeg 121 rrvygrivps rnlaaqqlvi keplgpvaaf tpwnfpinqi vrklgaalat gcsflvkape 181 etpaspaall qafvdagipp gtvglvfgnp aeisnylish piirkvtftg stpvgkqlaa 241 lagshmkrvt melgghapvi vaedadvala vkaagaakfr nagqvcispt rfIvhnslre 301 efartlvkyt eglklgdgla egttigplan arrltamahv lddarkkgat vaaggervgd 361 tgnffaptvl tdvpldadvf nnepfgpiaa irgfdtleea iaeanrlpfg lagyaftrsi 421 knahllsqkl elgmlwinqp aapspempfg gvkdsgygse ggpealeayl ntkavsimsv

SEQ ID NO:24

SeqID: ZP 03268788.1 GI:209520010

Protein name: Aldehyde Dehydrogenase [Burkholderia sp. H160]

1 maissytdtr llingewcda vsgktldvin patgqaigkv ahagiadldr aldaaqrgfe 61 awrkvpaher atimrkaaal vreraadigr lmtqeqgkpf aearvevlaa adiiewfade 121 grrvygrivp srnlaahsqv lkepigpvaa ftpwnfpvnq vvrklsasla cgcsflvkap 181 eetpaspaal lqaf eagvp pgtvglvfgd paeissylip hpvirkvtft gstpvgkqla 241 alagthmkra tmelgghapv ivaedadval avkaagaakf rnagqvcisp trflvhnsir 301 eefaaalvkh aeslklgdgl aegttlgpla narrlsamak vvedarktga kvatggervg 361 segnffaatv ltdvpleadv fnnepfgpva airgfdtlde aiteanrlpy glagyaytks 421 fanvhqlsqr mevgmlwinq patptpempf ggvkdsgygs eggpeameay lvtkavtima 481 v

SEQ ID NO:25

SeqID: YP_004022361.1 GI:312602516

Protein name: 6-oxohexanoate dehydrogenase [Burkholderia rhizoxinica HKI 454]

1 mvtssytdtr llidgqwcda asgktld vn patgqvigrv ahagiadldr alaaaqrgfd 61 twrkvpvher aatmrkaatl vreraegiar lmtqeqgkpf aearievlsa adiiewfade 121 grrvygrivp srnlavqqsv lkepigpvaa ftpwnfpvnq vvrklsaala cgcsflvkap 181 eetpaspagl lqafvdagvp agtiglvfgd paaissylia hpvirkvtft gstpvgkqla

241 alagahmkra tmelgghapv ivaedadial aikaaggakf rnagqvcisp trflvhnsir

301 eafeaalvkh aqglklgdgl aqgttlgpla narrltamtr ivenaratga tvatggervg

361 sagnffaptv ltnvprdadv fnqepfgpva avrgfdrled aiaeanrlpy glagyaftrs

421 vrnvhllshq levgmlwinq patpwpempf ggvkdsgygs eggpeameay lvtkavsvaa

481 v

SEQ ID NO:26

SeqID: YP_003605215.1 GL295676691

Protein name: Aldehyde Dehydrogenase [Burkholderia sp. CCGE1002]

1 maissytdtr llingewcda asgktldvin patgqaigkv ahagipdldr aleaaqrgfe 61 awrkvpaner atimrkaaal vrerasdigr lmtqeqgkpf aearvevlaa adiiewfade 121 grrvygrivp srnlaaqsqv lkepigpvaa ftpwnfpvnq vvrklsasla cgcsflvkap 181 eetpaspaal lqafveagvp pgtvglvfgd paeissylip hpvirkvtft gstpvgkqla 241 alagshmkra tmelgghapv ivaedadval avkaagaakf rnagqvcisp trflvhnsir 301 eefaaalvkh aeslklgdgl aegttlgpla narrlsamar vvddarktga kvatggervg 361 tegnffaatv ltdvpleadv fnnepfgpva airgfdklee aiaeanrlpy glagyaytks 421 fanvhllsqr mevgmlwinq patptpempf ggvkdsgygs eggpeameay lvtkavtvms 481 v

SEQ ID NO:27

SeqID: YP 558960.1 GI:91783754

Protein name: 2,5-dioxopentanoate dehydrogenase (NAD+) [Burkholderia xenovorans LB400]

1 maipsytdtr llingewcda asgktldvin patgqaigkv ahagiadldr alaaaqrgfe 61 awrkvpaner attmrraaal vrerasdigr lmtqeqgkpf aearievlaa adiiewfade 121 grrvygrivp srnlaaqqlv lkepigpvaa ftpwnfpvnq vvrklsaala cgcsflvkap 181 eetpaspaal lqafveagvp agtvglvfgd paeisgylip hpvirkvtft gstpvgkqla 241 alagahmkra tmelgghapv ivaedadval avkaaggakf rnagqvcisp trflvhnsir 301 eefaaalvkh aeglklgdgl aegttlgpla narrlsamsk vlddarktga kvetggervg 361 segnffaptv ltnvsleadv fnnepfgpia airgfdklee aiaeanrlpy glagyaftks 421 fsnvhllsqq vevgmlwinq patpspempf ggvkdsgygs eggpeamegy lvtkavsvma 481 v

SEQ ID NO:28

SeqID: ZP 06846085.1 GL296163325

Protein name: Aldehyde Dehydrogenase [Burkholderia sp. Chl-1]

1 maissytdtr llingewcda asgktldvvn patgqaigkv ahagiadldr alaaaqrgfe 61 awrkvpaner attmrraaal vrerasdigr lmtqeqgkpf aearvevlaa adiiewfade 121 grrvygrivp srnlaaqqlv lkepigpvaa ftpwnfpvnq vvrklsaala cgcsflvkap 181 eetpaspaal lqafveagvp agtvglvfgd paeissylip hpvirkvtft gstpvgkqla 241 alagahmkra tmelgghapv ivaedadval avkaaggakf rnagqvcisp trflvhnsir 301 eefaaalvkh aeglklgdgl aegttlgpla narrltamsk vlddarktga kvetggervg 361 segnffaptv ltnvsleadv fnnepfgpia airgfdklee aiaeanrlpy glagyaftks 421 fsnvhllsqq levgmlwinq patpspempf ggvkdsgygs eggpeamegy lvtkavsvma 481 v SEQ ID NO:29

SeqID: YP_001895827.1 GI: 187924185

Protein name: aldehyde dehydrogenase [Burkholderia phytofirmans PsJN]

1 matssytdtr llingewcda asgktldvin patgkaigkv ahagiadldr alaaaqrgfe 61 awrkvpaner attmrkaaal vrerasdigr Imtleqgkpf aearievlaa adiiewfade 121 grrvygrivp srnlaaqqlv lkepigpvaa ftpwnfpvnq vvrklsaala cgcsflvkap 181 eetpaspaal lqafveagvp agtvglvfgd paeissylip hpvirkvtft gstpvgkqla 241 alagshmkra tmelgghapv xvaedadval avkaaggakf rnagqvcisp trflvhnsir 301 eefaaalvkh aeglklgdgl aegttlgpla narrltamsk vlddarktga kvetggervg 361 segnffaptv ltnvslesdv fnnepfgpia airgfdklee aiaeanrlpf glagyaftks 421 ftnvhllsqq levgmlwinq patpspempf ggvkdsgygs eggpeamegy lvtkavsvms 481 v

SEQ ID NO:30

SeqID: YP_003907074.1 GL307729850

Protein name: aldehyde dehydrogenase [Burkholderia sp. CCGE1003]

1 maissytdtr llingewcda asgktidvln patgqvigtv ahagiadldr aleaaqrgfe 61 awrkvpaher aavmrkaaal vrerasdigr lmtqeqgkpf aeakievlaa adiiewfade 121 grrlygrvvp srnlaaqqlv lkepigpvaa ftpwnfpvnq ivrklsaala sgcsflvkap 181 eetpaspagl lqafveagvp agtvglvfgd paeisgylip hpvirkvtft gstpvgkqla 241 alagahmkra tmelgghapv ivaddadval avkaaggakf rnagqvcisp trflvhnsir 301 eefaaalvkh aeslklgdgl aegttlgpla narrltamsk vledarktga kvetggervg 361 segnffaptv ltnvsleadv fnnepfgpia airgfdklee aiaeanrlpf glagyaftks 421 fsnvhllsqq levgmlwinq patptpempf ggvkdsgygs eggpeameay lvtkavtvms 481 s

SEQ ID NO:31

SeqID: ZP_02887443.1 GI:170696312

Protein name: Aldehyde Dehydrogenase [Burkholderia graminis C4D1M]

1 maissytdtr llingewcda asgktidvln patgqvigkv ahagiadldr aleaaqrgfe 61 awrkvpaher aavmrkaaal vrerasdigr lmtqeqgkpf aeakvevlaa adiiewfade 121 grrlygrvvp srnlaaqqlv lkepigpvaa ftpwnfpvnq ivrklsaala sgcsflvkap 181 eetpaspagl lqafveagvp agtvglvfgd paeisnylip hpvirkvtft gstpvgkqla 241 slagahmkra tmelgghapv xvaedadval avkaaggakf rnagqvcisp trflvhnsir 301 eefaaalvkh aeglklgdgl adgttlgpla narrltamsk vlddarrtga kietggervg 361 tegnffaptv ltnvsleadv fnnepfgpia airgfdklee aiaeanrlpf glagyaftks 421 fanvhllsqq levgmlwinq patptpempf ggvkdsgygs eggpeameay lvtkavtvms 481 s

SEQ ID NO:32

SeqID: YP_001861563.1 GI: 186474221

Protein name: aldehyde dehydrogenase [Burkholderia phymatum STM815] 1 mvtsssytdt rllinnewcd aasgktldvv npatgkpigk vahagkadld raleaaqkgf 61 eawrkvpane rattmrkaag fvreradhia rlmtqeqgkp faearievls aadiiewfad 121 egrrvygr v psrnlnaqsl vikepigpva aftpwnfpvn qvvrklsaal asgcsflvka 181 peetpaspaq llqafvdagv pagtvglvfg dpaeissyli phpvirkvtf tgstpvgkql 241 aalagshmkr atmelgghap vivaedadva lavkaaggak frnagqvcis ptrflvhnsi 301 reafaaalvk haeglkvgdg laegtqlgpl anarrltama siidnarstg atvatggeri 361 gsegnffapt vltdvplead vfnnepfgpi aairgfdnxe daiaeanrlp fglagyaftk 421 sfrnvhllsq nlevgmlwxn qpatptpemp fggvkdsgyg seggpeamea ylvtkavtvm 481 av

SEQ ID NO:33

SeqID: YP 004228054.1 GI:323525901

Protein name: aldehyde dehydrogenase [Burkholderia sp. CCGEIOOI]

1 maissytdtr llingewcda asgktidvln patgqvigkv ahagiadldr aleaaqrgfe 61 awrkvpaher aavmrkaaal vrerasdigr lmtqeqgkpf aeakievlaa adiiewfade 121 grrlygrvvp srnlaaqqlv lkepigpvaa ftpwnfpvnq ivrklsaala sgcsflvkap 181 eetpaspagl lqafveagvp agtvglvfgd paeissylip hpvirkvtft gstpvgkqla 241 alagahmkra tmelgghapv ivaedadval avkaaggakf rnagqvcisp trflvhnsir 301 eefaaalvkh aeslklgdgl aegttlgpla narrltamsk vlddarktga kietggervg 361 segnffaptv ltnvsleadv fnnepfgpia airgfdklee aiaeanrlpf glagyaftks 421 fsnvhllsqq levgmlwinq patptpempf ggvkdsgygs eggpeameay lvtkavtvms 481

SEQ ID NO:34

SeqID: YP_004361425.1 GL330817720

Protein name: NAD-dependent aldehyde dehydrogenase [Burkholderia gladioli BSR3]

1 mtnttytdtq llingewcda esgktidvln patgkvigkv ahagiadldr aleaaqrgfe

61 twrkvtaydr aalmrkaaal vreradtiaq lmtqeqgkpl veakievlsa adiiewfade

121 grrvygrivp prnlavqqtv vkepvgpvaa ftpwnfpvnq vvrklsaala tgcsflvkap

181 eetpaspaql lrafvdagvp agvvglvygd paeisnylip hpvirkvtft gstpvgkqla

241 alagqhmkra tmelgghapv ivaedadldl avkaaggakf rnagqvcisp trflvhnsvr

301 edfakalvkh aeglkvgdgl algtnlgpla nsrrlgamek vvadarktga tvatggerig

361 segnffaptv ltdvpleadv fnnepfgpia airgfdsled aiteanrlpy glagyaftra

421 fknvhlltqr levgmlwinq patpwpempf ggvkdsgygs eggpealepy lvtksvtvta 481 a

SEQ ID NO:35

SeqID: YP_002912305.1 GI:238028074

Protein name: NAD-dependent aldehyde dehydrogenase [Burkholderia glumae BGR1]

1 mtntnytdtq llingewcda asgktldvvn patgqvigkv ahagiadldr aldaaqrgfe 61 twrkvsayer salmrkaaal vreransiaq lmtleqgkpl aearievlsa adiiewfade 121 grrvygrivp prnlavqqtv vkepvgpvaa ftpwnfpvnq vvrklsaala tgcsflvkap 181 eetpaspaql lrafvdagvp agvvglvygd paeisnylip hpvirkitft gstpvgkqla 241 alagqhmkra tmelgghapv ivaedadlel avkaaggakf rnagqvcisp trflvhnsvr 301 eafvkalvkh aeglkvgdgl eagtslgpla nprrltamek vvadarkaga tvatggerig 361 sagnffaptv ladvpldadv fnnepfgpva avrgfdsldd aiteanrlpy glagyaftrs 421 fknvhlltqr vevgmlwinq patpwpempf ggvkdsgygs eggpealepy lvtksvtvaa 481 v

SEQ ID NO:36

SeqID: ZP_04941711.1 GL254248391

Protein name: Succinate-semialdehyde dehydrogenase (NAD(P)+) [Burkholderia cenocepacia PC184]

1 mnpatgkpig kvahagiadl dralaaaqrg feawrkvpah eraatmrkaa alvreradai

61 aqlmtqeqgk pltearvevl saadiiewfa degrrvygri vpprnlnaqq tvvkepvgpv

121 aaftpwnfpv nq vrklsaa latgcsflvk apeetpaspa allrafvdag vpagviglvf

181 gdpaeissyl iphpvirkvt ftgstpvgkq laalagqhmk ratmelggha pvivaedadv

241 alavkaagga kfrnagqvci sptrflvhns irdeftralv khaeglkvgn gleegttlga

301 lanprrltam asvvdnarkv gasietgger igaegnffap tvianvplea dvfnnepfgp

361 vaairgfdkl edaiaeanrl pfglagyaft rsfanvhllt qrlevgmlwi nqpatpwpem

421 pfggvkdsgy gseggpeale pylvtksvtv mav

SEQ ID NO:37

SeqID: ZP 02382650.1 GL167590262

Protein name: Succinate-semialdehyde dehydrogenase (NAD(P)(+)) [Burkholderia ubonensis Bu]

1 mahvtytdtq llingewtda asgktidvvn patgkaigkv ahagiadldr alaaaqrgfe 61 qwrrvpaher aatmrkaaal vreradgiaq lmtqeqgkpl vearlevlaa adiiewfade 121 grrvygrivp prnlgaqqtv vkepvgpvaa ftpwnfpvnq vrklsaala tgcsflvkap 181 eetpaspaal lrafvdagvp agviglvygd paeisaylip hpvirkvtft gstpvgkhla 241 alagqhntkra tmelgghapv ivaedadval avkaaggakf rnagqvcisp trflvhnsir 301 deftralvkh aqglkvgngl degttlgala nprriaamts vvenaravga rvetggerig 361 tegnffaptv ladvpleadv fnnepfgpva airgfdsldd aiseanrlpy glagyaftrs 421 fanvhlltqr levgmlwinq patpwpempf ggvkdsgygs eggpealepy lvtksvtvma 481 v

SEQ ID NO:38

SeqID: YPJ72358.1 GL78062450

Protein name: 2,5-dioxopentanoate dehydrogenase (NAD+) [Burkholderia sp. 383]

1 manvtytdtq llidgewvda asgktidvvn patgkpigkv ahagiadldr alaaaqrgfd 61 awrkvpaher aatmrkaaal vreradaiaq lmtqeqgkpl tearvevlsa adiiewfade 121 grrvygrivp prnlgaqqtv vkepvgpvaa ftpwnfpvnq vvrklsaala tgcsflvkap 181 eetpaspaal lrafvdagvp agviglvygd paeissylip hpvirkvtft gstpvgkqla 241 amaglhmkra tmelgghapv ivaedadval avkaaggakf rnagqvcisp trflvhnsir 301 deftralvkh aeglkvgngl eegtalgala nprrltamas vvdnarkvga rietggerig 361 tegnffaptv iadvpleadv fnnepfgpva airgfdkldd aiaeanrlpf glagyaftrs 421 fanvhlltqr levgmlwinq patpwpempf ggvkdsgygs eggpealepy lvtksvtvma 481 v SEQ ID NO:39

SeqID: ZP_04947381.1 GL254254064

Protein name: NAD-dependent aldehyde dehydrogenase [Burkholderia dolosa

AU0158]

1 mwmanvtytd tqllidgewv daasgktidv vnpatgkaig kvahagiadl dralaaaqrg 61 feawrkvpah eraatmrkaa alvreradti aqlmtqeqgk plaesrievl saadiiewfa 121 degrrvygri vpprnlgaqq tvvkepvgpv aaftpwnfpv nqvvrklsaa latgcsflvk 181 apeetpaspa allrafvdag vpagviglvf gdpaeisayl iphpvirkvt ftgstpvgkq 241 laalagqhmk ratmelggha pvivaedadv alavkaagga kfrnagqvci sptrflvhns 301 irdeftralv khaeglkvgn gleegttlga lanprrltam as vdnarkv garietgger 361 igsegnffap tviadvplea dvfnnepfgp vaairgfdkl ddaiaeanrl pyglagyaft 421 rsfanvhllt qrlevgmlwi nqpatpwpem pfggvkdsgy gseggpeale pylvtksvtv 481 mav

SEQ ID NO:40

SeqID: BAE94276.1 GI:95102056

Protein name: alfa-ketoglutaric semialdehyde dehydrogenase [Azospirillum brasilense]

1 manvtytdtq llidgewvda asgktidvvn patgkpigrv ahagiadldr alaaaqsgfe 61 awrkvpaher aatmrkaaal vreradaiaq lmtqeqgkpl tearvevlsa adiie fade 121 grrvygrivp prnlgaqqtv vkepvgpvaa ftpwnfpvnq vvrklsaala tgcsflvkap 181 eetpaspaal lrafvdagvp agviglvygd paeissylip hpvirkvtft gstpvgkqla 241 slaglhmkra tmelgghapv ivaedadval avkaaggakf rnagqvcisp trflvhnsir 301 deftralvkh aeglkvgngl eegttlgala nprrltamas vidnarkvga sietggerig 361 segnffaptv ianvpldadv fnnepfgpva airgfdklee aiaeanrlpf glagyaftrs 421 fanvhlltqr levgmlwinq patpwpempf ggvkdsgygs eggpealepy lvtksvtvma 481 v

SEQ ID NO:41

SeqID: ZP 03583019.1 GI:221210038

Protein name: succinate-semialdehyde dehydrogenase [NADP+] (ssdh) [Burkholderia multivorans CGD1]

1 manvtytdtq llidgewvda asgktidvvn patgrvigkv ahagiadldr alaaaqrgfe 61 awrkvpaher aatmrkaaal vreradtiaq lmtqeqgkpl tearievlsa adiiewfade 121 grrvygrivp prnlgaqqtv vkepvgpvaa ftpwnfpvnq vvrklsaala tgcsflvkap 181 eetpaspaal lrafvdagvp agviglvygd paeissyvip hpvirkvtft gstpvgkqla 241 alagqnmkra tmelgghapv xvaedadval avkaaggakf rnagqvcisp trflvhnsir 301 deftralvkh aeglkvgngl eegttlgala nprrltamas vvenarkvga svetggerig 361 segnffaptv lanvpleadv fnnepfgpva airgfdkled aiaeanrlpy glagyaftrs 421 fanvhlltqr levgmlwinq patpwpempf ggvkdsgygs eggpealepy lvtksvtvma 481 v

SEQ ID NO:42

SeqID: YP 001779559.1 GL170738299

Protein name: aldehyde dehydrogenase [Burkholderia cenocepacia MCO-3] 1 manvtytdtq llidgewvda asgktidvvn patgkpigkv ahasiadldr alaaaqrgfe

61 awrkvpaher aatmrkaaal vreradtiaq lmtqeqgkpl tearvevlsa adiiewfade

121 grrvygrivp prnlgaqqtv vkepvgpvaa ftpwnfpvnq vvrklsaala tgcsfIvkap

181 eetpaspaal lrafvdagvp agviglvfgd paeissylip hpvirkvtft gstpvgkqla

241 alagqhmkra tmelgghapv ivaedadval avkaaggakf rnagqvcisp trflvhnsir

301 deftralvkh aeglkvgngl eegttlgala nprrltamas vvdnarkvga sietggerig

361 aegnffaptv ianvpleadv fnnepfgpva airgfdkled aiaeanrlpf glagyaftrs

421 fanvhlltqr levgmlwinq patpwpempf ggvkdsgygs eggpealepy lvtksvtvma

481 V

SEQ ID NO:43

SeqID: YP_001584188.1 GI:161520761

Protein name: aldehyde dehydrogenase [Burkholderia multivorans ATCC 17616]

1 manvtytdtq llidgewvda asgktidvvn patgkvigkv ahagiadldr alaaaqrgfe 61 awrkvpaher aatmrkaaar vreradtiaq lmtqeqgkpl tearievlsa adiiewfade 121 grrvygrivp prnlgaqqtv vkepvgpvaa ftpwnfpvnq vvrklsaala tgcsflvkap 181 eetpaspaal lrafvdagvp agviglvygd paeissyvip hpvirkvtft gstpvgkqla 241 alagqhmkra tmelgghapv ivaedadval avkaaggakf rnagqvcisp trflvhnsir 301 deftralvkh aeglkvgngl eegttlgala nprrltamas vvenarkvga svetggerig 361 segnffaptv Ianvpleadv fnnepfgpva airgfdkled aiaeanrlpy glagyaftrs 421 fanvhlltqr levgmlwinq patpwpempf ggvkdsgygs eggpealepy lvtksvtvma 481 v

SEQ ID NO:44

SeqID: EGD03606.1 GL325525897

Protein name: NADP-dependent succinate-semialdehyde dehydrogenase [Burkholderia sp. TJI49]

1 manvtytdtq llidgewvda asgktidvmn patgkvigkv ahagiadldr alaaaqrgfe 61 awrkvpaher aatmrkaaal vreradaiaq lmtqeqgkpl aearievlsa adiiewfade 121 grrvygrivp prnlgaqqtv vkepvgpvaa ftpwnfpvnq vvrklsaala tgcsflvkap 181 eetpaspaal lrafvdagvp agviglvygd paeissylip hpvirkvtft gstpvgkqla 241 alagqhmkra tmelgghapv ivaedadval avkaaggakf rnagqvcisp trflvhnsir 301 deftralvkh aeglkvgngl eegttlgala nprrltamas vvdnarkvga svetggerig 361 segnffaptv Ianvpleadv fnnepfgpva airgfdkled aiaeanrlpy glagyaftrs 421 fanvhlltqr levgmlwinq patpwpempf ggvkdsgygs eggpealepy lvtksvtvma 481 v

SEQ ID NO:45

SeqID: YP_002234153.1 GL206563390

Protein name: putative aldehyde dehydrogenase [Burkholderia cenocepacia J2315]

1 manvtytdtq llidgewvda asgktidvvn patgkpigkv ahagiadldr alaaaqrgfe 61 awrkvpaher aatmrkaaal vreradtiaq lmtqeqgkpl tearvevlsa adiiewfade 121 grrvygrivp prnlgaqqtv vkepvgpvaa ftpwnfpvnq vvrklsaala tgcsflvkap 181 eetpaspaal lrafvdagvp agviglvygd paeissylip hpvirkvtft gstpvgkqla 241 alagqhmkra tmelgghapv ivaedadval avkaaggakf rnagqvcisp trflvhnsir 301 deftralvkh aeglkvgngl eegttlgala nprrltamas vvdnarkvga sietggerxg

361 aegnffaptv ianvpleadv fnnepfgpva airgfdklee aiaeanrlpf glagyaftrs

421 fanvhlltqr levgml inq patpwpempf ggvkdsgygs eggpealepy Ivtksvtvma 481 v

SEQ ID NO:46

SeqID: ZP_03569460.1 GL221196413

Protein name: succinate-semialdehyde dehydrogenase [NADP+] (ssdh) [Burkholderia multivorans CGD2M]

1 manvtytdtq llidgewvda asgktidvvn patgkvigkv ahagiadldr alaaaqrgfe 61 awrkvpaher aatmrkaaal vreradtiaq lmtqeqgkpl tearievlsa adiiewfade 121 grrvygrivp prnlgaqqtv vkepvgpvaa ftpwnfpvnq vrklsaala tgcsflvkap 181 eetpaspaal lrafvdagvp agviglvygd paeissyvip hpvirkvtft gstpvgkqla 241 alagqhmkra tmelgghapv ivaedadval avkaaggakf rnagqvcisp trflvhnsxr 301 deftralvkh aeglkvgngl eegttlgala nprrltamas wenarkvga svetggerig 361 segnffaptv Ianvpleadv fnnepfgpva airgfdkled aiaeanrlpy glagyaftrs 421 fanvhlltqr levgmlwinq patpwpempf ggvkdsgygs eggpealepy Ivtksvtvma 481 v

SEQ ID NO:47

SeqID: YP_001117385.1 GI: 134293649

Protein name: 2,5-dioxopentanoate dehydrogenase (NAD+) [Burkholderia

vietnamiensis G4]

1 manvtytdtq llidgewvda asgktidvvn patgkaigkv ahagiadldr alaaaqrgfe 61 awrkvpaher aatmrkaaal vreradaiaq lmtqeqgkpl tearievlsa adiiewfade 121 grrvygrivp prnlgaqqmv vkepvgpvaa ftpwnfpvnq vvrklcaala tgcsflvkap 181 eetpaspaal lrafvdagvp agvvglvygd paeissylip hpvirkvtft gstpvgkqla 241 alagqhmkra tmelgghapv ivaedadval avkaaggakf rnagqvcisp trflvhnsxr 301 deftralvah aqglkigngl degttlgala nprrltamas wenarkvga sietggerxg 361 segnffaptv ianvpleadv fnnepfgpva airgfdkled aiseanrlpf glagyaftrs 421 fanvhlltqr levgmlwinq patpwpempf ggvkdsgygs eggpealepy Ivtksvtvma 481 v

SEQ ID NO:48

SeqID: YP 623820.1 GI: 107026309

Protein name: succinate-semialdehyde dehydrogenase (NAD(P)+) [Burkholderia cenocepacia AU 1054]

1 manvtytdtq llidgewvda asgktidvvn patgkpigkv ahagiadldr alaavqrgfe 61 awrkvpaher aatmrkaaal vreradtiaq lmtqeqgkpl tearvevlsa adiiewfade 121 grrvygrivp prnfnaqqtv vkepvgpvaa ftpwnfpvnq vvrklsaala tgcsflvkap 181 eetpaspaal lrafvdagvp agviglvfgd paeissylip hpvirkvtft gstpvgkqla 241 alagqhmkra tmelgghapv ivaedadval avkaaggakf rnagqvcisp trflvhnsxr 301 deftralvkh aeglkvgngl eegttlgala nprrltamas vvdnarkvga sietggerxg 361 aegnffaptv ianvpleadv fnnepfgpva airgfdkled aiaeanrlpf glagyaftrs 421 fanvhlltqr levgmlwinq patpwpempf ggvkdsgygs eggpealepy Ivtksvtvma 481 v SEQ ID NO:49

SeqID: ZP 02891604.1 GL170700605

Protein name: Aldehyde Dehydrogenase [Burkholderia ambifaria IOP40-10]

1 manvtytdtq llidgewvda asgktid vn patgkaigkv ahagiadldr alaaaqrgfe 61 awrkvpaner aatmrkaaal vreradtiaq lmtqeqgkpl tearvevlsa adiiewfade 121 grrvygrivp prnlgaqqmv vkepvgpvaa ftpwnfpvnq vvrklsaala tgcsflvkap 181 eetpaspaal lrafvdagvp agviglvygd paeissylia hpvirkvtft gstpvgkqla 241 alagqhmkra tmelgghapv ivaedadval avkaaggakf rnagqvcisp trflvhnsir 301 deftralvqh aeglkigngl eegttlgala nprrltamvs vvdnarkvga rietggerig 361 segnffaptv ianvpleadv fnnepfgpva airgfdkldd aiaeanrlpf glagyaftrs 421 fanvhlltqr levgmlwinq patpwpempf ggvkdsgygs eggpealepy lvtksvtvma 481 v

SEQ ID NO:50

SeqID: YP_001810977.1 GI:172063326

Protein name: aldehyde dehydrogenase [Burkholderia ambifaria MC40-6]

1 manvtytdtq llidgewvda asgktidvvn patgkaigkv ahagiadldr alvaaqrgfe 61 awrkvpaner aatmrkaaal vreradtiaq lmtqeqgkpl tearvevlsa adiiewfade 121 grrvygrivp prnlgaqqmv vkepvgpvaa ftpwnfpvnq vvrklsaala tgcsflvkap 181 eetpaspaal lrafvdagvp agviglvygd paeissylia hpvirkvtft gstpvgkqla 241 alagqhmkra tmelgghapv ivaedadval avkaaggakf rnagqvcisp trflvhnsir 301 deftralvqh aeglkigngl eegttlgala nprrltamas vvdnarkvga sietggerig 361 segnffaptv ianvpleadv fnnepfgpva airgfdkled aiaeanrlpf glagyaftrs 421 fanvhlltqr levgmlwinq patpwpempf ggvkdsgygs eggpealepy lvtksvtvma 481 v

SEQ ID NO:51

SeqID: ZP_02911594.1 GL171322894

Protein name: Aldehyde Dehydrogenase_ [Burkholderia ambifaria MEX-5]

1 manvtytdtq llidgewvda asgrtidvvn patgkaigkv ahagiadldr alaaaqrgfe 61 awrkvpaner aatmrkaaal vreradaiaq lmtqeqgkpl tearvevlsa adiiewfade 121 grrvygrivp prnlgaqqmv vkepvgpvaa ftpwnfpvnq vvrklsaala tgcsflvkap 181 eetpaspaal lrafvdagvp agviglvygd paeissylia hpvirkvtft gstpvgkqla 241 alagqhmkra tmelgghapv ivaedadval avkaaggakf rnagqvcisp trflvhnsir 301 deftralvqh aeglkigngl eegttlgala nprrltamas vvenarkvga sietggerig 361 segnffaptv ianvpleadv fnnepfgpva airgfdkled aiaeanrlpf glagyaftrs 421 fanvhlltqr levgmlwinq patpwpempf ggvkdsgygs eggpealepy lvtksvtvma 481 v

SEQ ID NO:52

SeqID: YP_775718.1 GL115358580

Protein name: succinate-semialdehyde dehydrogenase (NAD(P)(+)) [Burkholderia ambifaria AMMD] 1 manvtytdtq llidgewvda asgktidvvn patgkaigkv ahagiadldr alaaaqrgfe

61 awrkvpaner aatmrkaaal vreradaiaq lmtqeqgkpl tearvevlsa adiie fade

121 grrvygrivp prnlgaqqmv vkepvgpvaa ftpwnfpvnq vvrklsaala tgcsflvkap

181 eetpaspaal lrafvdagvp agviglvyge paeissylia hpvirkvtft gstpvgkqla

241 alagqhmkra tmelgghapv ivaedadval avkaaggakf rnagqvcisp trflvhnsxr

301 deftralvqh aeglkigngl eegttlgala nprrltamas vvenarkvga sietggerig

361 segnffaptv ianvpleadv fnnepfgpva airgfdkled aiaeanrlpf glagyaftrs

421 fanvhllsqr levgmlwinq patpwpempf ggvkdsgygs eggpealepy lvtksvtvma

481 v

SEQ ID NO:53

SeqID: NP_015264.1 GL6325196

Protein name: Aldehyde dehydrogenase, ALD6[Saccharomyces cerevisiae]

1 mtklhfdtae pvkitlpngl tyeqptglfi nnkfmkaqdg ktypvedpst entvcevssa

61 ttedveyaie cadrafhdte watqdprerg rllskladel esqidlvssi ealdngktla

121 largdvtiai nclrdaaaya dkvngrtint gdgymnfttl epigvcgqii pwnfpimmla

181 kiapalamg nvcilkpaav tplnalyfas lckkvgipag vvnivpgpgr tvgaaltndp

241 rxrklaftgs tevgksvavd ssesnlkkxt lelggksahl vfddanxkkt Ipnlvngxfk

301 nagqicssgs riyvqegiyd ellaafkayl eteikvgnpf dkanfqgait nrqqfdtimn

361 yidigkkega kiltggekvg dkgyfirptv fydvnedmri vkeeifgpvv tvakfktlee

421 gvemanssef glgsgietes lstglkvakm lkagtvwint yndfdsrvpf ggvkqsgygr

481 emgeevyhay tevkavrikl

SEQ ID NO:54

SeqID: NP_013893.1 GI:6323822

Protein name: Aldehyde dehydrogenase, ALD2 [Saccharomyces cerevisiae]

1 mptlytdiei pqlkislkqp lglfinnefc pssdgktiet vnpatgepit sfqaanekdv

61 dkavkaaraa fdnvwsktss eqrgiylsnl lklieeeqdt laaletldag kpyhsnakgd

121 laqxlqltry fagsadkfdk gatxpltfnk faytlkvpfg vvaqivpwny plamacwklq

181 galaagntvi ikpaentsls llyfatlikk agfppgvvni vpgygslvgq alashmdidk

241 isftgstkvg gfvleasgqs nlkdvtlecg gkspalvfed adldkaidwi aagifynsgq

301 nctansrvyv qssiydkfve kfketakkew dvagkfdpfd ekcivgpvis stqydriksy

361 iergkreekl dmfqtsefpi ggakgyfipp tiftdvpqts kllqdeifgp vvvvskftny

421 ddalklandt cyglasavft kdvkkahmfa rdikagtvwi nssndedvtv pfggfkmsgi

481 grelgqsgvd tylqtkavhi nlsldn

SEQ ID NO:55

SeqID: NP_013892.1 GI:6323821

Protein name: Aldehyde dehydrogenase, ALD3 [Saccharomyces cerevisiae]

1 mptlytdiei pqlkislkqp lglfinnefc pssdgktiet vnpatgepit sfqaanekdv

61 dkavkaaraa fdnvwsktss eqrgiylsnl lklieeeqdt laaletldag kpfhsnakqd

121 laqxieltry yagavdkfnm getxpltfnk faytlkvpfg vvaqivpwny plamacrkmq

181 galaagntvi ikpaentsls llyfatlikk agfppgvvnv ipgygsvvgk algthmdidk

241 isftgstkvg gsvleasgqs nlkditlecg gkspalvfed adldkaiewv angiffnsgq 301 xctansrvyv qssxydkfve kfketakkew dvagkfdpfd ekcivgpvis stqydriksy

361 iergkkeekl dmfqtsefpi ggakgyfipp txftdvpets kllrdexfgp vvvvskftny

421 ddalklandt cyglasavft kdvkkahmfa rdxkagtvwi nqtnqeeakv pfggfkmsgi

481 gresgdtgvd nylqiksvhv dlsldk

Claims

What is claimed is:

1. A recombinant cell modified to exhibit increased biosynthesis of pentanoic acid compared to a wild-type control.

2. A recombinant microbial cell modified to exhibit increased biosynthesis of 2- methylbutyric acid compared to a wild-type control.

3. The recombinant microbial cell any preceding claim wherein the microbial cell is a fungal cell.

4. The recombinant cell of claim 3 wherein the fungal cell is a member of the

Saccharomycetaceae family.

5. The recombinant cell of claim 3 wherein the fungal cell is Saccharomyces cerevisiae, Candida rugosa, or Candida albicans.

6. The recombinant cell of claim 1 or claim 2 wherein the microbial cell is a bacterial cell.

7. The recombinant cell of claim 6 wherein the bacterial cell is a member of the phylum Protobacteria.

8. The recombinant cell of claim 7 wherein the bacterial cell is a member of the Enterobacteriaceae family.

9. The recombinant cell of claim 8 wherein the bacterial cell is Escherichia coli.

10. The recombinant cell of claim 7 wherein the bacterial cell is a member of the Pseudomonaceae family.

11. The recombinant cell of claim 10 wherein the bacterial cell is Pseudomonas putida.

12. The recombinant cell of claim 6 wherein the bacterial cell is a member of the phylum Firmicutes.

13. The recombinant cell of claim 12 wherein the bacterial cell is a member of the Bacillaceae family.

14. The recombinant cell of claim 13 wherein the bacterial cell is Bacillus subtilis.

15. The recombinant cell of claim 12 wherein the bacterial cell is a member of the Streptococcaceae family.

16. The recombinant cell of claim 15 wherein the bacterial cell is Lactococcus lactis.

17. The recombinant cell of claim 12 wherein the bacterial cell is a member of the Clostridiaceae family.

18. The recombinant cell of claim 17 wherein the bacterial cell is Clostridium cellulolyticum.

19. The recombinant cell of claim 6 wherein the bacterial cell is a member of the phylum Cyanobacteria.

20. The recombinant cell of any preceding claim wherein the microbial cell is photosynthetic.

21. The recombinant cell of any preceding claim wherein the microbial cell is cellulolytic.

22. The recombinant cell of any one of claims 1 and 3-21 wherein the increased biosynthesis of pentanoic acid compared to a wild-type control comprises an increase in conversion of L-aspartate to L-threonine compared to a wild-type control, an increase in conversion of L-threonine to 2-ketobutyrate compared to a wild-type control, an increase in 2-ketobutyrate elongation activity compared to a wild-type control, an increase in 2- ketovalerate elongation activity compared to a wild-type control, an increase in ketoacid decarboxylase activity compared to a wild-type control, an increase in ketoacid

decarboxylase selectivity toward a predetermined substrate compared to a wild-type control, or an increase in aldehyde dehydrogenase activity compared to a wild-type control.

23. The recombinant cell of any one of claims 2-21 wherein the increased biosynthesis of 2-methylbutyric acid compared to a wild-type control comprises an increase in conversion of L-aspartate to L-threonine compared to a wild-type control, an increase in conversion of L-threonine to 2-ketobutyrate compared to a wild-type control, an increase in conversion of 2-ketobutyrate to 2-keto-3-methylvalerate, an increase in ketoacid

decarboxylase activity compared to a wild-type control, an increase in ketoacid

decarboxylase selectivity toward a predetermined substrate compared to a wild-type control, or an increase in aldehyde dehydrogenase activity compared to a wild-type control.

24. A method comprising:

incubating a recombinant cell of any one of claims 1 and 3-23 in medium that comprises a carbon source under conditions effective for the recombinant cell to produce pentanoic acid, wherein the carbon source comprises one or more of: glucose, pyruvate, L- aspartate, L-threonine, 2-ketobutyrate, 2-ketovalerate, 2-ketocaproate, valeraldehyde, C0₂, cellulose, xylose, sucrose, arabinose, or glycerol.

25. A method comprising :

incubating a recombinant cell of any one of claims 2-23 in medium that comprises a carbon source under conditions effective for the recombinant cell to produce 2- methylbutyric acid, wherein the carbon source comprises one or more of: glucose, pyruvate, L-aspartate, L-threonine, 2-ketobutyrate, 2-keto-3 -methyl alerate, 2-methyl butyraldehyde, C0₂, cellulose, xylose, sucrose, arabinose, or glycerol.

26. A method comprising:

introducing into a host cell a heterologous polynucleotide encoding at least one polypeptide that catalyzes conversion of a carbon source to pentanoic acid, wherein the at least one polynucleotide is operably linked to a promoter so that the modified host cell catalyzes conversion of the carbon source to pentanoic acid.

27. The method of claim 26 wherein the carbon source comprises one or more of: glucose, pyruvate, L-aspartate, L-threonine, 2-ketobutyrate, 2-ketovalerate, 2-ketocaproate, valeraldehyde, C0₂, cellulose, xylose, sucrose, arabinose, or glycerol.

28. A method comprising :

introducing into a host cell a heterologous polynucleotide encoding at least one polypeptide that catalyzes conversion of a carbon source to 2-methylbutyric acid, wherein the at least one polynucleotide is operably linked to a promoter so that the modified host cell catalyzes conversion of the carbon source to 2-methylbutyric acid.

29. The method of claim 28 wherein the carbon source comprises one or more of: glucose, pyruvate, L-aspartate, L-threonine, 2-ketobutyrate, 2-keto-3 -methyl valerate, 2- methyl butyraldehyde, C0₂, cellulose, xylose, sucrose, arabinose, or glycerol.

30. The method of any one of claims 24-29 wherein the host cell is a fungal cell.

31. The method of claim 30 wherein the fungal cell is a member of the

Saccharomycetaceae family.

32. The method of claim 31 wherein the fungal cell is Saccharomyces cerevisiae, Candida rugosa, or Candida albicans.

The method of any one of claims 24-29 wherein the host cell is a bacterial cell.

34. The method of claim 33 wherein the bacterial cell is a member of the phylum Protobacteria.

35. The method of claim 34 wherein the bacterial cell is a member of the

Enterobacteriaceae family.

36. The method of claim 35 wherein the bacterial cell is Escherichia coli.

37. The method of claim 34 wherein the bacterial cell is a member of the

Pseudomonaceae family.

38. The method of claim 37 wherein the bacterial cell is Pseudomonas putida.

39. The method of claim 33 wherein the bacterial cell is a member of the phylum Firmicutes.

40. The method of claim 39 wherein the bacterial cell is a member of the Bacillaceae family.

41. The method of claim 40 wherein the bacterial cell is Bacillus subtilis.

42. The method of claim 39 wherein the bacterial cell is a member of the

Streptococcaceae family.

43. The method of claim 42 wherein the bacterial cell is Lactococcus lactis.

44. The method of claim 39 wherein the bacterial cell is a member of the Clostridiaceae family.

45. The method of claim 44 wherein the bacterial cell is Clostridium cellulolyticum.

46. The method of claim 33 wherein the bacterial cell is a member of the phylum Cyanobacteria. The method of any one of claims 24-46 wherein the host cell is photosynthetic. The method of any one of claims 24-46 wherein the host cell is cellulolytic.