SPLIT INTEIN-BASED SELECTION FOR PEPTIDE BINDERS

Information

  • Patent Application
  • 20230227508
  • Publication Number
    20230227508
  • Date Filed
    June 11, 2021
    2 years ago
  • Date Published
    July 20, 2023
    10 months ago
Abstract
Disclosed herein, in some embodiments, non-naturally occurring proteins (e.g., non-naturally occurring modified proteins) that may be useful in the treatment of bacterial and viral infections, including SARS-CoV-2 infection, host cells comprising the same, and methods of treating bacterial and viral infections including SARS-CoV-2 infection. Also provided herein are host cells comprising fusion proteins for split intein-based selection of peptides that bind a target protein, methods of using the same, and methods of identifying peptides that bind a target protein.
Description
BACKGROUND OF THE INVENTION

Protein-protein interactions play an important role in elucidating the mechanisms of biological systems and in numerous clinical applications. For example, during viral infection, viral surface proteins bind to host cell receptors to promote internalization of the viral genome. Inhibitors of the interaction between a viral surface protein and host cell receptors may be used to prevent viral infection or spread of such an infection to other host cells. Elucidation of protein-protein interactions have also led to development of immunotherapies and antibodies, which has been useful in the treatment of cancer. Accordingly, efficient methods of identifying peptide binders of target proteins are warranted.


SUMMARY OF THE INVENTION

Aspects of the present disclosure relate to peptides binders of target proteins that may be useful in the treatment of disease and methods of identifying such peptides. Further aspects of the present disclosure provide non-naturally occurring peptides. In some embodiments, a non-naturally occurring peptide comprise:

    • (A) AACX1X2X3X4X5X6MPPX7X8X9X10X11X12C (SEQ ID NO: 1) (scaffold L1), wherein:
      • (i) X6 and X7 are each the amino acid S or T;
      • (ii) X1-X5 and X8-X12 are each any amino acid; and
      • (iii) the peptide comprises a thioether bridge that links C at position 3 in to S or T at position 9 in SEQ ID NO: 1 and a thioether bridge that links S or T at position 13 to C at position 19 in SEQ ID NO: 1;
    • (B) X1PX2TTX3X4TX5X6X7EX8X9DX10DEX11X12X13 (SEQ ID NO: 2) (scaffold L2), wherein:
      • (i) X2 is the amino acid H, Q, N, K, D, or E;
      • (ii) X6 is the amino acid F, L, S, I, M, T, V, or A;
      • (iii) X7 is the amino acid F, L, I, or V;
      • (iv) X1, X3-X5 and X8-X13 are each any amino acid; and
      • (v) the peptide comprises an ester bridge that links T at position 5 of SEQ ID NO: 2 to D at position 15 of SEQ ID NO: 2 and an ester bridge that links T at position 8 of SEQ ID NO: 2 to E at position 12 of SEQ ID NO: 2;
    • (C) X1CX2X3X4X5X6CX7X8X9X10X11 (SEQ ID NO: 3) (scaffold L3), wherein:
      • (i) X5 and X10 are each the amino acid D or E;
      • (ii) X1-X4, X6-X9, and X11 are each any amino acid; and
      • (iii) the peptide comprises a thioether bridge that links C at position 2 to D or E at position 6 of SEQ ID NO: 3 and a thioether bridge that links C at position 8 to D or E at position 12 of SEQ ID NO: 3;
    • (D) X1CX2X3CX4X5X6X7X8X9 (SEQ ID NO: 4) (scaffold L4), wherein:
      • (i) X4 and X7 are each the amino acid D or E;
      • (ii) X1-X3, X5-X6, and X8-X9 are each any amino acid; and
      • (iii) the peptide comprises a thioether bridge that links C at position 2 to D or E at position 6 of SEQ ID NO: 4 and a thioether bridge that links C at position 5 to D or E at position 9 of SEQ ID NO: 4; and/or
    • (E) X1CX2X3X4X5X6CX7X8CX9X10X11X12X13 (SEQ ID NO: 5), wherein:
      • (i) X5, X9, and X12 are each the amino acid D or E;
      • (ii) X1-X4, X6-X8, X10-X11, and X13 are each any amino acid; and
      • (iii) the peptide comprises a thioether bridge that links the C at position 2 to D or E at position 6 of SEQ ID NO: 5, a thioether bridge that links C at position 8 of SEQ ID NO: 5 with D or E at position 12 of SEQ ID NO: 5, and a thioether bridge that links C at position 11 with D or E at position 15 of SEQ ID NO: 5.


In some embodiments, the non-naturally occurring peptide comprises scaffold L5 and a sequence selected from SEQ ID NOS: 6-16; and/or scaffold L3 and a sequence selected from SEQ ID NOs: 17-25. In some embodiments, the non-naturally occurring peptide comprises scaffold L3 and SEQ ID NO: 24.


Further aspects of the present disclosure provide host cells comprising a heterologous nucleic acid encoding any of the non-naturally occurring peptides disclosed herein.


In some embodiments, the heterologous nucleic acid further encodes SEQ ID NO: 46.


In some embodiments, the heterologous nucleic acid comprises any one of SEQ ID NOs: 47-66.


Further aspects of the present disclosure provide:

    • (a) a first fusion protein comprising (i) a first fragment of a transcription factor, (ii) a first split intein, and (iii) a target protein;
    • (b) a second fusion protein comprising (i) a candidate peptide, (ii) a second split intein, and (iii) a second fragment of the transcription factor; wherein the first split intein and second split intein are complementary fragments; and
    • (c) an inducible promoter operably linked to at least one reporter gene, wherein the transcription factor induces transcription of the at least one reporter gene when the transcription factor is present as a full-length transcription factor.


In some embodiments,

    • (A) in (a), the first fusion protein comprises (i)-(iii) linked sequentially from the N-terminus to the C-terminus, the first fragment is a N-terminal fragment of the transcription factor and the first split intein is a N-terminal split intein; and
    • (B) in (b), (i)-(iii) are linked sequentially from the N-terminus to the C-terminus, wherein the second split intein is a C-terminal split intein, and the second fragment is a C-terminal fragment of the transcription factor; or
    • (C) in (a), from the N-terminus to the C-terminus, the first fusion protein comprises (iii) linked to (ii) linked to (i), wherein the first fragment is a C-terminal fragment of the transcription factor and the first split intein is a C-terminal split intein; and
    • (D) in (b), from the N-terminus to the C-terminus, the second fusion protein comprises (iii) linked to (ii) linked to (i), wherein the second split intein is a N-terminal split intein and the second fragment is a N-terminal fragment of the transcription factor.


In some embodiments, the cell is a eukaryotic or prokaryotic cell, optionally wherein the prokaryotic cell is a bacterial cell.


In some embodiments, the transcription factor is a sigma factor (a factor).


In some embodiments, the first fusion protein is encoded by a first heterologous nucleic acid and the second fusion is encoded by a second heterologous nucleic acid.


In some embodiments, the candidate peptide comprises a sequence selected from SEQ ID NOs: 6-25 or comprises the non-naturally occurring peptide of any one of claims 1 or 2, optionally wherein the candidate peptide further comprises SEQ ID NO: 46.


In some embodiments, the at least one reporter gene encodes a positive selection marker, a negative selection marker, and/or a fluorescent protein, optionally wherein the positive selection marker is an antibiotic resistance gene, optionally wherein the antibiotic resistance gene is chloramphenicol acetyltransferase (cat), optionally wherein the negative selection marker is the herpes simplex virus-thymidine kinase (hsvtk) gene.


In some embodiments, the inducible promoter is an ECF promoter.


In some embodiments, the target protein comprises viral receptor binding domain (RBD) of the SARS-CoV-2 spike protein.


In some embodiments, the RBD comprises SEQ ID NO: 71.


In some embodiments, the host cells further comprises one or more enzymes selected from ProcM, LynD, TgnB, or PapB, optionally wherein the host cell comprises a heterologous nucleic acid encoding the enzyme, optionally wherein the heterologous nucleic acid encoding the enzyme comprises an inducible promoter.


Further aspects of the disclosure provide methods of identifying a peptide that binds a target protein. In some embodiments, the methods comprise culturing any of the host cells disclosed herein and detecting transcription of the at least one reporter gene, thereby identifying the candidate peptide as being capable of binding to the target protein.


In some embodiments, the methods comprise incubating in a reaction vessel:

    • (a) a first fusion protein comprising (i) a first fragment of a transcription factor, (ii) a first split intein, and (iii) a target protein;
    • (b) a second fusion protein comprising (i) a candidate peptide, (ii) a second split intein, and (iii) a second fragment of the transcription factor; wherein the first and second split inteins belong to the same intein; and
    • (c) an inducible promoter operably linked to at least one reporter gene, wherein the transcription factor induces transcription of the at least one reporter gene when the transcription factor is present as a full-length transcription factor, and


detecting transcription of the reporter gene, thereby identifying the candidate peptide as being capable of binding to the target protein.


Further aspects of the present disclosure provide methods of treating a subject having or suspected of having a SARS-CoV-2 infection comprising administering an effective amount of any of the non-naturally occurring peptides disclosed herein.


In some embodiments, the method comprises repeating the method with a plurality of candidate peptides.


In some embodiments, culturing comprises positive and/or negative selection of the host cell.


In some embodiments, the method further comprises sequencing.


Further aspects of the disclosure provide libraries of peptides. In some embodiments, a library compress a plurality of peptides, wherein each peptide of the plurality of peptides has a length of n amino acids and has an amino acid sequence defined by a motif X1X2X3X4 . . . Xn, wherein n is 5-100, wherein each of X1-Xn is independently selected from a group consisting of up to 20 amino acids and at least one of X1-Xn within each peptide is an amino acid selected from a group consisting of 19 or fewer amino acids, and wherein the motif X1X2X3X4 . . . Xn is determined to be susceptible to post-translational modification by at least 2 distinct protein modification enzymes.


In some embodiments, less than 80% of the plurality of peptides are capable of being fully modified by the at least 2 distinct protein modification enzymes.


In some embodiments, at least one of X1-Xn is defined to be a single amino acid.


According to some aspects of the disclosure, compositions comprising host cells are provided. In some embodiments, a composition comprises a plurality of host cells, each host cell of the plurality comprising a peptide of a library disclosed herein, wherein the peptide comprised by each host cell is independent of the peptide comprised by each other host cell. In some embodiments, the composition comprises each peptide of the plurality of peptides. In some embodiments, the host cells are bacterial cells. In some embodiments, the peptide is encoded by a first nucleic acid sequence in the host cell. In some embodiments, each host cell further comprises at least one protein modifying enzyme. In some embodiments, the at least one protein modifying enzyme is encoded by a second nucleic acid sequence in the host cell.


Further aspects of the disclosure provide methods of designing amino acid motifs. In some embodiments, a method of designing an amino acid motif comprises:


(i) selecting one or more protein modifying enzymes;


(ii) identifying a recognition site (RS) sequence for each of the one or more protein modifying enzymes;


(iii) constructing a plurality of nucleic acid molecules, each nucleic acid molecule encoding a leader amino acid sequence comprising the RS sequence for each of the one or more protein modifying enzymes;


(iv) assigning a score to each of the plurality of nucleic acid molecules; and


(v) selecting one of the plurality of nucleic acid molecules based on step (iv),


to design the amino acid motif, wherein each RS sequence facilitates interaction of the corresponding protein modifying enzyme to a peptide defined by the amino acid motif, and wherein the leader amino acid sequence encoded by the nucleic acid molecule selected in step (v) is comprised within each peptide defined by the amino acid motif.


In some embodiments, each peptide defined by the amino acid motif further comprises a core sequence.


In some embodiments, the core sequence comprises one or more amino acids susceptible to modification by the one or more protein modifying enzymes.





BRIEF DESCRIPTION OF THE DRAWINGS

The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present disclosure, which can be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein. For purposes of clarity, not every component may be labeled in every drawing. It is to be understood that the data illustrated in the drawings in no way limit the scope of the disclosure. In the drawings:



FIG. 1 shows a schematic of the split intein-based selection. Positive selection is effected by the expression of a chloramphenicol acetyltransferase (cat); negative selection effected by expression of herpes simplex virus thymidine kinase (hsvtk). Both effectors are expressed as fluorescent fusion proteins to facilitate population analysis/sorting by cytometry/FACS.



FIGS. 2A-2G show positive and negative transcriptional selection systems. FIG. 2A shows a genetic representation of selection operon comprising two fused proteins: superfolder-GFP fused to chloramphenicol acetyl transferase (sfGFP-CAT) and Herpes Simplex Virus thymidine kinase fused to mScarlet-I (HSVtk-mScarlet-I). FIG. 2B shows a schematic representation of a positive selection conducted with chloramphenicol (Cm). Only cells that have expressed sfGFP-CAT will be able to grow in the presence of Cm. FIG. 2C shows a schematic representation of a negative selection conducted with the nucleoside analog dP. Cells that have expressed HSVtk-mScarlet-I will not survive in the presence of dP. FIG. 2D shows a demonstration of titratable positive selection growth rescue dependence on expression of sfGFP-CAT (quantified through GFP relative expression units (REUs)) and the applied concentrations of Cm. FIG. 2E shows a demonstration of titratable negative selection growth inhibition dependence on expression of HSVtk-mScarlet-I (quantified through RFP REUs) and the applied concentrations of dP. FIG. 2F shows a schematic representation of the relationship between GFP REUs and the expression of sfGFP-CAT. Since sfGFP is translationally-fused to CAT, expression of CAT can be directly monitored and quantified by observing cellular fluorescence in the green channel. FIG. 2G shows a schematic representation of the relationship between RFP REUs and the expression of HSVtk-mScarlet-I. Since mScarlet-I is translationally-fused to HSVtk, expression of HSVtk can be directly monitored and quantified by observing cellular fluorescence in the red channel.



FIG. 3 shows a design of RiPP libraries for selections. The structures on the right-hand side correspond to scaffolds L1-L5 (SEQ ID NOs: 1-5). Scaffold L1 is a non-limiting example of a lanthipeptide scaffold. Scaffold L2 is a non-limiting example of a microviridin scaffold. Scaffolds L3-L5 are non-limiting examples of a ranthipeptide scaffold.



FIG. 4 shows a schematic of selection methods for initial campaign.



FIGS. 5A-5C show selections profiling of PapB library 1 (L3). FIG. 5A shows ring topology and amino acid degeneracy of library. FIG. 5B shows iterative selection stringencies are assigned an “sl” (selection) designation. FIG. 5C shows cytometry profiling of populations post-selection (from left to right, after a first round, second round, and third round of selection, respectively). First round of selection lead to escape mutants as evidenced by high REU values without induction. Later rounds demonstrate ideal population distributions.



FIGS. 6A-6B include data showing PapB library 1 (L3) hits. FIG. 6A shows PapB library 1 (L3) hits comprising >1% of the final population that were sequentially enriched throughout rounds of selection. FIG. 6B shows amino acid sequences and predicted cyclization topologies.



FIGS. 7A-7C show selection profiling of PapB library 3 (L5). FIG. 7A shows ring topology and amino acid degeneracy of library. FIG. 7B shows iterative selection stringencies are assigned a “sl” (selection) designation. FIG. 7C shows cytometry profiling of populations post-selection (from left to right, after a first round, second round, and third round of selection, respectively). First round of selection lead to escape mutants as evidenced by high REU values without induction. Later rounds demonstrate ideal population distributions.



FIGS. 8A-8B include data showing PapB library 3 (L5) hits. FIG. 8A shows PapB library 3 (L5) hits comprising >1% of the final population that were sequentially enriched throughout rounds of selection. FIG. 8B shows amino acid sequences and predicted cyclization topologies.



FIGS. 9A-9C show individual confirmation assays of selection hits. FIG. 9A shows REU values of 20 hits against the RBD-intein. FIG. 9B shows fold specificity of hits against the RBD. Fold specificity is defined as (REU-RBD)/(REU-Mdm2) where REU-RBD is the REU value of peptide against RBD-intein as target and REU-Mdm2 is the REU value of peptide against Mdm2-intein as target. FIG. 9C shows amino acid sequence and predicted topology of primary hit from pilot selection.



FIGS. 10A-10D show leader-dependent enzyme design constraints. FIG. 10A illustrates design constraints for leader-dependent modifying enzymes. FIG. 10B shows a flowchart for data acquisition and analysis for determining recognition sites. FIG. 10C shows the alanine scan variants for determining important residues in the TgnA precursor peptide. Residues replaced with alanine are indicated by the thicker portions in the bottom left sequence schematics. ΔΔGi for each position is shown above the wild-type sequence. FIG. 10D shows the recognition site constraints for each of the leader-dependent enzymes. Secondary structure is shown above each peptide sequence. The recognition site for each of the leader-dependent enzymes is outlined by a box. Residues that had high ΔΔGi scores but were not included in the recognition sites are labeled with an asterisk in the PlpA2 schematic. Residues that were included in the recognition site to maintain secondary structure are labeled with a triangle in the TruE schematic. Scatter plots show spacing variants for each enzyme. The fit line is based on Equation 3 from Example 3 with fit parameters listed in Table 6. FIG. 10E shows insertion and spacing variants tested for TgnA. Deletions were at the site indicated by the notch in each variant schematic (of the top 10 shown), and insertions are indicated by the thicker portion on the rightmost end of the last three variants. Insertion/deletion size is listed for each variant, alongside fractional modification. The thicker portion at the lefthand side of each variant schematic represent the recognition site.



FIGS. 11A-11C show the core motifs required for enzyme modification. FIG. 11A shows single mutant variant data for TgnA variants. The wild-type sequence is listed at the top, and each row represents a different variant with only mutated residue shown. The dashed line separates poorly modified residues (<50% of wild-type) from well modified residues (>50% of wild-type). The sequences above the dashed line were used to build the motif. FIG. 11B shows leader-dependent enzyme motifs. FIG. 11C shows leader-independent enzyme motifs. In FIGS. 11B and 11C, for each motif, the enzyme name is in bold and shown above the peptide name. Amino acids shown below the boxed wild-type sequence were observed and well-modified. Amino acids shown above the boxed sequence were not tolerated. Unobserved amino acids are not shown, except for positions labeled with a star or dagger. The core position of the first motif residue is labeled above the position, with the +1 sites additionally annotated in PaaP and LynD. Chemical modifications are shown on the modified residue(s) which are bolded. Positions that are allowed to be any amino acid are noted with a star, and a dagger indicates that the position is allowed to be any residue except cysteine.



FIGS. 12A-12D show automated design of hybrid core motifs and multi-modification of core peptide. FIG. 12A illustrates a design algorithm that combines user input of desired modifications and their positions, with demonstrated design showing combination of PlpXY, LynD, and ThcoK constraints. FIG. 12B illustrates an expression construct, showing inducer control of precursor peptide and modifying enzymes, modification of the precursor peptide, and cleavage to generate the final molecule.



FIGS. 13A-13J illustrate the split intein system for in vivo detection of protein-protein interactions. FIG. 13A shows a schematic of the binding interaction between the SARS-CoV-2 spike protein and the human ACE2 receptor. The receptor binding domain (RBD) of Spike protein is darkened. FIG. 13B shows a structural representation of the spike-ACE2 interaction. Only the spike RBD and the two N-terminal helices of ACE2 are shown. PDB ID: 6M17 97. FIG. 13C shows a schematic for the detection of a binding event between a RiPP and target. FIG. 13D illustrates inducible interaction-mediated splicing. The median fluorescence is shown as a function of the expression of the two halves of the sensor proteins. The induction of PMI-and Mdm2-driven association (left) or split intein alone (right) are shown. FIG. 13E shows the specificity calculated using the data in FIG. 13D: (Mdm2*−PMI)/(no bait-no peptide). The white dot in the lower right quadrant marks the highest fold-change in expression. FIG. 13F shows the fluorescence measured from the circuit containing a binding pair (Mdm2:PMI) and non-binding pairs. The 3O6-AHL concentration for all inductions was 1 μM. Three replicates and the mean values are shown. FIG. 13G shows a schematic of the RiPP-containing half of the split intein system. The modified core residue positions are shaded, and the RS for the modifying enzyme is shown within the leader. FIG. 13H shows the structure of the wild-type PapA modified peptide with a dashed box around the region used to design the peptide library. FIG. 13I shows a library sequence weblogo for the 9 unmodified library variants observed. FIG. 13J shows a library sequence weblogo for the 5 modified library variants observed.



FIGS. 14A-14F show a selection system to identify RBD-binding RiPPs. FIG. 14A shows a genetic circuit diagram for the RBD-binding RiPP selection system that is distributed across three plasmids and two genomic regions. Three small molecules: 3OC6-AHL, aTc, and cumate control the expression of the RiPP peptide, modifying enzyme 1, and modifying enzyme 2 (if present), respectively. FIG. 14B shows a schematic of selection output under two conditions: with an RBD-binding RiPP (top) and without an RBD-binding RiPP (bottom). Binding is shown to result in the production of chloramphenicol acetyltransferase (CAT; squares), such that bacteria in which an RBD-binding RiPP is expressed are selected based on chloramphenicol (Cm) resistance. FIG. 14C shows an overview of the positive of selection applied. Selection rounds were conducted in the presence of RiPP peptide and modifying enzymes and used increasing Cm concentrations for increased stringency. FIG. 14D shows a core scaffold for the pap2c library (lbAMK-103). Predicted macrocyles are indicated by brackets above constrained residues and “X” residues correspond to NNK translated amino acids. FIG. 14E show cytometry distributions for positive selections on the pap2c library beginning with no selection, round 2, and round 3 of positive selections (0, 800, and 1200 μM Cm, respectively). Fluorescence of the sfGFP fused to CAT is reported. FIG. 14F shows the measured fluorescence induced by an RBD-specific hit isolated from genetic selection. The RBD-binding RiPP was used as peptide against the non-specific bait (Mdm2*) and specific bait (RBD). The means were calculated from median fluorescence intensity of three replicates.



FIGS. 15A-15F show characterization of AMK-1057, a cyclic peptide that binds human-derived Spike RBD in vitro. FIG. 15A show a schematic of the peptide expression, modification, cleavage and purification steps. TEV cleavage removes the SUMO tag and HPLC purification produces the final product. Following TEV cleavage, a single G from the leader is left at the N-terminus of the product peptide. FIG. 15B shows high-resolution MS of unmodified AMK-1057 (top trace) and singly modified AMK-1057 (bottom trace). FIG. 15C shows high-resolution MS/MS of modified AMK-1057 and fragment mapping to the amino acid sequence. Numbered peaks correspond to fragment ions observed and represented as lettered amino acids next to MS/MS spectrum. FIG. 15D shows structural annotation of AMK-1057. FIG. 15E shows binding of purified, modified AMK-1057 to Spike RBD296-531 derived from a human cell line. Vertical dotted line indicates the start of the dissociation phase of the measurements. FIG. 15F shows binding of purified, unmodified AMK-1057 to human-derived Spike RBD. Vertical dotted line indicates the start of the dissociation phase of the measurements.



FIGS. 16A-16B illustrates cell competition for ACE2 binding by AMK-1057:RBD complex. FIG. 16A shows a schematic of ACE2 receptor binding inhibition by binding of AMK-1057 to RBD. FIG. 16B shows cytometry distributions for positive control (top trace; cells incubated with RBD only), negative control (bottom trace; cells incubated with vehicle), and cells incubated with RBD pre-incubated with 5 μM or 50 μM AMK-1057. Fluorescence signal represents fluorescence from labeled RBD.



FIGS. 17A-17B show optimization of binding affinity by tuning peptide expression. FIG. 17A shows comparisons of measured peptide binding to an on-target bait or an off-target bait under conditions of low peptide expression. FIG. 17B shows comparisons of measured peptide binding to an on-target bait or an off-target bait under conditions of high peptide expression. The results demonstrate that tuning expression allows characterization of peptide binding.



FIGS. 18A-18B show directed evolution of AMK-1057. FIG. 18A shows variant enrichment for single amino acid substitutions. Heatmap shows variant enrichment relative to the parent peptide. Arrows indicate selected core positions with substitutions that yielded positive enrichment. FIG. 18B show cytometry data for consensus variants containing up to 3 amino acid substitutions per variant, at the three positions indicated by arrows in FIG. 18A. The labeled peptide name indicates the respective amino acids at each of the three selected positions (e.g., “IVE” indicates that the indicated core amino acids were IVE rather than AVE in the parent peptide).



FIGS. 19A-19C show competition of AMK-1057 binding to RBD, measured via bio-layer interferometry. FIG. 19A shows AMK-1057 interferometry results measured with RBD in the presence of B38 antibody that does not overlap with the RBD ACE2 binding site. FIG. 19B shows AMK-1057 interferometry results measured with RBD in the presence of CR3022 antibody which overlaps with the RBD ACE2 binding site. FIG. 19C shows AMK-1057 interferometry results measured with RBD and AMK-1057 alone.



FIG. 20 shows an outline of native RiPP biosynthesis and export.



FIG. 21 shows the data mining strategy used to identify candidate peptide clusters. HMP microbial genomes were scanned for RiPP BGCs using AntiSMASH 4.0, a sequence similarity network generated for BGCs using BiG-SCAPE, and visualized using Cytoscape.



FIG. 22 shows a sequence similarity network of human microbiome RiPP BGCs. antiSMASH 4.0 was used to identify BGCs from 2,229 HMP genome sequences. 2,233 RiPP BGCs were clustered using BiG-SCAPE and visualized with Cytoscape. Nodes represent individual clusters shaded according to biosynthetic class. BGC nodes with similar cluster architecture are attached by edges.



FIGS. 23A-23E show a platform for large-scale RiPP BGC mining from sequence data. FIG. 23A shows the typical organization and native processing of a lanthipeptide BGC (the BGC and cartoon structure of nisin is shown). A ribosomally produced precursor peptide (RiPP) is dehydrated, cyclized, and cleaved to produce a mature antimicrobial cyclic peptide, nisin. lanA, precursor peptide; lanBC, lanthionine synthetase; lanT, transport; lanIFEG, immunity; lanP, leader peptide cleavage; lanRK, transcriptional regulation. FIG. 23B shows the typical organization and native processing of a lasso peptide BGC (the BGC and cartoon structure of microcin J25 is shown). A RiPP is cleaved and cyclized to produce a mature antimicrobial cyclic peptide, microcin J25. lasA, precursor peptide; lasBC, lasso peptide synthetase; last, transporter. FIG. 23C shows an engineered peptide expression system for lanthipeptides. An N-terminal hexa-histidine-SUMO fusion tag (HS-tag) followed by a protease site and precursor peptide allows for stabilized expression of putative lanthipeptide peptide sequences. Expression with putative modifying enzymes followed by affinity purification and in vitro proteolysis yields mature, processed peptide for assaying biological activity. FIG. 23D shows an engineered peptide expression system for lasso peptides. A C-terminal HS-tag was used instead of N-terminal to allow for leader peptide cleavage as part of biosynthesis. FIG. 23E shows a schematic for screening of engineered peptides. In the screening method, DNA sequences for putative precursor peptides and core biosynthetic enzymes are synthesized on medium copy plasmid backbones and transformed into an expression strain of E. coli in 96-well density. Expression, purification, processing, LC-MS analysis, and biological activity testing can all be done in 96-well plates.



FIG. 24 shows a taxonomic tree of lanthipeptide and lasso peptide producing organisms selected for heterologous expression.



FIG. 25 shows an example RiPP BGC and basic two-plasmid expression system for heterologous expression. HS, hexa-histidine-SUMO fusion tag.



FIG. 26 shows LC-MS traces corresponding to the BGC cluster shown in FIG. 25. The larger trace shows total ion chromatogram (TIC) for the peptide expressed alone or with modifying enzyme. The inset trace shows mass shifts from mass spectra taken from TIC peaks. Mass loss corresponds to multiple dehydrations indicating enzymatic modification.



FIG. 27 shows the results of tandem MS and HSEE analysis to annotate peptide structure. Single letters correspond to amino acids; lowercase b indicates dehydrobutyrine.



FIGS. 28A-28E show results of analysis of data mined for putative tailoring enzymes using the Marionette expression system, which enables high-throughput assaying of such enzymes. FIG. 28A shows the relative abundance of pfam domain occurrence in genetic proximity to lanBC modifying enzymes involved in type I lanthipeptide biosynthesis. FIG. 28B shows the relative abundance of pfam domain occurrence in genetic proximity to lanM modifying enzymes involved in type II lanthipeptide biosynthesis. FIG. 28C shows the relative abundance of pfam domain occurrence in genetic proximity to lanM modifying enzymes involved in type III lanthipeptide biosynthesis. FIG. 28D shows the relative abundance of pfam domain occurrence in genetic proximity to lasBC modifying enzymes involved in lasso peptide biosynthesis. FIG. 28E shows a schematic of the strategy for mining tailoring enzymes using the Marionette collection of orthogonal inducible promoters. In the screening strategy, putative precursor peptides (lanA), core modifying enzymes (lanBC), and putative tailoring enzymes (lanH1-3) are synthesized on individual plasmids and a one-pot type IIs assembly reaction generates a single modifying enzyme plasmid for use in co-expression platform. Each putative enzyme is under control of a separate inducer, allowing for systematic interrogation of function.



FIG. 29 shows RiPPs mined from diverse strains of the human microbiome. Peptides are organized by producing organism niche. Gene clusters are highlighted for open reading frames that were synthesized and heterologously expressed. Arrows show putative peptides, putative lanthionine synthetases, and putative tailoring enzymes. TIC traces are shown to the right of clusters with shading indicating eluted peptides. The peptide structures shown are annotated through tandem MS and HSEE.



FIG. 30 shows lasso peptides identified by mining the human microbiome.



FIGS. 31A-31D show identified candidate lanthipeptide tailoring enzymes. FIGS. 31A, 31B, and 31C show source BGCs and producing organisms followed by TIC traces+/−expression of tailoring enzymes and MS of largest peak. Precursor peptides (lanA, lanA1, lanA2) and modifying enzymes (lanM, lanB, lanC) are displayed, as are putative tailoring enzymes (lanH1, lanH2, and lanH3). BLAST was used to assign hypothetical tailoring enzyme annotations. In FIG. 31A, a flavodoxin-containing protein causes the production of a peak difficult to resolve via MS. In FIG. 31B, combined expression of OsmC family peroxiredoxin and truncated N-terminus of a lanM results in generation of a peak with a mass shift of +535.4 Da. In FIG. 31C, combined expression of a hut-D-like cupin, SM1 toxin immunity, and KptA-like protein resulted in generation of a peak with a mass shift of −533.2 Da. FIG. 31D shows TIC traces for expression of peptide and different tailoring enzymes from the M. odoratimimus BGC shown in FIG. 31C. These results demonstrate that KptA-like protein is required for modification of the peptide. The modified peptide corresponds to mass observed in FIG. 31C.



FIGS. 32A-32D show phylogenetic analysis of lanthipeptide producers. FIG. 32A shows a phylogenetic tree of all lanthipeptide producers. Organisms with BGCs that were successfully expressed in E. coli and detected are shaded. The tree was generated using NCBI taxonomic identifiers. FIG. 32B shows type I lanthipeptide synthetase (LanBC) modifications, which use glutamyl-tRNA (tRNAGlu) to glutamylate Serine/Threonine residues for dehydration and subsequent cyclization. FIG. 32C shows type II/III lanthipeptide synthetase (LanM/K) modifications, which use ATP to phosphorylate Serine/Threonine residues for dehydration and subsequent cyclization. FIG. 32D shows a phylogenetic tree generated using tRNAGlu sequences from type I lanthipeptide producers investigated herein. Organisms with BGCs that were successfully expressed in E. coli and detected are shaded.



FIGS. 33A-33B show results of screens for RiPP antimicrobial activity. FIG. 33A shows select images of zones of inhibition from disc-diffusion assays of purified lanthipeptides. For each row of images, the compound ID, microbiome niche, and producing organism are listed. Indicator organisms used are organized in columns. Circles in each image highlight zones of inhibition observed. FIG. 33B shows a heat map displaying residual growth in the presence of a set amount of SPE-purified RiPP. Residual growth was calculated for all indicator organisms as a ratio of OD600 measured in comparison to growth and sterility controls. These data demonstrate that lanthipeptides mined from the human microbiome have unique antimicrobial fingerprints.



FIG. 34 shows heat maps displaying residual growth in the presence of serial dilutions of antimicrobial lanthipeptides. Compound ID, microbiome niche, and producing organisms are displayed above each antimicrobial profile. Each row corresponds to the indicator organism grown in the presence of a 2-fold serial dilution of SPE-purified peptide. These results demonstrate that lanthipeptides mined from the human microbiome are active against MDR pathogens.



FIGS. 35A-35F show sequence-activity relationships of selected peptides. FIG. 35A shows cluster-associated Streptococcus-derived lanthipeptide core sequences. Amino acid similarity is annotated by extent of blue shading and consensus identity displayed above core sequences. Alignment was generated using the Geneious global alignment tool with free end gaps and a Blosum62 cost matrix. FIG. 35B shows the antimicrobial profiles of selected lanthipeptides against human microbiome bacterial strains. FIG. 35C shows the predicted structure of the related lanthipeptides from hypothetical structural annotation. Modified amino acids are shown with thick outlines. ‘b’ indicates dehydrobutyrine and ‘a’ indicates dehydroalanine. FIG. 35D shows amino acid sequence alignment of Rothia-derived cluster-associated lasso peptide core sequences. Amino acid similarity is annotated by darkness of shading, and the consensus identity sequence is displayed above the cored sequences. Alignment was generated using the Geneious global alignment tool with free end gaps and a Blosum62 cost matrix. FIG. 35E shows the antimicrobial profiles of selected lasso peptides against human microbiome bacterial strains. FIG. 35F shows the predicted structure of the related lasso peptides from hypothetical structural annotation. Modified amino acids are shown with thick outlines.



FIG. 36 shows peptide motifs for modification by LynD, PlpXY, PalS, PadeK, PaaA, ThcoK, TgnB, LasF, and EpiD enzymes. In each motif, the amino acid(s) modified by each respective enzyme are bolded. The boxed core peptide sequence shows the parental sequence, and the amino acids annotated below each position show the options that are allowable for each modification enzyme. The left-most boxed amino acids in the LynD (LAELSEEAL (SEQ ID NO: 84)), PlpXY (LNEEELEAIAG (SEQ ID NO: 85)), PaaA (SQRISAIT (SEQ ID NO: 86)), and TgnB (PYIAKYV (SEQ ID NO: 87)) motifs show the leader recognition site (RS) sequences, and the distance ranges annotated above the LynD, PlpXY, and TgnB motifs indicate the limitation on available distances between the RS and the amino acid to be modified.



FIGS. 37A-37F show identification of a peptide motif to be modified by three distinct enzymes (two leader-dependent enzymes and one tailoring enzyme). FIG. 37A shows an example schematic of a peptide motif (leader+core) with three modifying enzymes. FIG. 37B shows an example motif with three particular modifications incorporated by three distinct enzymes (top) and the chemical structure of an example peptide with those modifications. FIG. 37C shows the peptide motif generated by combining the distinct motif restrictions for LynD, PlpXY, and ThcoK. In the right motif, the amino acids shown below each position in the peptide schematic indicate the allowable amino acids at each given position based on the combination of three enzyme restrictions. FIG. 37D shows a schematic of the screening method for identifying the leader sequence incorporating the LynD and PlpXY recognition sites (RSs) and the score calculated for each possible leader. FIG. 37E shows the identified peptide motif (leader+core) based on the combination of LynD, PlpXY, and ThcoK sequence restrictions. FIG. 37F shows 11 peptides isolated from screening the degenerate library built based on the motif shown in FIG. 37E. Amino acids that did not fall within the motif are shaded.



FIG. 38 shows peptide motifs built for modification by various combinations of distinct modifying enzymes, labeled to the left of each amino acid sequence. The modifications introduced by the specific combination of enzymes are shown on each amino acid sequence.



FIG. 39 shows a schematic of the Small Ubiquitin-like Modifier (SUMO) protein tag (top) used in an approach to stabilize ribosomally synthesized and post-translationally modified peptides (RiPPs), allowing modification of the core peptide sequence by modification enzymes, purification, and isolation of the modified peptide. The RiPP stabilization tag comprises an affinity-tag, a solubilization-tag, and a TEV or thrombin cleavage site, with flexible linkers separating elements. It stabilizes precursor peptides when attached to the N- or C-terminus, and is compatible with many diverse protein-modifying enzymes. Example peptide modifications facilitated thereby are also shown (bottom).



FIGS. 40A-40C show an overview of an expression system for producing modified peptides. FIG. 40A shows a schematic of N-terminal and C-terminal RiPP stabilization tags (RSTs). FIG. 40B shows a two-plasmid system used for expression of the RST-tagged precursor peptide (top) and modifying enzyme (bottom). The peptide-expressing plasmid is IPTG-inducible, and the modifying enzyme is cumate-inducible. FIG. 40C shows a schematic of the subsequent analysis steps following peptide synthesis. Peptides extracted from their host cells are analyzed by LCMS for mass shifts associated with modification. The low molecular weight of the RST allows for easier high confidence analysis of the modification.



FIG. 41 shows stabilization of unmodified peptides from diverse RiPP classes using the SUMO tag. SUMO protein successfully stabilized expression of seven precursor peptides with varying lengths and amino acid compositions, each from a different RiPP family, with two additional peptides stabilized after cleavage (presumably by endogenous E. coli proteases). In comparison, HIS6 tag only successfully showed four minor peptide peaks. Boxes in the microviridin, bottromycin, streptide, pyrroloquinoline quinone, lanthipeptide, thiopeptide, and pheganomycin traces indicate that the given peak was present in sample, absent in the negative control, and had the expected mass; boxes in the sactipeptide and trifolitoxin traces indicate that the given peak was present in sample, absent in the negative control, but did not have the expected mass.



FIGS. 42A-42E show characterization of RST-tagged haloduracin A1 (HalA1) and A2 (HalA2) peptides, demonstrating that RST-tagged peptides can be modified, cleaved, and purified as bioactive molecules. FIG. 42A shows schematics of both RST-tagged HalA1 and HalA2 peptides, which were engineered to have TEV cleavage sites in between the leader and core peptides, with RSTN tags. FIG. 42B shows the post-cleavage structures of HalA1 and HalA2. After expression and modification of HalA1 and HalA2, the peptides were purified by LCMS (FIG. 42C) and the SUMO tag and leader peptide were cleaved from the core (FIG. 42D). FIGS. 42C and 42D show LCMS traces for HalA1 (left) and HalA2 (right) during purification and following cleavage, respectively. FIG. 42E shows LC-MS/MS fragmentation spectra of cleaved HalA1 and HalA2, which demonstrate masses that match fragments of the structures shown in FIG. 42B. FIG. 42F shows the results of treatment of B. subtilis reporter strain with HalA1 and HalA2. The results demonstrate that HalA1 and HalA2 individually had minimal antibacterial activity, but both haloduracins together successfully inhibited bacterial growth of B. subtilis reporter strain.



FIG. 43 shows a bar chart of successful peptide/modifying enzyme combinations. Peptide plasmid number and gene name, modifying enzyme plasmid number and gene name, and replicate extract numbers are listed alongside fraction modified in TB (dark grey) and LB (light grey) medias. Dashed line demarcates 50% modification (half of peptide modified).



FIGS. 44A-44D show maps of plasmids used in Example 3. FIG. 44A shows N-term SUMO Backbone 2. FIG. 44B shows N-term SUMO Backbone 3, which is the same as N-term SUMO Backbone 2 but with flanking Bsa1 restriction sites around the peptide operon. FIG. 44C shows Cumate Modifying Enzyme Backbone. FIG. 44D shows Multi-Enzyme Backbone.



FIGS. 45A-45C show a multiply modified peptide library. FIG. 45A shows a hybrid motif combining the PlpXY, LynD, and ThcoK motifs, with modified positions bolded and showing modification where possible. The bolded tyrosine is excised in the modification process, but still shown in this motif. FIG. 45B shows the peptide sequence that was built, with degenerate nucleotide sequences shown above the peptide structure for each amino acid position, and the resulting amino acids encoded. FIG. 45C shows a set of peptide sequences that were isolated from the library. Amino acid residues that do not match the hybrid motif (shown in FIG. 45A) are shown shaded. The non-matching residues were not observed in the original data set, but were not unallowed. The degenerate nucleotide sequences resulted in production of certain peptides having certain amino acids not included in the hybrid motif. The bolded sequence labels (2582, 2583, 2585, and 2587) indicate the peptides that were successfully triply-modified.



FIG. 46 shows baseline fractional modification for modifying enzymes. Leader, core, and follower sequences were used to establish baseline. A SUMO tag is represented by a square at the beginning of each sequence. The modified residues are underlined.



FIGS. 47A-47D show leader and core amino acid sequence screening for TgnB enzyme. FIG. 47A shows results of an alanine scan (top) and deletion/addition scan (bottom) of the leader sequence, with the fraction modified, ratio modified, ΔΔG for each variant peptide and for each position of the leader sequence. FIG. 47B shows results of a peptide variant scan of the core sequence. The top amino acid sequence in bold represents the wild-type core sequence, and subsequent rows show the substituted amino acid(s) in each variant, alongside the fraction modified for each variant. FIG. 47C shows a core sequence amino acid variant tolerance summary, in which the wild-type sequence is boxed, and amino acids below the wild-type sequence represent amino acids tested at each position that were found to be tolerated, and amino acids shown above represent those tested and found to be not tolerated. FIG. 47D shows sequence constraints for the core motif, the recognition sequence, and the distance between the recognition sequence and the amino acid to be modified.



FIGS. 48A-48D show leader and core amino acid sequence screening for PlpXy enzyme. FIG. 48A shows results of an alanine scan of the leader sequence, with the fraction modified, ratio modified, ΔΔG for each variant peptide and for each position of the leader sequence (top) and candidate deletion/addition peptides (bottom). FIG. 48B shows results of a peptide variant scan of the core sequence. The top amino acid sequence in bold represents the wild-type core sequence, and subsequent rows show the substituted amino acid(s) in each variant, alongside the fraction modified for each variant. FIG. 48C shows a core sequence amino acid variant tolerance summary, in which the wild-type sequence is boxed, and amino acids below the wild-type sequence represent amino acids tested at each position that were found to be tolerated, and amino acids shown above represent those tested and found to be not tolerated. FIG. 48D shows sequence constraints for the core motif, the recognition sequence, and the distance between the recognition sequence and the amino acid to be modified.



FIGS. 49A-47C show leader and core amino acid sequence screening for PaaA enzyme. FIG. 49A shows results of an alanine scan (top) and deletion/addition scan (middle and bottom) of the leader sequence, with the fraction modified, ratio modified, ΔΔG for each variant peptide and for each position of the leader sequence. FIG. 49B shows a core sequence amino acid variant tolerance summary, in which the wild-type sequence is boxed, and amino acids below the wild-type sequence represent amino acids tested at each position that were found to be tolerated, and amino acids shown above represent those tested and found to be not tolerated. FIG. 49C shows sequence constraints for the core motif, the recognition sequence, and the distance between the recognition sequence and the amino acid to be modified.



FIGS. 50A-50D show leader and core amino acid sequence screening for LynD enzyme. FIG. 50A shows results of an alanine scan (top) and deletion/addition scan (bottom) of the leader sequence, with the fraction modified, ratio modified, ΔΔG for each variant peptide and for each position of the leader sequence. FIG. 50B shows results of a peptide variant scan of the core sequence. The top amino acid sequence in bold represents the wild-type core sequence, and subsequent rows show the substituted amino acid(s) in each variant, alongside the fraction modified for each variant. FIG. 50C shows a core sequence amino acid variant tolerance summary, in which the wild-type sequence is boxed, and amino acids below the wild-type sequence represent amino acids tested at each position that were found to be tolerated. Positions with sufficient diversity such that they are allowed to be any amino acid are annotated with a star. Positions with sufficient diversity such that they are allowed to be any amino acid except for cysteine are annotated with a dagger. FIG. 50D shows sequence constraints for the core motif, the recognition sequence, and the distance between the recognition sequence and the amino acid to be modified.



FIGS. 51A-51C show core amino acid sequence screening for EpiD enzyme. FIG. 51A shows results of a peptide variant scan of the core sequence. The top amino acid sequence in bold represents the wild-type core sequence, and subsequent rows show the substituted amino acid(s) in each variant, alongside the fraction modified for each variant. FIG. 51B shows a core sequence amino acid variant tolerance summary, in which the wild-type sequence is boxed, and amino acids below the wild-type sequence represent amino acids tested at each position that were found to be tolerated, and amino acids shown above represent those tested and found to be not tolerated. Positions with sufficient diversity such that they are allowed to be any amino acid are annotated with a star. FIG. 51C shows sequence constraints for the core motif.



FIGS. 52A-52C show core amino acid sequence screening for PalS enzyme. FIG. 52A shows results of a peptide variant scan of the core sequence. The top amino acid sequence in bold represents the wild-type core sequence, and subsequent rows show the substituted amino acid(s) in each variant, alongside the fraction modified for each variant. FIG. 52B shows a core sequence amino acid variant tolerance summary, in which the wild-type sequence is boxed, and amino acids below the wild-type sequence represent amino acids tested at each position that were found to be tolerated, and amino acids shown above represent those tested and found to be not tolerated. Positions with sufficient diversity such that they are allowed to be any amino acid are annotated with a star. FIG. 52C shows sequence constraints for the core motif.



FIGS. 53A-53C show core amino acid sequence screening for LasF enzyme. FIG. 53A shows results of a peptide variant scan of the core sequence. The top amino acid sequence in bold represents the wild-type core sequence, and subsequent rows show the substituted amino acid(s) in each variant, alongside the fraction modified for each variant. FIG. 53B shows a core sequence amino acid variant tolerance summary, in which the wild-type sequence is boxed, and amino acids below the wild-type sequence represent amino acids tested at each position that were found to be tolerated, and amino acids shown above represent those tested and found to be not tolerated. FIG. 53C shows sequence constraints for the core motif.



FIGS. 54A-54C show core amino acid sequence screening for PadeK enzyme. FIG. 54A shows results of a peptide variant scan of the core sequence. The top amino acid sequence in bold represents the wild-type core sequence, and subsequent rows show the substituted amino acid(s) in each variant, alongside the fraction modified for each variant. FIG. 54B shows a core sequence amino acid variant tolerance summary, in which the wild-type sequence is boxed, and amino acids below the wild-type sequence represent amino acids tested at each position that were found to be tolerated, and amino acids shown above represent those tested and found to be not tolerated. Positions with sufficient diversity such that they are allowed to be any amino acid are annotated with a star. FIG. 54C shows sequence constraints for the core motif.



FIGS. 55A-55C show core amino acid sequence screening for ThcoK enzyme. FIG. 55A shows results of a peptide variant scan of the core sequence. The top amino acid sequence in bold represents the wild-type core sequence, and subsequent rows show the substituted amino acid(s) in each variant, alongside the fraction modified for each variant. FIG. 55B shows a core sequence amino acid variant tolerance summary, in which the wild-type sequence is boxed, and amino acids below the wild-type sequence represent amino acids tested at each position that were found to be tolerated, and amino acids shown above represent those tested and found to be not tolerated. Positions with sufficient diversity such that they are allowed to be any amino acid are annotated with a star. FIG. 55C shows sequence constraints for the core motif.



FIG. 56 shows weblogos for the leader peptides of leader-dependent enzymes. Blastp results for each of the leaders (plus core and follower for PaaP) were aligned using Cobalt and visualized using Weblogo. Each weblogo was then aligned to the leader sequence used in Example 3. The x-axis corresponds to the position within each leader sequence and the recognition sites are outlined in boxes.



FIG. 58 shows a phylogenetic tree of species from which enzymes were mined. The tree was generated from the organisms listed in Table 13. Species from which functional enzymes were sourced are shown with a star (*).



FIG. 59 shows a summary of select non-limiting RiPP chemical modifications. Each box shows an example structure with the modified residue(s). The amino acids involved in each chemical modification are shown in the lower left corner of each box, for instances in which amino acids are chemically restrictive.





DETAILED DESCRIPTION OF THE INVENTION

Aspects of the present disclosure provide efficient methods of identifying peptide binders of target proteins using an intein-based system. As shown herein, the method is useful in identifying peptide binders of a target protein, including the viral receptor binding domain (RBD) of spike protein from SARS-CoV-2. In some embodiments, the methods disclosed herein have been used to identify modified peptide binders of RBD. Additional methods disclosed herein provide an efficient means of identifying peptides with particular properties and/or activity, such as biological activity. Libraries of peptides with useful characteristics are also provided, in addition to methods for their preparation and screening.


Without being bound by a particular theory, modified peptide binders have numerous advantages over traditional drug candidates including small molecule compounds and monoclonal antibodies (mABs). For example, small molecule compounds are often poor inhibitors of macromolecular interactions due to the physicochemical constraints of small molecule compounds; small molecule compounds are often not large enough to cover large binding interfaces. While mABs may be capable of occupying a larger binding surface area as compared to small molecule compounds, development of mABs is often slow, often taking about six months to identify a lead mAB against a target protein, have low stability, often require particular routes of administration (e.g., parenteral administration), and may have low cell penetrability. The methods and modified peptides described herein, in some embodiments, overcome many of these limitations. For example, in some embodiments, the peptide binders comprise modifications that increase stability, promote proteolytic resistance, and/or increase solubility.


Furthermore, conventional antibiotics used as drugs target diverse bacteria as part of their mode of action. This “broad-spectrum” activity has benefit in the treatment of life-threatening bacterial infections, as a single agent is able to address a large number of clinical indications. However, this broad-spectrum activity can also disrupt the subject's microbiome, leading to associated complications in health. The methods disclosed herein provide means for identifying peptides with antimicrobial activity, including narrow-spectrum activity. Narrow-spectrum antimicrobial agents are desirable to avoid microbiome disruptions and to mitigate selection pressure for widespread evolution of resistance to antibiotics. Narrow spectrum agents that can selectively remove specific bacteria are useful as both a subject-specific medicine, and as tool compounds to facilitate understanding of and manipulate the microbiome.


In early-stage drug discovery, candidate compounds are typically identified from two sources: natural products (e.g., isolated from natural sources such as plants or microbes) and combinatorial chemistry libraries of synthetic molecules. Inadequacies in ability to synthesize natural product-like molecules, as well as the prohibitive cost of identifying such molecules from nature, limit the ability to develop products (e.g., peptides) with desirable properties. In addition, molecules from combinatorial chemistry libraries lack the structural complexity necessary to identify ideal drug candidates. Engineered RiPPs provide the ability to biosynthesize structurally diverse small molecules (e.g., peptides) for screening and drug discovery.


In some embodiments, the methods disclosed herein allow for efficient methods of identifying candidate drugs against challenging therapeutic targets (e.g., targets that have been referred to as “undruggable”). Several cancer targets including KRAS, MYC, and transcription factors have been labeled as “undruggable targets” due to their large protein-protein interaction interfaces or due to the absence of protein pockets for binding. See, e.g., Whitfield et al., Front. Cell Dev. Biol. 5, 10 (2017) and McCormick et al., Clin. Cancer Res. 21, 1797-1801 (2015). In some embodiments, challenging therapeutic targets include particular microbes (e.g., drug-resistant bacteria, or bacteria of a class or species that is difficult to treat).


Split Intein-Based Selection

Aspects of the present disclosure provide methods of identifying peptide binders of a target protein using split intein-based selection system. Additional aspects of the present disclosure provide methods of identifying peptides with particular desired properties, such as biological activity using a split intein-based selection system. FIG. 1 provides a non-limiting example of a split intein-based selection system.


An intein is an internal amino acid sequence that is post-translationally autoprocessed. During protein splicing, an intein self-excises from a precursor protein and ligates the flanking N- and C-terminal amino acid sequences (exteins or external protein sequences) via a new peptide bond. For example, a precursor protein may comprise the following configuration: N-extein-intein-C-extein. Following protein splicing, the following peptide is produced: N-extein-C-extein.


The intein, however, may be provided as two separate fragments (split inteins) rather than as contiguous sequence. During trans-splicing, the two fragments of the intein have to associate before protein splicing can occur. As used herein, an N-terminal intein (N-intein) comprises the N-terminal sequence of an intein, while the C-terminal intein (C-intein) comprises the C-terminal sequence of the same intein. When split inteins are used, the N-intein is linked to the C′ terminal end of the N-extein; the C-intein is located at the N′ end of the C-extein. The N-extein and the C-intein may belong to the same protein of interest. For example, the N-extein may comprise an N-terminal fragment of a protein of interest, while the C-intein comprises the C-terminal fragment of the same protein of interest, such that when the N-intein and C-intein associate, a full-length protein of interest is formed. See, e.g., Shah and Muir, Chem Sci. 2014; 5(1):446-461.


Any complementary split intein pair may be used including those known in the art. Non-limiting examples of complementary split inteins include the N-terminal intein NpuDNAE intein N (SEQ ID NO: 68) and the C-terminal intein NpuDNAE intein C (SEQ ID NO: 67). See also, e.g., US20200055900 and Stevens et al., J Am Chem Soc. 2016 Feb. 24; 138(7):2162-5.


In some embodiments, the methods described herein comprise using split inteins. In general, unless indicated otherwise, the split intein-based selection system described herein comprises two fusion proteins and an inducible promoter operably linked to a reporter gene. For example, the first fusion protein generally comprises (i) a first fragment of a transcription factor, (ii) a first split intein, and (iii) a target protein, and the second fusion protein may comprise (i) a candidate peptide, (ii) a second split intein, and (iii) a second fragment of the transcription factor. The first and second split inteins are complementary fragments, such that association of the first split intein with the second split intein promotes trans-splicing and formation of a full-length transcription factor to drive expression from the inducible promoter. As described below, it may also be possible to use the split intein-based system described herein without the need for a reporter gene operably linked to an inducible promoter (e.g., the fragments of the transcription factor may be replaced with fragments of a reporter protein).


In some embodiments, the first fusion protein comprises (i) a first fragment of a transcription factor, (ii) a first split intein, and (iii) a target protein linked sequentially from the N-terminus to the C-terminus, in which the first fragment is an N-terminal fragment of the transcription factor and the first split intein is an N-terminal split intein; and the second fusion comprises: (i) a candidate peptide, (ii) a second split intein, and (iii) a second fragment of the transcription factor linked sequentially from the N-terminus to the C-terminus, in which the second split intein is a C-terminal split intein, and the second fragment is a C-terminal fragment of the transcription factor.


In some embodiments, from the N-terminus to the C-terminus, the first fusion protein comprises a target protein linked to a first split intein linked to a first fragment of a transcription factor in which the first fragment is a C-terminal fragment of the transcription factor and the first split intein is a C-terminal split intein; and from the N-terminus to the C-terminus, the second fusion protein comprises a second fragment of the transcription factor linked to a second split intein linked to a candidate peptide, in which the second split intein is a N-terminal split intein and the second fragment is a N-terminal fragment of the transcription factor.


The first and second fusion proteins of the split intein-based selection system described herein may be used together with a nucleic acid comprising an inducible promoter operably linked to at least one reporter gene. Without being bound by a particular theory, binding of the (i) target protein in the first fusion protein with (ii) the candidate peptide in the second fusion protein brings the complementary split-intein in each fusion protein together to allow for protein splicing and release of a full-length transcription factor. The full-length transcription factor may then drive transcription from its cognate promoter. As used herein, a transcription factor is a protein that controls transcription (e.g., drives expression of a nucleic acid that is operably linked to a promoter). In some embodiments, a transcription factor binds to a promoter and drives transcription from the promoter. In some embodiments a transcription factor is an initiation factor. In some embodiments, a transcription factor is a sigma factor.


The promoter is operably linked to a reporter gene. A promoter is a control region of a nucleic acid sequence at which initiation and rate of transcription of the remainder of a nucleic acid sequence are controlled. A promoter may also contain sub-regions at which regulatory proteins and molecules may bind, such as RNA polymerase and other transcription factors. A promoter drives expression or drives transcription of the nucleic acid sequence that it regulates. A promoter is considered to be ‘operably linked’ to a nucleotide sequence when it is in a correct functional location and orientation in relation to the nucleotide sequence to control (‘drive’) transcriptional initiation and/or expression of that sequence. Promoters may be constitutive or inducible.


An inducible promoter is a promoter that is regulated (e.g., activated or inactivated) by the presence or absence of a particular factor. Inducible promoters for use in accordance with the present disclosure include any inducible promoter described herein or known to one of ordinary skill in the art. Examples of inducible promoters include, without limitation, chemically/biochemically-regulated and physically-regulated promoters such as alcohol-regulated promoters, tetracycline-regulated promoters (e.g., anhydrotetracycline (aTc)-responsive promoters and other tetracycline responsive promoter systems, which include a tetracycline repressor protein, steroid-regulated promoters (e.g., promoters based on the rat glucocorticoid receptor, human estrogen receptor, moth ecdysone receptors, and promoters from the steroid/retinoid/thyroid 25 receptor superfamily), metal-regulated promoters (e.g., promoters derived from metallothionein (proteins that bind and sequester metal ions) genes from yeast, mouse and human), pathogenesis-regulated promoters (e.g., induced by salicylic acid, ethylene or benzothiadiazole (BTH)), temperature/heat-inducible promoters (e.g., heat shock promoters), pH-regulated promoters, and light-regulated promoters. A non-limiting example of an inducible system that uses a light-regulated promoter is provided in Wang et al., Nat. Methods. 2012 Feb. 12; 9(3):266-9.


Non-limiting examples of inducible promoters include the inducible T5 lacO promoter, which may be induced by Isopropyl β-d-1-thiogalactopyranoside (IPTG), pCym promoter, which may be induced by cumate and a sigma-factor sensitive promoter, including an extra-cytoplasmic function (ECF) promoter.


In some embodiments, the promoter operably linked to a reporter gene is an extra-cytoplasmic function (ECF) promoter and the transcription factor is a sigma factor. In some embodiments, a Sigma factor comprises the N-terminal sequence ECF20_992 N (SEQ ID NO: 70) and the C-terminal sequence ECF20_992 C (SEQ ID NO: 69). Initiation of transcription in bacteria requires a sigma factor (a factor or specificity factor). Sigma factors bind to bacterial RNA polymerase to form a holoenzyme and initiate transcription. Non-limiting examples of sigma factors include extracytoplasmic function (ECF) a factors, a70 (RpoD), a19 (FecI), a24 (RpoE), a28 (RpoF/FliA), a32 (RpoH), a38 (RpoS), and 654 (RpoN). In some embodiments, a sigma factor is not a housekeeping sigma factor. In some embodiments, a sigma factor that is used is not native to a host cell and allows for orthogonal gene expression. As a non-limiting example, a sigma factor from B. subtilis that is not naturally expressed in E. coli may be used in E. coli for orthogonal gene expression. See also, e.g., Bervoets et al., Nucleic Acids Res. 2018 Feb. 28; 46(4): 2133-2144 and Pinto et al., Nucleic Acids Res. 2018 Aug. 21; 46(14):7450-7464. As would be appreciated by one of ordinary skill in the art, a particular sigma factor may require particular promoter elements to promote transcription and/or a particular environmental trigger including, e.g., heat. In some embodiments, additional activator proteins may be required for a sigma factor to function.


Non-limiting examples of reporter genes include genes that encode fluorescent proteins, enzymes, and antibiotic resistance genes. A reporter gene may allow for positive or negative selection.


In some embodiments, a reporter gene encodes a selection marker, such as an antibiotic resistance gene (e.g., bsd, neo, hygB, pac, ble, or Sh bla) and/or a gene encoding a fluorescent protein (RFP, BFP, YFP, or GFP). In some embodiments, the antibiotic resistance gene is cat, which encodes chloramphenicol acetyltransferase. Cells may be selected for resistance to chloramphenicol by culturing the cells in the presence of chloramphenicol. In some embodiments, the selection marker enables selection of cells expressing a protein of interest (e.g., a full-length transcription factor). As would be appreciated by one of ordinary skill in the art, the effective amount of a selection agent may vary depending on the host cell and phenotype of interest.


Positive selection markers are selection markers that confer a selective advantage to a host cell. In some embodiments, positive selection is the use of such selection markers to confer a growth or survival advantage to a cell comprising a protein of interest. In some embodiments, positive selection is used to identify cells in which a candidate peptide binds a target protein. Without being bound by a particular theory, protein splicing of the fusion proteins in the split intein-based selection system disclosed herein is dependent on the association of the candidate peptide with the target protein; therefore, in the absence of a binding interaction or when the binding interaction is weak, expression of the reporter gene is low. In some embodiments, a candidate peptide binder of a target protein increases expression of the reporter gene in a host cell comprising the split intein-based selection system disclosed herein by at least 10%, at least 20%, at least 30%, at least 40%, at 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 110%, at least 120%, at least 130%, at least 140%, at least 150%, at least 200%, at least 300%, at least 400%, at least 500%, at least 600%, at least 700%, at least 800%, at least 900%, or at least 100% relative to a control. In some embodiments, a control is a control peptide that has non-specific binding to the same target protein of interest. In some embodiments, a control is the level of expression of the candidate peptide binder in a host cell that comprises a split intein-based selection system with a control target protein that is not of interest.


Negative selection markers are selection markers that confer a selective disadvantage to a host cell. In some embodiments, negative selection is the use of such selection markers to confer a growth or survival disadvantage to a cell comprising an undesirable phenotype. Non-limiting examples of negative selection markers include Herpes Simplex Virus-1 Thymidine Kinase (HsvTK). Cells expressing HsvTK can be selected against by contacting cells with nucleotide 6-(β-D-2-deoxyribofuranosyl)-3,4-dihydro8H-pyrimido [4,5-c][1,2] oxazin-7-one (dP). Without being bound by a particular theory, expression of HsvTK alone without the addition of dP does not confer a growth disadvantage, which allows for temporal control of selection. As a non-limiting example, negative selection may be used to deplete host cells comprising candidate peptides that bind off-target proteins (identify candidates that non-specifically bind to a target protein of interest); the reporter gene may comprise a negative selection gene. For example, the split intein-based selection system described herein may be used with the candidate peptide and an off-target control protein in place of the target protein of interest to identify candidate peptides that bind to the off-target protein. In this embodiment, the inducible promoter may be operably linked to a gene encoding a negative selection marker and cells expressing the negative selection marker may be depleted by contacting the cells with the negative selection agent. Without being bound by a particular theory, the expression of the negative selection marker in this system is indicative of binding between the candidate peptide and the off-target control protein. In some embodiments, a reporter gene in the split intein-based selection system described herein comprises a negative selection marker to deplete cells that comprise an undesirable candidate peptide. As a non-limiting example, it may be desirable to select for peptide binders that specifically bind a target protein when the peptide is modified (e.g., comprising one or more post-translational modifications) but not when the peptide is unmodified. In some embodiments, the unmodified peptide is used in place of the candidate peptide in the split intein-based selection system described herein along with an inducible promoter operably linked to a negative selection marker and driving expression of the negative selection marker. The cells may be contacted with the negative selection agent to deplete cells with an unmodified peptide that binds to the target protein of interest. Without being bound by a particular theory, formation of a full-length transcription factor and subsequent expression of the full-length transcription factor would be dependent on the unmodified peptide binding to the target peptide in this system.


Expression of a reporter gene may be detected by any suitable method known in the art, including by analysis of RNA (e.g., reverse transcription-polymerase chain reaction (RT-PCR)), by analysis of protein levels (e.g., immunoassays), by analysis of enzyme activity (e.g., analysis of catalytic activity), by contacting cells with one or more selection agents, or by fluorescence analysis. A reporter protein may be detected by any known method, including via fluorescence microscopy, an immunoassay (including a western blot or an ELISA), or flow cytometry.


As one of ordinary skill in the art would appreciate, any transcriptional or translational output may be coupled with the first and second fusion proteins described herein.


In some embodiments, the intein-based selection system comprises a fusion protein with (i) a first fragment of a reporter protein, (ii) a first split intein, and (iii) a target protein, and another fusion protein that comprises (i) a candidate peptide, (ii) a second split intein, and (iii) a second fragment of the reporter protein. The first and second split inteins are complementary fragments, such that association of the first split intein with the second split intein promotes trans-splicing. In this embodiment, the presence of a full-length reporter protein is indicative of the candidate protein binding the target protein.


Peptides

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a class of natural products that are modular and engineerable. In RiPP biosynthesis, the ribosome synthesizes a peptide using proteinogenic (i.e., amino acids that are biologically incorporated into proteins during translation) amino acids, and modifying enzymes subsequently bind to the peptide and modify it. Such post-translational modification introduces chemical diversity beyond the 20 standard amino acids, as well as structural diversity such as macrocyclization. Each modifying enzyme is constrained by a set of design rules, such as which amino acid(s) they can modify, the recognition site(s) (RSs) they will associate with, the distance (e.g., number of amino acids) between the RS and the amino acid residue(s) to be modified, and the amino acid context in which they can act (e.g., the amino acids in proximity to the target amino acid(s) that they modify). Synthetic peptides with particular activity (e.g., desired biological activity), and libraries thereof, can be constructed by incorporating the design constraints of one or a combination of modification enzymes into a peptide synthesis scheme.


In some embodiments, a RiPP comprises a leader amino acid sequence and a core amino acid sequence. In some embodiments, the leader and the core are connected via a cleavable linker (e.g., a protease-cleavable linker). In some embodiments, a RiPP comprises one or more (e.g., 1, 2, 3, 4, 5, 6, or more) recognition sites (RSs) for one or more distinct modification enzymes.


Aspects of the present disclosure relate to peptides for identification of binders to a target protein (e.g., candidate peptides or a plurality thereof) and peptides that may be useful in clinical applications. A candidate peptide is a peptide whose binding activity to a protein is being investigated. In some embodiments, a peptide comprises a sequence that is at least 60%, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NOs: 6-25 or 26-45, an amino acid sequence in Table 3 or any amino acid sequence disclosed herein, including fragments thereof.


The peptides described herein may be modified (e.g., the peptide may comprise a non-natural amino acid, a non-naturally occurring linkage, and/or a post-translational modification). In some embodiments, a modified peptide comprises a post-translational modification. In some embodiments, a modified peptide is produced recombinantly. In some embodiments, a modified peptide is produced synthetically. Without being bound by a particular theory, recombinant production of a modified peptide using a host cell may require expression of one or more protein modification enzymes. In some embodiments, the peptide is non-naturally occurring. In some embodiments, the peptide is naturally occurring.


Without being bound by a particular theory, a peptide comprising one or more modifications may be more stable (e.g., has reduced denaturation at a particular temperature), have increased bioavailability, and/or have increased solubility compared to a peptide not comprising the one or more modifications.


Non-limiting examples of post-translational modifications include formation of thioether bridges, formation of ester bridges, phosphorylation, glycosylation, acetylation, ubiquitylation/sumoylation, methylation, palmitoylation, myristoylation, prenylation, hydroxylation, GPI anchoring, ADP-ribosylation, pyrrolidone carboxylic acid, citrullination, S-nitrosylation, sulfation, amidation, nitration, oxidation, gamma-carboxyglutamic acid, topaquinone, lysine topaquinone, phosphopantetheine, quinone, hypusine, iodination, bromination, cysteine tryptophylquinone, formylation, and tryptophan tryptophylquinone.


In some embodiments, a peptide described herein is a ribosomally synthesized and post-translationally modified peptide (RiPP). RiPPs are ribosomally-produced peptides that comprise a post-translational modification. There are several subfamilies of RiPPs and RiPPs are grouped based on the biosynthetic machinery that produce the RiPP and structural characteristics. See, e.g., Table 1 below, which is based on Table 1 from Ortega and van der Donk, Cell Chem Biol. 2016 Jan. 21; 23(1):31-44; and Arnison et al., Nat Prod Rep. 2013 January;30(1):108-60.


In some embodiments, a modified peptide comprises two or more (e.g., at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20) non-contiguous amino acids that are linked. In some embodiments, a modified peptide comprises at least 1 pair, at least 2 pairs, at least 3 pairs, at least 4 pairs, at least 5 pairs, at least 6 pairs, at least 7 pairs, a least 8 pairs, at least 9 pairs, at least 10 pairs, at least 15 pairs, at least 20 pairs, at least 30 pairs, at least 40 pairs, or at least 50 pairs) of non-contiguous amino acids that are linked. As a non-limiting example, scaffold L1 in FIG. 3 comprises two pairs of non-contiguous amino acids that are linked. As will be understood by one of ordinary skill in the art, two or more amino acids may be linked as valency permits.


In some embodiments, a peptide comprises at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, a least 24, at least 25, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, at least 90, or at least 100 thioether bridges. In some embodiments, a peptide comprises at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, a least 24, at least 25, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, at least 90, or at least 100 ester bridges. In some embodiments, a peptide comprises a thioether bridge and an ester bridge.


As an example, lanthipeptides comprise Lan and/or MeLan thioether bis-amino acids. In some embodiments, a peptide is a lanthipeptide. In some embodiments, a lanthipeptide comprises scaffold Li: AACX1X2X3X4X5X6MPPX7X8X9X10X11X12C (SEQ ID NO: 1), wherein: X6 and X7 are each the amino acid S or T; X1-X5 and X8-X12 are each any amino acid; and the peptide comprises a thioether bridge that links C at position 3 to S or T at position 9 in SEQ ID NO: 1 and a thioether bridge that links S or T at position 13 to C at position 19 in SEQ ID NO: 1. See, e.g., L1 in FIG. 3.


In some embodiments, a peptide is a microviridin. Microviridins may comprise lactones made from Glu/Asp and Ser/Thr side chains and/or lactams made from Lys and Glu/Asp residues. In some embodiments, a microviridin comprises X1PX2TTX3X4TX5X6X7EX8X9DX10DEX11X12X13 (SEQ ID NO: 2) (scaffold L2), wherein: X2 is the amino acid H, Q, N, K, D, or E; X6 is the amino acid F, L, S, I, M, T, V, or A; X7 is the amino acid F, L, I, or V; X1, X3-X5 and X8-X13 are each any amino acid; and the peptide comprises an ester bridge that links T at position 5 of SEQ ID NO: 2 to D at position 15 of SEQ ID NO: 2 and an ester bridge that links T at position 8 of SEQ ID NO: 2 to E at position 12 of SEQ ID NO: 2. See, e.g., L2 in FIG. 3.


In some embodiments, a peptide comprises a sactipeptide (ranthipeptide). Sactipeptides comprise one or more intramolecular thioether linkages between Cys side chains and α-carbons of other amino acids. In some embodiments, a sactipeptide comprises: X1CX2X3X4X5X6CX7X8X9X10X11 (SEQ ID NO: 3) (scaffold L3), wherein: X5 and X10 are each the amino acid D or E; X1-X4, X6-X9, and X11 are each any amino acid; and the peptide comprises a thioether bridge that links C at position 2 to D or E at position 6 of SEQ ID NO: 3 and a thioether bridge that links C at position 8 to D or E at position 12 of SEQ ID NO: 3. See, e.g., L3 in FIG. 3. In some embodiments, a peptide comprising scaffold L3 comprises a sequence that is at least 60%, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a sequence selected from SEQ ID NOs: 17-25.


In some embodiments, a sactipeptide comprises X1CX2X3CX4X5X6X7X8X9 (SEQ ID NO: 4) (scaffold L4), wherein: X4 and X7 are each the amino acid D or E; X1-X3, X5-X6, and X8-X9 are each any amino acid; and the peptide comprises a thioether bridge that links C at position 2 to D or E at position 6 of SEQ ID NO: 4 and a thioether bridge that links C at position 5 to D or E at position 9 of SEQ ID NO: 4. See, e.g., L4 in FIG. 3. In some embodiments, a sactipeptide comprises X1CX2X3X4X5X6CX7X8CX9X10X11X12X13 (SEQ ID NO: 5), wherein: X5, X9, and X12 are each the amino acid D or E; X1-X4, X6-X8, X10-X11, and X13 are each any amino acid; and the peptide comprises a thioether bridge that links the C at position 2 to D or E at position 6 of SEQ ID NO: 5, a thioether bridge that links C at position 8 of SEQ ID NO: 5 with D or E at position 12 of SEQ ID NO: 5, and a thioether bridge that links C at position 11 with D or E at position 15 of SEQ ID NO: 5. See, e.g., L5 in FIG. 3. In some embodiments, a peptide comprising scaffold L5 comprises a sequence that is at least 60%, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a sequence selected from SEQ ID NOS: 6-16.


In some embodiments, a peptide described herein has biological activity, e.g., antimicrobial activity. In some embodiments, peptides having antimicrobial activity are modified from RiPPs of microbiome bacteria from a subject, such as a human subject. Non-limiting examples of bacteria from which RiPPs can be modified to have antimicrobial activity include the Flavobacteria, Proteobacteria, Actinobacteria, Erysipelotrichia, Clostridia, Bacilli provided in FIG. 24, or the bacteria provided in FIG. 32A and FIG. 32D. In some embodiments, a peptide having antimicrobial activity (e.g., a modified RiPP) comprises at least 15 (e.g., 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 39, 40, 41, or 42) consecutive amino acids of the sequence GTFSX1GX2X3X4X5X6X7X8X9X10X11GX12DGVX13X14TX15SHECHMNTWQFLX16TCCS (SEQ ID NO: 88) or GX12DGVX13X14TX15SHECHMNTWQFL (SEQ ID NO: 938); wherein: X1 is G or E; X2 is W or T; X3 is F or I; X4 is T or S; X5 is A or I; X6 is I or T; X7 is Q or L; X8 is L or S; X9 is T, V, or G; X10 is L, Y, or S; X11 is A, M, R, or G; X12 is R, G, N, W, or K; X13 is W, M, V, L or F; X14 is F, H, C, P, or K; X15 is G, L, W, V, or I; and X16 is L, F, or A. In some embodiments, a peptide having antimicrobial activity (e.g., a modified RiPP) comprises a sequence that is at least 60%, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a sequence selected from GGWFTAIQLTLAGRCGNWFTGSFECTSNNVKCG (SEQ ID NO: 89); GGDGVMHTLTHECHMNTWQFLLTCC (SEQ ID NO: 90); GTFSEGTISITLSVYMGNDGKVCTWTVECQNNCSHKK (SEQ ID NO: 91); GSRWWQGVLPTVSHECRMNSFQHIFTCC (SEQ ID NO: 92); or GGKNGVFKTISHECHLNTWAFLATCCS (SEQ ID NO: 93). In some embodiments, a peptide having antimicrobial activity (e.g., a modified RiPP) comprises a sequence selected from GGWFTAIQLTLAGRCGNWFTGSFECTSNNVKCG (SEQ ID NO: 88); GGDGVMHTLTHECHMNTWQFLLTCC (SEQ ID NO: 90); GTFSEGTISITLSVYMGNDGKVCTWTVECQNNCSHKK (SEQ ID NO: 91); GSRWWQGVLPTVSHECRMNSFQHIFTCC (SEQ ID NO: 92); and GGKNGVFKTISHECHLNTWAFLATCCS (SEQ ID NO: 93). In some embodiments, a peptide having antimicrobial activity (e.g., a modified RiPP) comprises a sequence that is at least 60%, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a sequence selected from IDTLDYEISHQELSGKSAAGWQTAFRLTMQGRCGGVFTLSYECATPHVSCG (SEQ ID NO: 97); GGWYTAFKLTLAGRCGLCFTCSYECTSNNVHC (SEQ ID NO: 98); and GWFTAIQLTLAGRCGNWFTGSFECTSNNVKCG (SEQ ID NO: 99). In some embodiments, a peptide having antimicrobial activity (e.g., a modified RiPP) comprises a sequence selected from IDTLDYEISHQELSGKSAAGWQTAFRLTMQGRCGGVFTLSYECATPHVSCG (SEQ ID NO: 97); GGWYTAFKLTLAGRCGLCFTCSYECTSNNVHC (SEQ ID NO: 98); and GWFTAIQLTLAGRCGNWFTGSFECTSNNVKCG (SEQ ID NO: 99). In some embodiments, a peptide having antimicrobial activity (e.g., a modified RiPP) comprises a sequence that is at least 60%, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a sequence selected from SEQ ID NOs: 115-147, 758-783, 820, and 821. In some embodiments, a peptide having antimicrobial activity (e.g., a modified RiPP) comprises a sequence of any one of SEQ ID NOs: 115-147, 758-783, 820, and 821. In some embodiments, a peptide having antimicrobial activity comprises at least 15 (e.g., 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more) consecutive amino acids of any one of Lacticin 481, AMK287, AMK417, AMK419, AMK687, or AMK691, or of of any one of SEQ ID NOs: 115-147, 758-783, 820, or 821. In some embodiments, a peptide having antimicrobial activity (e.g., a modified RiPP) comprises at least 15 (e.g., 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, or 34) consecutive amino acids of the sequence GGGWX1TAFX2LTLAGRCGX3X4FTX5SYECTSNNVX6CG (SEQ ID NO: 94), wherein: X1 is F, Y, or Q; X2 is Q, K, or R; X3 is N, L, or G; X4 is W, C, or V; X5 is G, C, or L; X6 is K, H, or S. In some embodiments, a peptide having antimicrobial activity (e.g., a modified RiPP) comprises a sequence that is at least 60%, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a sequence selected from GGGWFTAIQLTLAGRCGNWFTGSFECTSNNVKCG (SEQ ID NO: 100), GGGWYTAFKLTLAGRCCGLCFTCSYECTSNNVHC (SEQ ID NO: 101), and GWQTAFRLTMQGRCGGVFTLSYECATPHVSCG (SEQ ID NO: 96). In some embodiments, a peptide having antimicrobial activity (e.g., a modified RiPP) comprises a sequence selected from GGGWFTAIQLTLAGRCGNWFTGSFECTSNNVKCG (SEQ ID NO: 100), GGGWYTAFKLTLAGRCCGLCFTCSYECTSNNVHC (SEQ ID NO: 110), and GWQTAFRLTMQGRCGGVFTLSYECATPHVSCG (SEQ ID NO: 96).


In some embodiments, a peptide having antimicrobial activity (e.g., a modified RiPP) comprises at least 15 (e.g., 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, or 34) consecutive amino acids of the sequence GSX1GX2X3GVX4X5TX6SHECHMNTWQFLX7TCCS (SEQ ID NO: 95), wherein: X1 is R or G; X2 is G, W, or K; X3 is D, Q, or N; X4 is M, L, or F; X5 is H, P, or K; X6 is L, V, or I; and X7 is L, F, or A;. In some embodiments, a peptide having antimicrobial activity (e.g., a modified RiPP) comprises a sequence that is at least 60%, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a sequence selected from GGDGVMHTLTHECHMNTWQFLLTCC (SEQ ID NO: 90), GSRWWQGVLPTVSHECRMNSFQHIFTCC (SEQ ID NO: 92), and GGKNGVFKTISHECHLNTWAFLATCCS (SEQ ID NO: 93). In some embodiments, a peptide having antimicrobial activity (e.g., a modified RiPP) comprises a sequence selected from GGDGVMHTLTHECHMNTWQFLLTCC (SEQ ID NO: 90), GSRWWQGVLPTVSHECRMNSFQHIFTCC (SEQ ID NO: 92), and GGKNGVFKTISHECHLNTWAFLATCCS (SEQ ID NO: 93).


In some embodiments, a peptide having antimicrobial activity (e.g., a modified RiPP) comprises at least 15 (e.g., 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, or 42) consecutive amino acids of the sequence GWX1WGSYRDX2YGALRGPNX3X4FVGX5GGX6X7X8X9X10X11X12X13X14SWRLVPR (SEQ ID NO: 102), wherein: X1 is I, F, L, or Y; X2 is V or I; X3 is P, S, T, or K; X4 is P, G, N, or R; X5 is L, G, A, or R; X6 is V, F, or S; X7 is P, T, or S; X8 is P, G, or E; X9 is G or W; X10 is G or R; X11 is V or L; X12 is S or V; X13 is G or P; and X14 is G or R. In some embodiments, a peptide having antimicrobial activity (e.g., a modified RiPP) comprises a sequence that is at least 60%, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a sequence selected from GLIYGKYRDVLSGARLVTPPEVALRLVPR (SEQ ID NO: 103), GWFWGSYRDIFGALRGPNSGFEGGGGFTGGGVSGGSWRLVPR (SEQ ID NO: 104), GWLWGSYRDVYGVWHGPRTNFNGAGGSSEWRLVPR (SEQ ID NO: 105), and GWYWGNRRDIYGALRYANKRLVPR (SEQ ID NO: 106). In some embodiments, a peptide having antimicrobial activity (e.g., a modified RiPP) comprises a sequence selected from GLIYGKYRDVLSGARLVTPPEVALRLVPR (SEQ ID NO: 103), GWFWGSYRDIFGALRGPNSGFEGGGGFTGGGVSGGSWRLVPR (SEQ ID NO: 104), GWLWGSYRDVYGVWHGPRTNFNGAGGSSEWRLVPR (SEQ ID NO: 105), and GWYWGNRRDIYGALRYANKRLVPR (SEQ ID NO: 106).


In some embodiments, a peptide having antimicrobial activity (e.g., a modified RiPP) comprises a sequence that is at least 60%, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to GVGYbbYWGILPLVbKNPQIAPVaENbVKARLL (SEQ ID NO: 107), wherein ‘b’ is dehydrobutyrine and ‘a’ is dehydroalanine, and wherein a thioether bridge connects the dehydrobutyrine at position 15 to the alanine at position 21, and a thioether bridge connects the dehydrobutyrine at position 27 to the alanine at position 30. In some embodiments, a peptide having antimicrobial activity (e.g., a modified RiPP) comprises the sequence GVGYbbYWGILPLVbKNPQIAPVaENbVKARLL (SEQ ID NO: 107), wherein ‘b’ is dehydrobutyrine and ‘a’ is dehydroalanine, and wherein a thioether bridge connects the dehydrobutyrine at position 15 to the alanine at position 21, and a thioether bridge connects the dehydrobutyrine at position 27 to the alanine at position 30.


In some embodiments, a peptide having antimicrobial activity (e.g., a modified RiPP) comprises a sequence that is at least 60%, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a sequence provided in Table 12 (SEQ ID NOs: 115-147).


In some embodiments, a peptide having antimicrobial activity is selectively active against a particular class, genera, species, or strain of bacteria. In some embodiments, a peptide having antimicrobial activity does not kill commensal bacteria of a subject. In some embodiments, a peptide having antimicrobial activity kills pathogenic bacteria. In some embodiments, a peptide having antimicrobial activity is selective towards pathogenic bacteria over commensal bacteria. In some embodiments, a peptide having antimicrobial activity is selective towards bacteria of a first class, genera, species, or strain over bacteria of a second class, genera, species or strain. In some embodiments, being selective towards a first population of bacteria over a second population of bacteria means the peptide kills bacteria of the first population of bacteria at a concentration that is at least 5% lower (e.g., at least 10% lower, 15% lower, 20% lower, 25% lower, 30% lower, 35% lower, 40% lower, 45% lower, 50% lower, 55% lower, 60% lower, 65% lower, 70% lower, 75% lower 80% lower, 85% lower, 86% lower, 87% lower, 88% lower, 89% lower, 90% lower, 91% lower, 92% lower, 93% lower, 94% lower, 95% lower, 96% lower, 97% lower, 98% lower, or 99% lower) than the concentration that is required to kill bacteria of the second population. In some embodiments, being selective towards a first population of bacteria over a second population of bacteria means the peptide is capable of killing bacteria of the first population, but is unable to kill bacteria of the second population.


In some embodiments, a peptide having antimicrobial activity (e.g., a modified RiPP) disclosed herein comprises one or more post-translational modifications, such as modifications effected by one or more enzymes listed in Tables 5, 7, 8, 13, 14, and 17. Possible peptide post-translational modifications include, but are not limited to, phosphorylation (e.g., of serine, threonine, or tyrosine residues); glycosylation (e.g., N-glycosylation, O-glycosylation, glypiation, C-glycosylation, and phosphoglycosylation); ubiquitylation/ubiquitination; S-nitrosylation; methylation (e.g., N-methylation or O-methylation); N-acetylation; lipidation (e.g., C-terminal glycosyl phosphatidylinositol (GPI) anchor, N-terminal myristoylation, S-myristoylation, or S-prenylation); deamidation; eliminylation; prenylation; ADP-ribosylation; hydroxylation; polypeptide backbone modifications (e.g., stereoisomerization, dehydration, oxidation, cyclization), and any other post-translational modifications disclosed herein. Post-translational modifications are described further in Müller Biochemistry 2018, 57(2):177-187 (doi: 10.1021/acs.biochem.7b00861) and deGruyter et al. Biochemistry 2017, 56(30):3863-3873 (doi: 10.1021/acs.biochem.7b00536).


In some embodiments, one or more serine (S) and/or cysteine (C) residues of a peptide having antimicrobial activity disclosed herein is replaced with a dehydroalanine (e.g., by dehydration of a serine or cysteine). In some embodiments, one or more threonine (T) residues of a peptide having antimicrobial activity disclosed herein is replaced with a dehydrobutyrine (e.g., by dehydration of a threonine). In some embodiments, a peptide having antimicrobial activity (e.g. a modified RiPP) disclosed herein comprises one or more thioether bridges, one or more thioester bridges, and/or one or more other bridges. Any modified peptide disclosed herein can comprise any combination of post-translational modifications described herein (e.g., one or more dehydrated amino acids, one or more thioether bridges, one or more thioester bridges, and/or one or more other bridges).


Despite the structural diversity of RiPPs, RiPP biosynthesis generally begins with production of a precursor peptide by ribosomes; the precursor peptide generally comprises an N-terminal leader sequence and a C-terminal core sequence that comprises sites for post-translational modification. In some embodiments, biosynthesis requires a C-terminal recognition sequence. The leader sequence recruits the biosynthetic machinery and is, in some embodiments, cleaved by a peptidase to form a mature peptide. In some embodiments, a protein modification enzyme is a peptidase that cleaves the leader peptide.


In some embodiments, one or more protein modification enzymes (e.g., at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10) protein modification enzymes may be expressed in a cell to produce a modified peptide. In some embodiments, the protein modification enzyme is expressed from a heterologous nucleic acid. The expression of one or more protein modification enzymes may be under the control of an inducible promoter.


Protein modification enzymes including RiPP synthesis enzymes are known. As a non-limiting example, Prochlorosin (ProcM) is a member of the enzyme class that installs the macrocyclic thioether linkages that give rise to lanthipeptides. ProcM engages in dehydration-based chemistry that targets side chain serine/threonine residues. ProcA is a natural peptide substrate for ProcM. TgnB is a member of the enzyme class that installs the macrocyclic ester linkages that give rise to microviridins. TgnA is a natural peptide substrate for the modifying enzyme, TgnB. PapB is a member of the enzyme class that installs the macrocyclic thioether linkages that give rise to ranthipeptides, or sactipeptides. Freyrasin (PapB) engages in radical-based chemistry that targets main chain carbon atoms of aspartate/glutamate residues. LynD is a cyanobactin cyclodehydratase (PDB ID 4V1T). Additional non-limiting examples of protein modification enzymes including RiPP synthesis enzymes are provided in Table 7. See also, e.g., Ortega and van der Donk, Cell Chem Biol. 2016 Jan. 21; 23(1): 31-44. In some embodiments, a protein modification enzyme comprises a sequence that is at least 60%, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a sequence selected from SEQ ID NOs: 80-83, 174, 176, 179, 180, 183, 185, 187, 188, 190, 192, 247, 249-251, 253, 255, 256, 258, 262, 264, 265, 267, 270, 271, 274, 275, 279-281, 285, 289, 290, 292, 295, 296, 298, 300-303, 305, 308-310, 312, 313, 316, 318-322, 325, 327, 330, 332, 334, 335, 337, 338, 342, 343, 346, 349, 350, 354, 356, 360, 362, and 363. In some embodiments, a protein modification enzyme comprises a sequence selected from SEQ ID NOs: 80-83, 174, 176, 179, 180, 183, 185, 187, 188, 190, 192, 247, 249-251, 253, 255, 256, 258, 262, 264, 265, 267, 270, 271, 274, 275, 279-281, 285, 289, 290, 292, 295, 296, 298, 300-303, 305, 308-310, 312, 313, 316, 318-322, 325, 327, 330, 332, 334, 335, 337, 338, 342, 343, 346, 349, 350, 354, 356, 360, 362, and 363. See, e.g., Table 4, Table 7, Table 8, Table 9, and Table 17.


In some embodiments, the split intein-based selection methods described herein comprise sequencing to identify the candidate peptide in the host cell. In some embodiments, a host cell comprises a plasmid encoding the candidate peptide and the plasmid may be sequenced. Non-limiting examples of sequencing methods include next-generation sequence (NGS), nanopore sequencing, and Sanger sequencing.









TABLE 1







Non-limiting examples of RiPP modified peptides.








RiPP Subfamily
Defining Features





Amatoxins and
N-to-C cyclized peptides produced by fungi


Phallotoxins


Autoinducing
Peptides containing a cyclic ester or a thioester.


peptides


Bacterial head-to-
N-to-C cyclized peptides differing from cyanobactins in the biosynthetic machinery employed


tail cyclized
for macrocyclization


peptides


Bottromycins
An N-terminal macrocyclic amidine



Use a C-terminal follower peptide instead of N-terminal leader peptide.



Use a C-terminal follower peptide instead of N-terminal leader peptide.


Conopeptides
Venom peptides produced by snails. The degree and type of PTMs varies.


Cyanobactins
N-to-C macrocyclic peptides produced by cyanobacteria.



Sometimes further decorated with azole(in)es and/or prenylations.


Cyclotides
N-to-C cyclized peptides produced by plants containing a cysteine knot composed of three



disulfides


Glycocins
Glycosylated antimicrobial peptides


Lanthipeptides
Lan and/or MeLan thioether bis-amino acids


Lasso peptides
An N-terminal macrolactam with the C-terminal tail threaded through the ring.


Linaridins
Dehydroamino acids but lacking Lan/MeLan


Linear azol(in)e-
Linear peptides containing (methyl)oxazol(in)e or/and thiazol(in)e heterocycles


containing


peptides


Methanobactin
Peptidic chelators used by methanotrophic bacteria


Microcins
Produced by members of the Enterobacteriaceae Family.



Include lasso peptide and LAP families


Microviridins
Lactones made from Glu/Asp and Ser/Thr side chains and/or lactams made from Lys and



Glu/Asp residues


Orbitides
N-to-C cyclized peptides produced by plants lacking disulfides


Proteusins
Linear peptides containing D-amino acids and C-methylations


Pyrroloquinoline
Small molecules generated from the post-translational modification of a precursor peptide or


quinone (PQQ),
protein.


Pantocin, and


Thyroid hormones


Sactipeptides
Intramolecular thioether linkages between Cys side chains and α-carbons of other amino acids


(Ranthipeptides)


Streptide
A Trp-to-Lys carbon-carbon cross link


Thioamides
Peptides containing thioamide linkages installed post-translationally


Thiopeptides
A central six-membered nitrogen-containing ring



Additional PTMs include dehydrations and cyclodehydrations
















TABLE 7







Non-limiting examples of peptide modifying enzymes










Protein





modifi-





cation


Peptide


enzyme
Enzyme

interaction


name
class
Modification facilitated
mechanism





TgnB
lactone cyclase


embedded image


Leader- dependent





PaaA
glu-glu cyclase


embedded image


Leader- dependent





PlpXY
tyrosine excisionase


embedded image


Leader- dependent





LynD
thiazoline cyclase


embedded image


Leader- dependent





LasF
carboxylic acid methyl- transferase


embedded image


Tailoring





PalS
cysteine glycosyl- transferase


embedded image


Tailoring





EpiD
de- carboxylase


embedded image


Tailoring





ThcoK
serine kinase


embedded image


Tailoring





PadeK
serine kinase


embedded image


Tailoring









Methods of Engineering RiPPs and RiPP Libraries

Provided herein are methods for engineering RiPPs, such as to develop non-naturally occurring RiPPs with desired properties. Both the leader and core sequences of a RiPP can be engineered based on the methods provided. In a leader sequence, recognition site(s) (RS) for protein modifying enzymes can be engineered (e.g., added, removed, optimized, or moved), such as to enable the use of the corresponding protein modifying enzyme to incorporate a particular post-translational modification to a peptide, or to prevent a particular protein modifying enzyme from acting on a given RiPP. In a core sequence, the amino acid sequence can be engineered, such as to facilitate post-translational modification by a particular protein modifying enzyme.


The amino acid sequence of a RiPP (including its leader and core sequences, as well as any additional amino acids within the RiPP) determine which protein modifying enzymes interact with the RiPP. Leader-dependent protein modifying enzymes associate with an RS within the leader sequence of a RiPP, and facilitate modification of an amino acid or amino acids within the core sequence. Tailoring protein modification enzymes associate with a particular amino acid or amino acids within the core sequence of a RiPP, and facilitate modification of one or more of those amino acids.


To engineer a RiPP, e.g., so as to include a particular set of post-translational modifications on a peptide having a particular amino acid sequence, the protein modification enzymes that facilitate the particular set of post-translational modifications are first identified. Consensus leader RS sequences for each leader-dependent enzyme are then compiled. Each leader RS sequence is then incorporated (e.g., by encoding in a nucleic acid sequence to be translated into the RiPP) into the leader sequence of the engineered RiPP. In embodiments in which one or all of the RS sequences for a given engineered RiPP have constraints on the distance between the RS and the amino acid(s) to be modified, each RS is placed in the leader sequence according to its respective constraint(s). An optimized leader sequence can be identified by screening candidate leaders and calculating a position score (e.g. by quantifying the amount of peptide having the desired modification pattern for each candidate leader sequence and identifying the leader sequence generating the highest yield of modified peptide). A non-limiting example of this screening process to identify optimized leader sequences is demonstrated in FIGS. 10A-10E and in FIG. 37D. The engineered RiPP is then expressed in a host cell concurrently with the protein modification enzymes, thereby synthesizing the engineered RiPP comprising the combination of post-translational modifications. In some embodiments, the engineered RiPP is expressed from a plasmid comprising a nucleic acid sequence encoding the leader and core amino acid sequence of the RiPP. In some embodiments, the protein modification enzymes are expressed from a plasmid or a set of plasmids comprising nucleic acid sequences encoding the enzymes. In some embodiments, the engineered RiPP and protein modification enzymes are expressed from a bacterial genome, such as an E. coli Marionette genome. In some embodiments, the engineered RiPP is expressed under the control of an inducible promoter. In some embodiments, each protein modification enzyme is expressed under the control of independently inducible promoters (i.e., each enzyme is controlled by an orthogonal promoter).


The RiPP engineering method provided herein enables the synthesis of a given peptide comprising a particular amino acid sequence with a specific combination of post-translational modifications. Biosynthesis using engineered RiPPs, rather than chemical or other conventional synthesis mechanisms, has one or more benefits, including but not limited to increased yield, decreased cost, and decreased complexity of the synthesis relative to alternative synthesis methods (e.g., chemical synthesis).


To engineer a RiPP, it may also be desirable to build a library of RiPPs to be screened with a particular protein modification enzyme or a particular combination of protein modification enzymes to identify preferred RiPPs (e.g., having a particular desired property or combination of properties) that comprise the desired post-translational modifications. Degenerate peptide libraries (i.e., libraries in which each amino acid of each member of the library is chosen randomly from all 20 natural amino acid options) can be designed, but have the disadvantage of being too large to be screened by conventional means (or in some instances are too large to be synthesized). For example, a degenerate library of peptides of 8 amino acids in length comprises peptides with 2.56×1010 distinct amino acid sequences, a number which is impossible or unfeasible to synthesize and/or screen. Such libraries are either impossible or unfeasible to synthesize and/or screen based on cost (sequencing, materials/reagents, etc.), time, or other considerations. As such, provided herein are libraries of RiPPs comprising a plurality of peptide members defined by a particular amino acid sequence motif. A library of RiPPs, in some embodiments, comprises peptides that are each 5-100 amino acids (e.g., 10-100, 10-90, 10-80, 10-70, 10-60, 10-50, 10-40, 10-30, 10-20, 20-100, 20-90, 20-80, 20-70, 20-60, 20-50, 20-40, 20-30, 30-100, 30-90, 30-80, 30-70, 30-60, 30-50, 30-40, 40-100, 40-90, 40-80, 40-70, 40-60, 40-50, 50-100, 50-90, 50-80, 50-70, 50-60, or any range or combination thereof) in length. A library, in some embodiments, comprises peptides that are each defined by a particular amino acid motif X1X2X3X4 . . . Xn, wherein n is the number of amino acids within the peptide (i.e., the length of the peptide), wherein each of X1-Xn is independently chosen from 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acids, and wherein at least one of X1-Xn (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or all of X1-Xn) is chosen from fewer than 20 amino acids. In some embodiments, at least one of X1-Xn is restricted to a single amino acid. As a non-limiting example, X1 may be chosen from 3 amino acids, X2 may be chosen from 7 amino acids, X3 may be chosen from 2 amino acids, and so on. In some embodiments, the amino acid motif X1X2X3X4 . . . Xn is determined to be susceptible to modification by 1, 2, 3, 4, 5, 6, 7, 8, or more distinct protein modification enzymes. In some embodiments, the plurality of peptides of the library do not have random amino acid sequences.


In some embodiments, a library comprises peptides defined by a particular amino acid motif determined to be susceptible to modification by 1, 2, 3, 4, 5, 6, 7, 8, or more distinct protein modification enzymes. In some embodiments, less than 100% (e.g., less than 95%, less than 90%, less than 85%, less than 80%, less than 75%, less than 70%, less than 65%, less than 60%, less than 55%, less than 50%, less than 45%, less than 40%, less than 35%, less than 30%, less than 25%, less than 20%, less than 15%, less than 10%, less than 5%, less than 4%, less than 3%, less than 2%, or less than 1%) of the members of the peptide library are capable of being fully modified by the protein modification enzymes to which the amino acid motif was determined to be susceptible. In some embodiments, at least 1% (e.g., at least 2%, at least 3%, at least 4%, at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95%) of the members of the peptide library are capable of being fully modified by the protein modification enzymes to which the amino acid motif was determined to be susceptible.


In some embodiments, each member of a library disclosed herein comprises a SUMO tag. In some embodiments, each member of a library disclosed herein comprises a SUMO tag at its 5′ end. In some embodiments, each member of a library disclosed herein comprises a SUMO tag at its 3′ end. In some embodiments, each member of a library disclosed herein comprises a SUMO tag and a histidine tag at its 5′ end (e.g., the member comprises the structure [histidine tag]-[SUMO tag]-peptide or [SUMO tag]-[histidine tag]-peptide). In some embodiments, each member of a library disclosed herein comprises a SUMO tag and a histidine tag at its 3′ end (e.g., the member comprises the structure peptide-[histidine tag]-[SUMO tag] or peptide-[SUMO tag]-[histidine tag]-peptide). In some embodiments, each member of a library disclosed herein comprises a SUMO tag and a histidine tag at its 5′ end or at its 3′ end. In some embodiments, a histidine tag is a hexahistidine tag. In some embodiments, each member of a library disclosed herein comprises a tobacco etch virus protease (TEVp) cleavage site, or each member comprises two TEVp cleavage sites. In some embodiments, each member of a library disclosed herein comprises a TEVp cleavage site in between a RiPP peptide and a SUMO tag (e.g., the member comprises the structure peptide-[TEVp site]-[SUMO tag] or [SUMO tag]-[TEVp site]-peptide).


In some embodiments, a plurality of host cells comprises a library of peptides disclosed herein. In some embodiments, each host cell comprises a peptide of the library (e.g., each host cell comprises a peptide of the library and the peptide comprised by each host cell is independent of the peptides comprised by each other host cell). In some embodiments, each host cell is a bacterial cell. In some embodiments, each host cell comprises a nucleic acid sequence encoding the peptide. In some embodiments, each host cell further comprises a protein modifying enzyme. In some embodiments, the protein modifying enzyme is encoded by a nucleic acid sequence comprised by the host cell.


In some embodiments, a library is synthesized in a plurality of host cells. For example, in some embodiments, each member of the library is synthesized in a separate host cell. In some embodiments, each host cell is a bacterial cell. In some embodiments, a library is synthesized in a population of bacteria. In some embodiments, each bacterium of the population expresses a single member of the library. In some embodiments, each member of the library is synthesized in a host cell in which one or more protein modifying enzymes are also expressed.


In some embodiments, a library is capable of being screened by methods disclosed herein (e.g., using split-intein based selection). In some embodiments, screening of a library disclosed herein identifies one or more peptides with a desired functional property (e.g., a desired biological property). In some embodiments, screening of a library disclosed herein identifies one or more peptides with antimicrobial activity. In some embodiments, screening of a library disclosed herein identifies one or more peptides with binding activity to a target protein.


Target Proteins

The target protein may be any protein of interest. In some embodiments, a target protein is a cell surface receptor, antigen, transmembrane protein, glycoprotein, glycolipid or any other cell surface macromolecule. In some embodiments, the target protein is a viral protein or a fragment thereof. In some embodiments, the target protein comprises a receptor binding domain (RBD) from a coronavirus protein. In some embodiments, the coronavirus is 229E (alpha coronavirus), NL63 (alpha coronavirus), OC43 (beta coronavirus), HKU1 (beta coronavirus), MERS-CoV (the beta coronavirus that causes Middle East Respiratory Syndrome, or MERS), SARS-CoV (the beta coronavirus that causes severe acute respiratory syndrome, or SARS), or SARS-CoV-2 (the novel coronavirus that causes coronavirus disease 2019, or COVID-19). In some embodiments, the target protein is a bacterial protein or a fragment thereof. In some embodiments, the target protein is a bacterial enzyme. In some embodiments, the target protein is a bacterial outer-membrane protein. In some embodiments, the target protein is a bacterial toxin. In some embodiments, the target protein is a bacterial structural protein. In some embodiments, the target protein is a bacterial polymerase. In some embodiments, the target protein is a bacterial transcription regulator.


In some embodiments, the target protein is SARS-CoV-2 receptor binding domain (RBD) of the Spike protein. Spike protein is a surface glycoprotein that binds to angiotensin I converting enzyme 2 (ACE2) to promote viral entry. The al helix of ACE2 makes most of the binding contacts with the RBD and is provided as SEQ ID NO: 72.


In some embodiments, the target protein comprises a sequence that is at least 60%, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 71 (RBD). In some embodiments, the target protein comprises the amino acid sequence of SEQ ID NO: 71.


In some embodiments, the target protein comprises a sequence that is at least 60%, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 72 (al helix of ACE2). In some embodiments, the target protein comprises the amino acid sequence of SEQ ID NO: 72.


Non-limiting examples of known cellular receptors include ACVR2A, EGFR/HER1, HER2/ERBB2, ERBB3/HER3, CD32a/FCGR2A/Fc gamma RIIa, CD32b/FCGR2B/Fc gamma RIIb, CD16a/Fc gamma RIIIa, CD16b/Fc gamma RIII, CD155/PVR, TNFR1/TNFRSF1A/CD120a, TNFR2/TNFRSF1B/CD120b, 4-1BB/TNFRSF9/CD137, TRAIL R2/CD262/TNFRSF10B, TRAIL R4/CD264/TNFRSF10D, TNFRSF11A, TRAIL R1/CD261/TNFRSF10A, TRAILR3/TNFRSF10C, TACI/TNFRSF13B(CD267) HVEM/TNFRSF14/CD270, BCMA/TNFRSF17/CD269, GITR/TNFRSF18/CD357, FGFR2/CD332, CD23/FCER2, FCRL1/FCRH1, TIM-3/HAVCR2, IL1RL1/IL-1 R4, IL17RA/IL-17RA/CD217, IL-4R/CD124, IL7R/IL-7R/CD127, TrkA/NTRK1, PDGFRB/CD140b, TREM-2/TREM2, ACVR2B/Activin RIIB, FCGRT & B2M, CD89/FCAR, IL3RA/CD123, IGF1R/CD221/IGF-I R, Insulin Receptor/INSR/CD220, LILRB2/ILT4/LIR-2, VEGFR2/KDR/Flk-1/CD309, MCSF Receptor/CSF1R/CD115, EPHA3/Eph Receptor A3, CD16-2/FCGR4, FcERI/FCER1A, TIM-1/KIM-1/HACVR, IL6R/IL-6R/CD126, LILRB4/CD85k/ILT3, IL2RA/IL-2RA/CD25, CD122/IL-2RB, LDLR/LDL R/LDL Receptor, CD112/Nectin-2/PVRL2, and TFRC/CD71.


A peptide described herein may have a particular binding affinity for a target protein. Binding affinity is the apparent association constant or KA. The KA is the reciprocal of the dissociation constant (KD). The peptides identified by the methods described herein may have a binding affinity (KD) of at least 10−5, 10−6, 10−7, 10−8, 10−9, 10−10 M, or lower for a target protein. An increased binding affinity corresponds to a decreased KD. Higher affinity binding of a peptide for a first protein relative to a second protein can be indicated by a higher KA (or a smaller numerical value KD) for binding the first protein than the KA (or numerical value KD) for binding the second protein. In such cases, the peptide has specificity for the first protein (e.g., a first protein in a first conformation or mimic thereof) relative to the second protein (e.g., the same first protein in a second conformation or mimic thereof; or a second protein). In some embodiments, the peptides described herein have a higher binding affinity (a higher KA or smaller KD) to an appropriate protein as compared to the binding affinity of the same type of peptide produced using naturally occurring secretion signal peptides. Differences in binding affinity (e.g., for specificity or other comparisons) can be at least 1.5, 2, 3, 4, 5, 10, 15, 20, 37.5, 50, 70, 80, 91, 100, 500, 1000, 10,000 or 105 fold. In some embodiments, any of the peptides produced as provided herein may be further affinity matured to increase the binding affinity of the peptide to the target protein or epitope thereof.


Binding affinity (or binding specificity) can be determined by a variety of methods including equilibrium dialysis, equilibrium binding, gel filtration, ELISA, surface plasmon resonance, or spectroscopy (e.g., using a fluorescence assay). Non-limiting exemplary conditions for evaluating binding affinity are in HBS-P buffer (10 mM HEPES pH7.4, 150 mM NaCl, 0.005% (v/v) Surfactant P20). These techniques can be used to measure the concentration of bound binding protein as a function of target protein concentration. The concentration of bound binding protein ([Bound]) is generally related to the concentration of free target protein ([Free]) by the following equation:





[Bound]=[Free]/(Kd+[Free])


It is not always necessary to make an exact determination of KA, though, since sometimes it is sufficient to obtain a quantitative measurement of affinity, e.g., determined using a method such as ELISA, FACS analysis or magnetic immunoprecipitation, which is proportional to KA, and thus can be used for comparisons, such as determining whether a higher affinity is, e.g., 2-fold higher, to obtain a qualitative measurement of affinity, or to obtain an inference of affinity, e.g., by activity in a functional assay, e.g., an in vitro or in vivo assay.


In some embodiments, a peptide disclosed herein or identified through the methods disclosed herein decreases the binding affinity of a target peptide with a naturally occurring cognate binding partner. In some embodiments, a peptide disclosed herein or identified through the methods disclosed herein decreases the binding affinity of a target peptide with a naturally occurring cognate binding partner by at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 99%.


Host Cells

Aspects of the present disclosure provide host cells comprising any of the nucleic acids, fusion proteins, peptides, enzymes, selection markers and components of the split intein-based systems disclosed herein. In some embodiments, a host cell is a eukaryotic cell. In some embodiments, a host cell is a prokaryotic cell. In some embodiments, a host cell is a bacterial cell. In some embodiments, a host cell is an E. coli cell. As one of ordinary skill in the art would appreciate, components of the split intein-based systems disclosed herein may be selected based on the type of host cell used.


A nucleic acid may encode any of the fusion proteins, peptides, enzymes, selection markers and components of the split intein-based systems disclosed herein. As used herein, a heterologous nucleic acid is one that is introduced into a host cell. A nucleic acid, generally, is at least two nucleotides covalently linked together, and in some instances, may contain phosphodiester bonds (e.g., a phosphodiester “backbone”). A nucleic acid is considered “engineered” if it does not occur in nature. Examples of engineered nucleic acids include recombinant nucleic acids and synthetic nucleic acids.


Nucleic acids encoding any of the fusion proteins, peptides, enzymes, selection markers and components of the split intein-based system described herein may be introduced into a host cell using any known methods, including but not limited to chemical transfection, viral transduction and electroporation. In some embodiments, one or more nucleic acids that are introduced into a host cell integrate into the host cell genome; in some embodiments, one or more nucleic acids that are introduced in a host cell do not integrate into the host cell genome. The nucleic acids described herein may encode one or more of the fusion proteins, peptides, enzymes, selection markers and components of the split intein-based system disclosed herein. In some embodiments, a nucleic acid comprises a sequence that is at least 60%, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NOs: 47-66 or 73-79, a nucleic acid sequence in Table 3, or a nucleic acid sequence disclosed herein. In some embodiments, a nucleic acid comprises a nucleotide sequence of any one of SEQ ID NOs: 47-66 or 73-79, a nucleic acid sequence in Table 3, or a nucleic acid sequence disclosed herein. Any of the plasmids disclosed herein may be used.


It should be understood the methods of identifying peptides disclosed herein may or may not use host cells. In some embodiments, a split intein-based system disclosed herein is not used in a host cell. For example, in vitro methods comprising incubating a split intein-based system disclosed herein in a reaction vessel under suitable conditions is encompassed by the present disclosure.


Kits

Any of the host cells, nucleic acids, fusion proteins, peptides, enzymes, selection markers and components of the split intein-based systems disclosed herein, in some embodiments, may be assembled into pharmaceutical or diagnostic or research kits to facilitate their use in therapeutic, diagnostic or research applications. A kit may include one or more containers housing the components of the disclosure and instructions for use. Specifically, such kits may include one or more agents described herein, along with instructions describing the intended application and the proper use of these agents. In certain embodiments, agents in a kit may be in a pharmaceutical formulation and dosage suitable for a particular application and for a method of administration of the agents. Kits for research purposes may contain the components in appropriate concentrations or quantities for running various experiments.


In some embodiments, the instant disclosure relates to a kit for identifying a peptide that binds a target protein, the kit comprising a container housing any of the host cells, nucleic acids, fusion proteins, peptides, enzymes, and components of the split intein-based systems disclosed herein. In some embodiments, the kit further comprises instructions for identifying the peptide and/or performing the split intein-based selection.


In some embodiments, the instant disclosure relates to a kit comprising a container housing any of the nucleic acids disclosed herein. In some embodiments, the kit comprises a container housing a nucleic acid that comprises a sequence that is at least 60%, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NOs: 47-66 or 73-79, a nucleic acid sequence in Table 3, or a nucleic acid sequence disclosed herein; or that comprises the nucleotide sequence of any one of SEQ ID NOs: 47-66 or 73-79, a nucleic acid sequence in Table 3, or a nucleic acid sequence disclosed herein. In some embodiments, the instant disclosure relates to a kit comprising a container housing any of the peptides disclosed herein. In some embodiments, the kit comprises a container housing a peptide that comprises a sequence that is at least 60%, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NOs: 6-25 or 26-45, an amino acid sequence in Table 3 or any amino acid sequence disclosed herein, including fragments thereof; or that comprises the amino acid sequence of any one of SEQ ID NOs: 6-25 or 26-45, an amino acid sequence in Table 3 or any amino acid sequence disclosed herein, including fragments thereof. In addition, kits of the disclosure may include instructions, a negative and/or positive control, containers, diluents and buffers for the sample, sample preparation tubes and a printed or electronic table of reference peptide sequences for sequence comparisons.


The kit may be designed to facilitate use of the methods described herein by researchers and can take many forms. Each of the compositions of the kit, where applicable, may be provided in liquid form (e.g., in solution), or in solid form, (e.g., a dry powder). In certain cases, some of the compositions may be constitutable (e.g., reconstitutable) or otherwise processable (e.g., to an active form), for example, by the addition of a suitable solvent or other species (for example, water or a cell culture medium), which may or may not be provided with the kit. As used herein, “instructions” can define a component of instruction and/or promotion, and typically involve written instructions on or associated with packaging of the disclosure. Instructions also can include any oral or electronic instructions provided in any manner such that a user will clearly recognize that the instructions are to be associated with the kit, for example, audiovisual (e.g., videotape, DVD, etc.), Internet, and/or web-based communications, etc. The written instructions may be in a form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, which instructions can also reflect approval by the agency of manufacture, use or sale for animal administration. The kit may contain any one or more of the components described herein in one or more containers. As an example, in one embodiment, the kit may include instructions for mixing one or more components of the kit and/or isolating and mixing a sample and applying to a subject. The kit may include a container housing agents described herein. The agents may be in the form of a liquid, gel or solid (powder). The agents may be prepared sterilely, packaged in syringe and shipped refrigerated. Alternatively, it may be housed in a vial or other container for storage. A second container may have other agents prepared sterilely. Alternatively, the kit may include the active agents premixed and shipped in a syringe, vial, tube, or other container. The kit may have one or more or all of the components required to administer the agents to an animal, such as a syringe, topical application devices, or IV needle tubing and bag, particularly in the case of the kits for producing specific somatic animal models.


The kit may have a variety of forms, such as a blister pouch, a shrink-wrapped pouch, a vacuum sealable pouch, a sealable thermoformed tray, or a similar pouch or tray form, with the accessories loosely packed within the pouch, one or more tubes, containers, a box or a bag. The kit may be sterilized after the accessories are added, thereby allowing the individual accessories in the container to be otherwise unwrapped. The kits can be sterilized using any appropriate sterilization techniques, such as radiation sterilization, heat sterilization, or other sterilization methods known in the art. The kit may also include other components, depending on the specific application, for example, containers, cell media, salts, buffers, reagents, syringes, needles, a fabric, such as gauze, for applying or removing a disinfecting agent, disposable gloves, a support for the agents prior to administration etc.


Pharmaceutical Compositions and Uses Thereof

Any of the peptides (e.g., modified peptides) disclosed herein or identified by a method disclosed herein may be formulated in a pharmaceutical composition for administration to a subject. As used herein, a subject is a human, non-human primate, cow, horse, pig, sheep, goat, dog, cat, or rodent. In all embodiments, human subjects are preferred.


In some embodiments, the subject is a suspected of having a disease or has previously been diagnosed as having a disease. In some embodiments, the subject is a human suspected of having a disease, or a human having been previously diagnosed as having a disease. Methods for identifying subjects suspected of having a disease may include physical examination, subject's family medical history, subject's medical history, biopsy, viral tests (e.g., nasal swabs), antibody tests (e.g., serological testing), or a number of imaging technologies such as ultrasonography, X-ray imaging, computed tomography, magnetic resonance imaging, magnetic resonance spectroscopy, or positron emission tomography.


In some embodiments, the subject is suspected of having or has previously been diagnosed as having an infectious disease (e.g., a disease caused by a pathogen and/or virus). As a non-limiting example, the subject may have coronavirus disease 2019 (COVID-19), which is an infectious disease. COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 may be diagnosed using any suitable method including nasopharyngeal swabs and serology testing for antibodies against coronavirus.


In some embodiments, the subject is suspected of having or has previously been diagnosed as having cancer. The term “cancer” refers to a class of diseases characterized by the development of abnormal cells that proliferate uncontrollably and have the ability to infiltrate and destroy normal body tissues. See, e.g., Stedman's Medical Dictionary, 25th ed.; Hensyl ed.; Williams & Wilkins: Philadelphia, 1990. Exemplary cancers include, but are not limited to, acoustic neuroma; adenocarcinoma; adrenal gland cancer; anal cancer; angiosarcoma (e.g., lymphangiosarcoma, lymphangioendotheliosarcoma, hemangiosarcoma); appendix cancer; benign monoclonal gammopathy; biliary cancer (e.g., cholangiocarcinoma); bladder cancer; breast cancer (e.g., adenocarcinoma of the breast, papillary carcinoma of the breast, mammary cancer, medullary carcinoma of the breast); brain cancer (e.g., meningioma, glioblastomas, glioma (e.g., astrocytoma, oligodendroglioma), medulloblastoma); bronchus cancer; carcinoid tumor; cervical cancer (e.g., cervical adenocarcinoma); choriocarcinoma; chordoma; craniopharyngioma; colorectal cancer (e.g., colon cancer, rectal cancer, colorectal adenocarcinoma); connective tissue cancer; epithelial carcinoma; ependymoma; endotheliosarcoma (e.g., Kaposi's sarcoma, multiple idiopathic hemorrhagic sarcoma); endometrial cancer (e.g., uterine cancer, uterine sarcoma); esophageal cancer (e.g., adenocarcinoma of the esophagus, Barrett's adenocarcinoma); Ewing's sarcoma; ocular cancer (e.g., intraocular melanoma, retinoblastoma); familiar hypereosinophilia; gall bladder cancer; gastric cancer (e.g., stomach adenocarcinoma); gastrointestinal stromal tumor (GIST); germ cell cancer; head and neck cancer (e.g., head and neck squamous cell carcinoma, oral cancer (e.g., oral squamous cell carcinoma), throat cancer (e.g., laryngeal cancer, pharyngeal cancer, nasopharyngeal cancer, oropharyngeal cancer)); hematopoietic cancers (e.g., leukemia such as acute lymphocytic leukemia (ALL) (e.g., B-cell ALL, T-cell ALL), acute myelocytic leukemia (AML) (e.g., B-cell AML, T-cell AML), chronic myelocytic leukemia (CML) (e.g., B-cell CML, T-cell CML), and chronic lymphocytic leukemia (CLL) (e.g., B-cell CLL, T-cell CLL)); lymphoma such as Hodgkin lymphoma (HL) (e.g., B-cell HL, T-cell HL) and non-Hodgkin lymphoma (NHL) (e.g., B-cell NHL such as diffuse large cell lymphoma (DLCL) (e.g., diffuse large B-cell lymphoma), follicular lymphoma, chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), mantle cell lymphoma (MCL), marginal zone B-cell lymphomas (e.g., mucosa-associated lymphoid tissue (MALT) lymphomas, nodal marginal zone B-cell lymphoma, splenic marginal zone B-cell lymphoma), primary mediastinal B-cell lymphoma, Burkitt lymphoma, lymphoplasmacytic lymphoma (i.e., Waldenstram's macroglobulinemia), hairy cell leukemia (HCL), immunoblastic large cell lymphoma, precursor B-lymphoblastic lymphoma and primary central nervous system (CNS) lymphoma; and T-cell NHL such as precursor T-lymphoblastic lymphoma/leukemia, peripheral T-cell lymphoma (PTCL) (e.g., cutaneous T-cell lymphoma (CTCL) (e.g., mycosis fungoides, Sezary syndrome), angioimmunoblastic T-cell lymphoma, extranodal natural killer T-cell lymphoma, enteropathy type T-cell lymphoma, subcutaneous panniculitis-like T-cell lymphoma, and anaplastic large cell lymphoma); a mixture of one or more leukemia/lymphoma as described above; and multiple myeloma (MM)), heavy chain disease (e.g., alpha chain disease, gamma chain disease, mu chain disease); hemangioblastoma; hypopharynx cancer; inflammatory myofibroblastic tumors; immunocytic amyloidosis; kidney cancer (e.g., nephroblastoma a.k.a. Wilms' tumor, renal cell carcinoma); liver cancer (e.g., hepatocellular cancer (HCC), malignant hepatoma); lung cancer (e.g., bronchogenic carcinoma, small cell lung cancer (SCLC), non-small cell lung cancer (NSCLC), adenocarcinoma of the lung); leiomyosarcoma (LMS); mastocytosis (e.g., systemic mastocytosis); muscle cancer; myelodysplastic syndrome (MDS); mesothelioma; myeloproliferative disorder (MPD) (e.g., polycythemia vera (PV), essential thrombocytosis (ET), agnogenic myeloid metaplasia (AMM) a.k.a. myelofibrosis (MF), chronic idiopathic myelofibrosis, chronic myelocytic leukemia (CML), chronic neutrophilic leukemia (CNL), hypereosinophilic syndrome (HES)); neuroblastoma; neurofibroma (e.g., neurofibromatosis (NF) type 1 or type 2, schwannomatosis); neuroendocrine cancer (e.g., gastroenteropancreatic neuroendoctrine tumor (GEP-NET), carcinoid tumor); osteosarcoma (e.g., bone cancer); ovarian cancer (e.g., cystadenocarcinoma, ovarian embryonal carcinoma, ovarian adenocarcinoma); papillary adenocarcinoma; pancreatic cancer (e.g., pancreatic andenocarcinoma, intraductal papillary mucinous neoplasm (IPMN), Islet cell tumors); penile cancer (e.g., Paget's disease of the penis and scrotum); pinealoma; primitive neuroectodermal tumor (PNT); plasma cell neoplasia; paraneoplastic syndromes; intraepithelial neoplasms; prostate cancer (e.g., prostate adenocarcinoma); rectal cancer; rhabdomyosarcoma; salivary gland cancer; skin cancer (e.g., squamous cell carcinoma (SCC), keratoacanthoma (KA), melanoma, basal cell carcinoma (BCC)); small bowel cancer (e.g., appendix cancer); soft tissue sarcoma (e.g., malignant fibrous histiocytoma (MFH), liposarcoma, malignant peripheral nerve sheath tumor (MPNST), chondrosarcoma, fibrosarcoma, myxosarcoma); sebaceous gland carcinoma; small intestine cancer; sweat gland carcinoma; synovioma; testicular cancer (e.g., seminoma, testicular embryonal carcinoma); thyroid cancer (e.g., papillary carcinoma of the thyroid, papillary thyroid carcinoma (PTC), medullary thyroid cancer); urethral cancer; vaginal cancer; and vulvar cancer (e.g., Paget's disease of the vulva).


In some embodiments, the subject is suspected of having or has previously been diagnosed as having a bacterial infection (e.g., an infection caused by a pathogenic bacterium). Exemplary bacterial infections include, but are not limited to, pulmonary infections (e.g., upper respiratory infection or lower respiratory infections), urinary tract infections, skin infections (e.g., bacterial cellulitis), sexually transmitted infections, neurological infections (e.g., bacterial encephalitis, bacterial meningitis), cardiac infections (e.g., bacterial endocarditis, bacterial myocarditis, or bacterial pericarditis), gastrointestinal infections (e.g., gastric infections, bacterial gastroenteritis, bacterial pharyngitis), bacterial vaginosis, and Lyme disease. Bacterial infections can be caused by any bacterium, including, but not limited to, Gram-positive bacteria, Gram-negative bacteria, Streptococcus pneumoniae, Haemophilus species, Staphylococcus aureus, Mycobacterium tuberculosis, methicillin-resistant S. aureus, non-typhoidal Salmonella species, Salmonella typhi, Bacillus cereus, Clostridium perfringens, Clostridium botulinum, Escherichia coli (ETEC, EPEC, EHEC, EAEC, EIEC), Salmonella sp., Shigella sp., Campylobacter sp., Yersinia enterocolitica, Clostridium difficile, Vibrio cholerae, Vibrio parahemolyticus, Listeria monocytogenes, Aeromonas hydrophila, Plesiomonas sp., Neisseria meningitidis, Streptococcus pneumoniae, Haemophilus influenzae, Neisseria gonorrhoeae, Chlamydia trachomatis, Treponema pallidum, Borrelia burgdorferi, Vibrio cholerae, Clostridium tetani, and Bacillus anthracis.


A “plurality” of elements, as used throughout the application refers to two or more of the elements.


The peptides (e.g., modified peptides) of the invention are administered to the subject in an effective amount for detecting or modulating protein (e.g., enzyme) activity. An “effective amount”, for instance, is an amount required to confer therapeutic effect on a subject, either alone or in combination with at least one other active agent. The effective amount of a peptide of the invention described herein may vary depending upon the specific peptide used, the mode of delivery of the peptide, and whether it is used alone or in combination. The effective amount for any particular application can also vary depending on such factors as the disease being assessed or treated, the particular peptide being administered, the size of the subject, or the severity of the disease or condition as well as the detection method. One of ordinary skill in the art can empirically determine the effective amount of a particular molecule of the invention without necessitating undue experimentation. Combined with the teachings provided herein, by choosing among the various active peptides and weighing factors such as potency, relative bioavailability, patient body weight, severity of adverse side-effects and preferred mode of administration, an effective regimen can be planned.


Pharmaceutical compositions of the present invention comprise an effective amount of one or more agents, dissolved or dispersed in a pharmaceutically acceptable carrier. The phrases “pharmaceutical or pharmacologically acceptable” refers to molecular entities and compositions that do not produce an adverse, allergic or other untoward reaction when administered to an animal, such as, for example, a human, as appropriate. Moreover, for animal (e.g., human) administration, it will be understood that preparations should meet sterility, pyrogenicity, general safety and purity standards as required by FDA Office of Biological Standards.


As used herein, “pharmaceutically acceptable carrier” includes any and all solvents, dispersion media, coatings, surfactants, antioxidants, preservatives (e.g., antibacterial agents, antifungal agents), isotonic agents, absorption delaying agents, salts, preservatives, drugs, drug stabilizers, gels, binders, excipients, disintegration agents, lubricants, sweetening agents, flavoring agents, dyes, such like materials and combinations thereof, as would be known to one of ordinary skill in the art (see, for example, Remington's Pharmaceutical Sciences (1990), incorporated herein by reference). Except insofar as any conventional carrier is incompatible with the active ingredient, its use in the therapeutic or pharmaceutical compositions is contemplated. The agent may comprise different types of carriers depending on whether it is to be administered in solid, liquid or aerosol form, and whether it need to be sterile for such routes of administration as injection.


General considerations in the formulation and/or manufacture of pharmaceutical agents, such as compositions comprising any of the engineered cells disclosed herein, may be found, for example, in Remington: The Science and Practice of Pharmacy 21st ed., Lippincott Williams & Wilkins, 2005 (incorporated herein by reference in its entirety).


Suitable routes of administration include, for example, parenteral routes such as intravenous, intrathecal, parenchymal, or intraventricular injection.


EXAMPLES
Example 1: Plasmid Design for Split Intein-Based RiPP Selections

A three plasmid system was used to conduct selection experiments. All plasmids are low-medium copy number variants previously characterized1: the “peptide plasmid” is a pSC101 backbone with an ampicillin resistance cassette (working concentration of 100 ng/uL) and contains a Type IIs restriction site for insertion of RiPP/peptide sequences N-terminal to one half of the split intein/sigma factor under control of an inducible T5 lacO promoter (maximally induced with 1 mM IPTG). The “modifying enzyme plasmid” is a p15A backbone with a spectinomycin resistance cassette (working concentration of 50 ng/uL) and contains a Type IIs restriction site for inserting cognate RiPP modifying enzymes under control of an inducible pCym promoter (maximally induced with 100 uM cumate). The “selection plasmid” is a ColE1 backbone with a kanamycin resistance cassette (working concentration of 50 ng/uL) and contains two regions of expression. The first is a C-terminal fusion of the SARS-CoV-2 receptor binding domain (RBD) of the Spike protein2 to the other half of the split intein-sigma factor. The second expression region contains two open reading frames downstream of the ECF20_992 promoter. The first is a sfGFP-cat gene for expression of superfolder-green fluorescent protein (sfGFP) and a chloramphenicol acetyltransferase (CAT) and the second is hsvTK-mScarlet-I gene for expression of the red fluorescent protein mScarlet-I and, when in the presence of a nucleoside analog, the toxic gene product, herpes simplex virus thymidine kinase (HsvTK) 3 (FIG. 2A).


The three plasmid system allows for flexible selection methods. Inducible expression of the peptide and modifying enzyme plasmids results in production of modified RiPP libraries with C-terminal fusions to the split intein machinery. RiPPs that are able to bind to the target (in this case, the RBD) lead to productive intein association and splicing 4 of the split sigma factor, which induces expression of the selection cassettes. For positive selection of binders, increasing concentrations of chloramphenicol (cm) can be used to enrich for target binders (in this case, an RBD-intein fusion) that produce increasing amounts of CAT (FIG. 2B, FIG. 2D, and FIG. 2F). For negative selection of binders, increasing concentrations of nucleotide 6-(β-D-2-deoxyribofuranosyl)-3,4-dihydro8H-pyrimido [4,5-c][1,2] oxazin-7-one (dP) can be used to deplete target binders (in this case, a Mdm2-intein fusion; note any off-target protein fusion is suitable) that produce increasing amounts of HsvTK (FIG. 2C, FIG. 2E, and FIG. 2G).


For the generation of this initial round of RBD hits, a negative selection was not implemented. Current and future selections will utilize positive and negative selections in consecutive, discrete rounds to best evolve RiPP libraries toward high affinity and specific binders to the RBD.


Example 2: Identification of RiPP Binders of RBD
Design and Construction of RiPP Libraries and Cognate Modifying Enzymes

Five libraries were designed based on in-house understanding of RiPP biosynthetic constraints, (FIG. 3). Library 1 contains recognition sites (RS) for the enzymes ProcM and LynD, which install lanthionines and thiazolines, respectively. Library 2 contains RS for the enzymes TgnB and LynD, which install ester linkages and thiazolines, respectively. Libraries 3-5 contain the RS for the enzyme PapB, which installs thioethers. The predicted cyclization topologies and amino acid degeneracy are outlined for each library in FIG. 3.


Library sizes were as indicated in Table 2 based on serial dilutions and counting colony forming units (CFU)/mL.









TABLE 2







Library sizes









library
core mod
size





1
procM
6E+07


2
tgnB
1E+07


3
papB
1E+07


4
papB
1E+06


5
papB
1E+07









Selection Methods for Generation of Pilot Hits

Appropriate antibiotics were used at every stage for plasmid propagation, as detailed above. Inducers were used at maximum concentration where indicated, as detailed above. Transformation efficiencies were recorded via serial dilution and CFU/mL counts. Libraries were miniprepped and transformed into separate electrocompetent strains of E. coli Marionette-Clo5 containing cognate modifying enzyme and selection constructs (transformation efficiencies >108 CFU/mL). After a one-hour outgrowth, strains were diluted 1:50 for plasmid outgrowth and induction of library peptides and modifying enzymes. This culture was grown overnight at 30° C., with shaking at 250 RPM.


After overnight growth, libraries were diluted 1 mL in 100 mL TB medium in inducing conditions. Selections were grown at 30° C. for 20 hours, 250 RPM. 4 mL of each selection was miniprepped and modifying enzyme/selection plasmids were restriction digested using SacI/KpnI (NEB, per manufacturer's instructions). Resulting digests were column purified (Zymo) and re-transformed in strains containing modifying enzyme/selection plasmids. This step was done in order to eliminate escape mutants in the selection plasmid (for instance, mutations generating high-level, constitutive expression of cat-GFP; see FIGS. 5 and 7). FIG. 4 outlines the process graphically.


For this initial pilot screen, 3 rounds of positive selections were conducted, at 300, 800 and 1200 uM chloramphenicol. Cell populations were assessed via cytometry to observe shifts in REU values (FIGS. 5 and 7). Libraries 3 (FIGS. 5A, 5B, and 5C) and 5 (FIGS. 7A, 7B, and 7C) demonstrated ideal REU shifts over rounds of selection and were chosen for next-generation sequencing (NGS). Degenerate regions of the peptide library plasmid were amplified and submitted for Illumina sequencing (HiSeq) to generate quantitative reads of peptide populations. Peptide sequences that were enriched in iterative selection rounds and also comprised >1% of the final population are summarized in FIGS. 6A and 6B (Library 3) and FIGS. 8A and 8B (Library 5).


Confirmation of Pilot Hits

20 sequences were codon optimized, synthesized as gBlocks (IDT), and individually cloned into the peptide plasmid. These 20 peptide plasmids were co-transformed with the PapB modifying enzyme plasmid and either the RBD-intein or Mdm2-intein as target in the selection plasmid. After overnight induction of peptide/modifying enzyme at 30° C., cells were analyzed via cytometry and REU values determined (FIG. 9A). Fold specificity was determined by comparing the ratio of REU values of peptides either against RBD or Mdm2-intein fusions (FIG. 9B). One hit emerged as having high specificity for the RBD (FIG. 9C).


REFERENCES FROM EXAMPLES 1 AND 2



  • 1 Segall-Shapiro, T. H., Sontag, E. D. & Voigt, C. A. Engineered promoters enable constant gene expression at any copy number in bacteria. Nat. Biotechnol., doi:10.1038/nbt.4111 (2018).

  • 2 Lan, J. et al. Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature 581, 215-220, doi:10.1038/s41586-020-2180-5 (2020).

  • 3 Kawai-Noma, S. et al. Improvement of the dP-nucleoside-mediated herpes simplex virus thymidine kinase negative-selection system by manipulating dP metabolism genes. J Biosci Bioeng, doi:10.1016/j.jbiosc.2020.03.002 (2020).

  • 4 Stevens, A. J. et al. Design of a Split Intein with Exceptional Protein Splicing Activity. J. Am. Chem. Soc. 138, 2162-2165, doi:10.1021/jacs.5b13528 (2016).

  • 5 Meyer, A. J., Segall-Shapiro, T. H., Glassey, E., Zhang, J. & Voigt, C. A. Escherichia coli “Marionette” strains with 12 highly optimized small-molecule sensors. Nat. Chem. Biol., doi:10.1038/s41589-018-0168-3 (2018).



Example 3: De Novo Design of Enzyme-Modified Peptides

Chemically-modified peptides are made by all kingdoms of life, where the enzymatic decorating and reshaping are critical for function. Peptides could be designed de novo by harnessing the modifying enzymes from the deluge of genomics, but it is difficult to extract the rules guiding their use and combination. In this Example, a model that captures the minimal specificity constraints was developed to use enzymes gleaned from microbial gene clusters encoding RiPPs (ribosomally-synthesized and post-translationally modified peptides). They include the recognition site (RS) sequence and restrictions on its placement in the precursor peptide and the tolerance to variability of the released core. The rule sets were empirically parameterized using a pipeline to construct and evaluate the activities of enzymes against hundreds of precursor peptide variants in Escherichia coli. This was applied to nine enzymes from eight RiPPs classes, including those for which there is little prior characterization (lactone macrocyclase, tyramine excisionase, glutamate heterocyclase, cysteine heterocyclase, glycosyltransferase, serine kinases, decarboxylase, and methyl transferase). The rules can be algorithmically combined to computationally design new-to-nature RiPPs, demonstrated by creating a 13-mer that combines excision, heterocyclization, and phosphorylation (PlpXY, LynD, ThcoK). Formalizing enzyme rules provides a foundation for retrosynthesis, where peptides and libraries could be designed to facilitate therapeutic discovery and diversification.


INTRODUCTION

Across biology, peptides are chemically modified for diverse purposes, from enhancing antimicrobial potency to honing signaling specificity and nucleating inorganic materials [1-6]. In the pursuit of pharmaceutical or other applications, one would like to design patterns of modifications in a peptide, but this is challenging using total synthesis because routes are long and involve highly-functionalized and chiral molecules [7-9]. An alternative would be to encode the peptide as a gene that is expressed with enzymes that introduce the desired post-translational modifications (PTMs) [10-12]. The process of identifying a path to a target molecule is a form of retrosynthesis that requires knowing the rules by which enzymes can be combined to act on a peptide sequence [13].


Peptide secondary metabolites are often encoded in genomes as a RiPP where a precursor peptide is expressed that comprises a leader and core sequence [3]. An enzyme binds to a recognition site (RS) in the leader and modifies amino acid(s) in the core [14-16]. PTMs include the introduction of cycles, added moieties (e.g, methylation), or conversions (e.g., epimerization) [3, 17-19]. A leader can have up to three RSs, sometimes overlapping to save space [20-22]. Changing the distance dbetween the RS and the modified amino acid(s) can affect the efficiency and which amino acids are modified [22-31]. Some enzymes are more sensitive than others, likely due to flexibility or allostery [32-34]. Leader-independent “tailoring” enzymes add modifications before or after the proteolytic release of the core [3]. To date, up to eight modifying enzymes have been found to act on a single peptide (theiostrepton), but the number of modifications can be much larger (e.g., polytheonamide has 49 modifications by 7 enzymes) [22, 35, 36].


During evolution, core hypervariability around a PTM scaffold facilitates the exploration of functional space, for example to diversify antimicrobials against new threats [10, 11, 37-40]. By physically separating binding from catalysis, leader-dependent enzymes are highly tolerant to changes to the core sequence; typically, 40-90% of mutants are modified correctly [12, 16, 17, 19, 20, 26, 27, 31, 41-50]. The specificity of tailoring enzymes can vary, with some being sensitive to sequence or the peptide conformation and others being very broad, notably when they modify the termini [46, 51-55]. Taken together, the minimal rule set needed to repurpose an enzyme is: 1. the tolerance of the core sequence, and 2. the RS sequence and position constraints within the leader, if relevant (FIG. 10A).


Various approaches have been used to discern these rules. Importantly, when characterizing an enzyme for retrosynthesis, the constraints must be with respect to the chemistry performed and not function [42]. For example, in one study, only 41% of thiopeptide mutations that yielded the correct PTM also retained antibiotic activity [56]. While bioinformatics can be used to deduce the RS or enumerate core variability, drawing them from natural genomes implies functionality [57, 58]. Another approach is to evaluate the impact of mutants with libraries created though alanine-scanning, saturation mutagenesis, or core shuffling [42, 47, 59-66]. Billions can be evaluated using assays that screen for function or by panning for target binding [26, 47, 56, 62, 64, 67-72]. The throughput of chemical assays is more limited; electrospray ionization mass spectroscopy (ESI-MS) can characterize hundreds of variants [29, 33, 42, 73]. MALDI-MS and SAMDI-MS could scale to 104 variants or more, but they are currently limited by peptide length and require additional expensive processing steps when automated [31, 50, 56, 74, 75].


Early work has combined enzymes from different pathways to build novel compounds, but typically, these have been sourced from the same RiPPs family [39, 55, 76]. Some tailoring enzymes will modify nearly any core and this observation has been used to incorporate methyltransferases, decarboxylation or epimerases into unrelated pathways [46, 55, 77]. Combining enzymes across RiPP classes has proven more difficult. In pioneering work, Mitchell and van der Donk showed that leader-dependent enzymes from sactipeptide, lanthipeptide, and heterocycloanthracin pathways could be combined by creating leader chimeras combining the RSs [74]. Along with a tailoring enzyme, this was used to make a new 32-mer lanthipeptide containing a thiazoline and d-Alanine.


In this Example, enzyme specificity rules were formalized to facilitate their algorithmic combination to create a peptide with a defined PTM pattern. Four leader-dependent enzymes (TgnB, PlpXY, PaaP and LynD) and five tailoring enzymes (PalS, ThcoK, PadeK, EpiD, LasF) were selected to represent diverse chemical modifications, species, and RiPP classes (Table 5) [18, 54, 59, 78-81]. Most have little prior information in the literature regarding substrate preferences. Escherichia coli was selected as the chassis because RiPP enzymes often work in this host and the “Marionette” strains allow the independent control of up to a dozen genes [82-84]. An N-terminal SUMO RiPP stabilization tag (RST; as described in Example 8) was used to increase the concentration of precursor peptide and simplify leader cleavage, which can be difficult to predict [85]. Mutagenesis strategies were developed to efficiently extract the enzyme rules: recognition site, distance constraint, and core tolerance (FIG. 10A). An automation pipeline that spans oligo synthesis to ESI-MS analysis was used to evaluate over 1000 precursor peptide variants. The substrate rules were put into a form that simplifies their combination, to computationally design a precursor peptide that is modified by multiple enzymes. As a proof-of-principle, heterocyclized peptides that contain a thiazoline, beta-amino acid, and phosphorylated serine were designed and it was verified that 4/5 had the correct modifications, whereas there was an estimated 1 in 10 million chance of success if designed randomly. This Example lays out a strategy to mine RiPP enzymes with the data necessary to inform retrosynthesis algorithms to aid the design of desired post-translational patterns.


Results
Characterization of Leader-Dependent Enzymes

A microtiter-based peptide expression, purification, and analysis pipeline was adapted to study modification of many peptide mutants/variants by individual modifying enzymes. This is a two plasmid system, with modifying enzyme produced from a p15A medium-copy plasmid and precursor peptide expressed from a pSC101 origin mutated to maintain at medium copy number (var 2, [87], FIGS. 44A-44D). Modifying enzyme expression was controlled by the cumate-inducible CymR repressor with matching promoter due to the repressor's high expression and low leak, while precursor peptide expression was controlled by the IPTG-inducible lac repressor with the T5LacO promoter due to its high expression (leak was acceptable for precursor peptide expression) [84]. Peptide expression was stabilized with by the RST, which includes an N-terminal hexahistidine (HIS6) tag for affinity purification, a SUMO stabilization tag, and a TEV cleavage site for liberation of the precursor peptide from SUMO (with residues “GC” remaining with the liberated peptide—G from the TEV cleavage site and C for compatibility with SAMDI analysis). Ribosome binding sites (RBS) were custom designed for each modifying enzyme using the RBS calculator to normalize expression levels, while a single RBS was used with the peptides since the RST sequence was consistently downstream and insulated the RBS from different precursor peptide sequences[88, 89]. A ribozyme was also used for modifying enzyme expression to stabilize mRNA and minimize effects of different promotors on translation (required for multi-enzyme modification) [90].









TABLE 5







Enzymes investigated in Example 3.












RiPP Class
Enzyme
Enzyme
Peptide
Organism
Ref





microviridin
lactone cyclase
TgnB
TgnA*

Bacillus thuringiensis

58


pantocin
glu-glu cyclase
PaaA
PaaP

Pantoea agglomerans

59, 78, 136


spliceotide
tyrosine excisionase
PlpXY
PlpA2

Pleurocapsa sp.

18


cyanobactin
thiazoline cyclase
LynD
TruE*

Prochloron spp.

39


lasso peptide
carboxylic acid methyl-
LasF
LasA

Lentzea kentuckyensis

79, 113



transferase


glycocin
cysteine glycosyl-transferase
PalS
PalA

Aeribacillus pallidus

110 


lanthipeptide
de-carboxylase
EpiD
EpiA

Staphylococcus epidermidis

54, 106


lasso peptide
serine kinase
ThcoK
ThcoA

Thermobacillus composti

80, 81 


lasso peptide
serine kinase
PadeK
PadeA

Paenibacillus dendritiformis

80, 81 





*in this Example, truncated forms of the wild-type TgnA and TruE peptides were used, which only included one core sequence (see Table 8).






Nine RiPP modifying enzymes were selected for analysis in this Example (Table 5; see also Table 7). Four of the selected enzymes were leader dependent and needed recognition sites and spacing constraints elucidated. Three of those (PlpXY, LynD, and PaaA) contained the RiPP recognition element (RRE) domain previously shown to be responsible for leader binding [14, 15], while TgnB is an ATP-Grasp microviridin-class enzyme with a less-studied binding mechanism. These four enzymes are from different bacteria genera, catalyze diverse chemical modifications, and result in different physicochemical properties in the modified peptide:


(1) TgnB, from Bacillus thuringiensis, covalently links glutamate/aspartate residues with serine/threonine residues to form the bi-cyclic depsipeptide thuringeinin[58]. The resulting cyclic peptide is a potent antidigestive (digestive protease inhibitor) and is rigid and constrained, both properties of interest in the peptide drug-discovery community [6]. The enzyme was codon optimized and synthesized, and used to modify a truncated peptide substrate with only one core (versus the three-core repeat in the native TgnA peptide)[58].


(2) PlpXY, from Pleurocapsa sp. PCC 7319, excises tyramine (the amine, alpha carbon, and sidechain of tyrosine) by breaking the peptide backbone and re-fusing it, resulting in a ketone containing beta-amino acid [18]. The modification is interesting both in its chemical reactivity (it can be used as a click substrate), and its uniqueness—no other RiPP enzyme known alters the peptide backbone as extensively. The enzyme PlpX and its RiPP recognition element PlpY were both codon-optimized and expressed as a two-gene operon and used to modify PlpA2, one of three core peptides in the cluster.


(3) PaaA, an antibiotic from Pantoea agglomerans, performs a Claisen condensation between two adjacent glutamate residues, resulting in the fused-ring heterocycle indolizidine [78]. This alkaloid moiety is not typically associated with RiPP biosynthesis, but is prevalent in many bioactive small molecules [91]. The enzyme was codon optimized and was used to modify its native precursor peptide (also codon optimized).


(4) LynD, from Lyngbya sp., dehydrates a cysteine with a peptide backbone amide to form a five-membered heterocycle. The resulting heterocycle, thiazoline, spans what was the amide bond, creating a protease resistant backbone[92]. Thiazolines retain the planar structure of the amide [92] and can be oxidized to aromatic thiazoles by cyclodehydratases found in some RiPP clusters[93]. Due to their valuable properties, thiazol(in)e heterocycles are frequently found in bioactive natural products and approved drugs[92]. LynD was codon optimized, and was used to modify a single-core truncation of TruE, a precursor peptide from a homologous pathway.


To generate the peptide expression plasmids, and leader mutants thereof, some were ordered as oligos, PCR amplified, and cloned into TypeIIs expression vectors, but a majority were synthesized and assembled by Twist Biosciences. From Twist, peptide vectors were rehydrated and immediately co-transformed with their cognate modifying enzyme plasmid in microtiter 96-well plates. Because only clonal, sequence verified plasmids were used, co-transformants were directly selected for by growing in LB supplemented with kanamycin and carbenicillin, without plating on agar and picking colonies. After overnight incubation, stationary phase cultures were diluted 1:100 into expression media and maximally-induced at approximately mid-log to decrease potential toxicity effects on growth[94]. A high-velocity microtiter plate shaker was required due to the use of deep 96-well plates. It was found that shaking below 900 r.p.m. led to cell sedimentation and highly variable expression. The peptide/enzyme expressions were conducted in TB media, such that conditions for all enzymes were identical.


Liquid-chromatography coupled to mass spectrometry (LC-MS) was used for peptide analysis. SUMO-tagged peptides were analyzed directly (without tag removal) in order to decrease the number of processing steps and reduce peptide-to-peptide run variability (the tag buffers against the chromatographic properties and solubility of diverse peptides). Peptides purified and eluted via IMAC were directly injected on the LC-MS for analysis. Since all of the modifications studied in this Example resulted in a change in mass between the unmodified and modified peptide, extracted compound chromatograms could be generated based on the expected masses of the unmodified, partially modified (if relevant), and modified peptides. If a chromatogram contained a peak, it was fit with a skewed gaussian[96], and the resulting fit was used to calculate peak area. Peak areas for modified, partially modified (if applicable), and unmodified peptide were summed to calculate the total peptide observed, which was then used to calculate the fraction of each peptide modification state.


While this process was chosen due to its simplicity and scalability, it does have two limitations: 1) Modified, partially modified, and unmodified peptide masses were sometimes not fully resolved in the MS. For the tagged large peptides analyzed (15-25 kDa), the isotope distribution could span 15-25 Da. If the modification being studied caused a mass shift of <15-25 Da, the isotope distributions between the unmodified and modified peptides would not be fully resolved, leading to crossover during integration of the modified and unmodified peptides. Similarly, spurious sodium adducts could cause a 22 Da mass shift, resulting in overlap with enzyme-catalyzed 14 Da (LasF) and 18 Da (TgnB and LynD) mass shifts, also affecting integrations and fraction modified calculations. 2) Multiple charge states are required to reliably annotate a peptide as present, which raises the limit of detection. On the machine that was used, the SUMO-tagged peptide limit of detection was estimated to be a peak area of ˜104-5. The median peak size observed was ˜106, meaning that a peptide with a fraction modified of 0.0 could actually have been as high as 0.1, if the modified peptide intensity was just below the detection threshold, or fraction modified of 1.0 could have been as low as 0.9 (though this would have had no effect on intermediate values of fraction modified). Most of the overlapping isotope effects were solved by extracting ECCs using a small m/z window around the expected mass of each peptide, such that regions of isotope overlap were ignored. For any remaining effects of overlapped isotope distribution, as well as sodium adduct and high limit of detection effects, the effects should largely have been dependent on the modification mass shift and the peptide being studied. Therefore, the effects could be countered by only comparing fraction modified within the same modification, since the effects should be similar (and cancel out) for similar peptides with the same modification.


Using the outlined pipeline, the four leader-dependent modifying enzymes were used to assay for modification (FIG. 46). Fraction of peptide modified varied between the enzymes (0.32-0.94), qualitatively in agreement with data presented in previous publications[18, 39, 58, 78]. PaaA and LynD were the most efficient, with 94% and 83% of their peptide modified, respectively. TgnB was distributive[58], like other microviridins[97], meaning that the enzyme binds, forms a single lactone, unbinds, and the process repeats until all lactones are formed. Both lactones were formed in 65% of the peptide, with the remaining 35% evenly split between unmodified and a single lactone modification. The lowest fraction modified was observed for PlpXY, with 32% of PlpA2 modified, although this was similar to the low-turnover shown previously [18]. Encouragingly, the platform gave reproducible values, with standard deviations as low as 2% (LynD and TgnB) and not above 3.8% (PlpXY).


Identification of Recognition Sites within Leaders


A simple approach was taken to deduce each enzyme's RS sequence(s). Alanine scanning is effective in finding the RSs, by measuring when the modification to the core is disrupted [60]. However, making a single substitution at every position is inefficient, particularly for long leaders and provides unnecessary resolution given that the smallest RS known is 7 amino acids[98] (excluding protease sites). Instead, blocks of 4-5 alanines were used to scan the leader and measure the impact on the fraction modified (block size dependent on leader length). The block was iteratively moved by 2-3 residues for each mutant (FIG. 10B). As an example, only 14 mutants of the 42-residue TgnA leader needed to be made to identify the RS for TgnB (FIG. 10C). When the alanine block disrupts the RS, the efficiency of modification drops dramatically, in this case at the far N-terminus of the leader. The results of these experiments for the leader-dependent enzymes are shown FIGS. 47A-47D, 48A-48D, 49A-49C, and 50A-50D.


A thermodynamic model was derived to infer the per-residue contribution to the binding of the modifying enzyme. This was simplified by assuming that the reaction follows Michaelis-Menten kinetics, where reversible binding to the leader precedes modification and release. This treats the binding and unbinding as being at quasi-steady state with respect to the production and degradation of the peptide; in other words, the ratio modified ρ, is the equilibrium value. Then, the change in the free energy of binding of the variant n with respect to the wild-type is










ΔΔ


G
n


=



Δ


G
n


-

Δ


G
wt



=


-
RT



ln

(



ρ


π


ρ
wt


)







(

Equation


1

)







where R is the gas constant and T is temperature. If the contribution of each residue i of a mutant contributes additively to the free energy change, then





ΔΔGni=1MΔΔGi  (Equation 2)


where M is the number of mutated residues. An algorithm was developed to assign ΔΔGi values using all of the variant data. Initially, the contribution of ΔΔGn was divided equally amongst the mutated residues (for example, divided by 5 for a 5-alanine block in which none of the wild-type residues replaced by the block were originally alanines). However, some residues were mutated in two variants, so the residue was assigned a ΔΔGi value of the mean of the two ΔΔGn/M values. The resulting ΔΔGi assignments violated equation 2 (ΔΔGi values will not sum to ΔΔGn within a variant), so ΔΔGi values were adjusted iteratively and in small increments (similar to a force-directed graph) until the constraint of equation 2 was satisfied for all variants.


The result of this calculation is shown in FIG. 10C for TgnA/TgnB. Eleven residues at the N-terminal end were determined to have high ΔΔGi values. This was in agreement with previously published observations that deletion of residues −42 through −35 or −34 through −29 residues at the N-terminus of the TgnA leader peptide knocks out TgnB modification while deletions in other sections of the leader are tolerated [58], as well as high conservation of residues −40 through −33 in TgnA homologs (FIG. 56). These data were mapped to the leader sequence in FIG. 10D, shaded according to the magnitude of ΔΔGi. Because ΔΔGi values were based on alanine-block replacements, they may not accurately depict the edge of an RS. The RS defined for the specificity rule is outlined by a box in FIG. 10D. For several enzymes, it did not exactly correspond to the regions of high ΔΔGi because additional information was incorporated into the designation; either expanding it to be conservative or shrinking it if there was information that the residues were not important.


One source of additional information was leader structure. A Deep Convolutional Neural Field algorithm (RaptorX Structure Property Prediction) was used to predict the secondary structure of the leaders (FIG. 10D) [99]. Of the four peptides, TgnA was the only leader RS that did not align with an alpha-helical region, which was surprising given that the TgnB homolog MdnC recognizes an alpha-helix in the MdnA leader[98]. The sequence itself is also similar, with TgnB recognizing “YRPYIAKYVEE (SEQ ID NO: 108)”, with bolded residues aligning closely with the “PFFARFL (SEQ ID NO: 109)” recognition site highly conserved in microviridin leader peptides[98]. Analysis of the MdnA peptide with RaptorX predicted an alpha-helix at the RS, indicating that the TgnA sequence may elude secondary structure prediction by this algorithm or the TgnB enzyme does not bind a helix like MdnC. Closer investigation of the secondary structure prediction from RaptorX showed that the recognition site is ˜10 times more likely to have a helix than anywhere else in the leader peptide, but ˜3 times less likely than beta-sheet or coil at those positions. Importantly, this showed that secondary structure alone cannot reliably predict an RS. PlpXY, PaaA, and LynD all bind to the RS via a RiPP recognition element (RRE) which has been shown to bind to alpha-helical peptides [14]. Indeed, the high ΔΔGi residues corresponded to regions predicted to adopt a helical structure. In the case of LynD, even though only three residues were calculated to have a high ΔΔGi, the boundaries of the RS were extended to encompass more of the helix (FIG. 10D). In contrast, the final glycine was removed from the PlpXY recognition site in PlpA2 because it was not part of the helix, and the “GG” leader motif is commonly necessary for cleavage between the leader and core, not for modifying enzyme recognition [100].


Sequence conservation within peptide homologs was also incorporated. Encouragingly, for all of the leader peptides, regions of high ΔΔGi values corresponded to regions of high conservation in weblogos of peptide homologs (FIG. 56). Similar to structural predictions, sequence homology was used to inform the boundaries of the recognition sites. The LynD recognition site did not include the full helix (“SQ” at the beginning is not included) because those positions had poor conservation in TruE homologs (FIG. 56). The resulting LynD recognition site, “LAELSEEAL (SEQ ID NO: 110)” is highly conserved in other cyanobactin peptides [39], and has been shown to be sufficient for modification with LynD homologs[76]. While the first two residues of the TgnB leader were kept in the recognition site, lower conservation at those positions may indicate that they are not necessary. Finally, the two positions N-terminal to the PlpA2 RS (“NE”) were not included because they are not conserved in PlpA2 homologs.


While the alanine scans showed that sequences in the RSs are necessary, and homologous sequences and structural predictions can help validate those data and inform boundaries, they did not prove that the RS is sufficient for modification. For each of the peptides, truncations were tested to remove sequence that should be unnecessary. The TgnA RS is at the N-terminus of the leader, so only truncations between the RS and the core were possible. The effect of truncations on RS-to-modification spacing versus sequence importance could not be differentiated, but truncations of various sizes were generally tolerated. Most truncations were modified over half as well as wild-type, and were modified as well as or better than similarly-sized insertions, indicating that the modifying enzyme is sensitive to changes in RS-modification site spacing. Previously reported deletions scanned through the TgnA leader also agreed with annotation of the TgnB RS as necessary and sufficient for modification, where only deletions that included RS residues were unmodified [58]. Both the TruE and PlpA2 peptides included sequences N-terminal to the RS, removal of which was well-tolerated by each respective modifying enzyme, with fraction modified similar to that of full-length leader (FIG. 48A and FIG. 50A). Removal of residues between the LynD RS and the core was also tolerated by LynD (FIG. 50A). The PaaP RS consisted of nearly the entire leader, so leader truncations were not tested, but truncations to the follower peptide were tested to determine if it is necessary for modification. Previous work has shown that truncation or removal of the follower peptide is not tolerated by PaaA [78], but that the follower sequence can be mutated without breaking modification [59]. Similarly, removal of only three amino acids from the C-terminus of the follower was observed to decrease modification from 89% to 39%, with removal of nine amino acids breaking modification. While the sequence is important for modification, scanning site saturation mutagenesis of the entire peptide showed that the sequence in the follower is mutable, unlike residues in the RS of the leader[59]. Based on this, the follower was treated as an extension of the core peptide, rather than as a “structural” element of the peptide. The sequence constraints in the follower were therefore elucidated later as part of the core sequence motif.


The final recognition site sequences are outlined in boxes in FIG. 10D and are listed in Table 5. The sites were similarly sized, ranging from 9-12 amino acids, but varied in their placement in the leader, ranging from N-terminal (TgnB) to C-terminal (PaaA and PlpXY) and between (LynD). The sites contained large numbers of hydrophobic amino acids (L/I/A/F/V/P), in agreement with observations that hydrophobic interactions are a contributor to affinity between modifying enzymes and RSs [14] and protein-protein interactions as a whole [101]. They differed in the charged residues present, with LynD and PlpXY containing negatively charged glutamate residues and PaaA and TgnB containing a single arginine and lysine, respectively. Given the helicity of the RSs (all but TgnB), charged residues may be solvent exposed (opposite the binding face), or participate in salt-bridges as part of the interaction. The annotated RSs also agreed with previously published work on these enzymes, when available. Deletion of amino acids in the N-terminus of TgnA precluded modification by TgnB [58], in agreement with annotation of the RS at the N-terminus of the leader. The four leader residues previously shown to be important for modification of PaaP by PaaA [59] were all included within the annotated RS. The LynD RS, as annotated, has previously been used both in vivo and in vitro with LynD and homologs of LynD [39, 42, 102]. This is the first known description of the PlpXY RS in PlpA2.


Determination of RS Spacing Constraints

Variants were designed to alter the spacing d between the RS and the modified residue. An alternative would be to define d as the distance to the start of the core sequence, which could be more intuitive for enzymes that modify multiple core amino acids, such as TgnB [58]. However, the distance to the modification was selected as it was more likely to be the physical distance to the modification site itself that influences modification rather than the distance to the core/leader cleavage site. Additionally, during forward engineering of precursor peptides, it functions as a constraint on core length by keeping modifications from being allowed at infinite core positions away from the leader. As such, d was defined as the number of residues between the RS and the modified amino acid. If multiple amino acids were modified (for example the two lactone cycles in TgnB modification), it was the distance to the first modified amino acid.


Changing d from its optimal value was expected to lead to lower modification efficiencies. In its simplest form, this can be treated as an energy well, where a wider well corresponds to more core positions being modifiable if RS position in the leader is kept constant. In contrast, a steep well indicates that the modification can only occur at a single residue, optimally spaced from the RS. A spring model is the simplest way to model this effect, which has been applied to similar biophysical phenomena, such as modeling the impact on ribosome binding that results from different spacing between the Shine-Delgarno and ATG start sites [88]. Using a spring model, RS-to-modification distances less than optimal would be “stretched” for modification, while distances greater than optimal would be “compressed”. The following equation can be derived from Hooke's Law,










ΔΔ


G
n


=


1
2

[



κ
s



H

(

d
-

d
0


)




(

d
-

d
0


)

2


+



κ
c

(

1
-

H

(

d
-

d
0


)


)




(

d
-

d
0


)

2



]





(

Equation


3

)







where d0 is the optimum spacing, κs and κc are the stretching and compression spring constants, and H(x) is a step function. Equation 3 could be changed to reflect other functions; for example, it might take on the form of a steep step function if there is a distance at which suddenly an enzyme is no longer active. It also does not have to be monotonic, with more complex forms modeling enzymes that exhibit multiple local minima or periodic behavior. In its current form, the stretching and compression constants define the width of the energy well described above, with small values of κ corresponding to a wide energy well with high spacing tolerance and large values corresponding to a narrow energy well with low spacing tolerance.


Leader variants were designed for each modifying enzyme to perturb the RS spacing, starting with TgnB. TgnA* has 35 residues between the RS and the first modified residue, with 31 of those being in the leader. Five truncation variants were designed by removing residues at the C-terminus of the leader, starting with two amino acids and increasing in increments of four amino acids to the longest truncation of 18 amino acids, representing over half of the spacer. Three insertion variants were also designed using a TEV cleavage site (amino acid sequence ENLYFQ (SEQ ID NO: 111)) and glycines as a spacer: the TEV site alone is a 6 amino acid insertion, TEV site followed by triple-glycine is +9 amino acids, and TEV site flanked by triple-glycines is +12. Each of these 8 variants was assayed for modification, and the fraction modified for the variants is shown in FIG. 10E. Values were converted to ΔΔG. (using equation 1) for each variant and plotted against the RS-modification distance. With the exception of the longest insertion variant, increased spacing deviations from optimal corresponded with decreased modification. The trend was fit with equation 3 to calculate the stretching and compression spring constants (Table 6) as 30 and 100 J·mol−1·AA−2, respectively, where do is set to the wild-type distance. These values implied that the enzyme was more tolerant of shorter spacer distances than longer, surprising given that the wild-type TgnA peptide contains a leader with three cores in tandem [58], with leader to modification distances of 35, 56, and 77. With a compression constant of 100 J·mol−1·AA−2, the farthest modification was predicted to have a ΔΔGn of 176.6 kJ/mol, effectively unmodified. While the data collected was used to fit the spring constants, this data indicated that a more complicated model, including variations of equation 3 with periodic behavior, may be necessary for distributive/multi-core enzymes like TgnB [103]. It is worth noting that modification of the full TgnA peptide using this expression platform was not observed[104], so it is also possible that the TgnA* spacing parameters described here are specific to the single core TgnA* peptide expressed as a SUMO fusion.









TABLE 6







RS spacing constraints


Parametera












Enzyme
d0
κ1
κ2
















TgnB
37
 100
 30



PlpXY
6
 20
3390



PaaA
0
40000b
40000b



LynD
11
  8
 100








aParameters for Equation 3.





bNo indel tolerated; Fit for ΔΔGn = 20 at d-d0 = 1







PlpXY is known to be tolerant to varying core positions, since there are two precursor peptides associated with the cluster that have RS to modification distances of 6 (PlpA2) and 21 (PlpA1). The leader peptide (and RS sequence) of PlpA1 differs from PlpA2, so modification of the two was not directly compared, since modification differences due to distance cannot be separated from RS sequence differences. Instead, spacing parameters were elucidated similarly to TgnA*, using engineered insertion/deletion variants of PlpA2. Since the RS is one residue away from the C-terminus of the leader peptide and the modified tyrosine is also close to the N-terminus of the core, only three deletion variants were tested: deletion of the final glycine (−1), the final glycine and first two residues of the core (−3), and the final glycine and first four residues of the core (−5). The same insertion variants were tested as for TgnA*/B: insertion of a TEV cleavage site (+6), TEV cleavage site followed by a triple-glycine (+9), and TEV cleavage site flanked by triple-glycines (+12). The variants were assayed for modification, with variant effect on modification converted to ΔΔGn and fit with spring constants (FIG. 10D and Table 6). As expected, increases to RS-to-modification distance were well tolerated, with variants having near-wild-type modification, in agreement with the large spacing observed in PlpA1.


The PaaA RS has very rigid placement restrictions (FIG. 49A). The RS in the leader directly abuts the modified residues in the core, making it impossible to delete amino acids. Deletions that cut into the defined RS were found to abolish modification, while adding a small GGG spacer between the RS and the modification was also not tolerated. Therefore, a ΔΔGn of 20 was assigned for d values −1 and +1 from d0, and solved for both κ constants using those values, with ΔΔGn=0 at d0.


LynD, and homologous cyanobactin heterocyclases, are known to be tolerant to spacing changes in the precursor peptide [39, 42]. In nature, it modifies the LynE peptide, which includes the same “LAELSEEAL (SEQ ID NO: 110)” RS defined in the truncated TruE* peptide, with three tandem cores and modified cystines spaced 9, 12, 24, 27, 39, and 42 amino acids from the RS [39]. In the full-length TruE peptide, which was modified with LynD in this Example, LynD modifies cysteines in two tandem cores, with RS-to-modification distances of 6 and 27 amino acids (FIG. 50A). Modification of the full-length TruE peptide was compared with modification of the truncated TruE* peptide to identify a compression spring constant of 8 J·mol−1·AA−2. A single deletion variant, with five of the six leader residues between the RS and core removed, was fit with a stretching spring constant of 100 J·mol−1·AA−2 and tested.


Tolerance to Core Mutations

Libraries varying the core of each RiPP were made to determine modifying enzyme tolerance to different amino acids. In general, the approach of using scanning site saturation mutagenesis (SSSM) was followed and applied to positions surrounding the modified residue(s) [56, 59]. Degenerate oligonucleotides, with codons replaced by NNK mixed bases, were used to build libraries and isolate core sequence variants. Typically, a single residue would be varied at a time, with all single-residue NNK libraries pooled together such that an individual library member has a random amino acid at a single random position (also known as a saturation mutagenesis single variant library or single codon randomization library, abbreviated as sSSSM for single SSSM). The pooled oligonucleotide libraries were cloned and individual variants were isolated and sequence verified. To increase coverage at each position, the number of core positions in the libraries was decreased and included only those surrounding and necessary for the modification. For cores with long C-terminal “tails” after the modification, truncations were made to the peptide's C-terminus to determine the minimal sequence necessary for modification. All four modifications were close to the N-terminus of the core, so the entire core N-terminal to the modification was always included in the libraries. PaaA and TgnB modifications used wild-type leaders for modification, while leaders with long N-terminal regions before the RS (TruE* and PlpA2) used N-terminal leader truncations shown to be sufficient for modification during leader/RS characterization (FIGS. 48A-48B and 50A-50B). The core libraries were cloned into the same expression system described above and used with identical growth/expression conditions.


The raw data for the TgnA* core library are shown in FIG. 11A. For this library, the entire core sequence of 21 amino acids were included and 48 single-mutant variants were generated and analyzed. The library was composed of 21 oligonucleotides, each with a different core codon replaced by NNK, pooled together and assembled with the leader peptide into the peptide expression plasmid. The resulting sSSSM library was then co-transformed with the TgnB expression plasmid, and plated on agar such that each colony contained a unique peptide variant along with the modifying enzyme. Individual colonies were picked and peptide sequence verified before assaying for modification. As can be seen in FIG. 11A, the variants span all levels of modification. A criterion of 50% of the wild-type activity was set to consider an amino acid as being accepted. This conservative threshold was selected because, assuming additive effects, the multiple mutations that would arise from de novo peptide design would rapidly decrease the fraction modified. Of the variants tested, 25, or 52%, were modified above this threshold (FIG. 47B). Accepted amino acids at each position were then compiled into a core summary motif, shown in FIG. 47C, where accepted amino acids appear below the wild-type sequence and unaccepted appear above the sequence. Finally, amino acids that were observed unallowed/allowed at each position were compared with the other two core repeats present in the TgnA peptide (only one core repeat was used in TgnA*). Only a single amino acid of overlap was present between observed amino acid variants and the other natural cores—core position 20 is a tyrosine in the other cores. Though tyrosine was originally disallowed at position 20 since its fraction modified was slightly below the cutoff, the motif was updated to include it based on its presence in the natural core. Based on the same principle, the final core motif was updated to include all of the amino acids present in the other wild-type cores, and used to generate the motif shown in FIG. 11B.


Although the TgnA* library was designed to generate single-mutant variants, several variants were isolated with two mutations and one with three, which provided an opportunity to investigate mutation additivity (FIGS. 47A-47D). Mutations are additive when the free energy change of a double mutant is the sum of the individual mutations, ΔΔG12=ΔΔG1+ΔΔG2. This is equivalent to multiplying the modified ratio from individual mutations for the double mutant. Two instances of non-additivity were found, both of which showed the compensatory recovery of a bad mutation. For example, in TgnA, the A14S mutation decreased the activity, but this could be compensated when both E9L and T4L were present, returning the triple mutant to wild-type activity. Similarly, P2L could be recovered by adding Y19A. Non-additivity was not observed for any of the other leader-dependent enzymes.


For PlpA2 modification by PlpXY, truncations to the C-terminus were first investigated to identify residues necessary for modification. Increments of three amino acids were removed from the C-terminus of the peptide until modification broke. Removal of 12 amino acids was tolerated, with fraction modified within error of modification of the wild-type peptide, while removal of 15 amino acids was not modified at all. This was in agreement with previous work which showed that the proline at position 11 was necessary for modification [18]. Based on this data, a library was built to include positions 1-12 of the core peptide. A similar sSSSM library was built as described for TgnA*, with 41 single-mutation variants isolated and assayed. In contrast to TgnA*, only half of the variants were tolerated, with one variant removed because of high variance amongst replicates (FIG. 48B). From this data, G7, V9, and P11 were observed to be restricted positions, with all tested mutations at those positions showing no activity (FIG. 48B). A core motif was built for PlpA2, shown in FIG. 11B. The observations were similar to those of Morinaka, et al[18]. They observed G7 to be essential, with replacement by an alanine not tolerated. At the methionine at position 5, mutations with 30 L, V, W, D, and T were tested, with L well tolerated, V poorly tolerated, and no tolerance for W, D, or T. Morinaka, et al annotated L and V as tolerated at that position, and F and E as not (similar to W and D, respectively)[18].


Based both on the six cysteines modified by LynD in the native LynE substrate [39] and the two cysteines modified in the TruE substrate, LynD was anticipated to be extremely permissive of different amino acid residues surrounding the modified cysteine residue. In the TruE* peptide, both the entire core (five amino acids preceding the modification) and the follower (four amino acids after the modification) were included in the library, with the follower treated as core peptide rather than a structural element (similarly to PaaP follower in its library). Given the number of residues in the library, and the potentially high tolerance of diverse amino acids, a saturation mutagenesis library of all positions simultaneously was used, allowing the core sequence to be xxxxxCxxxx (SEQ ID NO: 112), where x is any amino acid. A single degenerate oligonucleotide, with all core and follower codons except the cysteine replaced by NNK, was used to build the library. In the resultant variants, peptides with more than one cysteine were screened out, since it was impossible to tell which ones were modified via LC-MS. Twenty-four variants were isolated and assayed, in addition to 10 variants that were synthesized to have charged and/or bulky polar residues flanking the modified cysteine (native flanking residues are usually small and/or hydrophobic). All of the custom/designed variants were well modified, showing that LynD tolerated charged or bulky polar side chains at the modification site. Of the 24 random variants, 17 were modified above the half-of-wild-type threshold. At all of the positions included in the library, tolerated amino acids were physiochemically diverse, consistently including 5-6 of the 6 physicochemical groupings used to classify amino acids (positive, negative, polar, aliphatic, aromatic, G/P). Based on this, the motif was trimmed to include only the positions adjacent to the modified cysteine. Those two positions were updated to allow 19 amino acids, all except cysteine, since modification of adjacent cysteines was not investigated (FIG. 11B).


Tailoring Enzyme Tolerance to Core Mutations

The same expression/analysis pipeline described for leader-dependent modifying enzymes was applied to leader-independent tailoring enzymes. Tailoring enzymes do not bind recognition sites in the leader, instead they bind directly to the site of modification in the core, with specificity presumably determined by the amino acids around the modification. As such, these enzymes have no RS or RS spacing constraints, but do have core sequence constraints that can be elucidated similarly to the core constraints of leader-dependent modifying enzymes. To maintain consistency between all enzymes, expression conditions were equivalent to those described for modifying enzymes: peptides were expressed as a SUMO fusion and expressed and modified in TB media in 96-well plate format.


Of the nine enzymes selected for characterization (Table 5), five were leader-independent tailoring enzymes. One of the enzymes modifies the side chain of an internal peptide residue while others modify the C-terminal residue side chain or carboxyl group. In contrast to the leader-dependent modifying enzymes, where all were from different RiPP classes, three of the five tailoring enzymes came from lasso peptide clusters, highlighting the compatibility of lasso peptide tailoring enzymes have with heterologous expression in this platform. The tailoring enzymes catalyze diverse transformations and have been sourced from diverse bacterial species (Table 5):


(1) EpiD is an oxidative decarboxylase from the epidermin biosynthetic pathway, a type 1 lanthipeptide antibiotic identified from Staphylococcus epidermidis[105, 106]. It is an integral tailoring enzyme for formation of the aviCys macrocyclization, though without the other enzymes in the pathway the aviCys cycle is not formed and decarboxylation results in an enethiolate [107], with a corresponding loss of mass of −46 Da. This modification is valuable both for its potential for forming constrained aviCys macrocycles[6] when combined with other enzymes and also for removing the carboxy group, decreasing polarity and potentially increasing membrane permeability[108, 109].


(2) PalS is a glycosyltransferase that catalyzes the class-defining glycosylation of pallidocin, a glycocin antibiotic[110]. In pallidocin, a cysteine is glycosylated, causing a gain of mass of +162 Da. Glycosylation can play diverse roles in small molecules, often used in antibiotics to inhibit peptidoglycan biosynthesis by glycopeptides[111] and now proposed as a strategy for improving peptide bioavailability during drug design[112].


(3) LasF is a methyltransferase from the lasso peptide antibiotic lassomycin[l13]. It methylates the carboxyl group on the C-terminus to form a methyl ester, causing a gain in mass of +14 Da. Similar to EpiD decarboxylation, the methyl ester is uncharged (unlike the carboxyl group), potentially aiding membrane permeability[108, 109].


(4) ThcoK and (5) PadeK are both kinases from lasso peptide clusters that install 1-3 phosphates on the C-terminal serine of their respective peptides[80, 81]. Because multiple phosphate groups can be added, the gain in mass can be +80, +160, and +240, corresponding to +1, +2, and +3 phosphates, respectively. Naturally, their biological role is unknown, but synthetically they can be used to modify substrate pKa/log P properties or create phosphopeptide mimetics that act as signal transduction inhibitors[114]. Both ThcoK and PadeK were included to enable phosphorylation of a greater number of peptides by investigating two kinases with presumably different sequence constraints. Since these enzymes install a variable number of phosphates, any number of phosphates to be “modified” was considered, meaning that fraction modified is the fraction of peptide that has 1, 2, or 3 phosphates installed.


Each of these tailoring enzymes catalyze a mass shift that can be assayed via LC-MS, in the same manner that leader-dependent modification was assayed. The five tailoring enzymes and their respective wild-type precursor peptides were first assayed for modification (FIG. 46). Fraction of peptide modified varied between the enzymes (0.29-1.0). PadeK was the only poorly modified enzyme, which was surprising since both previous work[81] and its homolog ThcoK showed efficient modification (FIG. 46). Peptide-enzyme pairs had similar modification between replicates (fraction modified standard deviation of 0.026-0.081), except PalA modification by PalS, which had a standard deviation of 0.58. The large variance between PalA replicates was caused by the detection limit of the LC-MS: poor LC-MS signal was observed for wild-type PalA peptide due to proteolytic cleavage of the leader by endogenous E. coli proteases. This caused full length (uncut) peptide to be low abundance (near the detection limit of the LC-MS), and in two replicates unmodified peptide did not pass detection thresholds (fraction modified is 1.0) while in the third replicate both modified and unmodified peptide did not pass (fraction modified is assigned 0.0). This problem was solved by removal of the leader (and most of the core peptide) during elucidation of the core motif, described further below.


Similar to leader-dependent modifying enzymes, core motifs were elucidated using scanning site saturation mutagenesis. Since tailoring enzymes do not require the leader (or a majority of the core), most of the precursor peptide was truncated to investigate only those residues surrounding the modification. Each peptide library was limited to eight varying positions. For tailoring enzymes that modified the amino acid side chain (PadeK, ThcoK, and PalS), the modified residue was not included in the library since it was necessary for modification, so the total peptide size was truncated to 9 amino acids. For the two enzymes that modified the carboxy group on the C-terminus (LasF and EpiD), the C-terminal residue was included in the library, so the total peptide size was truncated to the C-terminal 8 amino acids. The positions were numbered based on their position in the wild-type (full-length) core, not their position in the truncated version.


Initial libraries varying single amino acids at a time (like those used with TgnB, PlpXY, and PaaA) resulted in variants that were well modified (FIGS. 51A-51C, 52A-52C, 53A-53C, 54A-54C, and 55A-55C), indicating that the core motifs were very permissive. To accelerate exploration of amino acid sequence space, libraries that had multiple mutated positions were also designed. Several library architectures were used, including NNK-NNK (two adjacent randomized positions, abbreviated dSSSM for double SSSM), NNK—NNK—NNK (three adjacent randomized positions, abbreviated tSSSM for triple SSSM) or NNK-www-NNK (two randomized positions flanking a wild-type residue, w denoting a wild-type nucleotide, abbreviated dfSSSM for double flanking SSSM). These architectures were scanned through the truncated core and pooled such that variants had 2-3 mutated AAs at a random location. To build the motifs (FIG. 11C), the same cut-off of 50% of modification of the truncated wild-type peptide sequence was used for acceptance of amino acids at each position. When building summaries of tolerated amino acids at each position, unallowed amino acids were assigned using only single-mutation data, since the amino acid responsible for decreasing modification below the 50% threshold could not be determined when there were multiple mutations in a variant.


Finally, each motif was analyzed and minimized based on tolerated amino acids at each position. If every observed mutant at a position was accepted in the tolerance summary, and those tolerated amino acids spanned 4+ of the 6 physicochemical amino acid classes used, the position was annotated as unconstrained and allowed to be any amino acid. Unconstrained positions on the edge of a motif could then be removed from the motif entirely. During golden-gate/typeIIs assembly of the libraries, assembly bias that lowered the number of amino acid variants at the N- and C-termini of the library was observed, so terminal positions were often removed from the motif if they didn't meet the 4+ criteria above, but had unconstrained positions between them and the modified residue. For example, in the PadeK tolerance summary (FIG. 54B), core positions E17, D18, and V19 met the criteria to be unconstrained, but position D16 at the N-terminus only had one mutant observed due to assembly bias. It is unlikely that position 16 was constrained, while 17, 18, and 19 were not, so positions 16 -19 were removed from the PadeK motif (FIG. 11C).


The EpiA peptide was truncated to include the eight C-terminal residues (positions 15 through 22). EpiD modification was investigated using sSSSM, dSSSM, and dfSSSM libraries, each of which were cloned separately and a total of 33 variants isolated and assayed between the libraries. For many of the variants, the replicates varied more than what was observed for other enzyme peptide variants. Analysis of the raw chromatograms showed large peaks that were above the detection limit, but the spectra were noisier than spectra from other peptides/enzymes, for unknown reasons. Despite the lower quality data, trends were visible: mutations close to the N-terminus were observed to be well modified and those close to the C-terminus (modification site) were poorly modified. Position 20 did not tolerate negatively charged aspartate/glutamate amino acids, while hydrophobic (L), polar (S, N, and Y), and positively charged (R) amino acids were tolerated. Positions 17, 18, and 19 were found to be very permissive and all mutations at positions 15 and 16 were tolerated, so positions 15-19 were removed from the core motif, which is shown in FIG. 11C. EpiD substrate tolerance has been investigated in vitro, using neutral loss mass spectrometry to measure modification[54]. The final three residues were also annotated as important for modification, but observed V, I, L, F, Y, and W tolerated at position 20 and A, S, V, T, C, I, and L tolerated at position 21 (with all other amino acids measured and not tolerated). None of the tolerated amino acids were not tolerated in the variants tested, but several additional amino acids were observed to be tolerated at both of those positions (N, R, and S at position 20 and H at position 21). The discrepancy may be explained by non-additive effects described earlier—those amino acids were observed as tolerated based on variants that included multiple mutations, but they may not be tolerated in isolation. Indeed, Y20S was not tolerated in isolation, but modification was recovered with S19N mutation (FIG. 51A).


The PalA peptide was truncated to include the four amino acids to either side of the glycosylated cysteine (9 amino acids total). Three libraries were designed: sSSSM, dSSSM, and dfSSSM, with 74 total variants assayed for modification by PalS (Supplementary Note 10). A majority of variants (40) were 100% modified, with only 14 variants showing intermediate levels of modification and the remaining 20 not tolerated. Of those that weren't tolerated, all but two included mutations flanking the modified cysteine (positions 24 and 26). The remaining two were G22F and G27I single mutation variants, both surprising given the diverse amino acids tolerated at both of those positions. While there were multiple examples of variants with overlapping amino acids at a position, investigating non-additivity was impossible, since most variants were not at quasi-steady state but were fully modified. Mutation S29G had a lower fraction modified (0.81) than S29G with Y28F (1.0), but was within the S29G standard deviation of +/−0.24. In another example, F23K was fully modified while F23K with G24R as poorly modified (0.19). Assuming additivity, G24R was the offending mutation, except F23G with G24R was well modified (0.79). This may be an example of non-additivity, but because the F23K single mutant variant was fully modified it's possible that the F23K mutation was detrimental to modification, but not enough to lower the fraction modified below 1.0. Only when combined with another slightly detrimental mutation, G24R, did F23K mutation bring modification down significantly. Without a clear indication of non-additivity, the core tolerance summary was assembled using all the variants, observed positions 21, 23, and 28 to be unconstrained, and updated the core motif to include positions 22-27 (FIG. 11C).


The LasA peptide was truncated to include the C-terminal eight amino acids, all of which were varied in the library. Both sSSSM and dSSSM libraries were constructed, with 37 variants isolated and assayed for modification. Mutations to LasF had greater impact on the activity of the enzyme compared to variants for other tailoring enzymes. None of the variants with multiple mutations were well modified, and only 5 single-mutant variants had wild-type levels of modification. Hydrophobic amino acids (A, V, L, F, and W) were generally allowed in all positions. Mutation of the C-terminal isoleucine to tyrosine and cysteine was not tolerated, in agreement with data for a LasF homolog showing mutation of the C-terminal residue led to a 4-fold reduction in methylation. The variant data was used to build the core tolerance summary (FIG. 53B) and core motif (FIG. 11C), with no other physicochemical or positional trends.


PadeK and ThcoK were both truncated to include the C-terminal nine amino acids, with the final serine not included in the library since its side chain is modified. Both of these enzymes were very tolerant to diverse core sequences, so sSSSM, dSSSM, dfSSSM, and tSSSM libraries were all used to elucidate core constraints. In total, 31 PadeA variants and 34 ThcoA variants were tested. ThcoK was the most tolerant enzyme investigated: only one variant was below the modification threshold, with the mutation adjacent to the modified cysteine. Positions 16 through 21 all passed the criteria for being unconstrained, so positions 15 through 21 were removed from the motif, leaving only the modified serine, and the preceding residue. PadeK was more constrained: it only showed high specificity at the penultimate core residue and at core positions 22 and 21, respectively (adjacent to the ultimate/modified serine) (FIG. 11C). The ThcoK motif was decreased to the final two residues and the PadeK motif was decreased to the final four residues. Only 2 of 20 random single-mutation variants in ThcoA decreased ThcoK modification below 50%, and both were adjacent to the modified residue (FIG. 55A).


Design of Peptides with Multiple PTMs


A design algorithm was developed to create a library of core variants enriched for a desired modification pattern (FIG. 12A). Each modification imposes new constraints on the precursor peptide sequence. To this end, the algorithm had two objectives. First, the leader must place the RS sequences with the correct spacing to the amino acids they modify. If present, gaps between RSs and/or between the RS and the core must be filled by the algorithm. Second, the constraints on the core sequence have to be combined to create a pattern of tolerated amino acids for all of the modifications. The core also needs to be scanned to predict potential off-target modifications.


Leader design proceeds by moving the RS sequences with respect to the core and calculating their contribution to a scoring function. The maximum leader length is a parameter that can be set in the algorithm, with a default value of L=40 amino acids. The score S of RS placement m is the predicted effect of RS-to-modification distance d compared to optimal distance d0.










S
m



e




-

κ
1




H

(

d
-

d
0


)



(

d
-

d
0


)


-



κ
2

(

1
-

H

(

d
-

d
0


)


)



(

d
-

d
0


)




2

RT







(

Equation


4

)







which is bounded to the range 0-1 (inclusive). The total score for a RS placement in a leader p for a set of M enzymes is defined as






S
pm=1NSm  (Equation 5)


The algorithm then seeks to identify the optimum p that maximizes the score. This can be found simply by enumerating all possible placement combinations of the RS sequences.


There are several use cases in which it is beneficial to save space by overlapping the RS sequences, as sometimes occurs in natural leaders. For instance, the constraints on d might be too rigid to separate them. It could also free other space in the leader for additional enzymes to bind. Finally, shorter leaders could facilitate the use of specific DNA oligosynthesis techniques in building a library. To this end, an algorithmic approach was developed to evaluate overlapping RS sequences. If two RS sequences could overlap without any amino acid mismatches, then this was done without penalty. However, in most cases, overlap would require an imperfect RS for at least one enzyme. To capture this, an additional term was calculated to modify the score,










S
mn

=




(

a
-
z

)



(

b
-
z

)


ab

.





(

Equation


6

)







In Equation 6, a and b are the lengths of RS1 and RS2 and z is the number of mismatched residues (BLOSUM62 score less than or equal to 0) in the overlap of the two recognition sites. The fraction was bounded to the range of 0-1 (inclusive) and simply included in the product of terms for the total score (Equation 5). If more than two RSs were being combined, more than one pair of RSs may overlap, and Smn was calculated for each overlapping pair and included with Equation 5. At mismatched overlapping RS positions, a random choice between the two possible amino acids can be made, or one RS can be given priority over the other in selecting the amino acid.


Typically, if tolerated, a TEV protease site was included between the leader and the core so the core could be released and recovered after purification. When used, the TEV sequence constraints were treated as an additional leader-dependent modifying enzyme. The six amino acid TEV sequence ENLYFQ (SEQ ID NO: 111) was added as an RS, with fixed placement (high κ constants), such that it contributed to the calculation of Sp. TEV cleavage occurs after this sequence and was permissive to different amino acids at the first position of the core, except P, and reduced efficiency for L/E/I/V [115]. This core constraint was added as a core motif, with placement specified at position 1 of the core. In addition to this, there may be a gap between the RS sequences or between the last RS and the core. There are multiple options for filling these gaps provided by the algorithm: (1) GGS repeats; (2) choosing random amino acids (additional sequence constraints can be optionally added at any leader position); (3) spacer sequences taken from wild-type leaders of the enzymes being combined; and (4) nothing, the leader is returned with gaps to be filled in manually.


The final step was to design the core (FIG. 12A). First, the positions to be modified were fixed. The rules for each enzyme were then aligned to these positions. They were then combined to create a motif over the length of the sequence, where an amino acid was only allowed at a residue if it was allowed by all the enzymes at that position. Additional constraints can be added by the user, at any position, to encode a pharmacophore of interest, limit combinatorial complexity, or influence hydrophobicity or other physicochemical properties. Positions not restricted by an enzyme sequence constraint can be any amino acid. A library can then be generated of size N that randomly assigns amino acids from those allowed at each position. Optionally, this library can be filtered to remove sequences that have motifs at off-target sites that could potentially be modified by the enzymes. The output can serve to guide pooled oligo synthesis strategies.


Forward Design of a Synthetic RiPP

The algorithm was applied to design precursor peptides that can be modified by four enzymes: two leader-dependent modifying enzymes (LynD and PlpXY), one tailoring enzyme (ThcoK), and TEV protease (FIGS. 12A-12B). The core was defined to be 13 amino acids, with a thiazoline, excised tyrosine and phosphorylated serine at positions 2, 6 and 13, respectively. TEV cleavage was specified at position 1. The LynD, PlpXY, and TEV recognition sequences had to be combined into the leader sequence. It was hypothesized that the LynD and PlpXY RSs could overlap because the alanine-scan variants through the RSs for both enzymes were well tolerated (FIGS. 50A and 48A), indicating sequence plasticity. Then, the scores of all combinations of the LynD and PlpXY sequences, including overlaps, were calculated. This is shown in FIG. 12A, where there is a pareto-optimal boundary between the best scores and minimum leader size. A variant was chosen that had a high score but shortened the leader by having the RS sequences overlap by six amino acids (two mismatches).


A core motif was then designed by combining the rules associated with the three enzymes and including the restriction from the TEV protease that a proline cannot appear in the first position. Considering the variability allowed at each position, this resulted in 21,000 peptides that conformed to the rules. This was in contrast to the ˜1013 peptides that would result from all 20 amino acids being allowed at all non-modified positions. An oligo pool was built and designed to access a subset of the allowed peptides and cloned and sequence verified one that matched the enzyme restrictions and ten that had imperfect matches (FIGS. 45A-45C). To enable modification with multiple enzymes, a Marionette derivative of NEB Express E. coli was used, such that all inducible systems were encoded in the genome. Enzyme genes lynD, plpXY, and thcoK were placed under aTc-, OHC14-, and cumate-inducible systems, respectively, and assembled together onto a spectinomycin-resistant p15A backbone (FIG. 12B). The engineered leader-core was cloned under the same IPTG-inducible expression plasmid used above, which included its own copy of lac (in addition to the lacI encoded in the Marionette genome cassette), but this did not affect peptide expression. This created an artificial biosynthetic gene cluster of four genes, all under independent, inducible, control.


Expression and peptide modification was investigated in the same manner as for individual enzymes. Each of the eleven peptide plasmids were co-transformed with the multi-enzyme plasmid. Overnight cultures were diluted 1:100 into TB media, fully induced after 3 hours at 30° C., and incubated for 20 hours. Cultures were then lysed, affinity purified, and assayed via LC-MS.


All possible combinations of modification were searched (dehydration from LynD modification (−18 Da), tyramine excision from PlpXY modification (−135 Da), and phosphorylation from ThcoK modification (+80 Da)). For four of the peptides, masses were identified that matched expected triple-modification masses, suggesting a success rate of 80% for the hybrid core motif. The peptide variant with the highest fraction of triply modified peptide was selected for validation.


The co-transformed strain was struck out, and three colonies were individually grown up at small scale, affinity purified, and TEV cleaved. The final molecule was assayed via LC-MS/MS, where the mass and observed fragments matched the expected peptide structure.


DISCUSSION

This Example abstracted the substrate preferences of RiPP enzymes as “rules,” applicable to the constraint-based design of precursor peptides. Computational design can be used to guide the selection of enzymes to decorate a natural product [116], identify scaffolds to splice in a binding sequence [61, 117], or design large screening libraries enriched in modified peptides [62]. While RiPPs are generally very tolerant, the success rate declines rapidly as more constraints are added. For the example in FIGS. 12A and 12B, the enzyme rules estimated that only 1 in 300 million random peptides (holding the modified amino acids constant) would lead to a triply modified peptide. A library built according to these rules would contain 31,500 predicted unique compounds. Creating a large library for an exact set of core sequences has been historically difficult, where construction required random mutagenesis (e.g., NNK), but it is now trivial using custom pooled DNA synthesis services [118].


Chemical retrosynthetic planning algorithms use “rules,” extracted from the literature, to represent how a chemical moiety will be converted by a reaction [13, 119-121]. There is a trade-off between accuracy and path discovery: if every rule is specific to only one chemical, this would be the most reliable, but it would not be possible to predict paths to new chemicals. Algorithms balance these needs by specifying rules with respect to the number of atoms from the reaction center n; if n=0, then it is just the reaction itself and as n gets larger, this increases the accuracy as more of the chemical context is incorporated into the rule. This approach has been extended to enzymes using the same rules-based method of defining allowable enzyme substrates based on the substrate reaction center and surrounding atoms/functional groups [13].


Considering rules for RiPP enzymes, simply defining the chemistry performed by an enzyme and assuming perfect promiscuity for the other core positions is the philosophical equivalent to n=0. This assumption has implicitly appeared in the literature for RiPP design when highly tolerant enzymes were combined without restricting the core sequence [11, 23-25, 27]. Simultaneously, other retrosynthesis studies have engineered multiply modified peptides by generating peptide chimeras, with an enzyme effectively modifying its wild-type substrate [74, 76, 77], the equivalent of a large and un-engineerable n-value. The rules defined in this Example are the next level of constraints, representing the minimal information to capture substrate specificity. However, they incorporate a number of assumptions, including the additive combination of amino acid tolerances derived from single-mutant data. Indeed, incidences of non-additive compensatory effects from multiple mutations were observed. The next level of accuracy in rules could account for higher-order effects requiring more sequence knowledge of the core, such as charge, hydrophobicity, secondary structure, and loop entropy, all of which have been cited as important in determining RiPP enzyme specificity [22, 26, 42, 45, 47, 76, 122]. Similarly, in the leader it was assumed that recognition sites and spacing alone were determining factors of modification, but TgnB recognition site spacing variants varied in modification based solely on spacer sequence, indicating that leader sequence outside of the recognition site may affect modification (FIG. 10D), possibly due to spacer structure/flexibility. Mapping additional leader/core rules could be aided with artificial intelligence, which has been applied for this purpose to define rules for chemical retrosynthesis and has been applied to predict protein-protein interactions[121, 123].


However, many RiPP enzyme have properties, or gaps in knowledge, that make their function difficult to capture as a “rule.” Enzymes with wide RS spacing tolerance are often progressive, with difficult-to-predict behavior where single leader mutations change the modification pattern [20, 32, 34]. Kinetics are also a complicating factor, as enzymes in the same pathway can have orders-of-magnitude differences in time scales, from less than an hour to days[10, 33, 36, 124]. Imperfect leader sequences have been observed to alter enzyme kinetics, not just binding[33]. The order of operations also matters for cases in which later modifications require earlier ones to occur, for example, when a cyclization or epimerization orients an amino acid such that it is accessible for a subsequent modification[20, 30, 32, 61, 125, 126]. Tailoring enzymes can require that the released core peptide adopt a particular shape [42, 47, 52, 127].


This Example provides a new type of RiPP enzyme mining effort that differs from the approach of discovering new bioactive compounds by finding and reconstructing entire gene clusters from metagenomics data [65, 128]. Screens can be established to identify modifying enzymes along with simple approaches to define the minimal rule sets for their use. Because the goal is to combine them into a pathway, these enzymes need to be screened under a common set of conditions, whether it be in vivo or in vitro [76] and jettisoning those that do not work in this standardized context or that exhibit odd or unpredictable behaviors. These conditions may not reveal the precise role of enzymes in nature, but they provide the necessary information for forward design of artificial pathways. The “ideal” enzyme for retrosynthesis can also begin to be defined. One might think that it is a very tolerant enzyme regarding spacing to the modification, but broad substrate specificity can lead to unpredictable modification of multiple core residues and slow kinetics [33]. Instead, when given the option, it may better to have multiple enzymes on hand that differ in the distance from the RS where they modify their residue, such as appears to be the case in bottromycin biosynthesis [21]. Enzyme engineering, such as directed evolution, could be used to widen or tune substrate specificity specifically for the purpose of retrosynthesis. On last count, there are 300,000 RiPP clusters in the genomic databases with 4.6 million enzymes spanning ˜40 classes [129-134]. Finding subsets that work well together and characterizing their rules under common conditions would enable an enormous functional space to be algorithmically or combinatorially explored, providing unprecedented access to an emerging therapeutic modality: medium-sized constrained molecules, which are already showing promise for disrupting protein-protein interactions and other therapeutic targets that have traditionally been considered “undruggable”.


Materials and Methods
Strains, Plasmids, Media, and Chemicals.


E. coli NEB 10-beta (C3019I, New England BioLabs, Ipswich, Mass., USA) was used for all routine cloning. E. coli NEB Express (C2523I, New England BioLabs, Ipswich, Mass., USA) was used to express precursor peptides with single modifying enzymes, and the Marionette derivative of E. coli NEB Express (Marionette X) was used to express precursor peptides with multiple modifying enzymes. Plasmids for precursor peptide expression and modifying enzyme expression were used as follows: precursor peptide genes used a pSC101 origin variant (var 2) [87] and single modifying enzyme plasmids contained p15A origins of replication and kanamycin resistance. Plasmids with multiple modifying enzymes contained p15A origins of replication and spectinomycin resistance. LB-Miller (B244620, BD, Franklin Lakes, N.J., USA) and TB (T0311, Teknova, Hollister, Calif., USA) supplemented with 0.4% glycerol (BDH1172-4LP, VWR, OH, USA) were used for peptide expression and modification. 2xYT liquid media (B244020, BD, Franklin Lakes, N.J., USA) and 2xYT+2% agar (B214010, BD, Franklin Lakes, N.J., USA) plates were used for routine cloning and strain maintenance. SOB liquid media (S0210, Teknova, Hollister, Calif., USA) was used for making competent cells. SOC liquid media (B9020S, New England BioLabs, Iwsich, Mass., USA) was used for outgrowth. Cells were induced with the following chemicals: cuminic acid ≥98% purity from Millipore Sigma (268402, Millipore Sigma, Saint Louis, Mo., USA) added as 1000× stock (200 mM) in EtOH or DMSO; isopropyl β-D-1-thiogalactopyranoside (IPTG) ≥99% purity (I2481C, Gold Biotechnology, Saint Louis, Mo., USA) added as 1000× stock (1 M) in water or DMSO. Cells were selected with the following antibiotics: kanamycin (K-120-10, Gold Biotechnology, Saint Louis, Mo., USA) as 1000× stock (50 mg/ml in H2O); carbenicillin (C-103-5, Gold Biotechnology, Saint Louis, Mo., USA) added as 1000× stock (100 mg/ml in H2O); spectinomycin (22189-32-8, Gold Biotechnology, Saint Louis, Mo., USA). Liquid chromatography was performed with Optima Acetonitrile (A996-4, Thermo Fisher Scientific, MA, USA) and water (Milli-Q Advantage A10, Millipore Sigma, Saint Louis, Mo., USA) supplemented with LC-MS Grade Formic Acid (85178, Thermo Fisher Scientific). The following solvents/chemicals were also used: Ethanol (V1001, Decon Labs, King of Prussia, Pa., USA), Methanol (3016-16, Avantor, Center Valley, Pa., USA), dimethyl sulfoxide (DMSO) (32434, Alfa Aesar, Ward Hill, Mass., USA), Imidazole (IX0005, Millipore Sigma, Saint Louis, Mo., USA), sodium chloride (X190, VWR, OH, USA), sodium phosphate monobasic monohydrate (20233, USB Corporation, Cleveland, Ohio, USA), sodium phosphate dibasic anhydrous (204855000, Acros, N.J., USA), guanidine hydrochloride (50950, Millipore Sigma, Saint Louis, Mo., USA), tris (75825, Affymetrix, Cleveland, Ohio, USA), TCEP (51805-45-9, Gold Biotechnology, Saint Louis, Mo., USA), and EDTA (0.5M stock, 15694, USB Corporation, Cleveland, Ohio, USA). DNA oligos and oligo pools were ordered from Integrated DNA Technologies (San Francisco, Calif., USA) and enzymes and peptide plasmids were assembled/cloned in-house or synthesized by Twist Biosciences (San Francisco, Calif., USA). Enzymes and peptides were codon optimized using an in-house optimization tool.


Peptide Expression and Purification.

Saturated cultures in LB were diluted 1:100 into 1 ml TB in deep well plates, incubated for 3 hours (Multitron Pro, 30° C., 900 r.p.m.), supplemented with appropriate inducers, and incubated for an additional 20 hours (Multitron Pro, 30° C., 900 r.p.m.). For purification, plates were centrifuged (Legend XFR, 4,500 g, 4° C., 20 min), pellets were resuspended in 850 μl lysis buffer (5 M guanidinium hydrochloride, 300 mM NaCl, 50 mM sodium phosphate, pH 7.5), frozen (liquid nitrogen, −196° C.), thawed (Multitron Pro at 37° C., 900 r.p.m), and clarified via centrifugation (Legend XFR, 4,500 g, 4° C., 40 min). Peptides were affinity purified using His MultiTrap TALON plates (29-0005-96, GE Life Sciences), following manufacturer instructions, using 1×500 μl water and 2×500 μl lysis buffer for column equilibration, 2×500 μl wash buffer (300 mM NaCl, 50 mM sodium phosphate, 5 mM imidazole, pH 7.5), and 1×200 μl elution buffer (300 mM NaCl, 50 mM sodium phosphate, 150 mM imidazole, pH 7.5).


Liquid Chromatography/Mass Spectrometry.

All chromatography was performed using mobile phases ACN (acetonitrile supplemented with 0.1% formic acid and 0.1% water) and water (supplemented with 0.1% formic acid). LC-MS was performed on one of two mass spectrometers: “QQQ” is an Agilent 1260 Infinity liquid chromatograph with binary pump configured in low-dwell volume mode, high-performance autosampler chilled to 18° C., and column oven, coupled to an Agilent 6420 QQQ mass spectrometer equipped with an Agilent electrospray ionization (ESI) source; nitrogen gas is supplied by a Parker Nitroflowlab and ESI source parameters are 350° C. gas temp at 12 L/min flow rate, 15 psi nebulizer voltage, 4000 V capillary voltage, 135 V fragmentor voltage, and 7 V cell accelerator voltage. “QTOF” is an Agilent 1260 Infinity II liquid chromatograph with binary pump configured in low-dwell volume mode and column oven set to 40° C., coupled to an Agilent 6545 QTOF mass spectrometer equipped with an Agilent electrospray ionization (ESI) source; nitrogen gas is building supplied and ESI source parameters are 350° C. gas temperature, 12 L/min gas flow, 30 psig nebulizer pressure, 350° C. sheath gas temperature, 8 L/min sheath gas flow, 3000 V capillary voltage, 1000 V nozzle voltage, 135 V fragmentor voltage, 15 V skimmer voltage, 600 V Oct 1 RF Vpp; the mass spectrometer was run in MS mode with reference mass enabled and tuned in positive mode with standard mass range (3200 m/z) and 2 GHz extended dynamic range.


LCMS Data Analysis and Peak Integration.

mzXML files were parsed and imported into python to a long-form pandas dataframe and filtered for signals between 1-6 min and 500-2,500 Da. For each extract, the expected molecular weight of unmodified, modified, and partially modified (if applicable) peptides were calculated. For each molecular weight, all charge state [M+xH]x+ (x is number of protons/charges) masses were calculated and extracted as an EIC with a mass window of +/−5/x Da for extracts analyzed with “QQQ” and 2/x Da for extracts analyzed with “QTOF”. Charge state EIC intensities were summed together at each timepoint to generate an extracted compound chromatogram (ECC). If present, an ECC peak is fit with a skewed gaussian with parameters peak area, retention time, peak width, and peak skew. Peaks are considered real/trustworthy based on the following criteria: greater than 8 charge states present/observed at the same retention time (+/−0.2 min) with at least 4 being consecutive charge states, only one “large” peak in the ECC (i.e. no peaks greater than 80% of the largest peak height in the chromatogram), and not more than 2 “small” peaks (i.e. <3 peaks greater than 40% of the largest peak height), peak skew between 0 and 1.5, peak width less than or equal to 0.25. Within an extract, “total peptide” is defined as the sum of the peak areas of unmodified, modified, and partially modified (if applicable) peptides if the modification mass shift is >15 Da and is defined as the sum of the peak areas of unmodified and modified peptides otherwise (due to overlapping isotope distributions). Fraction modified is defined as the modified peptide peak area divided by the “total peptide”. Peak integrations and masses for each extract are listed in Supplementary Table 6. All analysis is done in python 3.5 using pandas, scipy, numpy, and matplotlib libraries.


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Example 4: Selection for Constrained Peptides that Bind to the SARS-CoV-2 Spike Protein

Peptide secondary metabolites are common in nature and have diverse functions, from antibiotics to cross-kingdom signaling, that have been harnessed as pharmaceuticals. Their amino acid structure simplifies binding to protein targets and they have constraints and chemical modifications that enhance affinity, stability and solubility. A method to design large libraries of modified peptides in Escherichia coli and screen them in vivo to identify those that bind to a target-of-interest was developed in this Example. Constrained peptide scaffolds were produced using modified enzymes gleaned from microbial RiPP (ribosomally synthesized and post-translationally modified peptides) pathways and diversified to build large libraries. RiPP binding to a target protein leads to the intein-catalyzed release of a 6 factor. This circuit was used to drive a selection, which could evaluate 108 variants in a single experiment. This was applied to the discovery of a 1625 Da constrained peptide (AMK-1057) that binds with 990±5 nM affinity to the SARS-CoV-2 Spike receptor binding domain (RBD), a potential therapeutic target.


INTRODUCTION

Bacteria and fungi secrete modified peptides that can act on eukaryotic cells by binding to cell-surface proteins, inhibiting enzymes or affecting protein-protein interactions [1-3]. They can be produced by large non-ribosomal peptide synthases or encoded by genes and post-translationally modified (RiPPs) [4-8]. As pharmaceuticals, cyclic peptides are approved for the treatment of cancer, inflammation, and infection and increasing numbers are entering all phases of clinical development for diverse indications [9-12]. They have shown promise for blocking viral entry into human cells [13,14]. For example, the FDA-approved HIV therapeutic Enfuvirtide is a 36 amino acid (aa) linear peptide that binds to a transmembrane glycoprotein; however, it suffers from rapid proteolysis, thus requiring twice daily injections [15]. Crosslinking HIV-1 mimetic peptides makes them proteolytically-stable, acid-resistant, and orally bioavailable [16].


Discovering peptides that bind to a therapeutic target requires methods to: (1) create massive pools of chemical diversity, and (2) identify hits in an efficient manner. Synthetic chemistry can be used to create libraries of modified peptides, including cycles and glycosylation, which are screened individually in assays that can be automated [17-24]. Encoding the peptide with its genetic material facilitates the panning for those that bind to a target, for example, using fluorescence activated cell sorting (FACS) [18-20,23, 25-29]. This can be done through yeast display, mRNA-peptide fusions and phage display, which have been used to find modified peptides that are antibiotics or bind human therapeutic targets [26, 29-36]. Cyclization can be performed enzymatically, chemically, or with split inteins, which are naturally occurring proteins that splice two separately-expressed peptides into an excised intein and a product [37,38].


If target binding can be linked to gene expression, this can be used to drive a reporter for screening or a marker that allows cells to survive a selection. The classic example is a two-hybrid system where a “bait” protein fused to DNA-binding domain recruits the “prey” protein fused to an activator that turns on a promoter when bound [39-44]. This can be used to find molecules that disrupt the bait-prey interaction, which has been applied to the discovery of linear peptides that are antivirals or block cancer signaling or progression [40, 45-47]. An E. coli version led to the discovery of a cyclized RiPP μM inhibitor of the p6-UEV protein-protein interaction necessary for HIV budding [41,44]. Protein-protein interactions have also been detected using split inteins where, upon binding, a reporter (epitope, fluorescent protein or a factor) is released, but this has not been applied to molecular discovery [48,49].


Infection by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of COVID-19, is dependent upon cell recognition and entry mediated by the interaction of viral surface glycoprotein (Spike) receptor binding domain (RBD) and host receptor angiotensin-converting enzyme 2 (ACE2) (FIG. 13A, FIG. 13B) [50-53]. The high affinity of RBD to human ACE2 (44.2 nM) has been suggested to contribute to the contagiousness of SARS-CoV-2 [54]. Serum isolated from convalescent coronavirus patients, used for treatment, contains mixtures of antibodies targeting viral epitopes, with Spike protein being the predominant target neutralized [55,56]. Targeted drug discovery efforts from companies including Astra Zeneca/Vanderbilt University, Celltrion, Eli Lilly/AbCellera, Eli Lilly/Junshi, and Tychan have yielded monoclonal antibodies (>1000 aa) specific to Spike protein in various stages of clinical development [57]. So-called nanobodies (˜100 aa) have been evolved in the laboratory to bind to Spike (with 4.5 nM affinity) [58]. Computational protein design was used to develop a “miniprotein” (56 aa), the best of which bound with sub-nM affinity and neutralized virus at 0.15 nM concentration [59]. A biotinylated 23 aa peptide taken from the N-terminal region of ACE2 binds to the Spike RBD with a KD of 1.3 μM [60]. A cyclic peptide based on the SARS-CoV-2 Mpro C-terminal autolytic cleavage site was shown to have an IC50 of 150 μM for the viral protease, another potential therapeutic target [61].


A genetic circuit in E. coli that responds when a modified peptide binds to a single bait protein was developed and used to drive a selection to identify hits that bind to the SARS-CoV-2 Spike RBD. Libraries of modified peptides were produced by artificially combining enzymes from microbial RiPP pathway that introduces thioether-based macrocycles to constrain the peptide (Paenibacillus polymyxa PapB) [62-64] and vary the unmodified core residues. Each candidate RiPP was fused to a C-terminal intein and one half of a split a factor (RiPP-NpuCC) and modified in this context (FIG. 13C). The bait (Spike RBD) was fused to the complementary intein and the other half of the σ factor (σN-NpuN-Bait). In this system, when the modified RiPP binds to the bait, the complete σ factor is released, binds to a promoter and facilitates the expression of a reporter and/or selection marker. Rounds of positive selection were used to identify RiPPs that bound to the bait RBD in the circuit. From these selections, a 14 aa thioether-cyclized peptide (termed AMK-1057) that binds human-derived SARS-CoV-2 Spike RBD with a KD of 990±5 nM was identified.


Results
A Genetic Circuit to Detect Modified Peptide Binding to a Target

The genetic circuit described in this Example converts a binding event into a transcriptional response (e.g., the expression of a reporter protein; FIG. 13C). It is based on two fusion proteins that, upon binding, release a σ factor that recruits RNA polymerase to a promoter, resulting in expression of the reporter downstream of the promoter. Each fusion protein comprises one half of a split intein from Nostoc punctiforme PCC73102 (Npu). The Npu intein was selected because of its stability and rapid splicing kinetics [38]. The σ factor ECF20_992 was chosen based on previous development by the inventors of a split version of it [65,66]. The N-terminus of the fusion protein had the leader peptide that recruits modifying enzymes and the core sequence of the RiPP followed by a flexible 20 aa linker. Successful splicing of full length σ factor resulted in the activation of the P20_992 promoter, thereby turning on the downstream genes (e.g., a reporter gene; FIG. 13C). To develop the sensor, the well-studied interaction between the proteins p53 and Mdm2 was selected as a test case [67]. Specifically, residues 17-124 of Mdm2 (Mdm2*) and a high affinity (KD=0.5 nM) variant of residues 15-29 of p53 (PMI) [68,69] were used as bait and peptide fusions to the σN-NpuN and NpuCC fragments, respectively. The two genes were placed under the control of the PLuxB and PTac promoters in E. coli Marionette Clone 70 (a derivative of NEB 10β). For characterization, sfGFP was cloned downstream of P20_992 and fluorescence was measured using flow cytometry as a function of the inducers 3O6-AHL and IPTG (FIG. 13D, left panel). The dynamic range between uninduced and fully-induced was 114-fold, and expression varied over orders-of-magnitude while still allowing a response to be observed.


It is important that the expression of the σN-NpuN and NpuCC fragments, in the absence of bait or peptide, does not induce the circuit. The experiments described above were repeated for these fragments lacking bait or peptide. At maximal expression of the σN-NpuN and NpuCC fragments (lacking bait or peptide), the output promoter was activated, albeit at 8-fold lower activity than when the bait and peptide were included (FIG. 13D, right panel). This difference was maximized to >200-fold when σN-NpuN was fully induced and NpuCC fragment was uninduced (FIG. 13D, right panel). To simplify this implementation, the σN-NpuN-bait protein was placed under the control of a constitutive promoter. The peptide-NpuCC was kept under 3OC6-AHL control so that its intracellular concentration could be varied during rounds of selection to preferentially select for higher-affinity binders.


The inducible range of the sensor was then determined when either the bait or peptide were swapped to disrupt the interaction. When a peptide based on the N-terminal residues 19-56 of ACE2 (ACE2*), which does not bind to the Mdm2* target, was used, the fluorescent output of the circuit dropped 15-fold. Similarly, when the target peptide was swapped to be residues 328-533 of the SARS-CoV-2 Spike protein (RBD) 51, to which PMI does not bind, the output dropped 93-fold (FIG. 13F).


The peptide needs to be able to be modified by RiPP enzymes in the context of its fusion to C-terminal NpuCC (FIG. 13F). The RiPP enzymes were recruited by binding to an N-terminal leader sequence and then modifying the core sequence [4]. Natural RiPPs are proteolytically released from the leader, but for the selections used in this Example, they remain fused because the cognate protease was not co-expressed. Examples have been published where leaders do not interfere with the binding of the core sequence to its target [27,41]. RiPP enzymes often exhibit relaxed substrate specificity for the unmodified core residues [72-74]. In many cases, tags and fusions can be made to the C-terminus without impacting the modification [27,74,75].


A preliminary experiment was performed to ensure that an enzyme of interest could modify a large fraction of core sequences in a library without being impacted by the C-terminal fusion (FIG. 13G). The PapA/PapB peptide/enzyme pair from the Paenibacillus polymyxa freyrasin biosynthetic gene cluster was selected as a test case [63]. PapB introduces a thioether macrocycle between core C and D/E residues and was shown to be tolerant to amino acid diversity at the unmodified residues [63,73]. Based on this system, a simplified core and leader peptide containing two cycles was designed (FIG. 13H). A library was constructed allowing full (NNK) degeneracy at 9 unconserved amino acid positions and D/E at the two macrocyclized positions, resulting in 1012 theoretical diversity. Nineteen random members from this library were selected, co-expressed with PapB, and evaluated for cyclization by measurement of the mass shift observed using LCMS. Of the original set, 14 were the proper core peptide (1 frame shift) and could be observed by LC-MS, and of these 36% were modified correctly. Thus, a large fraction of a highly diverse library contained the expected modification. The modification did not seem to bias the core amino acid content for the small set analyzed (FIG. 13I, FIG. 13J).


Selection System for Finding SARS-CoV-2 Spike RBD Binders

The genetic system used for the selections, involving nine genes, is shown in FIG. 14A. It has been previously demonstrated that the SARS-CoV-2 Spike RBD can be expressed in E. coli and, despite the protein being non-glycosylated, a similar antibody binding profile to that produced from human cells results [76,77]. This domain was used to build σN-npuN-RBD, which was placed under the control of the weak J23105 constitutive promoter. The peptide library was inserted into the RiPP-npuCC gene and controlled with 3OC6-AHL. The modifying enzyme was placed under the control of the cumate-inducible promoter. When the a factor is released, the P20_992 promoter drives the expression of an operon containing a fluorescent protein selectable marker fusion sfGFP-cat. This enabled positive selection by the addition of chloramphenicol (Cm) to the media.


The libraries of modified peptides were constructed using oligo synthesis with NNK codons at the varied residues and cloned into a low copy pSC101 plasmid. The library was transformed using electrocompetence, which was found to limit the library size to 108 per transformation. Then, multiple rounds of positive selection were performed. The details for each library are described further below. When a RiPP binds the target, expression of Cat is increased, thereby conferring chloramphenicol resistance to the host cell (FIG. 14B). Over rounds of positive selection, increased stringency can be applied by increasing the concentration of Cm or decreasing peptide induction with 3OC6-AHL (FIG. 14C).


Library Design and Selection

The library was based on the simplified PapB-modified core structure shown in FIG. 14D which produces 13 aa cyclized peptides. After transformation, rounds of positive selection were performed, after which the surviving plasmids were isolated and retransformed after each round (FIG. 14C). Cells were grown overnight in increasing concentrations of Cm: Round 1 (300 μM), Round 2 (800 μM) and Round 3 (1200 μM). sfGFP expression was measured after each round using flow cytometry, showing a continuous increase in the fluorescence after each round of selection (FIG. 14E). Notably, when using 300 μM Cm for the initial selection, two peaks were observed: one lower (˜2,000 AU) and much higher (˜10,000 AU). This higher peak was attributed to escape mutants from the selection plasmid breaking. To eliminate escapes from round to round, non-peptide plasmid was digested and re-transformed into the expression strain, eliminating the peak corresponding to escapes (FIG. 14E). All selection rounds were then analyzed using next-generation sequencing (NGS). The number of unique RiPP sequences decreased after each round, indicating enrichment: 139,320 (Round 1), 88,229 (Round 2) and 63,344 (Round 3). The abundance of each sequence was calculated and 32 were found to represent >1% of the population each after Round 3. These were further reduced to 20 by only considering those that showed consistent enrichment from Round 1 to 2 and from Round 2 to 3.


The 20 hits from this library were codon optimized, re-synthesized and cloned into the RiPP-npuCC plasmid and re-assessed in freshly transformed cells. Testing of newly synthesized constructs was intended to eliminate any cheater behavior that may have arisen throughout the selection process. These constructs were transformed into selection strains containing cognate modifying enzymes and either Spike RBD or Mdm2* as bait, with the latter intended to measure off-target binding. The circuit output was measured using flow cytometry under the same growth conditions and inducer concentrations used for the selections. The core sequence VCKYGEWCEIVEI (SEQ ID NO: 24) demonstrated a strong transcriptional output and 14-fold specificity for the Spike RBD as bait over Mdm2* (FIG. 14F).


AMK-1057 Binds Human Cell-Derived SARS-CoV-2 RBD

The core sequence VCKYGEWCEIVEI (SEQ ID NO: 24) underwent liter-scale production, cleavage and purification (FIG. 15A). The peptide gene was cloned as a C-terminal fusion to a hexa-histidine-Small Ubiquitin-like Modifier (SUMO) tag under control of the PT5LacO promoter and strong ribosome binding site (no longer in the context of the NpuCC fragment). SUMO is a small (12 kDa) tag often used in heterologous protein purification that has been found to be effective in stabilizing RiPP peptide expression while not interfering with modifying enzyme activity [78]. A Tobacco etch virus (TEV) cleavage site was added between the leader and core regions for downstream processing. This left a glycine on the N-terminus of the pap2c_1 peptide, thus producing a 14 aa peptide that, in its modified form, was named AMK-1057. Note there is also a TEV site upstream of the leader sequence, liberating it from SUMO as well so that it can be used as a control.


Co-expression of this peptide fusion with PapB in E. coli Marionette X (NEB Express derivative) cells followed by Ni-NTA affinity purification yielded tagged and modified pap2c_1. A peak corresponding to unmodified peptide was also detected. Dialysis of Ni-NTA purified peptide, TEV cleavage, solid phase extraction (SPE) and semiprep HPLC purification led to the isolation of three peptides: leader (yield: 200 μg/L), unmodified core (640 μg/L) and modified core (360 μg/L).


High resolution LCMS analysis of both modified (expected m/z: 1625.7338; observed m/z: 1625.7332) and unmodified (expected m/z: 1627.7494; observed m/z: 1627.7484) peptide showed a mass shift corresponding to formation of a single cycle, despite the library being based on a two-cycle scaffold (FIG. 15B). The macrocycle found in AMK-1057 is formed through the covalent linkage of a side chain cysteine sulfur atom to the CP on the downstream glutamate residue, a linkage that is stable to standard collision-induced dissociation conditions [63]. This property was used to annotate the macrocycle placement via high-resolution tandem MS (HR-MS/MS) and hypothetical structure enumeration and evaluation (FIG. 15C) [79]. Fragmentation analysis indicated that the macrocycle forms at the C-terminal end of AMK-1057, between C9 and E13 (FIG. 15D).


In vitro binding experiments were then performed using Expi293F human cell-derived and purified RBD. Bio-layer interferometry (BLI) was used to measure the affinity of AMK-1057 to Spike RBD as 990±5 nM (FIG. 15E). Neither the purified unmodified core peptide (FIG. 15F) nor the leader sequence (not shown) showed any binding to the target.


DISCUSSION

This Example demonstrates a technique to capture modified peptides that bind to a single target protein. There are several advantages over a two-hybrid screen, including that the binding target does not have to be known (or be a protein) or able to be expressed in a heterologous host, and hits will not be discovered against the “wrong” target (in this case, to human ACE2). As a relevant example of the importance of this capability, clinically relevant betacoronaviruses to date share a common Spike protein for host recognition, but the host receptor is not known a priori [50]. This allows for the search for binders to begin before their cellular targets have been fully elucidated. The libraries provided in this Example are based on natural products built with RiPP enzymes, a family that has been rapidly growing and for which there are many interesting chemical conversions, including halogenation, backbone N-methylation, and β-amino acid formation [80-82]. Larger biologics, such as antibodies, can have problems with stability and are limited in possible modes of delivery [59]. In contrast, cyclic peptides can exhibit improved stability, be cell-permeable thereby enabling access to intracellular antiviral targets, and be suitable for administration via inhalation [83-86].


Using this approach, a small peptide binder to SARS-Cov Spike RBD was identified. At ˜1600 Da, AMK-1057 is a size that is common for peptide secondary metabolites and approaches the threshold for the commonly used definition of a small molecule (˜900 Da) [9]. At <1 μM binding, AMK-1057 is in the higher range of natural RiPPs binding to their target (e.g., lassomycin at 0.41 μM, microcin J25 at 2 μM) and some peptidic drugs (e.g., vancomycin at ˜1 μM) [87-89]. As the first hit to emerge from a selection, it is ripe for further optimization through additional diversification and medicinal chemistry. This work represents a critical initial step of drug discovery. Putative therapeutics targeting viral fusion need to progressively tested in assays for the blockage of viral entry into cell lines [90-93], followed by animal models [92,93]. A human organ-chip has also been developed to screen repurposed drug compound collections that inhibit viral pseudoparticles expressing SARS-CoV-2 Spike from infecting human lung epithelial cells [94]. Combining molecular diversity creation using the method provided herein with a selection circuit in the same cell enables massive libraries to be evaluated to populate these pharmaceutical discovery pipelines with binders to a target-of-interest with minimal biochemical information.


Materials and Methods
Strains, Media, and Chemicals.


E. coli NEB 10-beta (C3019I, New England BioLabs, Ipswich, Mass., USA) was used for all routine cloning. E. coli Marionette-Clo 70 was used for all selection experiments. E. coli Marionette-X, a Marionette-compatible derivative of NEB Express (C2523I, New England BioLabs, Ipswich, Mass., USA) was used for large-scale peptide expression experiments. TB (T0311, Teknova, Hollister, Calif., USA) supplemented with 0.4% glycerol (BDH1172-4LP, VWR, OH, USA) was used for peptide expression and modification. 2xYT liquid media (B244020, BD, Franklin Lakes, N.J., USA) and 2xYT+2% agar (B214010, BD, Franklin Lakes, N.J., USA) plates were used for routine cloning and strain maintenance. SOB liquid media (S0210, Teknova, Hollister, Calif., USA) was used for making competent cells. SOC liquid media (B9020S, New England BioLabs, Ipswich, Mass., USA) was used for outgrowth. Unless noted otherwise, cells were induced with the following chemicals: cuminic acid (268402, Millipore Sigma, Saint Louis, Mo., USA) added as 1000× stock (200 mM) in EtOH or DMSO; 3-oxohexanoyl-homoserine lactone (3OC6-AHL) (K3007, Millipore Sigma, Saint Louis, Mo., USA) added as a 1000× stock (1 mM) in DMSO; anhydrotetracycline (aTc) (37919, Millipore Sigma, Saint Louis, Mo., USA) added as a 1000× stock (100 PM) in DMSO; isopropyl β-D-1-thiogalactopyranoside (IPTG) (I2481C, Gold Biotechnology, Saint Louis, Mo., USA) added as 1000× stock (1 M) in water. Cells were selected with the following antibiotics: carbenicillin (carb, C-103-5, Gold Biotechnology, Saint Louis, Mo., USA) added as 1000× stock (100 mg/mL in H2O); kanamycin (kan, K-120-10, Gold Biotechnology, Saint Louis, Mo., USA) as 1000× stock (50 mg/mL in H2O); spectinomycin (spec, S-140-5, Gold Biotechnology, Saint Louis, Mo., USA); and chloramphenicol (Cm, C-105-5, Gold Biotechnology, Saint Louis, Mo., USA). Liquid chromatography was performed with Optima Acetonitrile (A996-4, Thermo Fisher Scientific, MA, USA) and water (Milli-Q Advantage A10, Millipore Sigma, Saint Louis, Mo., USA) supplemented with LCMS Grade Formic Acid (85178, Thermo Fisher Scientific). The following solvents/chemicals were also used: Ethanol (V1001, Decon Labs, King of Prussia, Pa., USA), Methanol (3016-16, Avantor, Center Valley, Pa., USA), Ammonium bicarbonate (A6141 Millipore Sigma, Saint Louis, Mo., USA), dimethyl sulfoxide (DMSO) (32434, Alfa Aesar, Ward Hill, Mass., USA), Imidazole (IX0005, Millipore Sigma, Saint Louis, Mo., USA), sodium chloride (X190, VWR, OH, USA), sodium phosphate monobasic monohydrate (20233, USB Corporation, Cleveland, Ohio, USA), sodium phosphate dibasic anhydrous (204855000, Acros, N.J., USA), guanidine hydrochloride (50950, Millipore Sigma, Saint Louis, Mo., USA), tris (75825, Affymetrix, Cleveland, Ohio, USA), TCEP (51805-45-9, Gold Biotechnology, Saint Louis, Mo., USA), and EDTA (0.5M stock, 15694, USB Corporation, Cleveland, Ohio, USA). DNA oligos and gBlocks were ordered from Integrated DNA Technologies (IDT) (San Francisco, Calif., USA).


Plasmids and Genes.

Plasmids pTHSS-1282 and pAMK-267 were constructed from the parental pTHSS-1193 backbone, which has a pSC101 origin variant (var 2) and ampicillin resistance [95]. Plasmids pTHSS-1282 and pAMK-267 contain a flexible linker sequence (GSSRGGKGGPGGRGGVGGGGGIGG (SEQ ID NO: 113)) between the peptide/sfGFP and NpuC regions. Plasmids pAMK-925, pTHSS-2132, pAMK-866, and pAMK-870, were constructed from the parental pTHSS-1458 backbone, which has a colE1* origin variant and a kanamycin resistance marker [95]. All plasmids carrying modifying enzymes were constructed from the parental pEG01_189 backbone and contain a p15A origin of replication and spectinomycin resistance [78]. The parental backbone pTHSS-2012, which has a p15a origin and spectinomycin resistance was used for additional cloning experiments [95]. The plasmid pTHSS-1282 that contains the P20_992 promoter expressing sfGFP was constructed from pTHSS-1193. The plasmids pAMK-926 and pTHSS-2137 that contain the PLux promoter expressing NpuCC and PMI-NpuCC, respectively, were constructed from pTHSS-2012. The plasmids pAMK-925 and pTHSS-2132 that contain the PTac promoter expressing σN-NpuN and residues 17-124 of Mdm2 (Mdm2*)-σN-NpuN, respectively, were constructed from pTHSS-1458. The plasmid pAMK-870 that contains the constitutive PJ23105 promoter expressing Mdm2*-σN-NpuN and the P20_992 promoter expressing CAT-sfGFP was constructed from pTHSS-1458. The plasmid pAMK-866 that contains the constitutive PJ23105 promoter expressing 328-533 of the SARS-CoV-2 Spike protein (RBD)-σN-NpuN and the P20_992 promoter expressing CAT-sfGFP was constructed from pTHSS-1458. The peptide cloning plasmid pAMK-267, constructed from pTHSS-1193, contains the PLux promoter upstream of an RBS-His tag-SapI-sfGFP-SapI-NpuCC where the sfGFP gene can be replaced by a peptide gene through Type IIs assembly methods using the enzyme SapI (NEB). The RBS from pAMK-267 was chosen from a library of RBS variants upstream of a His tag-PMI-NpuCC that was tuned for co-expression with constructs containing the PJ23105 promoter expressing Mdm2*-σN-NpuN. The N-terminal His tag in pAMK-267 was left in place to provide a constant 11 aa for consistent levels of expression between different peptide sequences. The plasmid pAMK-670 that contains the PLux promoter expressing PMI-NpuCC was constructed from pAMK-267. The plasmid pAMK-857 that contains the PLux promoter expressing N-terminal residues 19-56 of ACE2 (ACE2*)-NpuCC was constructed from pAMK-267. The pTHSS-1193 and pTHSS-1458 backbones have origin variants that alter their copy numbers, making them approximately equivalent to a p15a backbone. Genes encoding Npu intein, PMI, Mdm2*, ACE2*, and RBD were synthesized as gBlocks. The ECF20_992 gene was sourced from a previous publication [65].


Cytometry Analysis.

Fluorescence characterization was performed on a BD LSR Fortessa flow cytometer with HTS attachment (BD, Franklin Lakes, N.J., USA). Samples were prepared by diluting overnight cultures 1:400 by adding 0.5 μl of cell culture into 200 μl of PBS containing 1 mg/mL Kan. All samples were run in standard mode at a flow rate of 0.5 μl/s. Fluorescence measurements were made using the blue (488 nm) laser and all data was derived from the FITC-A channel (PMT voltage of 400 V). The FSC and SSC voltages were 650 V and 270 V, respectively. At least 30,000 events were collected for each sample and the Cytoflow Python package was used for downstream analysis. Gating was completed by fitting a 2D Gaussian function to the FSC and SSC distributions and excluding all events greater than three standard deviations from the mean. When presented, the median value is used.


Evaluation of the Split-Intein σ Factor Circuit.

Strains of E. coli Marionette Clo harboring a combination of plasmids pTHSS-1282, pTHSS-2132, and pTHSS-2137 or pTHSS-1282, pAMK-925, and pAMK-926 were used for assessing intein splicing with or without PMI-Mdm2* induced association, respectively. Strains were grown in 1 mL of LB+ antibiotics for 20 hr in a deep well 96-well plate (1896-2000, USA Scientific, FL, USA) at 30° C., 900 rpm in an Infors HT Multitron Pro (Infors USA, MD, USA). Cultures were then diluted 1:100 into fresh 1 mL of LB+ antibiotics and serial 1:10 dilutions of inducers (IPTG, 10−3-103 μM; 3O6-AHL, 10−3-103 nM) for 20 hr in a deep well 96-well plate at 30° C., 900 rpm in the Multitron Pro. 0.5 μl of saturated cell culture were then diluted into 200 μl of PBS containing 1 mg/mL kan for cytometry analysis.


Two-Hybrid Assay for RBD/Mdm2* Association.

To assay for protein-protein mediated splicing the following plasmid combinations were transformed into E. coli Marionette Clo and fluorescence was measured via cytometry: pAMK-866/pAMK-670 (RBD/PMI); pAMK-866/pAMK-857 (RBD/ACE2*); pAMK-870/pAMK-670 (Mdm2*/PMI); pAMK-870/pAMK-857 (Mdm2*/ACE2*). Strains were grown in 1 mL of LB+ antibiotics for 20 hr in a deep well 96-well plate at 30° C., 900 rpm in a Multitron Pro. Cultures were then diluted 1:100 into fresh 1 mL of LB+ antibiotics+1 μM 3O6-AHL (full induction of peptide plasmid) for 20 hr in a deep well 96-well plate at 30° C., 900 rpm in the Multitron Pro. 0.5 μl of saturated cell culture were then diluted into 200 μl of PBS containing 1 mg/mL Kan for cytometry analysis.


Library Generation.

The Pap library was designed with diversity at the ends and middle of the peptide and included either glutamate or aspartate as a cyclization partner, for a final sequence design of “XCXXX[D/E]XCXXX[D/E]X (SEQ ID NO: 114)”. Using the degenerate nucleotide sequences “NNK” to encode any amino acid and “GAW” for aspartate or glutamate, a library of 1012 peptides encoded by 1014 unique codon sequences was generated. The library of plasmids lbAMK-103, which contains the PLux promoter expressing the Pap library-NpuCC was constructed from pAMK-267. The pap library was amplified from pEG03_283 using degenerate oligonucleotides oAMK-915/916 (IDT). Gel purification was used to isolate the 124 bp amplicon, which was then cloned into pAMK-267 using the type IIS restriction enzyme SapI (NEB).


Linear insert and plasmid were mixed at a 1:1 molar ratio (200 fmol each) along with 10 μl 1×DNA ligase buffer, 2 μl T4 DNA ligase (HC) (20 U/μl) (M1794, Promega, Madison, Wis., USA) and 4 μl SapI in 100 μl total volume. Reactions were cycled 25 times for 2 min at 37° C. and 5 min at 16° C. then incubated for 30 min at 50° C., 30 min at 37° C., and 10 min at 80° C. in a DNA Engine cycler (Bio-Rad, Hercules, Calif., USA). An additional 2 μl SapI was then added, and the assembly was incubated for 1 h at 37° C. Assemblies were then purified using Zymo Spin I columns (Zymo Research, Irvine, Calif., USA). Library assemblies were initially transformed into electrocompetent NEB 10βE. coli (C3020K, NEB, Ipswich, Mass., USA). 1.5×107 colony forming units (CFU)/mL were observed for lbAMK-103. Total transformants were estimated by colony counting after 107-fold dilution and plating of liquid outgrowths on selective media.


Calculation of the Modified Fraction of the Library.

The initial, unselected papA library was transformed and plated to resolve individual colonies. A set of 19 random colonies were picked and sequenced via colony PCR. Of the 19 sequenced colonies, 18 were properly assembled. These 18 library members were then assessed for post-translational modification via LCMS. The 9 unmodified and 5 modified library sequences were then aligned and WebLogos generated (weblogo.berkeley.edu/logo.cgi) with default parameters, except without small sample correction.


Selection of Pap Library lbAMK-103.


Assembled library of plasmids lbAMK-103 was transformed into an electrocompetent Marionette Clo strain harboring the PapB modifying enzyme plasmid, pEG06_044, and the selection plasmid, pAMK-866 (all non-assembly transformation steps were >1×108 efficiency). A 1 mL of liquid outgrowth of library transformants was diluted 1:50 in TB+Carb/Kan/Spec+1 μM 3OC6-AHL and 100 μM cumate to induce peptide+modifying enzyme, and grown at 30° C., 250 r.p.m. for 20 h. For the first round of selection, cultures were then diluted 1:100 in TB Carb/Kan/Spec+1 μM 3OC6-AHL and 100 μM cumate+300 μM Cm and grown at 30° C., 250 r.p.m. for at least 20 h (until cultures were saturated). A 0.5 μL aliquot of was taken for cytometry analysis and 2 mL of culture was also taken to harvest plasmid. A 5 μL sample of purified plasmid was stored for NGS analysis and the rest was digested with 1 μL SapI (NEB) for 1 hour at 37° C. to remove the background pEG06_044/pAMK-866 plasmid. The selected lbAMK-103 plasmid was then re-transformed into the strain of electrocompetent E. coli Marionette Clo strain harboring the PapB modifying enzyme, pEG06_046, and the selection plasmid, pAMK-866. The selection process was repeated once more with a Cm concentration of 800 μM and then once more with a Cm concentration of 1200 μM.


Ngs Analysis.

Library construction for NGS was performed using the protocol for “KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series” (KK8504, Roche). First, miniprepped library plasmids were amplified with Q5 polymerase (#M0492L, New England BioLabs, Ipswich, Mass., USA) with the primers oAMK-946/947 (Pap library) and oAMK-997/998 (Tgn/Lyn library). A 150 bp band was isolated via gel extraction. Indexed adapters were ligated and reamplified with 10 cycles of PCR. Gel extraction was then used to isolate the resultant 260 bp PCR product. Sample concentrations were calculated using a BioAnalyzer on a High Sense DNA chip (5067-4626, Agilent). Samples were diluted to 2 nM, denatured, and further diluted to 10 μM, with a 10% phiX spike in. Samples were run on a HiSeq 2500 using HiSeq v2 reagents for Paired End Clustering and a 200 cycle SBS kit (PE-402-4002 and FC-402-4021, Illumina). Forward and reverse reads were both 110 cycles, with an 8-cycle single index read. Base-calling and demultiplexing were performed using the bcl2fastq software (Illumina) with default settings. After basecalling and indexing, sequences were identified and aligned using the leader sequence and then binned by sequence.


Validation of sequences from NGS. Hit peptides from NGS were resynthesized as gBlocks (IDT). These gBlocks were used as template for PCR to introduce SapI restriction sites compatible for re-cloning into the pAMK-267 library backbone. Newly reconstructed library members were transformed into Marionette-Clo cells containing modifying enzyme and selection plasmids and were then plated on media containing Carb/Kan/Spec. Individual transformants were then cultured in TB+Carb/Kan/Spec in a deep well 96-well plate (1896-2000, USA Scientific, FL, USA) and incubated overnight (Multitron Pro, 30° C., 900 rpm). These cultures were then subcultured 1:100 in TB+Carb/Kan/Spec either fully induced (1 μM 3OC6-AHL, and 100 μM cumate) or uninduced and incubated for 20 hr (Multitron Pro, 30° C., 900 rpm) before taking 0.5 μL for standard flow cytometry analysis.


Peptide Purification.

Potential peptide hit gBlocks were cloned into the peptide expression plasmid, pEG03-119 78 using their flanking SapI restriction sites. The peptide and modifying enzyme plasmids were co-transformed into E. coli Marionette-X, streaked onto 2xYT agar with carb/spec and incubated at 30° C. overnight. Individual colonies were used to inoculate 20 mL of LB in a 125 mL shake flask and incubated overnight at 30° C. and 250 rpm in an Innova44 (Eppendorf, N.Y., USA). A 5 mL aliquot of overnight starter culture was diluted in 500 mL total volume TB with carb/spec in Fernbach flasks and grown at 30° C. and 250 rpm until reaching OD600 of 0.8-1.0, at which point 1 mM IPTG and 200 μM cumate were added. Induced cultures were grown for a further 20 h at 30° C. and 250 rpm and then centrifuged (4,000 g, 4° C., 10 min) in a Sorvall RC 6+ centrifuge (Thermo Fisher Scientific, MA, USA). Pellets were resuspended in 30 mL lysis buffer (5 M guanidinium hydrochloride, 300 mM NaCl, 10 mM imidazole, 50 mM sodium phosphate, pH 7.5), and freeze-thawed twice (frozen in −80° C. freezer; thawed in innova44 incubator at 30° C., 250 rpm). Cell lysates were centrifuged (Eppendorf 5424, 20,000 g, 18° C., 45 min) in a Sorvall RC 6+ centrifuge (Thermo Fisher Scientific, MA, USA) and the peptides affinity purified via gravity-flow using 3 mL resin-bed volume of Ni-NTA agarose resin (88223, Thermo Fisher Scientific, MA, USA), following manufacturer instructions, using 2 resin-bed volumes water and lysis buffer for column equilibration, 4 resin-bed volumes of wash buffer (5 M guanidinium hydrochloride, 300 mM NaCl, 25 mM imidazole, 50 mM sodium phosphate, pH 7.5), 4 resin-bed volumes of elution buffer (5 M guanidinium hydrochloride, 300 mM NaCl, 250 mM imidazole, 50 mM sodium phosphate, pH 7.5). Eluate from Ni-NTA purification was then subjected to solid-phase extraction (SPE) using Strata-XL 500 mg tubes (8B-S043-HCH, Phenomenex, CA, USA). The solid phase was first conditioned with 4 bed volumes of methanol and then water. Eluate was then loaded, washed with 8 bed volumes of 10 mM NH4CO3, and eluted with 8 bed volumes of 1:1 acetonitrile:aqueous 10 mM NH4CO3. Solvent was removed via lyophilization at −80 C for 24-48 hours. To cleave the SUMO and leader peptide from the core, the extracted peptide was resuspended in 20 mL TE buffer and 100 μl of 20 mg/mL TEV protease and incubated overnight at room temperature with slow orbital shaking. The cleaved peptides were then desalted using a Strata-X PRO 500 mg SPE tubes (8B-S536-HCH, Phenomenex, CA, USA). The solid phase was first conditioned with 4 bed volumes of methanol and then water. Eluate was then loaded, washed with 8 bed volumes of 10 mM NH4CO3, and eluted with 8 bed volumes of 1:1 acetonitrile:aqueous 10 mM NH4CO3. Solvent was removed via lyophilization at −80 C for 24-48 hours. After solvent removal, a 5 mL aliquot of the mixture resuspended in 10:90 acetonitrile:water was injected into a Agilent Technologies 1260 Infinity system HPLC (Agilent Technologies, Santa Clara, Calif.) and separated using a 150 mm×10 cm Aeris PEPTIDE XB-C18 column (100 Å, 5 μm) at a flow rate of 2 mL/min. Separation was carried out with a gradient program, with 0.1% formic acid as solvent A and acetonitrile with 0.1% formic acid as solvent B. The % B was held at 25% for 3 minutes, then increased to 50% over the next 17 minutes. The eluent was passed through a diode array detector (DAD) and absorbance at 270 nm was recorded. Detected peaks were collected using an Agilent G1364B Fraction Collector and again solvent was removed via lyophilization at −80 C for 24-48 hours. Samples were resuspended in 1 mL of 1:1 acetonitrile:aqueous 10 mM NH4CO3 in pre-weighed 2 mL microcentrifuge tubes (Eppendorf) and solvent was removed via lyophilization at −80 C for 24-48 hours. Yields were measured by comparing mass of empty tubes to tubes containing lyophilized powder.


Liquid Chromatography/Mass Spectrometry.

All chromatography was performed using the mobile phases ACN (acetonitrile supplemented with 0.1% formic acid and 0.1% water) and water (supplemented with 0.1% formic acid). The “QTOF” was an Agilent 1260 Infinity II liquid chromatograph with binary pump configured in low-dwell volume mode and column oven set to 40° C., coupled to an Agilent 6545 QTOF mass spectrometer equipped with an Agilent electrospray ionization (ESI) source. ESI source parameters are 350° C. gas temperature, 12 L/min gas flow, 30 psig nebulizer pressure, 350° C. sheath gas temperature, 8 L/min sheath gas flow, 3000 V capillary voltage, 1000 V nozzle voltage, 135 V fragmentor voltage, 15 V skimmer voltage, 600 V Oct 1 RF Vpp; the mass spectrometer was run in MS mode with reference mass enabled and tuned in positive mode with standard mass range (3200 m/z) and 2 GHz extended dynamic range. QTOF analysis was performed with a Phenomenex Aeris PEPTIDE XB-C18 2.6 μm 50 mm×2.1 mm column. The flow rate was set at 0.5 mL/min and 5 μl sample was injected. The gradient used was 20% ACN for 0.5 min, 20% to 55% ACN over 5.5 min, 55% to 90% ACN over 0.5 minutes, 90% ACN for 1.5 min, with 0.8 min re-equilibration. Accurate mass predictions of peptides were generated using the online resource, ChemCalc [96].


Bio-Layer Interferometry.

Assays were performed on an Octet Red (ForteBio) instrument at 30° C. with shaking at 1,000 rpm. Ni-NTA biosensors (18-5101, ForteBio, Bohemia, N.Y., USA) were hydrated in 1× kinetics buffer (diluted from 10× buffer; 18-5032, ForteBio, Bohemia, N.Y., USA) for 30 min before the measurement. Expi293F human cell-derived and purified SARS-CoV-2 RBD (RBD296-531) was loaded at 10-20 μg/mL in 1× Kinetics Buffer for 300 s prior to baseline equilibration for 180 s in 1× kinetics buffer. Association reactions of the peptide to RBD296-531 were carried out in 1× kinetics buffer at various concentrations in a two-fold dilution series from 80 mM to 1.25 mM was carried out for 900 s. Then dissociation reactions were observed for 900 s. Response data were generated using ForteBio data analysis software.


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Example 5: Optimization of Peptide Binders

AMK-1057, a small peptide binder, was evaluated for cell competition between the Receptor Binding Domain (RBD) of the SARS-CoV-2 Spike protein and the human ACE2 receptor. RBD incubated with and without AMK-1057 was mixed with ACE2 cells, washed, and quantified via flow cytometry (FIG. 16A). Measurement of a fluorescence marker on the RBD demonstrated a slight decrease in binding of RBD to ACE2-expressing cells after the RBD was pre-incubated with the RBD, relative to RBD in the absence of AMK-1057, and the effect was stronger with higher concentration of AMK-1057 (FIG. 16B). The results demonstrate that the high nanomolar binding of AMK-1057 to RBD is not sufficient to robustly block RBD-ACE2 binding. A two-hybrid system was constructed to evaluate the effect of construct expression level on binding. Peptides with published KD values were tested in the presence of on-target or off-target baits under conditions in which the peptides were expressed at a low level (FIG. 18B) or a high level (FIG. 18C). The results demonstrated that expression level of a given peptide can affect the ability to detect its binding to bait, and that lower expression allowed observation of differences in binding between on-target and off-target baits, whereas higher expression masked this effect to some extent. Scanning site saturation mutagenesis was performed on the core residues of AMK-1057 and variant enrichment was monitored using next-generation sequencing (FIG. 19A). Three positions that showed positive variant enrichment relative to the parent sequence were selected (arrows in FIG. 19A) and constructs expressing various combinations of amino acid substitutions at these positions were generated and evaluated for binding via flow cytometry. Each of the tested combinations of AMK-1057 variants showed improved binding relative to the parent peptide (FIG. 19B). The results demonstrate that screening of peptides with individual amino acid substitutions allows prediction of improved peptides with multiple substitutions.


Bio-layer interferometry was used to assay AMK-1057 competition for binding to RBD in the presence of B38 and CR3022 antibodies as well as purified ACE2 for the purpose of mapping what region of the RBD AMK-1057 may bind. RBD binding to AMK-1057 was not affected by the presence of B38 (FIG. 20A), CR3022 (FIG. 20B), or ACE2 (FIG. 20C).


Example 6: Large Scale Genome Mining of the Human Microbiome for Targeted Antibiotic Discovery

The human microbiome harbors substantial biosynthetic potential for specialized metabolites with roles in host-microbe and microbe-microbe interactions. Analysis of genomic sequence data from the Human Microbiome Project shows an untapped source of post-translationally modified peptides, a class of molecule demonstrated to have important effects on human health and disease. Genome mining approaches, wherein DNA sequences are synthesized de novo and heterologously expressed in chassis organisms, can be leveraged to access the molecules encoded in human microbiome sequence data. However, robust methods for large-scale interrogation of sequence space through DNA synthesis and heterologous expression have yet to be developed. Here, 78 biosynthetic gene clusters were selected for post-translationally modified peptides from a diverse set of human microbiome strains from all niches of the human body. Production of peptides was shown in a format suitable for screening their biological activity and novel molecules with unique spectra of antimicrobial activity against members of the human microbiome and pathogenic bacteria of clinical significance were identified. This work demonstrates that large-scale genome mining of peptidic natural products and functional assaying for their biological activity is possible through a DNA sequence-to-molecule pipeline.


Revealing how the human microbiome affects health at a mechanistic level will continue to be critical in understanding disease and developing new therapies1. Discovery and characterization of specialized metabolites (small molecules, peptides) is of particular interest due to their important role in biological systems and pharmaceutical potential as standalone agents or effectors in cell-based therapeutics2. Traditional approaches to the isolation of specialized metabolites from the human microbiome have been hampered by access to putative producing organisms and difficulties in eliciting production. A number of bioinformatics tools are now available to parse ever-increasing DNA sequence data, annotate biosynthetic gene clusters, and assign basic molecular predictions3. These tools make possible a “sequence-to-molecule” approach, wherein mining DNA sequence databases, selecting gene clusters for DNA synthesis, and heterologous expression can yield specialized metabolites of value. However, the rate of molecular production is orders of magnitude behind in silico identification of the encoding DNA. Production of molecules is handicapped by difficulties with the large size of many gene clusters, appropriate heterologous production hosts, and standardized approaches for their purification as well as structural elucidation4.


Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a class of specialized metabolite particularly abundant in human microbiome DNA sequence data5-7. RiPPs are defined by a conserved biosynthetic logic wherein a precursor peptide (comprised of a “leader” and “core” region) is ribosomally produced, the core subsequently altered by modifying enzymes that often recognize sequence motifs in the leader, then ultimately processed and exported (FIG. 20). For example, lanthipeptides are polycyclic peptides defined by the presence of thioether macrocycles formed via addition of a cysteine thiol to dehydrated serine and threonine residues (dehydroalanine and dehydrobutyrine, respectively). Dehydration of the core peptide and subsequent cyclization are catalyzed by a single, bifunctional enzyme or by two separate proteins, depending on the class of lanthipeptide5. Lasso peptides are formed via a complex of 2-3 proteins that recognize leader motifs, cleave the leader peptide, and use the resulting free amine to form an isopeptide bond with a downstream carboxyl side chain from an Asp/Glu residue5. The resulting constrained peptides are not only structurally diverse but also enriched in biological activity. RiPPs produced by the human microbiome are responsible for a remarkable range of microbe-host interactions8,9 as well as microbe-microbe interactions10-13 with pronounced effects upon human health.


As of 2015, 100 lanthipeptides had been discovered from microbes14 and half that number of lasso peptides15. New computational approaches to RiPP genome mining have yielded impressive advances in the discovery of RiPP subclasses and scaffolds but actual molecular discovery is relatively low (˜1-5 molecules per report) and functional assaying is either absent or narrow in scope16-21. The flexible biosynthesis afforded by RiPPs has also led to a number of innovative strategies for generating large libraries around a given peptide scaffold linked to a functional output. These include libraries based on the lasso peptide microcin J2522, the thiopeptide thiocillin23, and the lanthipeptides nisin, prochlorosin, haloduracin, and lacticin 48124-28. While of outstanding value, these approaches all require specialized assays and selections and do not exploit specific biological activities afforded by natural evolution. There is a need for higher throughput approaches to purify, express, and structurally annotate RiPPs that can then be tested in diverse functional assays. Here, an E. coli-based expression system was used to mine 78 RiPP gene clusters to generate 23 new lanthipeptides and lasso peptides from the human microbiome. The established pipeline was able to go from DNA sequence information to a structurally and functionally annotated molecule in relatively high-throughput. These 23 structurally annotated RiPPs, combined with 7 RiPPs with unknown modification, were demonstrated to have unique scaffolds and spectra of antimicrobial activity when tested against a large panel of human microbiome-associated strains. A subset of these RiPPs were shown to possess activity against multidrug resistant (MDR) clinical isolates of human pathogens, including vancomycin resistant Enterococcus and methicillin-resistant Staphylococcus aureus. This provides a robust method for accessing a vast and underexplored chemical space of the human microbiome.


Results
Selection of Human Microbiome RiPP Gene Clusters for Heterologous Expression

AntiSMASH29 was used to identify 2,233 RiPP gene clusters from 2,231 genomes of the Human Microbiome Project (HMP)30. BiG-SCAPE31 was then used to generate a sequence similarity map of these gene clusters to visualize the abundance of different subclasses of RiPP (FIG. 21 and FIG. 22). Previously identified RiPP gene clusters from the Joint Genome Institute (JGI)6,32 were also included in the analysis. Clusters were not prioritized based on any perceived contribution to health of a producing organisms; pathogens are an equally useful source of biologically active molecules with therapeutic potential33,34. From this survey, it was decided to pursue genome mining of two RiPP subclasses enriched in the human microbiome: lanthipeptides and lasso peptides.


In addition to the defining biosynthetic enzymes described above (LanBC, LanM, LanK for lanthipeptides; LasBC for lasso peptides), “tailoring enzymes” that further chemically diversify peptides can be encoded in gene clusters. Tailoring enzymes can modify bioactivity of peptides and have promise in functioning as catalysts for engineering RiPPs35 so open reading frames encoding putative tailoring enzymes were included in the mining workflow. Novel tailoring enzymes were not identifiable by existing in silico methods so a script was developed to identify and count the presence of all protein family (pfam) domains found in gene clusters annotated by AntiSMASH. These pfam counts were converted to relative abundance by dividing raw counts by the presence of core biosynthetic enzymes (lanBC/M/K; lasBC) and rank-ordered to profile prevalence of certain pfam domains in each subclass of RiPP investigated here (FIGS. 28A-28D). Certain pfam domains feasibly associated with biosynthesis (acetyltransferases, flavoproteins, epimerases, methyltransferases, dehydrogenases, aminotransferases, and glycosyltransferases) were modestly enriched. This analysis was coupled to manual inspection of each cluster for putative tailoring enzymes, then candidate genes were synthesized and assembled into single expression plasmids using an orthogonal set of inducible promoters36 (FIG. 28E).


78 gene clusters were selected from 68 diverse organisms spanning 6 classes and occupying airway, gastrointestinal (GI) tract, oral, skin, and urogenital (UG) tract microbiomes (FIG. 24, Table 11). A two-plasmid expression system was used wherein putative precursor peptides and modifying enzymes are synthesized and assembled in plasmids under control of inducible promoters (FIG. 25), singly- or doubly-transformed into E. coli, and analyzed by liquid chromatography-mass spectrometry (LC-MS) for retention and mass shifts indicative of peptide modification (FIG. 26)37. Peptides were engineered to possess either an N-terminal or C-terminal (lanthipeptides and lasso peptides, respectively) hexa-histidine-small ubiquitin-like modifier (SUMO) tag for affinity purification and increased peptide stability (HS-tag) (FIGS. 23A and 23B). Peptides were also engineered to possess protease sites in order to remove the HS-tag and leader peptide (FIGS. 23C and 23D), which enabled structural annotation of lanthipeptides through hypothetical structure enumeration and evaluation (HSEE)38 (FIG. 27). The entire process of assembly, transformation, growth, and purification was optimized for the use of 96-well microtiter plates (FIG. 23E)37.









TABLE 11







Bacterial strains used in Example 6.












Species
Niche
Strain
Source
Media
Growth






Streptococcus pneumoniae

Airways

Streptococcus pneumoniae

Ribbick lab
TSBb
anaerobic




TIGR4



Dolosigranulum pigrum

Airways

Dolosigranulum

ATCC
TSBb
aerobic





pigrum Aguirre et al.





(ATCC ® 51524 ™)



Staphylococcus caprae

Airways

Staphylococcus

ATCC
TSBb
aerobic





caprae (ATCC ® 55133 ™)




Staphylococcus capitis

Airways,

Staphylococcus capitis

Voigt lab
TSBb
aerobic



skin
TA281 (JAB794)



Staphylococcus epidermis

Airways,

Staphylococcus epidermidis

Voigt lab
TSBb
aerobic



skin
TA278 (JAB793)



Streptococcus infantarius

Gut

Streptococcus infantarius

Voigt lab
TSBb
anaerobic




subsp. infantarius ATCC-




BAA-102 (JAB516)



Bacteroides

dorei

Gut
aa_0143_0002_h6
OpenBiome
BHIs
anaerobic



Bacteroides

faecis

Gut
aa_0143_0089_f9
OpenBiome
BHIs
anaerobic



Bacteroides

thetaiotaomicron

Gut
af_0058_0071_a4
OpenBiome
BHIs
anaerobic



Bifidobacterium

adolescentis

Gut
ao_0067_0069_a1
OpenBiome
BHIs
anaerobic



Bifidobacterium

longum

Gut
am_0171_0090_c1
OpenBiome
BHIs
anaerobic



Citrobacter

amalonaticus

Gut
ao_0067_0062_a8
OpenBiome
BHIs
anaerobic



Enterococcus

avium

Gut
ao_0067_0069_c1
OpenBiome
BHIs
anaerobic



Enterococcus

durans

Gut
am_0171_0068_e1
OpenBiome
BHIs
anaerobic



Enterococcus

mundtii

Gut
am_0171_0068_d4
OpenBiome
BHIs
anaerobic



Leuconostoc

lactis

Gut
aa_0143_0055_c12
OpenBiome
BHIs
anaerobic



Paeniclostridium

sordellii

Gut
av_0103_0069_f8
OpenBiome
BHIs
anaerobic



Parabacteroides

distasonis

Gut
cx_0004_0077_a10
OpenBiome
BHIs
anaerobic



Parabacteroides

goldsteinii

Gut
aa_0143_0055_a8
OpenBiome
BHIs
anaerobic



Pediococcus

acidilactici

Gut
cx_0004_0082_e12
OpenBiome
BHIs
anaerobic



Ruthenibacterium

lacta-

Gut
am_0070_0084_c5
OpenBiome
BHIs
anaerobic



tiformans




Sellimonas

intestinalis

Gut
am_0224_0084_c8
OpenBiome
BHIs
anaerobic



Veillonella

dispar

Gut
bj_0095_0068_g5
OpenBiome
BHIs
anaerobic



Streptococcus sobrinius

oral

Streptococcus sobrinius 6715

Ribbick lab
TSBb
anaerobic



Streptococcus mitis

oral

Streptococcus

ATCC
TSBb
anaerobic





mitis Andrewes and Horder





emend. Judicial Commission




(ATCC ® 49456 ™)



Streptococcus gordonii

oral

Streptococcus gordonii Kilian

ATCC
TSBb
anaerobic




et al. (ATCC ® 33399 ™)



Streptococcus mutans

oral

Streptococcus mutans UA159

Ribbick lab
TSBb
anaerobic



Rothia dentocariosa

oral

Rothia dentocariosa (Onishi)

ATCC
TSBb
aerobic




Georg and Brown




(ATCC ® 17931 ™)



Corynebacterium striatum

Skin

Corynebacterium

ATCC
TSBb
aerobic





striatum (Chester) Eberson





(ATCC ® 6940)



Micrococcus luteus

Skin

Micrococcus

Wright lab
TSBb
aerobic





luteus (Schroeter) Cohn





(ATCC ® 10240 ™)



Staphylococcus aureus

Skin

Staphylococcus aureus subsp.

Voigt lab
TSBb
aerobic





aureus ATCC-19685





(JAB849)



Staphylococcus hominis

Skin

Staphylococcus

ATCC
TSBb
aerobic





hominis subsp. hominis Kloos





and Schleifer




(ATCC ® 27844 ™)



Streptococcus dysgalactiae

Skin

Streptococcus dysgalactiae

Voigt lab
TSBb
aerobic




TA380 (JAB792)



Streptococcus sanguinis

Skin, oral

Streptococcus

Ribbick lab
TSBb
anaerobic





sanguinis White and Niven





emend. Kilian et al.




(ATCC ® 10556 ™)



Lactobacillus crispatus JV-V01

vagina

L. crispatus JV-V01

Mitchell lab
MRS
anaerobic



Lactobacillus jensenii ATCC

vagina

L. jensenii ATCC 25258

Mitchell lab
MRS
anaerobic


25258



Lactobacillus gasseri ATCC

vagina

L. gasseri ATCC 33323

Mitchell lab
MRS
anaerobic


33323



Acinetobacter baumannii

pathogen
0033
CDC
TSBb
aerobic



Aspergillus fumigatus

pathogen
0731
CDC
SDA
aerobic



Campylobacter jejuni

pathogen
0412
CDC
TSBb
aerobic



Candida albicans

pathogen
0761
CDC
SDA
aerobic



Enterococcus faecalis

pathogen
0679
CDC
TSBb
aerobic



Enterococcus faecium

pathogen
0572
CDC
TSBb
aerobic



Escherichia coli

pathogen
0011
CDC
TSBb
aerobic



Klebsiella pneumoniae

pathogen
0112
CDC
TSBb
aerobic



Pseudomonas aeruginosa

pathogen
0508
CDC
TSBb
aerobic



Salmonella Typhimurium

pathogen
0408
CDC
TSBb
aerobic



Staphylococcus aureus

pathogen
0215
CDC
TSBb
aerobic










E. coli is an Effective Chassis Organism for Genome Mining of RiPPs


Application of this workflow to the selected gene clusters resulted in the detection and subsequent structural annotation of 18 lanthipeptides and 5 lasso peptides (FIG. 29). FIG. 29 shows total ion chromatograms (TICs) of TALON purified microtiter plate expressions. The HS-peptides were clearly identifiable via their mass shifts (water losses, −18 Da) using a low-resolution instrument and the detected peaks are highlighted. All of the peptides highlighted in FIG. 29 were successfully expressed, purified, dialyzed, cleaved, and SPE purified at 0.5 L scale and then subject to liquid chromatography tandem mass spectrometry (LC-MS/MS). Structures were annotated using HSEE, which is a method wherein all hypothetical modified peptide structures are enumerated in silico and compared to observed fragments from the MS/MS experiment37,38. N-Ethylmaleimide was used to determine the extent of cyclization for lanthipeptides and infer macrocycle topology via absence of fragmentation, as was demonstrated previously39-45. RiPPs from all microbiome niches were discovered but with varying rates of success: airways/other (2/11, 18%), GI (4/29, 14%), oral (11/23, 48%), skin (2/7, 29%), and UG (3/6, 50%).


7 lanthipeptide clusters generated retention/mass shifts in the presence of modifying enzymes but mass shifts weren't consistent with known modification patterns. Of particular interest were several producing strains that showed modifications via retention time/mass shift when putative tailoring enzymes were expressed (FIG. 31A-31D). For both above examples the mass spectra could be difficult to deconvolute, but expression differences were clear with the addition of modifying enzyme(s), as in HMLn020 (sAMK-730 from Bifidobacterium sp.) (FIG. 31A). In another example, expression of the core biosynthetic enzymes and putative peptide lanA2 from cluster HMLn034 (sAMK-740 from Dolosigranulum pigrum) resulted in production and mass detection of a 6×-dehyrated peptide lacking the last eight residues of its C-terminus, presumably from unanticipated proteolysis via E. coli enzymes. Additional expression of putative tailoring enzymes resulted in the production and detection of a higher molecular weight peptide consistent with a modified sequence lacking the last three residues of its C-terminus (FIG. 31B). Most strikingly, expression of the core biosynthetic enzymes and a putative peptide from cluster HMLn009 (sAMK-720 Myroides odoratimimus) did not result in any modification of the precursor peptide but additional expression of three putative tailoring enzymes resulted in a mass shift of −533.2 Da (FIG. 31C). Expression of one gene in particular, a KptA-like protein, was shown to be necessary for the observed modification. Homologs of KptA have been implicated in peptide modification46. Selective induction of the Marionette orthogonal expression system enabled the simultaneous expression of all putative genes and systematic interrogation of their contribution to biosynthesis, demonstrating its utility in genome mining via construction of a single strain.


A diverse selection of producing organisms were selected from which to mine lanthipeptide sequences for heterologous expression and whether gene clusters from particular genera were more or less suitable for expression in E. coli was investigated. To this end, a taxonomic tree of all lanthipeptide-producing organisms (with E. coli BL21 for reference) selected for this study was generated. Strains from which that successfully produced a RiPP were highlighted to detect trends (FIG. 32A). Lanthipeptides originating from all Classes of strains used in this study were successfully expressed and no obvious trends in failures or successes observed. The biosynthesis of type I lanthipeptides was next considered. Type I lanthipeptides are unusual in their requirement for glutamyl-tRNA (tRNAGlu) to activate Ser/Thr residues for dehydration (FIG. 32B) as opposed to using ATP, as in type II-IV lanthipeptide biosynthesis (FIG. 32C)47. Sequence differences in tRNAGlu have been shown to be important in heterologous expression of lanB-type enzymes48. Sequences for tRNAGlu from all species mined for type I lanthipeptide biosynthesis were used to generate a phylogenetic tree. Sequence homology of tRNAGlu was not important in analysis of successful production using E. coli as chassis, but no gene clusters from strains possessing alternative anticodon loops (CTC as opposed to TTC) were successfully produced, consistent with previous reports and predictions48.


Heterologous Expression of RiPP Gene Clusters Suitable for Functional Assaying

96-well microtiter growths (2×1 mL TB media) were purified and processed and optimal conditions for assaying biological activity were considered. Agar plate-based assays that demonstrate antimicrobial activity via zones of inhibition are an ideal method since compounds do not suffer dilution as in liquid-based readouts of optical density. Microtiter-purified RiPPs were initially tested against a subset of human microbiome-associated strains (Staphylococcus aureus, Streptococcus infantarius, Streptococcus dysgalactiae, Pediococcus acidilactici, Pseudofalnovifractor spp., and Bacteroides faecis) to assess this plate-based method and several producing strains (sAMK-287, sAMK-687, sAMK-691) showed varying zones of inhibition against this initial test set of indicator strains (FIG. 33A). While clear activity was observed in some cases, inconsistencies in colony density ruled out this method as a systematic means for detecting antimicrobial activity of RiPPs against a diverse panel of strains.


To streamline functional assaying, 96-well microtiter growths were optimized for a large collection of indicator strains sourced from a variety of niches found in the human microbiome (Table 11). The large-scale antimicrobial profiling of 30 SPE purified RiPPs (including both peptides that were confirmed via the structural annotation pipeline as well as putative modified peptides) showed that 8/30 demonstrated unique antimicrobial “fingerprints”. Of these active peptides, 7/8 could be grouped either through a common source cluster (AMK-286, 287, 916; AMK-917, 1009, 1010) or a common structural scaffold (AMK-417, 687, 691). The eighth, AMK-720, is an uncharacterized modified peptide that showed exceptionally broad antimicrobial activity. The structure and biosynthesis of AMK-720 are still under investigation, but structure-function relationships for the other three groups of peptides are described below.


Human Microbiome RiPPs Possess Unique Antimicrobial Fingerprints

The type II lanthipeptides AMK-286, AMK-287, and AMK-916 were based on genes from an oral strain of Streptococcus and share identical modification profiles (FIGS. 35A and 35C), including the consistent presence of a phosphoryl group on the most N-terminal threonine residue, which is a novel observation for enzymes of this class. Several features were apparent from the antimicrobial activity patterns of these related molecules (FIG. 35B). They (in particular AMK-287) demonstrated pronounced activity against strains of the alimentary tract, including Bifidobacterium adolescenits, Bifidobacterium longum, Sellimonas intestinalis, and Streptococcus dysgalactiae. The interplay between the oral microbiome and alimentary tract is complex and elucidating chemical mechanisms by which oral strains can disrupt and colonize the gut is critical to understanding the roles of certain strains in health and disease49. B. adolescenits and B. longum, for instance, are associated with anxiety and depression in mammals via substantial production of gamma-Aminobutyric acid50. These Streptococcus-derived RiPPs also demonstrated remarkably narrow spectrum activity with respect to other Streptococci (only significant activity observed against 1/5 Streptococcal strains). This suggested that an oral-derived Streptococcus produced a suite of molecules lacking activity against closely related members of the oral microbiomes51.


The lasso peptides AMK-917, 1009, and 1010 are from an oral strain of Rothia dentocariosa and exhibit conserved primary amino acid sequence about the lariat structure, with some degeneracy (FIGS. 35D-35F). The predicted amino acid sequences of these lasso peptides are substantially longer than others that were expressed in this study (Table 12) and antimicrobial activity tracked inversely with length of the core (FIG. 35E). The use of a C-terminal Factor Xa cleavage site (which leaves an “RLVPR (SEQ ID NO: 714)” scar) likely further exacerbated this negative trend. AMK-1008 was another predicted lasso peptide from the same gene cluster that was not observed during heterologous expression and had a much longer core sequence (AMK-917, 24 aa; AMK-1008, 37 aa; AMK-1009, 30 aa; and AMK-1010, 19 aa). Based on the amino acid sequence alignment (FIG. 35D), it was determined that AMK-1008 and AMK-1009 may be processed by non-cluster associated proteases that cleave before or after the “GG” at position 25. As such, discovery and application of scarless C-terminal proteases as well as iterations on core sequences used in heterologous expression will likely be important in genome mining lasso peptides.


Amino acid sequence alignments showed that AMK-417, 687, and 691 belong to the same family of RiPPs as lacticin 481 and the structural annotation was consistent with a similar cyclization pattern (FIGS. 57A-57C). Because AMK-687 displayed such remarkable antimicrobial activity and 2/5 strains were from the vaginal microbiome, the activity of these peptides was tested against Lactobacillus crispatus, a dominant member of the healthy vaginal microbiome52. AMK-687 displayed even more pronounced activity against this related strain while AMK-691 also demonstrated activity but other lanthipeptides tested were inactive (FIG. 57D). The strong activity of AMK-687 was noteworthy because Lactobacillus iners is implicated in transition of a healthy vaginal microbiome to an unhealthy one via depletion of the predominant Lactobacillus crispatus and related strains, but the exact mechanisms by which this dysbiosis occurs are largely unknown53.









TABLE 12







Microbiome RiPPs










Strain


SEQ ID


designation
Producing organism
Core primary amino acid sequence
NO





sAMK271

Streptococcus_pneumoniae_

GTDGADPRSTIICSATLSFIASYLGSAQTRCGKDN
115



SPAR95
KKK






sAMK285

Streptococcus_sp._

GIDTLDYEISHQELSGKSAAGWQTAFRLTMQGR
116



M334
CGGVFTLSYECATPHVSCG






sAMK286
Streptococcus_sp._
GGGWYTAFKLTLAGRCGLCFTCSYECTSNNVHC
117



M334







sAMK287

Streptococcus_sp._

GGWFTAIQLTLAGRCGNWFTGSFECTSNNVKCG
118



M334







sAMK293

Rothiadentocariosa

GTAFPGWYSKVIGNRGRVCTVTVECMSVCQ
119





sAMK298

Ruminococcus

GVGYTTYWGILPLVTKNPQICPVSENTVKCRLL
120




flavefaciens








sAMK299

Ruminococcus

GASTLPCAEVVVTVTGIIVKATTGFDWCPTGACT
121




flavefaciens

HSCRF






sAMK360

Clostridium spp.

GEAVSYTLNCTHFLTILCC
122





sAMK416

Corynebacterium_

GTHPSTLIPISIALCPTTRCSRRC
123




matruchotii_ATCC_14266








sAMK417

Gardnerella_vaginalis_

GGDGVMHTLTHECHMNTWQFLLTCC
124



5-1







sAMK418

Rothia_dentocariosa_

GGHGGGYSGGGYSGGGNSGGGNYCGNGCGNY
125



M567
NFGFGF






sAMK419

Clostridium_botulinum_

GTFSEGTISITLSVYMGNDGKVCTWTVECQNNCS
126



H04402_065
HKK






sAMK 421

Myroidesodoratimimus

GGGNSSKLYGSKGASCTCGNGVTCGTQQTKSGF
127



CIP 103059
EE






sAMK687

Lactobacillus iners

GSRWWQGVLPTVSHECRMNSFQHIFTCC
128





sAMK691

Streptococcus pyogenes

GGKNGVFKTISHECHLNTWAFLATCCS
129





sAMK692

Streptococcus pyogenes

GRGHGVNTISAECRWNSLQAIFTCC
130





sAMK695

Mobiluncus mulieris

GTSIPCGTLIIATLTQCFNDTLVWGSCRLGTRACC
131





sAMK696

Streptococcus

GMRFSTFSTNRCGNWSAFSWENC
132




pneumoniae








sAMK702

Lactobacillus delbrueckii

GGGAGLEDSKSFSLICIGSRVGDGNHSSHKKHHK
133




GKKH






sAMK715

Streptococcus agalactiae

GVTSKSLCTPGCKTGILMTCAIKTATCGCHFG
134





sAMK717

Staphylococcus caprae

GNTSLIWCTPGCAKNL
135





sAMK720

Myroides odoratimimus

GHVELMNADKVKCKSTSTTKSCSSTSTTSVD
136





sAMK725

Streptococcus sanguinis

GVGSRYLCTPGSCWKWVCFTTTVK
137





sAMK731

Streptococcus agalactiae

GAGHGVNTISAECRWNSLQAIFSCC
138





sAMK732

Streptococcus agalactiae

GGKNGVFKTISHECHLNTWAFLATCCS
139





sAMK734

Eubacterium sp.

GNMVIRARWTITSKCPSSIGHCC
140





sAMK740

Dolosigranulumpigrum

GTANTYCRCYSGRHSCGRACTITAECPVFTVACC
141





sAMK916

Streptococcus_sp._

GWQTAFRLTMQGRCGGVFTLSYECATPHVSCG
142



M334







sAMK917

Rothiaaeria F0474

GLIYGKYRDVLSGARLVTPPEVALRLVPR
143





sAMK989

Enterococcus faecalis

GLWTGKFRDVFGGRALFQVVIYYRLVPR
144





sAMK995

Sphingobium

GTSYGESLDATFPDGTPRGELTFSRLVPR
145




yanoikuyae








sAMK1009

Rothiaaeria FO474

GWLWGSYRDVYGVWHGPRTNFNGAGGSSEWR
146




LVPR






sAMK1010

Rothiaaeria F0474

GWYWGNRRDIYGALRYANKRLVPR
147









Based on the large antimicrobial activity dataset, four peptides (AMK-287, 417, 687, and 691) were selected to characterize their activity against clinical isolates of MDR pathogens. SPE-purified peptides from liter scale fermentations were used to profile dose-dependent killing of methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus faecium (VRE), and Streptococcus pneumoniae (FIG. 34). Dose-dependent antimicrobial activity was observed against at least one strain for all four peptides, with AMK-687 demonstrating particularly potent and broad-spectrum antimicrobial activity against all four isolates. Importantly, the clinical isolate of E. faecium was susceptible to these RiPPs despite a normal microbiome-associated E. faecium demonstrating robust growth in the presence of the same peptides (FIG. 33B). AMK-287 demonstrated pronounced activity against Streptococcus pneumoniae, again noteworthy given the narrow spectrum of activity against other strains of Streptococcus in the initial activity fingerprinting assay (FIG. 33B).


DISCUSSION

Attempts to address, at a mechanistic level, the dynamics of the microbiome commonly rely on a kind of “forward genetics” approach (start with a phenotype and move toward microbial genetic determinants)1. Here instead, a group of molecules were systematically assessed to functionally profile them for their potential to shape the microbiome. RiPPs sourced from the human microbiome may hold specific advantages as narrow spectrum antimicrobials for combating MDR pathogens. Traditional antibiotics can exacerbate the evolution of resistance or are causative of disease outright through their broad-spectrum activity disrupting the human microbiome54. Lanthipeptides with antimicrobial activity act primarily through targeting the cell envelope55, which is an attractive strategy to sidestep resistance mechanisms linked to enzymatic modification and efflux. Cyclic peptide natural products (or mimetics) targeting the bacterial outer envelope are being investigated and studied in clinical trials, including those active against Gram-negative pathogens56-58.


Several of the molecules discovered here serve as excellent scaffolds for further examining structure-activity relationships of the variable cyclic regions. The 96-well microtiter expression pipeline enables both rapid assessment of biosynthetic constraints for modifying enzyme/peptide pairs and functional assaying against indicator organisms of interest. Modifying enzymes that are associated with multiple substrate peptides can also serve as effective biocatalysts for selections of modified peptides with de novo activity25,39. Cell-free expression approaches, as demonstrated for unmodified bacteriocins59, offer a useful method for initial activity testing, but scalable production routes must be considered. Systematic heterologous expression and engineering of RiPP gene clusters (e.g., as provided herein) addresses the production issue and also advances peptides' potential as cell-based effectors in living therapeutics60. Emerging technology for the delivery of genetic programs to diverse bacteria61,62 coupled with responsive, in situ peptide production to sidestep unfavorable pharmacokinetic properties63 further highlights the therapeutic potential of peptides.


Semi-purified RiPPs were produced directly from sequence information without downstream assay constraints from as little as 2 mL microwell fermentations. Expression of RiPPs scaled well to liter volumes and methods were established for rapidly purifying and generating screening plates of peptides dissolved in an organic solvent/water mixture. These plates can be frozen, stored, and treated in similar fashion to small molecule libraries, enabling their broad assaying. The enumeration of medium-sized natural products in this format is of particular value since, compared to small molecules, they are under sampled in most natural products screening collections64. Medium-sized modalities exhibit greater efficacy in binding 15 to and disrupting non-enzymatic function of macromolecular targets65.


The scale at which RiPP gene clusters were constructed, expressed, and characterized in this study is unprecedented but precludes widespread, in-depth structural characterization. The application of high-resolution tandem mass spectrometry to characterize post-translationally modified peptides, however, is an acceptable level of structural annotation, as evidenced by comparable studies9-11, 39-45. The workflows described here enable discovery, prioritization, and optimization of a limited number of molecules, which can be scaled in production volume for more rigorous structural and functional characterization as appropriate.


In summary, a platform was developed for streamlined genome mining of RiPP gene clusters. Rapid assessment of modification through 96-well expression, purification, and LC-MS analysis enabled small molecule and novel enzyme discovery. Application of this pipeline toward genome mining of the human microbiome yielded constrained peptides with unique antimicrobial fingerprints when tested against a large subset of strains from the human microbiome. These molecules were shown to be active against MDR bacterial pathogens. Systematic discovery and functional profiling of human microbiome-derived antimicrobials able to selectively target endogenous microflora and pathogens has significant potential for both engineering the microbiome and developing therapeutics to address antimicrobial resistance.


Methods
Materials and Methods

Strains, media, and chemicals. E. coli NEB 10-beta (C3019I, New England BioLabs, Ipswich, Mass., USA) was used for all routine cloning. E. coli NEB Express (C2523I, New England BioLabs, Ipswich, Mass., USA) and E. coli Marionette-X, a Marionette-compatible derivative of NEB Express were used for liter-scale peptide expression experiments. TB (T0311, Teknova, Hollister, Calif., USA) supplemented with 0.4% glycerol (BDH1172-4LP, VWR, OH, USA) was used for peptide expression and modification. 2xYT liquid media (B244020, BD, Franklin Lakes, N.J., USA) and 2xYT+2% agar (B214010, BD, Franklin Lakes, N.J., USA) plates were used for routine cloning and strain maintenance. Other media include Tryptic Soy Broth (TSB; BD211825, BD, Franklin Lakes, N.J., USA), Brain Heart Infusion (BHI; BD237500, BD, Franklin Lakes, N.J., USA),


Lactobacilli MRS broth (MRS; BD288130, BD, Franklin Lakes, N.J., USA), and Sabouraud Dextrose Broth (SDB; BD288130, BD, Franklin Lakes, N.J., USA). SOB liquid media (S0210, Teknova, Hollister, Calif., USA) was used for making competent cells. SOC liquid media (B9020S, New England BioLabs, Iwsich, Mass., USA) was used for outgrowth. Unless noted otherwise, cells were induced with the following chemicals: cuminic acid (268402, Millipore Sigma, Saint Louis, Mo., USA) added as 1000× stock (200 mM) in EtOH or DMSO; 3-oxohexanoyl-homoserine lactone (3OC6-AHL) (K3007, Millipore Sigma, Saint Louis, Mo., USA) added as a 1000× stock (1 mM) in DMSO; anhydrotetracycline (aTc) (37919, Millipore Sigma, Saint Louis, Mo., USA) added as a 1000× stock (100 μM) in DMSO; isopropyl β-D-1-thiogalactopyranoside (IPTG) (I2481C, Gold Biotechnology, Saint Louis, Mo., USA) added as 1000× stock (1 M) in water; Sodium salicylate (S3007, Millipore Sigma, Saint Louis, Mo., USA), N-(3-Hydroxytetradecanoyl)-DL-homoserine lactone (3OC14-AHL; 51481, Millipore Sigma, Saint Louis, Mo., USA. Cells were selected with the following antibiotics: carbenicillin (carb, C-103-5, Gold Biotechnology, Saint Louis, Mo., USA) added as 1000× stock (100 mg/mL in H2O); kanamycin (kan, K-120-10, Gold Biotechnology, Saint Louis, Mo., USA) as 1000× stock (50 mg/mL in H2O); and spectinomycin (spec, S-140-5, Gold Biotechnology, Saint Louis, Mo., USA). Liquid chromatography was performed with Optima Acetonitrile (A996-4, Thermo Fisher Scientific, MA, USA) and water (Milli-Q Advantage A10, Millipore Sigma, Saint Louis, Mo., USA) supplemented with LCMS Grade Formic Acid (85178, Thermo Fisher Scientific). The following solvents/chemicals were also used: Ethanol (V1001, Decon Labs, King of Prussia, Pa., USA), Methanol (3016-16, Avantor, Center Valley, Pa., USA), Ammonium bicarbonate (A6141 Millipore Sigma, Saint Louis, Mo., USA), dimethyl sulfoxide (DMSO) (32434, Alfa Aesar, Ward Hill, Mass., USA), Imidazole (IX0005, Millipore Sigma, Saint Louis, Mo., USA), sodium chloride (X190, VWR, OH, USA), sodium phosphate monobasic monohydrate (20233, USB Corporation, Cleveland, Ohio, USA), sodium phosphate dibasic anhydrous (204855000, Acros, N.J., USA), guanidine hydrochloride (50950, Millipore Sigma, Saint Louis, Mo., USA), tris (75825, Affymetrix, Cleveland, Ohio, USA), TCEP (51805-45-9, Gold Biotechnology, Saint Louis, Mo., USA), and EDTA (0.5M stock, 15694, USB Corporation, Cleveland, Ohio, USA), dimethyl formamide (A13547, Alfa Aesar, MA, USA), defibrinated sheep blood (R54012, Thermo Fisher Scientific, MA, USA), hemin (51280, Sigma Aldrich), vitamin K1 (V3501, Sigma Aldrich), and L-cysteine (C7532, Sigma Aldrich). DNA oligos and gBlocks were ordered from Integrated DNA Technologies (IDT) (San Francisco, Calif., USA).


Computational detection and clustering of RiPP gene clusters. Genome datasets for projects “HMP1” and “HMP2” were obtained from the Human Microbiome Project online portal. These 2,229 genomes were used as the database for running AntiSMASH 4.0 using default parameters with ClusterFinder-based border predictions 29. Output from this analysis was analyzed using BiG-SCAPE with distance cut-off filters of 0.2, 0.4, 0.6, 0.8, and 1.0. The resulting similarity network matrices were visualized with Cytoscape and distance cutoff of 0.8 chosen for FIGS. 28A-28D.


Peptide expression in 96-well plates and purification. Plasmids were transformed into either E. coli NEB Express or E. coli Marionette-X using 30 μL of competent cells and 1 μL of each plasmid being transformed in a PCR strip tubes (1402-4700, USA Scientific, FL, USA or 951020401, Eppendorf, N.Y., USA). Transformations were incubated on ice (20-30 min), heat shocked (42° C., 30 sec), and incubated on ice again (5 min). Cells were then transferred to a deep well 96-well plate (1896-2000, USA Scientific, FL, USA) with 120 μL of SOC. After outgrowth (Multitron Pro, 1 hr, 30° C.) in an Infors HT Multitron Pro (Infors USA, MD, USA), 900 μL LB was added with appropriate antibiotics (at 1.1× for 1× final concentration) and incubated (Multitron Pro, 30° C., 900 r.p.m.) until all wells reached saturation (12-30 hours). Overnight cultures were diluted 1:100 into 1 ml TB in deep well plates. After 3 hours incubation (Multitron Pro, 30° C., 900 r.p.m.), appropriate inducer was added (1 μl IPTG or 1l1 IPTG and 1 μl cumate), and cultures were incubated for 20 hours (Multitron Pro, 30° C., 900 r.p.m.). To purify the peptides, the 96-well plates were centrifuged (Legend XFR, 4,500 g, 4° C., 20 min), pellets were resuspended in 600 μL lysis buffer, and freeze-thawed twice (frozen at −80° C.; thawed in Multitron Pro at 37° C., 900 r.p.m). Cell lysates were centrifuged (Legend XFR, 4,500 g, 4° C., 60 min) and peptides affinity purified using His MultiTrap TALON plates (29-0005-96, GE Life Sciences, Marlborough, Mass., USA), following manufacturer instructions, using 1×600 μL water and 2×600 μL lysis buffer for column equilibration, 2×600 μL wash buffer, and 1×200 μL elution buffer.


Liter-scale RiPP expression and purification. Glycerol stocks of strains generated from 96-well transformations were used to inoculate 20 mL of LB in a 125 mL shake flask and incubated overnight at 30° C. and 250 rpm in an Innova44 (Eppendorf, N.Y., USA). A 5 mL aliquot of overnight starter culture was diluted in 500 mL total volume TB with carb/spec in Fernbach flasks and grown at 30° C. and 250 rpm until reaching OD600 0.8-1.0, at which point 1 mM IPTG and 200 μM cumate are added. Induced cultures were grown for a further 20 h at 18° C. and 250 rpm and then centrifuged (4,000 g, 4° C., 10 min) in a Sorvall RC 6+ centrifuge (Thermo Fisher Scientific, MA, USA). Pellets were resuspended in 30 mL lysis buffer (5 M guanidinium hydrochloride, 300 mM NaCl, 10 mM imidazole, 50 mM sodium phosphate, pH 7.5), and freeze-thawed twice (frozen in −80° C. freezer; thawed in innova44 incubator at 30° C., 250 rpm). Cell lysates were centrifuged (20,000 g, 12° C., 45 min) and the peptides affinity purified via gravity-flow using 3 mL resin-bed volume of Ni-NTA agarose resin (88223, Thermo Fisher Scientific, MA, USA), following manufacturer instructions, using 2 resin-bed volumes water and lysis buffer for column equilibration, 4 resin-bed volumes of wash buffer (5 M guanidinium hydrochloride, 300 mM NaCl, 25 mM imidazole, 50 mM sodium phosphate, pH 7.5), 4 resin-bed volumes of elution buffer buffer (5 M guanidinium hydrochloride, 300 mM NaCl, 250 mM imidazole, 50 mM sodium phosphate, pH 7.5). Eluates were diluted to 30 mL with lysis buffer, transferred to Spectra/Por 3 RC Dialysis Membrane Tubing 3500 Dalton MWCO (132725, Spectrum, CA, USA) and dialyzed overnight at room temperature in 1× phosphate buffered saline (PBS; 6505-4L, CalBiochem, CA, USA). Dialyzed solutions were centrifuged (4,000 g, 4° C., 10 min) to remove any precipitate. To cleave the SUMO and leader peptide from the core, TCEP (1 mM final concentration) and 3 mg of TEV protease (30 mg lyophilizate, Gene and Cell Technologies, CA, USA) were added and tubes incubated overnight at room temperature with slow orbital shaking. Cleaved peptide solutions were centrifuged (4,000 g, 4° C., 10 min) to remove any precipitate and then desalted using a Strata-X PRO 500 mg SPE tube (8B-S536-HCH, Phenomenex, CA, USA). The solid phase was first conditioned with 4 bed volumes of methanol and then water. Eluate was then loaded, washed with 8 bed volumes of water, and eluted with 8 bed volumes of 1:1 acetonitrile:water+0.1% formic acid. Solvent was removed via lyophilization at −80 C for 24-48 hours.


Liquid chromatography/mass spectrometry. All chromatography was performed using mobile phases ACN (acetonitrile supplemented with 0.1% formic acid and 0.1% water) and water (supplemented with 0.1% formic acid). LC-MS was performed on one of two mass spectrometers: “QQQ” is an Agilent 1260 Infinity liquid chromatograph with binary pump configured in low-dwell volume mode, high-performance autosampler chilled to 18° C., and column oven, coupled to an Agilent 6420 QQQ mass spectrometer equipped with an Agilent electrospray ionization (ESI) source; nitrogen gas is supplied by a Parker Nitroflowlab and ESI source parameters are 350° C. gas temp at 12 L/min flow rate, 15 psi nebulizer voltage, 4000 V capillary voltage, 135 V fragmentor voltage, and 7 V cell accelerator voltage. “qTOF” is an Agilent 1260 Infinity II liquid chromatograph with binary pump configured in low-dwell volume mode and column oven set to 40° C., coupled to an Agilent 6545 qTOF mass spectrometer equipped with an Agilent electrospray ionization (ESI) source; nitrogen gas is building supplied and ESI source parameters are 350° C. gas temperature, 12 L/min gas flow, 30 psig nebulizer pressure, 350° C. sheath gas temperature, 8 L/min sheath gas flow, 3000 V capillary voltage, 1000 V nozzle voltage, 135 V fragmentor voltage, 15 V skimmer voltage, 600 V Oct 1 RF Vpp; the mass spectrometer was run in MS mode with reference mass enabled and tuned in positive mode with standard mass range (3200 m/z) and 2 GHz extended dynamic range. When using the QQQ, analysis was done with a Phenomenex Aeris PEPTIDE XB-C18 2.6 □m 50 mm×2.1 mm column with column oven set to 40° C. Flow rate was 0.6 ml/min. Gradient was 10% ACN for 0.5 min, 10% to 60% ACN over 6 min, 60% to 90% ACN over 1 min, 90% ACN for 1 min, with 1 min re-equilibration. The mass spectrometer was run in positive mode, 500-2000 m/z range with a 300 ms scan time. Injections were 5 □L (as a starting point, injection volumes were occasionally adjusted depending on the yield of the 96-well prep). When using the qTOF, analysis was done with a Phenomenex Aeris PEPTIDE XB-C18 2.6 □m 50 mm×2.1 mm column. Flow rate was set at 0.5 ml/min. The flow rate was set at 0.5 mL/min and 5 μL sample was injected. The gradient used was 10% ACN for 1.0 min, 10% to 70% ACN over 5.0 min, 70% to 90% ACN over 0.5 minutes, 90% ACN for 1.0 min, with 1.0 min re-equilibration. Injections were 5 μL (as a starting point, injection volumes were occasionally adjusted depending on the yield of the 96-well prep).


Peptide screening plate prep. Lyophilized liter-scale preps were resuspended in 540 μL DMF and vortexed for 5 seconds. To this was added 3060 μL of H2O and the mixture was vortexed for 5 seconds to make a solution of peptide in 15% DMF. All mixtures were centrifuged (Legend XFR, 4,000 g, 4° C., 10 min) to remove any insoluble material and then split into 2 96-well 2 mL plates. From this, 12 μL of each peptide was aliquoted into 290 96-well screening plates (3788, Corning), which were then used for downstream LC-MS/MS analysis and functional assay screening. Plates were covered and kept at −20° C. for up to one year.


LC-MS/MS data acquisition. All chromatography was performed using the mobile phases ACN (acetonitrile supplemented with 0.1% formic acid and 0.1% water) and water (supplemented with 0.1% formic acid). MS/MS data were acquired on an Agilent 1260 Infinity II liquid chromatograph with binary pump configured in low-dwell volume mode and column oven set to 40° C., coupled to an Agilent 6545 qTOF mass spectrometer equipped with an Agilent electrospray ionization (ESI) source. Nitrogen gas is building-supplied and ESI source parameters are 350° C. gas temperature, 12 L/min gas flow, 30 psig nebulizer pressure, 350° C. sheath gas temperature, 8 L/min sheath gas flow, 3000 V capillary voltage, 1000 V nozzle voltage, 135 V fragmentor voltage, 15 V skimmer voltage, 600 V Oct 1 RF Vpp; the mass spectrometer was run in MS mode with reference mass enabled and tuned in positive mode with standard mass range (3200 m/z) and 2 GHz extended dynamic range. For this analysis, 4 peptide screening plates were thawed and resuspended in a total of 100 □L PBS/DMF mixture. To this mixture, TCEP was added to a final concentration of 1 mM. Samples were split in two and NEM (12.5 mM final concentration) was added to one group of samples to label free cysteine residues. For the targeted MS/MS, 4 spectra/s were sampled with fixed collision energies of 30, 45, 60, and 75 V. A narrow isolation width (1.3 m/z) and observed monoisotopic mass (exact masses found in Supplementary Fig. xx) was used for fragmentation of each peptide. Sample analysis was performed with a Phenomenex Aeris PEPTIDE XB-C18 2.6 □m 50 mm×2.1 mm column. The flow rate was set at 0.5 mL/min and 5 □L sample was injected. The gradient used was 10% ACN for 1.0 min, 10% to 70% ACN over 5.0 min, 70% to 90% ACN over 0.5 minutes, 90% ACN for 1.0 min, with 1.0 min re-equilibration. Accurate mass predictions of peptides were generated using the online resource, ChemCalc 68. Indicator strain growth. Indicator strains were grown using the annotated media. The following specialized media mixtures were used: TSB supplemented with 5% defibrinated sheep blood (TSBb) and BHI supplemented with hemin, vitamin K1, and L-cysteine (BHIs). To make BHIs, 10 mL of hemin solution (50 mg hemin, 1 mL 1 N NaOH, 100 mL H2O, filter sterilized) and 200 μL of diluted vitamin K1 solution (150 μL vitamin K1 solution, 30 mL 95% ethanol, filter sterilized) were added to sterile 1 L sterile BHI supplemented with 0.5 g L-cysteine. Agar plates of all media types were generated by addition of 2% agar. For strains sourced from OpenBiome and individual labs, strains were first purified by streaking on agar media plates. For strains sourced from ATCC and CDC, product protocols were followed to activate lyophilizates and strains were grown on agar plates of the annotated media type. All strains were grown on solid media until uniform colonies were observed. Individual colonies were used to inoculate sterile 96-well microtiter plates of the corresponding media type. Once wells reached sufficient density (24-72 hours of growth, see additional culturing conditions below), liquid glycerol stocks were generated by the addition of 500 μL culture and 500 μL 50% glycerol. Multiple glycerol stock plates were generated and frozen at −80° C. for subsequent assaying described below.


Antimicrobial assays. All materials were additionally sterilized by exposure to UV light for 10 minutes in laminar flow cabinet. Glycerol stocks of microbiome strains were subcultured in liquid media. Strains were grown for 24-48 hours, diluted 1:200 into fresh media, and 100 μL added to thawed peptide screening plates previously generated. Compounds were aliquoted in wells C1-E12 with wells B1-B12 and F1-F12 containing 15% DMF controls. Additional media was added to wells surrounding the assay wells to mitigate evaporation. All growth plates contained wells B1-B12 with a no growth control (15% DMF plus 100 μL media) and wells F1-F12 with a growth control (15% DMF plus 100 μL diluted culture). Plates were manually inspected for sufficient control growth after 24 or 48 hours and optical density measured using a The OD600 was measured using a Synergy H1 Hybrid Reader (8041000, BioTek). Automated plate shaking was found to be insufficient to break up pellets formed by some strains and therefore all pellets were manually broken up by mild pipetting with care taken to not introduce bubbles. Residual growth was calculated by measuring the OD600 of all plate wells. All measurements were done in triplicate on three separate days. Dilution series experiments were performed as above with new compound preps. Compounds were mixed with media at 4× the final concentration. Serial two-fold dilutions into the same media composition generated a compound dilution series at 2× the final assay concentration. Diluted indicator cultures were added 1:1 to this mixture to generate a 1× compound concentration in all wells.


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Example 7: Combining Enzymes to Multiply Modify Peptides

Combining peptide sequence constraints for peptide-modifying enzymes, such as those identified through methods described in the previous examples and shown in FIG. 36, offers the attractive possibility of incorporating multiple distinct modifications into a peptide library, increasing diversity of peptides that can be generated and the flexibility of options available for designing features into a library.


As a proof of principle, the modification patterns of three enzymes were combined and analyzed to develop core and leader sequence motifs. As shown in FIG. 37A, incorporating multiple distinct recognition sites (RSs) into the leader sequence of a peptide and utilizing the corresponding enzymes, as well as incorporating design limitations based on tailoring enzymes, can allow the incorporation of combinations of modifications into a peptide that are not constrained by a given native BGC. As an example, combining the design rules for LynD, PlpXY, and ThcoK modifying enzymes allows for the generation of an amino acid sequence motif that is able to be modified by three distinct enzymes, a library of such peptides can be produced and combined with the respective modification enzymes, and candidate peptides for a given function (e.g., binding to a particular target protein) can be identified (FIG. 37B). The core sequence constraints identified for these three enzymes were combined to design a motif of allowable amino acids forming the range of options for core sequences that can be modified by the particular combination of three enzymes (FIG. 37C). Similarly, the recognition sites for the two leader-dependent enzymes were analyzed, and an array of chimeric leaders were generated by varying the positioning and overlap of the two RSs and scoring each output (FIG. 37D).


After analyzing the core and leader sequence variant possibilities, a chimeric leader and hybrid core motif were identified combining the options for LynD, PlpXY, and ThcoK modifications (FIG. 37E). The resulting motif provides 11,520 possible peptide sequences. This informed design strategy enables the generation of libraries of this order of magnitude which can be screened, whereas absent the incorporation of design limitations based on the selected modifying enzymes, screening a library of unconstrained peptides of the same length would be infeasible, as there would be 2013 or roughly 1016 possible options—a library which would be impossible to screen using any available techniques. To the contrary, the rationally designed library of ˜104 peptides was able to be screened using the methods provided here, thereby enabling the identification of candidates with the desired modification patterns. The hybrid motif was encoded as a degenerate library, and 11 library members were isolated (FIG. 37F). Certain of the library members included amino acids that theoretically were not allowed based on the hybrid motif (shaded in FIG. 37F), as a result of the degenerate codons that were used to encode certain amino acid positions.


Similar methods were applied to additional combinations of modification enzymes: (a) ThcoK and LynD; (b) PadeK and LynD; (c) LynD and LasF; (d) PalS, PlpXY and PadeK; (e) LasF and PalS; (f) PlpXY, ThcoK and LynD; (g) PadeK and PalS; and (h) ThcoK and PalS. A selection of peptides were identified for these combinations (FIG. 38).


Example 8: Functional Expression of Diverse Post-Translational Peptide-Modifying Enzymes in E. coli

RiPPs (ribosomally-synthesized and post-translationally modified peptides) are a class of pharmaceutically-relevant natural products expressed as precursor peptides before being enzymatically processed into their final functional forms. Bioinformatic methods have illuminated hundreds of thousands of RiPP enzymes in sequence databases and the number of characterized chemical modifications is growing rapidly; however, it has proven difficult to functionally express them in a heterologous host. A major challenge is peptide stability, which is addressed in this Example by design of a RiPP stabilization tag (RST) based on a small ubiquitin-like modifier (SUMO) domain that can be fused to the N- or C-terminus of the precursor peptide and proteolytically removed after modification. This is demonstrated to stabilize a set of eight RiPPs representative of diverse phyla without interfering with the activity of associated modifying enzymes. Further, using Escherichia coli for heterologous expression, a common set of media and growth conditions were identified in which 24 modifying enzymes, representative of diverse chemistries, were shown to be functional. The high success rate and broad applicability of this system enables RiPP discovery through high-throughput “mining” as well as retrosynthesis through the artificial combination of enzymes from different pathways to create a desired non-natural peptide.


INTRODUCTION

Metagenomics has led to a deluge of microbial genomes, leading to high-throughput efforts to “mine” the molecules made by organisms by rebuilding pathways and screening for functions-of-interest[1-3]. Because these genes are gleaned from sequence databases, the organism or genomic DNA may not be available, thus necessitating the use of DNA synthesis and a heterologous host to obtain the chemical product[4-6]. RiPPs (ribosomally-synthesized and post-translationally modified peptides) are a potentially rich source of functional diversity that are encoded in gene clusters as a precursor peptide that is enzymatically modified before being proteolytically released[7-14]. Because the peptidic product is made by the ribosome, rather than by a large megasynthase, the probability of successful heterologous expression was determined to be high. However, expressed peptides are often unstable in vivo, and post-translational modifying enzymes may not function in new contexts[15-17]. As a result, only a small fraction of the thousands of known RiPP pathways have been explored[13].


RiPPs are classified by the chemical modifications made to the peptide. Some are defined by cyclization chemistry, including lanthipeptides (lanthionine macrocyclizations), thiopeptides ((4+2) cycloaddition of dehydrated serine/threonine), lasso peptides (N-terminal macrocyclization with asp/glu), graspetides (lactone/lactam macrocyclizations), bottromycin (macrolactamidine macrocyclization), ranthipeptides (Non-Cα thioether macrocyclizations), pantocins (glutamate crosslink), and sactipeptides (sactionine macrocyclizations)[7, 14]. Others are defined by individual modifications, like glycocins (side chain glycosylation), microcin C (aminoacyl adenylation or cytidylation), comX (indole cyclization and prenylation), sulfatyrotide (tyrosine sulfation), spliceotide (β-amino acids from backbone splicing), and cyanobactins (N-terminal proteolysis). Precursor peptide organization varies between RiPP classes. Modifying enzymes can either bind to a leader/follower sequence in the precursor peptide or directly modify the core. The core consists of 2 to over 50 amino acids and there can be multiple cores in one precursor peptide[17-20]. Leader peptides range from 7 to over 80 amino acids and can recruit multiple modifying enzymes that can have overlapping binding sequences[21-23]. The diversity in chemistry and genetic encoding complicates the creation of general engineering tools that can be systematically used for mining efforts across RiPP classes.


Tools have been developed to aid heterologous production, including multi-plasmid inducible systems and exploration of E. coli, various Streptomyces strains, and Microvirgula aerodentrificans as expression hosts[17, 30-33]. In vitro methods have also been used to engineer production of new molecules or study biosynthesis[34-37]. Gene cluster regulation may not function properly in a new host. To overcome this, the precursor peptide and modifying enzymes can be cloned and expressed separately[17, 33]. However, precursor peptides have been observed to often be unstable due to host proteases, thus necessitating the use of stabilization tags[15, 16, 24]. Large tags must be removed before peptide modifications can be observed by mass spectrometry, such as in the case of maltose binding protein (MBP, 45 kD), green fluorescent protein (GFP, 27 kD) and glutathione-S-transferase (GST, 26 kD)[38]. In contrast, the small ubiquitin-like modifier tag (SUMO, 12 kD) is smaller, thus allowing modifications to be observed prior to its removal. Further, it can be removed using SUMO protease immediately after purification without desalting[39], which simplifies its use in high-throughput formats. SUMO has been used for expression of both eukaryotic and prokaryotic antimicrobial peptides in E. coli [40-42] as well as a post-translationally modified lanthipeptide from Lactococcus[43] and a xenorceptide from Xenorhabdus[44].


Here, a RiPP Stabilization Tag (RST) was developed. The RST is a SUMO-based tag for high-throughput RiPP production and was demonstrated to work with diverse classes and modifying enzymes. Versions were made for fusion to the N- or C-terminus of the precursor peptide. Each version contains a HIS6 tag to enable purification in 96-well format. TEV and thrombin protease cleavage sites were included for the N- and C-terminal versions, respectively. Optimized E. coli inducible systems[45] were used to express tagged precursor peptides and modifying enzymes from separate plasmids. The ability for the RST to stabilize the peptide was validated by testing precursor peptides from 9 RiPP classes. As an example, it was demonstrated that the B. halodurans antibiotic peptide haloduracin A1/A2 can be expressed in E. coli and completely modified while attached to the RST, and further that the peptide is functional upon proteolytic cleavage of the RST. Fifty (50) precursor peptides were tested with 47 modifying enzymes and 39 peptides were identified that were expressed as RST fusions, and 24 were identified that were able to be modified with the RST attached. This Example demonstrates the broad applicability of the RST tag for high-throughput mining efforts that span RiPP classes and modifying enzyme chemistries. In addition, these enzymes were all expressed in the same heterologous host (E. coli) under uniform culture conditions and induction times. This provides a roadmap for selecting those enzymes that can be artificially combined to build retrosynthetic pathways for producing non-natural RiPP molecules with desired properties.


Results
Expression System for Modified Peptides

Two versions of the RiPP stabilization tag (RST) were designed to allow fusion to either the N- or C-terminus (termed RSTN and RSTC, respectively) of a precursor peptide (FIG. 39 and FIG. 40A). In most instances in this Example, the N-terminal version was used. The C-terminal version is a useful alternative either when there is a modification at the N-terminus, or when the leader peptide is removed during modification. For purification, a HIS6 tag was placed at the terminus of the RST. A linker sequence was designed to connect SUMO to the precursor peptide, adapted from a recombinant protein expression system[46]. The linkers were built to include cleavage sites for orthogonal proteases: TEV (for RSTN) or Thrombin (for RSTC). The RST was designed such that it can be removed using either TEV/Thrombin or SUMO protease (for RSTN). Treatment of RSTN-tagged peptides with TEV leaves a GC scar at the N-terminus, where the cysteine is included to allow SAMDI (self-assembled monolayers on gold for matrix-assisted laser desorption/ionization) mass spectroscopy[47, 48].


A two-plasmid system was used to separately express the precursor peptide and modifying enzyme, thus enabling combinations to be tested rapidly through co-transformations (FIG. 40B). The inducible system for the precursor peptide was selected to maximize its expression. To this end, the IPTG-inducible PT5LacO promoter[45] was used and a strong ribosome binding site (RBS) designed using the RBS Calculator[49, 50]. For the modifying enzyme, the cumate-inducible PCymR* or ahl-inducible PLuxB plasmids were used because of their high dynamic range (low off and high on)[45]. A different RBS was calculated for each modifying enzyme to maximize the probability of successful expression and to bias toward similar expression levels. When expressing RSTC-fused peptide, a small N-terminal region of the RSTN tag (FIG. 40A) was used to keep the RBS strength (and associated expression level) relatively constant across different precursor peptides.


Expression and purification protocols were first developed for low-throughput growth in 250 ml flasks in LB media. The tagged precursor peptide and modifying enzyme were induced simultaneously. After induction with 1 mM IPTG and 200 μM cumate (for PCymR*) or 10 μM 3OC6-AHL (for PLuxB), cultures were grown at 18° C. for 20 hours with shaking. Then, the peptide was purified using immobilized metal affinity chromatography (IMAC) and analyzed using LC-MS.


An example of the production of a modified peptide in flasks is shown in FIG. 40C using a variant of the trunkamide precursor peptide (TruE*) and cognate modifying enzyme TruD. Two samples were prepared: (1) the TruE* peptide expressed using a first-generation version of RSTN (RSTN*) co-transformed with the plasmid containing PLuxB-controlled truD (pEG1128); and (2) the TruE* peptide expressed as an MBP fusion, also co-transformed with pEG1128. From the LC-MS spectra, the observed mass for each of the peptides, as well as the expected error given the resolution of the mass spectrometer were calculated. TruD catalyzes the formation of a thiazole from cysteine, causing a loss of water and a corresponding mass shift of −18 Da. The larger MBP obfuscated the observation of this expected mass shift because it is equal to the standard deviation of the measurement (18 Da). In contrast, the standard deviation of the RSTN fusion is 6 Da and the expected and observed mass matched (FIG. 40C). Therefore, it was concluded that the mass shift that occurs due to post-translational modification could be observed without removing the RST, even using a low-resolution quadrupole mass spectrometer.


Next, RST stabilization of diverse precursor peptides across RiPP classes was tested (FIG. 41). The following examples from each class were selected: microviridin L from graspetides, bottromycin from bottromycins, streptide from streptides, PQQ from pyrroloquinoline quinones, subtilosin A from sactipeptides, trifolitoxin from linear azole peptides, prochlorosin from lanthipeptides, thiomuracin from thiopeptides, and pheganomycin from guanidinotides (peptides described in [14, 20, 29, 51-57]). This set encompasses a wide range of lengths, amino acid compositions, number of modifying enzyme binding sites, N- and C-terminal leaders/followers, and pheganomycin has two cores.


The ability for RSTN* to stabilize the unmodified peptides was tested. Expression was measured in the absence of modifying enzymes to account for any stabilization affect that arises from peptide modification. Expression and purification were performed at the 250 mL flask scale, as described above. First, precursor peptide expression when fused only to a N-terminal HIS6 tag was evaluated. This tag led to only three of nine peptides being detected by LC-MS (FIG. 41). Trifolitoxin was also detected, but it was cleaved in E. coli, resulting in a truncated peptide. In contrast, when the precursor peptides were fused to RSTN*, large peaks appeared for all of the peptides. These peaks corresponded to the expected masses, except for trifolitoxin and subtilosin A, the latter of which is cleaved in the leader.


Production of Active Haloduracin

Next, the production of a biologically-active product was evaluated using the expression system provided herein. Modifications were directed at an RST-fused peptide, after which the tag was cleaved and the activity of the product tested. Haloduracin was selected, a two-component lanthipeptide that had previously been expressed and purified from E. coli and shown to have antibiotic activity[34]. Genes encoding haloduracin A1 and haloduracin A2 peptides fused to RSTN were synthesized, as were genes encoding corresponding HalM1 and HalM2 modifying enzymes from Bacillus subtilis (FIGS. 42A-42F). An additional TEV protease cleavage site was added between the leader and core regions of the precursor peptide (FIG. 42A) to allow the core to be cleaved and recovered as an active product (FIG. 42B). Such cleavage leaves a single N-terminal glycine on the released core sequence. The peptide-enzyme genes were cloned into the two-plasmid system (FIG. 40B) and transformed as pairs into E. coli NEB Express.


A high-throughput 96-well system for expression and purification was developed, which was tested using haloduracin. Cultures were grown in 2 mL of TB media in deep well plates (two 1 mL wells for each peptide), where they are each induced with 1 mM IPTG/200 μM cumate for 20 hours at 30° C. with shaking. The cells were lysed, affinity-purified and desalted using solid phase extraction, all in 96-well format. Then, the samples were treated with TEV protease to remove RSTN and the leader peptide, and desalted again to concentrate the core peptide (FIG. 42D). The presence of the cleaved cores was verified by LC-MS (FIG. 42D) and LC-MS/MS to confirm that SUMO did not disrupt or alter the lanthionine macrocyclizations present in both molecules (FIG. 42E). For both, the predicted structures were in close agreement with previous reports ([34, 58, 59]). For HalA2, seven of eight Ser/Thr residues were dehydrated and assignment of the single unmodified residue was previously localized to Thr18, Thr22, or Ser23 [34, 58, 59]. A low abundance fragment was observed, suggesting the presence of a dehydrated Ser23, in contrast to a previous report wherein mutation of Ser23 to Ala did not affect the overall number of dehydrations observed [58].


To assay for antimicrobial activity, the cleaved and desalted core peptides were resuspended in 50 μL 1:1 methanol:water. Bacillus subtilis PY79 was used as indicator strain and was spread on a LB-agar surface, on which 5 μL of either or both haloduracins or a solvent control was added. Individually, the haloduracin peptides showed limited activity (FIG. 42F, left two panels), but combined they formed a clear halo of growth inhibition (FIG. 42F, rightmost panel), indicating that both peptides were properly modified and cyclized. The solvent control showed no effect on bacterial growth.


High-Throughput Assay of Diverse Modifying Enzymes

A set of 47 modifying enzymes and their cognate 50 precursor peptides was collated from the literature. The complete list of pathways and enzymes is provided in Table 13 and Table 14, and the subset ultimately found to be active in this Example is provided in Table 15. The selected modifying enzymes are representative of 13 bacterial RiPP classes from diverse genera and catalyze 22 different chemical transformations, including glycosylation, radical carbon-carbon bond focpation and cysteine heterocyclization. The precursor peptide and modifying enzyme genes were codon optimized for E. coli and synthesized, or amplified when the source DNA was available, and cloned into the two-plasmid system. The precursor peptides were tagged with RSTN, except for macrocyclization of lasso peptides, which were fused to RSTC. The plasmids containing the modifying enzymes and precursor peptides were co-transformed into E. coli NEB Express.









TABLE 13







Modification enzymes












Cluster





RiPP Class
Name
Molecule Name(s)
Producing organism
Biological Activity





Lasso-peptide
Las
lassomycin

Lentzea kentuckyensis

Antibiotic



Cap
capistruin

Burkholderia thailandensis E264

Antibiotic



Albsa
albusnodin

Streptomyces albus

Unknown



Atx
astexin 1-3

Asticcacaulis excentricus

Unknown



Cln
caulonodin I-VII

Caulobacter sp. K31

Unknown



Cseg
caulosegnins I-III

Caulobacter segnis

Unknown



Pade
Paeninodin

Paenibacillus dendritiformis C454

Unknown



Thco
unnamed

Thermobacillus composti KWC4

Unknown



Papo
unnamed

Paenibacillus polymyxa CR1

Unknown



Stsp
unnamed

Streptomyces sp. Amel2xC10

Unknown


Glycocin
Lcn
listeriocytocin

Listeria monocytogenes SLCC2540

Unknown



Pal
pallidocin

Aeribacillus pallidus 8

Antibiotic


Microcin C
Bam
unnamed

Bacillus amyloliquefaciens DSM7

Antibiotic


ComX
Com
ComX

Bacillus subtilus

quorum sensing


Pantocin
Paa
pantocin

Pantoea agglomerans

Antibiotic


Sulfa-tyrotide
Rax
RaxX

Xanthomonas oryzae

Plant signaling


Splice-otide
Plp
unnamed

Pleurocapsa sp. PCC7319

Unknown



Pcp
unnamed

Pleurocapsa sp. PCC7327

Unknown


Lanthi-peptide
Crn
carnolysin A1′

Carnobacterium maltaromaticum C2

Antibiotic




carnolysin A2′



Sgb
unnamed

S. globisporus subsp. globisporus

Unknown





NRRL B2293



Bsj
bicereucins

Bacillus cereus SJ1

Antibiotic



Ltn
lacticin S

Lactococcus lactis

Antibiotic




lacticin 3147



Proc
prochlorosins

Prochlorococcus MIT9313

Unknown



Mcb
microcin B17

Escherichia coli

Antibiotic



Mib
micro-bisporicin

Microbispora corallina

Antibiotic



Cin
cinnamycin

Streptomyces cinnamoneus

Antibiotic






cinnamoneus DSM 40005




Hal
haloduracin A1

Bacillus halodurans C-125

Antibiotic




haloduracin A2



Epi
epidermin

Staphylococcus epidermidis

Antibiotic


Micro-viridin
AMdn
unnamed

Anabaena sp. PCC7120

Unknown



Psn
plesiocin

Plesiocystis pacifica

protease inhibitor



Mdn
microviridin L

Microcystis aeruginosa NIES843

protease inhibitor



Tgn
unnamed

Bacillus thuringiensis serovar

Unknown





huazhongensis BGSC 4BD


Cyano-bactin
Tru
trunkamide

Prochloron spp.

Unknown




patellins



Lyn
unnamed

Prochloron spp.

Unknown



Kgp
kawaguchi-peptin

Microcystis aeruginosa NIES-88

Unknown


Thio-peptide
Pbt
GE2270

Planobispora rosea

Antibiotic


Sacti-peptide
Alb/Sbo
subtilosin A

Bacillus subtilis subsp. spizizenii

Antibiotic



Pap
freyrasin

Paenibacillus polymyxa ATCC 842

Antibiotic
















TABLE 14







Enzyme-mediated modifications










Peptide Type
Enzyme Type
Mass Shifta
Enzyme Name





Lassopeptide
Amino-
−Leader (leader
LasBCD, CapBC, AlbsBC,



peptidase + cyclase
cleavage) −18 Da
AtxBC, Cln1BC, Cln2BC,




(cyclization)
Cln3BC, CsegBC



Acetyl-transferase
+42 Da (acetylation)
AlbsT



Kinase
+80 Da (phosphorylation)
PadeK, ThcoK, PapoK



O-methyl-transferase
+14 Da (methylation)
LasF, StspM


Glycocin
Glycosyl-transferase
+162.14 Da (glycosylation)
LcnG, PalS


Microcin
cytidylyl-transferase
+305.18 Da (cytidylation)
BamB


ComX
Prenyl transferase
+204.4 Da (prenylation)
ComQ


Pantocin
Claisen
−80 Da (Claisen condensation and
PaaA




decarboxylation)


Sulfatyrotide
Sulfo-transferase
+80 Da (sulfation)
RaxST


Spliceotide
rSAM tyrosinase
−135 Da (tyramine excision)
PlpXY, PcpXY


Lanthipeptide
LanM: Dehydratase +
−18 Da (dehydration)
CmM, SgbL, BsjM, LtnM1,



thioether cyclase

LtnM2, ProcM, HalM1, HalM2



TOMM
−18 Da (dehydration)
McbCD



halogenase
+34.5 Da (chlorination)
MibHS



P450
+16 Da (hydroxylation)
MibO, CinX



De-carboxylase
−44 Da (decarboxylation)
MibD, EpiD


Microviridin
Lactone cyclase
−18 Da (dehydration)
AMdnC, PsnB, MdnC, TgnB


Cyanobactin
TOMM
−18 Da (dehydration)
TruD, LynD



Prenyl transferase
+136.2 Da (prenylation)
KgpF


Thiopeptide
P450
+16 Da (hydroxylation)
PbtO



N-methyl-transferase
+14 Da (methylation)
PbtM1


Sactipeptide
rSAM cyclase
−2 Da (dehydrogenation)
AlbA


SCIFF/
rSAM cyclase
−2 Da (dehydrogenation)
PapB


Ranthipeptide






aMass shift listed is for a single modification. Enzymes can multiply-modify their peptide substrate, resulting in a total mass shift that is multiplied by the integer number of modifications performed.












The cultures were grown following the high-throughput protocol in 96-well plates. Both TB and LB media have been used previously to functionally express certain RiPPs in E. coli. The choice of media can impact the function of an enzyme; for example, radical S-adenosyl-L-methionine (rSAM) enzymes are more active in TB than LB, the latter requiring a reduction in shake speed and/or increased iron-sulfur cluster biosynthesis [22, 60, 61]. For applications requiring the high-throughput mining or the artificial combination of RiPP enzymes (retrosynthesis), it is desirable to have a single set of culture conditions. To this end, the ability for the enzymes to modify their precursor peptides was evaluated following the same culture conditions either in LB or TB (Table 15 and FIG. 43). All of the enzymes and precursor peptides were expressed in 1 mL of media in deep-well plates with shaking. Induction by 1 mM IPTG and 200 μM cumate was performed for 20 hours at 30° C., after which the modified peptide was purified and desalted. In all cases, the modification could be observed by LC-MS without cleaving RSTN. In total, 24/47 (51%) of the enzymes tested were found to be active against at least one peptide in one of the medias tested. The % modified values shown in Table 14 were calculated from the extracted compound chromatograms (ECCs) based on the expected charge state m/z's for unmodified, partially modified (if relevant) and modified peptide molar masses. More enzymes (24) had activity in TB than LB (20) and, on average, the % modified was higher. As expected, rSAM enzymes (AlbA, PapB, PlpXY) were found to be more active in TB and several only had activity in this media. Similarly, RaxST is a sulfur-requiring enzyme that was found to be more active in TB.


The 25 modified peptides shown in Table 14 showed the exact mass change that was expected to result from the modification shown. However, some modifications could occur at different positions than the wild-type modification, leading to a different peptide with the same mass. In instances in which multiple modification products are possible, the addition of an RST could change where the modification occurs. To test for this outcome, several modifications were selected from different classes for evaluation by LC-MS/MS. The following were selected for structural annotation: PsnA2 macrolactonization by PsnB, and PapA sactionine macrocyclization by PapB. The precursor peptides were modified to contain a TEV cleavage site between the leader and core peptides. The modifying enzymes and precursor peptides were expressed following the high-throughput protocol, the RST and leader peptide removed using TEV protease, and the modified core analyzed with LC-MS/MS. Fragmentation of PsnA2 was observed between the core repeats, with each core repeat fragment mass corresponding to two lactone macrocyclizations per repeat, in agreement with previously published results[19]. Within each core repeat, MS/MS was not able to validate the cyclization topology within each core, which was previously determined by analyzing partially hydrolyzed modified peptide. Without using high collision energies, fragmentation products of PapA were only observed outside of predicted C-D ring structures, in agreement with published MS/MS spectra[61].


Of the enzymes tested, 23 of the 47 did not correctly modify a peptide when co-expressed in E. coli. Patterns based on the phylogeny from which the pathway was sourced were sought, noting that the sources spanned cyanobacteria, actinobacteria, proteobacteria, and firmicutes (FIG. 58). Each of these phyla provided functional examples. The least successful phylum, Actinobacteria, yielded 2/7 functional pathways, but this was not too different from the 5/9 success rate of Proteobacteria, of which E. coli is a member. Therefore, it was determined that there is no relationship between similarity to E. coli and the likelihood of success. Enzymes categorized according to most modification chemical transformation types had at least one enzyme that was functional (FIG. 59), but both prenyl transferases (ComQ and KgpF) and all three P450 oxidases (MibO, CinX, and PbtO) were not functional. For other non-functional chemical transformation types, only one example was tested (acetyl-transferase: AlbsT, halogenase: MibHS, and N-methyl transferase: PbtM1).


DISCUSSION

While the number of characterized RiPP enzymes is growing rapidly in the literature, the conditions under which each enzyme is characterized vary across studies. This poses a challenge for high-throughput screening efforts if the conditions have to be re-optimized for each pathway. This Example presents a side-by-side survey of recombinant RiPP enzymes in E. coli, using the same growth and induction methods. Further, this Example provides protocols for every step to be performed in 96-well plate format under conditions that are consistent with high-throughput screening platforms [2, 70-72]. The RSTs address the problem of precursor peptide stability, for which degradation and solubility are the dominant causes of unobservable product. Their use increases the probability that a pathway will be successfully expressed in a new host; in other words, they increase the “hit rate” of screening efforts. The RSTs do not interfere with the action of modifying enzymes, facilitate high-throughput purification and do not need to be removed prior to LC-MS analysis of modifications. Software was developed to rapidly analyze LC-MS data. Collectively, this presents a suite of tools that enable the high-throughput screening of RiPP pathways mined from sequence databases [13, 73, 74]. In this manuscript, the action of only a single enzyme at a time was investigated. To mine complete RiPP-encoding gene clusters, additional enzyme genes can either be assembled as operons or placed under the control of different inducible promoters (e.g., E. coli Marionette as described in the preceding Examples).


The fraction of enzymes found to be functional in E. coli under common conditions was surprisingly high, especially considering the diversity in the source genera and chemistries. The success rate was much higher than the successful transfer of other natural products genes, such as non-ribosomal peptide synthases, which also produce peptidic products. These results imply that RiPP enzymes can be combined from different sources to create synthetic pathways from which all the enzymes can be functionally expressed. Indeed, several examples have been published demonstrating the artificial combination of RiPP enzymes from different source species and pathways to make products not observed in nature [30, 75, 76]. Knowing that roughly half of RiPP enzymes are functionally compatible with E. coli dramatically expands the potential peptide chemical space that can be explored through the artificial mixing-and-matching of these enzymes. Fully enabling this requires a better understanding of the rules for designing precursor peptides that can be acted on by multiple modifying enzymes, such as the rules provided herein and in the preceding Examples. Collectively, these tools for the mining and de novo design of RiPPs enable the exploration of the vast universe of modified peptides for novel antibiotics, intercellular communication channels, and signaling molecules that influence animal and plant physiology.


Materials and Methods

Strains, plasmids, media, and chemicals. E. coli NEB 10-beta (C3019I, New England BioLabs, Ipswich, Mass., USA) was used for all routine cloning. E. coli BL21 (C2530H, New England BioLabs, Ipswich, Mass., USA) was used to characterize RSTs and linker variants in low-throughput (flask) cultures. E. coli NEB Express (C2523I, New England BioLabs, Ipswich, Mass., USA) was used to express all other experiments. All plasmids containing RST-fused purcursor peptide genes use a pSC101 origin variant (var 2) with ampicillin resistance[77]. All plasmids carrying modifying enzyme genes contain p15A origins of replication and kanamycin resistance. LB-Miller media (B244620, BD, Franklin Lakes, N.J., USA) or TB media (T0311, Teknova, Hollister, Calif., USA) supplemented with 0.4% glycerol (BDH1172-4LP, VWR, OH, USA) were used for peptide expression and modification. 2xYT liquid media (B244020, BD, Franklin Lakes, N.J., USA) and 2xYT+2% agar (B214010, BD, Franklin Lakes, N.J., USA) plates were used for routine cloning and strain maintenance. SOB liquid media (S0210, Teknova, Hollister, Calif., USA) was used for making competent cells. SOC liquid media (B9020S, New England BioLabs, Iwsich, Mass., USA) was used for outgrowth. Cells were induced with the following chemicals: cumate (cuminic acid) ≥98% purity from Millipore Sigma (268402, Millipore Sigma, Saint Louis, Mo., USA) added as 1000× stock (200 mM) in EtOH or DMSO; isopropyl β-D-1-thiogalactopyranoside (IPTG) ≥99% purity (I2481C, Gold Biotechnology, Saint Louis, Mo., USA) added as 1000× stock (1 M) in water or DMSO; 3OC6-AHL from Millipore Sigma (K3007, Millipore Sigma, Saint Louis, Mo., USA) added as a 1000× stock (10 mM) in DMF. Cells were selected with the following antibiotics: 50 μg/ml kanamycin (K-120-10, Gold Biotechnology, Saint Louis, Mo., USA); 100 μg/ml carbenicillin (C-103-5, Gold Biotechnology, Saint Louis, Mo., USA); 30 μg/ml chloramphenicol. Liquid chromatography was performed with Optima Acetonitrile (A996-4, Thermo Fisher Scientific, MA, USA) and water (Milli-Q Advantage A10, Millipore Sigma, Saint Louis, Mo., USA) supplemented with LC-MS Grade Formic Acid (85178, Thermo Fisher Scientific). DNA oligos and gblocks were ordered from Integrated DNA Technologies (San Francisco, Calif., USA).


Gene design. A list of plasmids and corresponding plasmid maps are provided in Table 16. Amino acid sequences of all modifying enzymes and peptides are provided in Table 17. Sequences of genetic parts and full plasmids are provided in Table 18 and Table 19.









TABLE 16







Plasmids used in this Example












Name
Origin
Marker
Backbone
Gene
Description





pEG1128
p15A
Kan
bEG_S7
truD
pLux modifying enzyme expression plasmid


pEG2192
pSC101 var2
Amp
bEG_S5
papoA
RSTN peptide expression plasmid


pEG2194
pSC101 var2
Amp
bEG_S5
bamA
RSTN peptide expression plasmid


pEG2195
pSC101 var2
Amp
bEG_S5
epiA
RSTN peptide expression plasmid


pEG2199
pSC101 var2
Amp
bEG_S5
halA1
RSTN peptide expression plasmid


pEG2200
pSC101 var2
Amp
bEG_S5
halA2
RSTN peptide expression plasmid


pEG2312
pSC101 var2
Amp
bEG_S5
papA_tev
RSTN peptide expression plasmid


pEG2575
pSC101 var2
Amp
bEG_S5
psnA2_tev
RSTN peptide expression plasmid


pEG3017
pSC101 var2
Cm
bEG_S1
truE*
MBP-tag peptide expression plasmid


pEG3045
pSC101 var2
Amp
bEG_S2
mdnA
HIS-tag peptide expression plasmid


pEG3046
pSC101 var2
Amp
bEG_S2
bmbC
HIS-tag peptide expression plasmid


pEG3047
pSC101 var2
Amp
bEG_S2
strA
HIS-tag peptide expression plasmid


pEG3048
pSC101 var2
Amp
bEG_S2
pqqA
HIS-tag peptide expression plasmid


pEG3049
pSC101 var2
Amp
bEG_S2
sboA
HIS-tag peptide expression plasmid


pEG3051
pSC101 var2
Amp
bEG_S2
tfxA
HIS-tag peptide expression plasmid


pEG3052
pSC101 var2
Amp
bEG_S2
procA1.7
HIS-tag peptide expression plasmid


pEG3053
pSC101 var2
Amp
bEG_S2
tbtA
HIS-tag peptide expression plasmid


pEG3055
pSC101 var2
Amp
bEG_S2
pgm2
HIS-tag peptide expression plasmid


pEG3057
pSC101 var2
Amp
bEG_S3
truE*
RSTN* peptide expression plasmid


pEG3058
pSC101 var2
Amp
bEG_S2
mdnA
RSTN* peptide expression plasmid


pEG3059
pSC101 var2
Amp
bEG_S2
sboA
RSTN* peptide expression plasmid


pEG3060
pSC101 var2
Amp
bEG_S2
pqqA
RSTN* peptide expression plasmid


pEG3061
pSC101 var2
Amp
bEG_S2
strA
RSTN* peptide expression plasmid


pEG3062
pSC101 var2
Amp
bEG_S2
bmbC
RSTN* peptide expression plasmid


pEG3063
pSC101 var2
Amp
bEG_S2
tfxA
RSTN* peptide expression plasmid


pEG3064
pSC101 var2
Amp
bEG_S2
procA1.7
RSTN* peptide expression plasmid


pEG3065
pSC101 var2
Amp
bEG_S2
tbtA
RSTN* peptide expression plasmid


pEG3067
pSC101 var2
Amp
bEG_S2
pgm2
RSTN* peptide expression plasmid


pEG3121
pSC101 var2
Amp
bEG_S4
mdnA*
RSTN peptide expression plasmid


pEG3128
pSC101 var2
Amp
bEG_S4
procA*
RSTN peptide expression plasmid


pEG3132
pSC101 var2
Amp
bEG_S4
paaP
RSTN peptide expression plasmid


pEG3157
pSC101 var2
Amp
bEG_S5
mibA
RSTN peptide expression plasmid


pEG3161
pSC101 var2
Amp
bEG_S5
plpA1
RSTN peptide expression plasmid


pEG3162
pSC101 var2
Amp
bEG_S5
plpA2
RSTN peptide expression plasmid


pEG3165
pSC101 var2
Amp
bEG_S5
pbtA
RSTN peptide expression plasmid


pEG3172
pSC101 var2
Amp
bEG_S5
ltnA1
RSTN peptide expression plasmid


pEG3173
pSC101 var2
Amp
bEG_S5
ltnA2
RSTN peptide expression plasmid


pEG3174
pSC101 var2
Amp
bEG_S5
crnA1
RSTN peptide expression plasmid


pEG3175
pSC101 var2
Amp
bEG_S5
crnA2
RSTN peptide expression plasmid


pEG3176
pSC101 var2
Amp
bEG_S5
bsjA2
RSTN peptide expression plasmid


pEG3177
pSC101 var2
Amp
bEG_S5
bsjA3
RSTN peptide expression plasmid


pEG3178
pSC101 var2
Amp
bEG_S5
cinA
RSTN peptide expression plasmid


pEG3180
pSC101 var2
Amp
bEG_S5
lasA
RSTN peptide expression plasmid


pEG3181
pSC101 var2
Amp
bEG_S5
albsA
RSTN peptide expression plasmid


pEG3182
pSC101 var2
Amp
bEG_S5
mcbA
RSTN peptide expression plasmid


pEG3194
pSC101 var2
Amp
bEG_S5
psnA2
RSTN peptide expression plasmid


pEG3197
pSC101 var2
Amp
bEG_S5
aMdnA
RSTN peptide expression plasmid


pEG3212
pSC101 var2
Amp
bEG_S6
capA
RSTC peptide expression plasmid


pEG3213
pSC101 var2
Amp
bEG_S6
lasA
RSTC peptide expression plasmid


pEG3214
pSC101 var2
Amp
bEG_S6
albsA
RSTC peptide expression plasmid


pEG3215
pSC101 var2
Amp
bEG_S6
atxA1
RSTC peptide expression plasmid


pEG3248
pSC101 var2
Amp
bEG_S4
sboA
RSTN peptide expression plasmid


pEG3283
pSC101 var2
Amp
bEG_S5
papA
RSTN peptide expression plasmid


pEG3286
pSC101 var2
Amp
bEG_S5
pcpA
RSTN peptide expression plasmid


pEG3553
pSC101 var2
Amp
bEG_S6
cln1A1
RSTC peptide expression plasmid


pEG3554
pSC101 var2
Amp
bEG_S6
cln1A2
RSTC peptide expression plasmid


pEG3555
pSC101 var2
Amp
bEG_S6
cln2A1
RSTC peptide expression plasmid


pEG3556
pSC101 var2
Amp
bEG_S6
cln2A2
RSTC peptide expression plasmid


pEG3557
pSC101 var2
Amp
bEG_S6
cln3A1
RSTC peptide expression plasmid


pEG3558
pSC101 var2
Amp
bEG_S6
cln3A2
RSTC peptide expression plasmid


pEG3559
pSC101 var2
Amp
bEG_S6
cln3A3
RSTC peptide expression plasmid


pEG3560
pSC101 var2
Amp
bEG_S6
csegA1
RSTC peptide expression plasmid


pEG3561
pSC101 var2
Amp
bEG_S6
csegA2
RSTC peptide expression plasmid


pEG3562
pSC101 var2
Amp
bEG_S6
csegA3
RSTC peptide expression plasmid


pEG3563
pSC101 var2
Amp
bEG_S5
padeA
RSTN peptide expression plasmid


pEG3564
pSC101 var2
Amp
bEG_S5
thcoA
RSTN peptide expression plasmid


pEG3565
pSC101 var2
Amp
bEG_S5
stspA
RSTN peptide expression plasmid


pEG3567
pSC101 var2
Amp
bEG_S5
lcnA
RSTN peptide expression plasmid


pEG3568
pSC101 var2
Amp
bEG_S5
pal A
RSTN peptide expression plasmid


pEG3570
pSC101 var2
Amp
bEG_S5
raxX
RSTN peptide expression plasmid


pEG3571
pSC101 var2
Amp
bEG_S5
comX
RSTN peptide expression plasmid


pEG3572
pSC101 var2
Amp
bEG_S5
kgpE
RSTN peptide expression plasmid


pEG3574
pSC101 var2
Amp
bEG_S5
tgnA*
RSTN peptide expression plasmid


pEG3871
pSC101 var2
Amp
bEG_S5
sgbA
RSTN peptide expression plasmid


pEG3905
pSC101 var2
Amp
bEG_S5
truE
RSTN peptide expression plasmid


pEG7034
p15A
Kan
bEG_S9
truD
pCym modifying enzyme expression plasmid


pEG7035
p15A
Kan
bEG_S9
alba
pCym modifying enzyme expression plasmid


pEG7037
p15A
Kan
bEG_S9
mdnC
pCym modifying enzyme expression plasmid


pEG7043
p15A
Kan
bEG_S9
procM
pCym modifying enzyme expression plasmid


pEG7047
p15A
Kan
bEG_S9
mibHS
pCym modifying enzyme expression plasmid


pEG7048
p15A
Kan
bEG_S9
mibD
pCym modifying enzyme expression plasmid


pEG7056
p15A
Kan
bEG_S9
plpXY
pCym modifying enzyme expression plasmid


pEG7058
p15A
Kan
bEG_S9
pbtO
pCym modifying enzyme expression plasmid


pEG7059
p15A
Kan
bEG_S9
pbtM1
pCym modifying enzyme expression plasmid


pEG7060
p15A
Kan
bEG_S9
paaA
pCym modifying enzyme expression plasmid


pEG7066
p15A
Kan
bEG_S9
cinX
pCym modifying enzyme expression plasmid


pEG7067
p15A
Kan
bEG_S9
capBC
pCym modifying enzyme expression plasmid


pEG7068
p15A
Kan
bEG_S9
lasBCD
pCym modifying enzyme expression plasmid


pEG7069
p15A
Kan
bEG_S9
lasF
pCym modifying enzyme expression plasmid


pEG7070
p15A
Kan
bEG_S9
albsBC
pCym modifying enzyme expression plasmid


pEG7071
p15A
Kan
bEG_S9
albsT
pCym modifying enzyme expression plasmid


pEG7073
p15A
Kan
bEG_S9
mcbCD
pCym modifying enzyme expression plasmid


pEG7074
p15A
Kan
bEG_S9
mibO
pCym modifying enzyme expression plasmid


pEG7076
p15A
Kan
bEG_S9
ltnM1
pCym modifying enzyme expression plasmid


pEG7077
p15A
Kan
bEG_S9
ltnM2
pCym modifying enzyme expression plasmid


pEG7078
p15A
Kan
bEG_S9
crnM
pCym modifying enzyme expression plasmid


pEG7079
p15A
Kan
bEG_S9
bsjM
pCym modifying enzyme expression plasmid


pEG7127
p15A
Kan
bEG_S9
psnB
pCym modifying enzyme expression plasmid


pEG7130
p15A
Kan
bEG_S9
amdnC
pCym modifying enzyme expression plasmid


pEG7132
p15A
Kan
bEG_S9
atxBC
pCym modifying enzyme expression plasmid


pEG7133
p15A
Kan
bEG_S9
cln1BC
pCym modifying enzyme expression plasmid


pEG7134
p15A
Kan
bEG_S9
cln2BC
pCym modifying enzyme expression plasmid


pEG7135
p15A
Kan
bEG_S9
cln3BC
pCym modifying enzyme expression plasmid


pEG7136
p15A
Kan
bEG_S9
csegBC
pCym modifying enzyme expression plasmid


pEG7137
p15A
Kan
bEG_S9
padeK
pCym modifying enzyme expression plasmid


pEG7138
p15A
Kan
bEG_S9
thcoK
pCym modifying enzyme expression plasmid


pEG7139
p15A
Kan
bEG_S9
stspM
pCym modifying enzyme expression plasmid


pEG7141
p15A
Kan
bEG_S9
lcnG
pCym modifying enzyme expression plasmid


pEG7142
p15A
Kan
bEG_S9
palS
pCym modifying enzyme expression plasmid


pEG7143
p15A
Kan
bEG_S9
sgbL
pCym modifying enzyme expression plasmid


pEG7144
p15A
Kan
bEG_S9
raxST
pCym modifying enzyme expression plasmid


pEG7145
p15A
Kan
bEG_S9
comQ
pCym modifying enzyme expression plasmid


pEG7146
p15A
Kan
bEG_S9
kgpF
pCym modifying enzyme expression plasmid


pEG7147
p15A
Kan
bEG_S9
tgnB
pCym modifying enzyme expression plasmid


pEG7149
p15A
Kan
bEG_S9
papB
pCym modifying enzyme expression plasmid


pEG7152
p15A
Kan
bEG_S9
pcpXY
pCym modifying enzyme expression plasmid


pEG7160
p15A
Kan
bEG_S9
lynD
pCym modifying enzyme expression plasmid


pEG7166
p15A
Kan
bEG_S9
papoK
pCym modifying enzyme expression plasmid


pEG7169
p15A
Kan
bEG_S9
epiD
pCym modifying enzyme expression plasmid


pEG7171
p15A
Kan
bEG_S9
bamB
pCym modifying enzyme expression plasmid


pEG7172
p15A
Kan
bEG_S8
halM1
pCym modifying enzyme expression plasmid


pEG7173
p15A
Kan
bEG_S8
halM2
pCym modifying enzyme expression plasmid









Peptide expression/modification from flasks and purification. Plasmids were transformed into E. coli BL21, struck out on 2xYT agar with carbenicillin (or chloramphenicol for pEG3017) and kanamycin (if co-transforming modifying enzyme) and incubated (30° C., overnight). Individual colonies were used to inoculate 3 mL of LB media in a culture tube (352059, Corning, N.Y., USA) and incubated overnight (30° C., 250 r.p.m.) in an Innova44 (Eppendorf, N.Y., USA). Aliquots (500 l) were taken from the overnight cultures and subcultured into 50 mL of LB media in a 250 mL Erlenmeyer flask. After 3 hours incubation (Innova44, 30° C., 250 r.p.m.), IPTG and 3OC6-AHL (if inducing modifying enzyme) was added to final concentrations of 1 mM and 10 μM and cultures were incubated for 20 hours (Innova44, 18° C., 250 r.p.m.) (note: IPTG was not added for pEG3017, where the MBP-tagged peptide is constitutively expressed). The 50 mL cultures were transferred to a falcon tube (352070, Corning, N.Y., USA), centrifuged (4,500 g, 4° C., 20 min) in a Sorvall Legend XFR Centrifuge (Thermo Fisher Scientific, MA, USA), pellets were resuspended in 600 μl lysis buffer (5 M guanidinium hydrochloride, 300 mM NaCl, 50 mM sodium phosphate, pH 7.5), and freeze-thawed twice (frozen in −80° C. freezer; thawed in innova44 incubator at 30° C., 250 r.p.m). Cell lysates were centrifuged (Eppendorf 5424, 21,130 g, room temperature, 15 min) in an Eppendorf 5424 Centrifuge (Eppendorf, N.Y., USA) and the peptides affinity purified using His SpinTrap TALON columns (29-0005-93, GE Life Sciences (now Cytiva), Marlborough, Mass., USA), following manufacturer instructions, using 600 μL lysis buffer twice for column equilibration, loading 600 □L clarified lysate, two washes with 600 μL wash buffer (300 mM NaCl, 50 mM sodium phosphate, 5 mM imidazole, pH 7.5), and 200 μL elution buffer (300 mM NaCl, 50 mM sodium phosphate, 200 mM imidazole, pH 7.5) for elution. Purifications used an Eppendorf 5424 centrifuge.


Calculation of peptide molar masses. For large peptides/proteins, mass was calculated as described for ESIprot79: five consecutively charged m/z's (m1, m2, m3, m4, m5) were taken from the spectra and used to calculate the charge states (z1, z2, z3, z4, z5) for each of the peaks. For peaks m1 and m2, which have charge states, z1 and z2, where z2=z1−1 (peak 1 has one proton more than peak 2): z1=(m2−1)/(m2−m1). Charges z1, z2, z3, and z4 were calculated using each of the four pairs of consecutively charged masses (m1 and m2, m2 and m3, m3 and m4, m4 and m5), subtracted by the number of protons the peak has compared to m5, and averaged together and rounded to the nearest integer to calculate the lowest charge (z5). Charges z1-4 are recalculated based on charge z5 (z1=z5+4, z2=z5+3, etc.), uncharged masses are calculated from each of the five m/z's: uncharged mass=zx(observed m/z)−zx.


Peptide expression in 96-well plates. Plasmids were transformed into E. coli NEB Express using 15 μL of competent cells and 1 μL of each plasmid being transformed in a 96-well PCR plate (1402-9596, USA Scientific, FL, USA or 951020401, Eppendorf, N.Y., USA). Transformations were incubated on ice (20-30 min), heat shocked (40° C., 30 sec), and incubated on ice again (5 min). Cells were then transferred to a deep well 96-well plate (1896-2000, USA Scientific, FL, USA) with 100 μL of SOC media. After outgrowth (Multitron Pro, 1 hr, 37° C.) in an Infors HT Multitron Pro (Infors USA, MD, USA), 400 μL LB media was added with appropriate antibiotics (100 μg/ml carbenicillin and 50 μg/ml kanamycin) and incubated (Multitron Pro, 30° C., 900 r.p.m.) until all wells reached stationary phase (cultures were visibly saturated, 12-30 hours). Overnight cultures were diluted 1:100 into 1 mL LB or TB media (with same antibiotics as previous culture) in deep well plates. After a 3 hour incubation (Multitron Pro, 30° C., 900 r.p.m.), appropriate inducer was added (1 mM IPTG or 200 μM cumate) and cultures were incubated for 20 hours (Multitron Pro, 30° C., 900 r.p.m.). The 96-well plates were centrifuged (Legend XFR, 4,500 g, 4° C., 20 min) and media discarded. Pellets were either purified immediately or frozen at −20 C until purification.


Haloduracin production and purification. Haloduracin was produced following the 96-well expression protocol described above, with each sample being produced in two wells of 1 mL TB media to double the amount of product produced. Culture pellets were resuspended in 800 L lysis buffer, freeze-thawed (frozen at −80° C.; thawed in Multitron Pro at 37° C., 900 r.p.m), and centrifuged (Legend XFR, 4,500 g, 4° C., 30 min). Peptides were affinity purified using HIS MultiTrap TALON plates, using 500 μL water and two 500 μL lysis buffer washes for column equilibration (Legend XFR, 500 g, 4° C., 2 min), loading 600 μL of both matching sample's clarified lysates iteratively (load one, then centrifuge, then load the second, then centrifuge) (Legend XFR, 100 g, 4° C., 5 min), washing twice with 500 μL wash buffer, and eluting three times with 200 μL elution buffer to maximize titer. Purification was followed by solid-phase extraction (SPE) using Strata-XL microtiter plates (8E-S043-TGB, Phenomenex, CA, USA). Plates were conditioned with 1 mL methanol wash followed by 1 mL water wash. All 600 μL of TALON eluent was loaded, washed twice with 1 mL water, and then eluted twice with 500 μl 1:1 acetonitrile:water (supplemented with 0.1% formic acid). Plates with eluent were dried down at room temperature in a Savant Speedvac SPD2010 (Thermo Fisher Scientific, MA, USA), samples resuspended in 40 μL TE buffer (10 mM tris, 1 mM EDTA) with 20 μL 2 mg/mL TEV protease, and then incubated (stationary, 30° C., 8 hr). Cut fractions were desalted using a Strata-X SPE plate (8E-S100-TGB, Phenomenex, CA, USA) with same condition/wash/elution/drying steps as above. Dried down samples were resuspended in 50 μL 1:1 methanol:water.


Proteolytic cleavage and removal of SUMO. For purification of haloduracin for antimicrobial assays, TEV protease was purified as described previously 78 [Addgene #8827, concentrated to 2 mg/mL in TEV buffer (25 mM Tris-HCl, pH 8.0, 50 mM NaCl, 1 mM TCEP, 50% glycerol)]. For MS/MS analysis, TEV protease was prepared as a 50 mg/mL solution of 10% (w/w) TEV lyophilizate (Gene and Cell Technologies, CA, USA) in TEV Buffer.


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SEQUENCES USED IN THE EXAMPLES









TABLE 3







Non-limiting example of peptides (e.g., modified peptides)













Peptide
Leader
Core




Name
Sequence
sequence
sequence
Mod
Coding sequence (CDS)





gAMK-
MLKQINVIAGV
MLKQINVIAGV
ACTACEQCSK
L5
ATGCTGAAACAGATCAAC


174
KEPIRAYACTA
KEPIRAY
CDTNEK

GTTATTGCGGGTGTGAAA



CEQCSKCDTNE
(SEQ ID NO: 46)
(SEQ ID NO: 6)

GAGCCGATTCGCGCGTAC



K



GCCTGTACCGCATGTGAG



(SEQ ID NO: 26)



CAATGCAGTAAATGTGAC







ACCAATGAGAAG







(SEQ ID NO: 47)





gAMK-
MLKQINVIAGV
MLKQINVIAGV
ECPADETCMH
L5
ATGCTGAAACAGATAAAC


175
KEPIRAYECPA
KEPIRAY
CESHEM

GTCATTGCAGGCGTCAAG



DETCMHCESH
(SEQ ID NO: 46)
(SEQ ID NO: 7)

GAACCCATTCGCGCGTAT



EM



GAATGTCCGGCCGATGAA



(SEQ ID NO: 27)



ACTTGTATGCATTGCGAAT







CGCATGAGATG







(SEQ ID NO: 48)





gAMK-
MLKQINVIAGV
MLKQINVIAGV
HCIFIESCDVC
L5
ATGCTGAAACAGATCAAC


176
KEPIRAYHCIFI
KEPIRAY
ELNEP

GTGATAGCCGGGGTCAAA



ESCDVCELNEP
(SEQ ID NO: 46)
(SEQ ID NO: 8)

GAGCCCATTCGCGCATAT



(SEQ ID NO: 28)



CACTGCATTTTTATTGAAA







GCTGTGACGTGTGCGAAC







TGAATGAACCG







(SEQ ID NO: 49)





gAMK-
MLKQINVIAGV
MLKQINVIAGV
KCEKREECAD
L5
ATGCTGAAGCAAATCAAC


177
KEPIRAYKCEK
KEPIRAY
CDHLEF

GTTATCGCCGGAGTTAAG



REECADCDHLE
(SEQ ID NO: 46)
(SEQ ID NO: 9)

GAACCTATTCGTGCGTATA



F



AATGTGAAAAACGGGAAG



(SEQ ID NO: 29)



AGTGTGCTGATTGCGATC







ACCTTGAATTT







(SEQ ID NO: 50)





gAMK-
MLKQINVIAGV
MLKQINVIAGV
KCTSKECCIQC
L5
ATGCTGAAACAGATCAAC


178
KEPIRAYKCTS
KEPIRAY
EGSES

GTCATTGCCGGCGTCAAA



KECCIQCEGSE
(SEQ ID NO: 46)
(SEQ ID NO:

GAACCAATCCGTGCTTAC



S

10)

AAGTGTACGTCAAAAGAA



(SEQ ID NO: 30)



TGCTGTATCCAGTGTGAA







GGAAGTGAAAGC







(SEQ ID NO: 51)





gAMK-
MLKQINVIAGV
MLKQINVIAGV
MCVFCEICVM
L5
ATGTTAAAACAAATTAAC


179
KEPIRAYMCVF
KEPIRAY
CDTHEM

GTGATCGCCGGGGTTAAA



CEICVMCDTHE
(SEQ ID NO: 46)
(SEQ ID NO:

GAACCCATCCGTGCGTAT



M

11)

ATGTGTGTATTTTGTGAAA



(SEQ ID NO: 31)



TTTGTGTGATGTGTGACAC







CCATGAAATG







(SEQ ID NO: 52)





gAMK-
MLKQINVIAGV
MLKQINVIAGV
PCGKREPCNT
L5
ATGCTGAAGCAGATAAAT


180
KEPIRAYPCGK
KEPIRAY
CEHFET

GTTATCGCGGGCGTCAAG



REPCNTCEHFE
(SEQ ID NO: 46)
(SEQ ID NO:

GAACCGATCCGTGCCTAT



T

12)

CCGTGTGGTAAACGCGAG



(SEQ ID NO: 32)



CCGTGTAATACCTGCGAA







CATTTCGAAACG







(SEQ ID NO: 53)





gAMK-
MLKQINVIAGV
MLKQINVIAGV
PCTTTEACTA
L5
ATGCTGAAACAGATCAAC


181
KEPIRAYPCTT
KEPIRAY
CDSSDA

GTCATTGCTGGTGTTAAAG



TEACTACDSSD
(SEQ ID NO: 46)
(SEQ ID NO:

AACCGATTCGCGCTTATCC



A

13)

GTGTACCACCACGGAAGC



(SEQ ID NO: 33)



GTGCACAGCCTGCGATTCT







AGTGATGCG







(SEQ ID NO: 54)





gAMK-
MLKQINVIAGV
MLKQINVIAGV
RCRCPENCLS
L5
ATGCTGAAACAGATTAAC


182
KEPIRAYRCRC
KEPIRAY
CEPPER

GTTATCGCGGGCGTCAAA



PENCLSCEPPE
(SEQ ID NO: 46)
(SEQ ID NO:

GAACCCATCAGAGCGTAT



R

14)

CGTTGTCGTTGCCCTGAGA



(SEQ ID NO: 34)



ACTGCCTGTCGTGCGAAC







CGCCGGAGCGT







(SEQ ID NO: 55)





gAMK-
MLKQINVIAGV
MLKQINVIAGV
SCTPDEVCPLC
L5
ATGCTGAAGCAAATCAAT


183
KEPIRAYSCTP
KEPIRAY
EPCEP

GTGATCGCGGGCGTTAAA



DEVCPLCEPCE
(SEQ ID NO: 46)
(SEQ ID NO:

GAGCCGATCCGGGCCTAC



P

15)

TCTTGTACCCCGGATGAA



(SEQ ID NO: 35)



GTATGTCCGCTCTGCGAGC







CATGCGAACCG







(SEQ ID NO: 56)





gAMK-
MLKQINVIAGV
MLKQINVIAGV
TCTMAEKCQI
L5
ATGCTGAAGCAAATTAAC


184
KEPIRAYTCTM
KEPIRAY
CDVSEG

GTGATTGCTGGTGTCAAG



AEKCQICDVSE
(SEQ ID NO: 46)
(SEQ ID NO:

GAACCTATCCGTGCGTAC



G

16)

ACATGTACGATGGCGGAG



(SEQ ID NO: 36)



AAATGCCAAATTTGCGAT







GTGAGCGAAGGG







(SEQ ID NO: 57)





gAMK-
MLKQINVIAGV
MLKQINVIAGV
ACTNPDPCTD
L3
ATGCTCAAACAAATCAAC


185
KAPIRAYACTN
KAPIRAY
EEI

GTGATCGCGGGAGTCAAA



PDPCTDEEI
(SEQ ID NO: 46)
(SEQ ID NO:

GCACCGATCCGCGCCTAC



(SEQ ID NO: 37)

17)

GCTTGCACAAACCCGGAC







CCTTGCACGGATGAAGAA







ATC







(SEQ ID NO: 58)





gAMK-
MLKQINVIAGV
MLKQINVIAGV
PCEVLDNCTN
L3
ATGCTTAAGCAGATAAAC


186
KAPIRAYPCEV
KAPIRAY
PDH

GTGATCGCCGGCGTGAAA



LDNCTNPDH
(SEQ ID NO: 46)
(SEQ ID NO:

GCGCCGATCCGCGCGTAC



(SEQ ID NO: 38)

18)

CCGTGTGAAGTGTTGGAT







AATTGCACAAATCCAGAC







CAT







(SEQ ID NO: 59)





gAMK-
MLKQINVIAGV
MLKQINVIAGV
ACTNPDPCTD
L3
ATGCTGAAGCAAATCAAT


187
KEPIRAYACTN
KEPIRAY
EEI

GTGATTGCCGGGGTAAAA



PDPCTDEEI
(SEQ ID NO: 46)
(SEQ ID NO:

GAACCGATACGCGCGTAC



(SEQ ID NO: 39)

19)

GCCTGTACTAACCCTGATC







CGTGTACCGATGAGGAAA







TC







(SEQ ID NO: 60)





gAMK-
MLKQINVIAGV
MLKQINVIAGV
KCDEGDHCGT
L3
ATGCTGAAACAGATTAAT


188
KEPIRAYKCDE
KEPIRAY
KDL

GTGATTGCCGGAGTTAAG



GDHCGTKDL
(SEQ ID NO: 46)
(SEQ ID NO:

GAACCAATTCGCGCTTAT



(SEQ ID NO: 40)

20)

AAATGCGACGAAGGTGAT







CATTGTGGCACTAAAGAT







CTG







(SEQ ID NO: 61)





gAMK-
MLKQINVIAGV
MLKQINVIAGV
PCEVLDNCTK
L3
ATGCTGAAACAGATTAAT


189
KEPIRAYPCEV
KEPIRAY
PDH

GTGATCGCGGGTGTAAAG



LDNCTKPDH
(SEQ ID NO: 46)
(SEQ ID NO:

GAACCGATCAGAGCGTAT



(SEQ ID NO: 41)

21)

CCATGCGAAGTTTTAGAC







AACTGCACTAAACCCGAC







CAC







(SEQ ID NO: 62)





gAMK-
MLKQINVIAGV
MLKQINVIAGV
PCEVLDNCTN
L3
ATGCTGAAACAAATTAAC


190
KEPIRAYPCEV
KEPIRAY
PDH

GTTATTGCGGGTGTTAAA



LDNCTNPDH
(SEQ ID NO: 46)
(SEQ ID NO:

GAACCGATCCGTGCCTAT



(SEQ ID NO: 42)

22)

CCATGCGAGGTGTTGGAT







AATTGCACCAACCCTGAT







CAT







(SEQ ID NO: 63)





gAMK-
MLKQINVIAGV
MLKQINVIAGV
QCPWHERCD
L3
ATGTTAAAGCAGATCAAT


191
KEPIRAYQCPW
KEPIRAY
QCEP

GTGATCGCAGGGGTGAAA



HERCDQCEP
(SEQ ID NO: 46)
(SEQ ID NO:

GAACCGATACGCGCATAC



(SEQ ID NO: 43)

23)

CAGTGCCCATGGCATGAA







CGTTGTGATCAGTGCGAG







CCG







(SEQ ID NO: 64)





gAMK-
MLKQINVIAGV
MLKQINVIAGV
VCKYGEWCEI
L3
ATGCTGAAGCAGATTAAC


192
KEPIRAYVCKY
KEPIRAY
VEI

GTTATTGCCGGAGTTAAA



GEWCEIVEI
(SEQ ID NO: 46)
(SEQ ID NO:

GAACCCATACGCGCGTAC



(SEQ ID NO: 44)

24)

GTGTGTAAATATGGTGAA







TGGTGTGAGATCGTCGAA







ATC







(SEQ ID NO: 65)





gAMK-
MLKQINVIAGV
MLKQINVIAGV
YCNITERCHS
L3
ATGCTTAAACAAATTAAC


193
KEPIRAYYCNI
KEPIRAY
DEH

GTGATCGCTGGTGTTAAG



TERCHSDEH
(SEQ ID NO: 46)
(SEQ ID NO:

GAACCGATCCGCGCGTAT



(SEQ ID NO: 45)

25)

TATTGCAATATCACCGAA







CGCTGCCATTCGGATGAG







CAT







(SEQ ID NO: 66)









The protein modification enzyme used with the sequences in Table 3 was PapB. The modification (mod) refers to the scaffold for the core peptide and correspond to L3 and L5 in FIG. 3.









TABLE 4







Non-limiting examples of protein modification enzyme sequences








Protein



modification



enzyme
Amino acid sequence





LynD
MQSTPLLQIQPHFHVEVIEPKQVYLLGEQANHALTGQLYCQILPLLNGQYTLEQIVE



KLDGEVPPEYIDYVLERLAEKGYLTEAAPELSSEVAAFWSELGIAPPVAAEALRQPV



TLTPVGNISEVTVAALTTALRDIGISVQTPTEAGSPTALNVVLTDDYLQPELAKINKQ



ALESQQTWLLVKPVGSVLWLGPVFVPGKTGCWDCLAHRLRGNREVEASVLRQKQ



AQQQRNGQSGSVIGCLPTARATLPSTLQTGLQFAATEIAKWIVKYHVNATAPGTVF



FPTLDGKIITLNHSILDLKSHILIKRSQCPTCGDPKILQHRGFEPLKLESRPKQFTSDGG



HRGTTPEQTVQKYQHLISPVTGVVTELVRITDPANPLVHTYRAGHSFGSATSLRGLR



NTLKHKSSGKGKTDSQSKASGLCEAVERYSGIFQGDEPRKRATLAELGDLAIHPEQC



LCFSDGQYANRETLNEQATVAHDWIPQRFDASQAIEWTPVWSLTEQTHKYLPTALC



YYHYPLPPEHRFARGDSNGNAAGNTLEEAILQGFMELVERDGVALWWYNRLRRPA



VDLGSFNEPYFVQLQQFYRENDRDLWVLDLTADLGIPAFAGVSNRKTGSSERLILGF



GAHLDPTIAILRAVTEVNQIGLELDKVPDENLKSDATDWLITEKLADHPYLLPDTTQ



PLKTAQDYPKRWSDDIYTDVMTCVNIAQQAGLETLVIDQTRPDIGLNVVKVTVPG



MRHFWSRFGEGRLYDVPVKLGWLDEPLTEAQMNPTPMPF (SEQ ID NO: 80)





PapB
MANLIQDREDELIHFHPYKLFEVDSKTFFYNVVTNAIFEIDSLIIDILHSKGKNEEHVV



KDLAERYELSQVREAIQNMKEAYIIATDANISDVEKMGILDNSQRVFKLSSLTLFMV



QECNLRCTYCYGEEGEYNQKGKMTSEIARSAVDFLIQQSGEIEQLNITFFGGEPLLNF



PLIQETVQYVHEQSEIHNKKFSFSITTNGTLITPKIKNFFYKHHFAVQTSIDGDEKTHN



FNRFFKGGQGSYDLLLKRTEEMRNDRKIGARGTVTPAELDLSKSFDHLVKLGFRKI



YLSPALYSLSDDHYDTLSKEMVKLVEQFRELLEREDYVTAKKMSNVLGMLSKIHSG



GPRIHFCGAGTNAAAVDVRGNLFPCHRFVGEDECSIGNLFDEDPLSKQYNFIENSTV



RNRTTCSKCWAKNLCGGGCHQENFAENGNVNQPVGKLCKVTKNFINATINLYLQL



TQEQRSILFG (SEQ ID NO: 81)





ProcM
MESPSSWKTSWLAAIAPDEPHKFDRRLEWDELSEENFFAALNSEPASLEEDDPCFEE



ALQDALEALKAAWDLPLLPVDNNLNRPFVDVWWPIRCHSAESLRQSFVSDSAGLA



DEIFDQLADSLLDRLCALGDQVLWEAFNKERTPGTMLLAHLGAAGDGSGPPVREH



YERFIQSHRRNGLAPLLKEFPVLGRLIGTVLSLWFQGSVEMLQRICADRTVLQQCFA



IPCGHHLKTVKQGLSDPHRGGRAVAVLEFADPNSTANSSMHVVYKPKDMAVDAA



YQATLADLNTHSDLSPLRTLAIHNGNGYGYMEHVVHHLCANDKELTNFYFNAGRL



TALLHLLGCTDCHHENLIACGDQLLLIDTETLLEADLPDHISDASSTTAQPKPSSLQK



QFQRSVLRSGLLPQWMFLGESKLAIDISALGMSPPNKPERIALGWLGFNSDGMMPG



RVSQPVEIPTSLPVGIGEVNPFDRFLEDFCDGFSMQSEALIKLRNRWLDVNGVLAHF



AGLPRRIVLRATRVYFTIQRQQLEPTALRSPLAQALKLEQLTRSFLLAESKPLHWPIF



AAEVKQMQHLDIPFFTHLIDADALQLGGLEQELPGFIQTSGLAAAYERLRNLDTDEI



AFQLRLIRGAVEARELHTTPESSPTLPPPATPEALMSSSAETSLEAAKRIAHRLLELAI



RDSQGQVEWLGMDLGADGESFSFGPVGLSLYGGSIGIAHLLQRLQAQQVSLMDAD



AIQTAILQPLVGLVDQPSDDGRRRWWRDQPLGLSGCGGTLLALTLQGEQAMANSL



LAAALPRFIEADQQLDLIGGCAGLIGSLVQLGTESALQLALRAGDHLIAQQNEEGA



WSSSSSQPGLLGFSHGTAGYAAALAHLHAFSADERYRTAAAAALAYERARFNKDA



GNWPDYRSIGRDSDSDEPSFMASWCHGAPGIALGRACLWGTALWDEECTKEIGIGL



QTTAAVSSVSTDHLCCGSLGLMVLLEMLSAGPWPIDNQLRSHCQDVAFQYRLQAL



QRCSAEPIKLRCFGTKEGLLVLPGFFTGLSGMGLALLEDDPSRAVVSQLISAGLWPT



E (SEQ ID NO: 82)





TgnB
MKTILIITNTLDLTVDYIINRYNHTAKFFRLNTDRFFDYDINITNSGTSIRNRKSNLIINI



QEIHSLYYRKITLPNLDGYESKYWTLMQREMMSIVEGIAETAGNFALTRPSVLRKA



DNKIVQMKLAEEIGFILPQSLITNSNQAAASFCNKNNTSIVKPLSTGRILGKNKIGIIQT



NLVETHENIQGLELSPAYFQDYIPKDTEIRLTIVGNKLFGANIKSTNQVDWRKNDAL



LEYKPANIPDKIAKMCLEMMEKLEINFAAFDFIIRNGDYIFLELNANGQWLWLEDIL



KFDISNTIINYLLGEPI (SEQ ID NO: 83)





















NpuDNAE intein C:


GFIASNCW (SEQ ID NO: 67)





NpuDNAE intein N:


CLSYETEILTVEYGLLPIGKIVEKRIECTVYSVDNNGNIYTQPVAQWHDRGEQEVFEYCLEDGSLIRATKD


HKFMTVDGQMLPIDEIFERELDLMRVDNLPNIKIATRKYLGKQNVYDIGVERDHNFALKN (SEQ ID NO:


68)





ECF20_992 C:


LDTRPAPDEQLEASAQSRRMAQALDQLPDRQREAIVLQYYQELSNTEAAALMQISVEALESLLSRARRN


LRSHLAEAPGADLSGRRKP (SEQ ID NO: 69)





ECF20_992 N:


NETDPDLELLKRIGNNDAQAVKEMVTRKLPRLLALASRLLGDADEARDIAQESFLRIWKQAASWRSEQA


RFDTWLHRVALNLCYDRLRRRKEHVPVDSEHACEA (SEQ ID NO: 70)





SARS-CoV-2 RBD:


RFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYA


DSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFER


DISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNL


(SEQID NO: 71)





ACE2a1:


STIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITE (SEQ ID NO: 72)





lbAMK-101 (plasmid encoding lanthipeptide RiPP library N-terminal to sigma-intein):


tgccacctgacgtctaagaaGAATTCGCGGCCGCTTCTAGAGGGAGccaattattgaaggcctccctaacggggggcctttttttgtttctggtc


tcccgcttaacgatcgttggctgacctgtaggatcgtacaggtTTACGcaagaaaatggtttgtTACAGTcgaataaaagctgtcaccggatgtgctttccggt


ctgatgagtccgtgaggacgaaacagcctctacaaataattttgtttaaTCCATCTCTATGGCGGATTTTatgtcatattaccaccatcaccatcatca


cATGTCAGAAGAACAACTCAAGGCATTCATTGCCAAGGTTCAAGCAGACACTTCACTGCAGGAACA


GCTCAAAGTAGAAGGTGCTGATGTTGTTGCTATTGCTAAAGCCTCAGGGTTCGCGATTACCACAGAG


CTGGCGGAGCTTTCTGAGGAGGCTCTGTCTGATGATGAGCTGGAGGGAGTCGCGGGAGGCGCGGCA


TGCNNKNNKNNKNNKNNKWCGATGCCGCCTWCGNNKNNKNNKNNKNNKTGCCGAggaggtAAGggagg


aCCTggaggtCGGggaggtGTTggaggtGGTggaggaATTggaggtGGTTTTATCGCTTCCAACTGCTGGCTGGATAC


CCGTCCGGCACCGGATGAACAGCTGGAAGCAAGCGCACAGAGCCGTCGTATGGCACAGGCACTGGA


TCAGCTGCCGGATCGTCAGCGTGAAGCAATTGTTCTGCAGTATTATCAAGAACTGAGCAATACCGAA


GCAGCAGCACTGATGCAAATTAGCGTTGAAGCCCTGGAAAGCCTGCTGAGCCGTGCACGTCGTAAT


CTGCGTAGCCATCTGGCCGAAGCACCGGGTGCAGATCTGAGCGGTCGTCGCAAACCGtaaaggtgatactttc


agccaaaaaacttaagaccgccggtcttgtccactaccttgcagtaatgcggtggacaggatcggcggttttcttttctcttctcaaAGACCgTCCAATGGC


GGCGCgccatcgaatggcgcaaaacctttcgcggtatggcatgatagcgcccggaagagagtcaattcagggtggtgaatatgaaaaacataaatgccgacga


cacatacagaataattaataaaattaaagcttgtagaagcaataatgatattaatcaatgcttatctgatatgactaaaatggtacattgtgaatattatttactcgcgatcattt


atcctcattctatggttaaatctgatatttcaatcctagataattaccctaaaaaatggaggcaatattatgatgacgctaatttaataaaatatgatcctatagtagattattcta


actccaatcattcaccaattaattggaatatatttgaaaacaatgctgtaaataaaaaatctccaaatgtaattaaagaagcgaaaacatcaggtcttatcactgggtttagtt


tccctattcatacggctaacaatggcttcggaatgcttagttttgcacattcagaaaaagacaactatatagatagtttatttttacatgcgtgtatgaacataccattaattgtt


ccttctctagttgataattatcgaaaaataaatatagcaaataataaatcaaacaacgatttaaccaaaagagaaaaagaatgtttagcgtgggcatgcgaaggaaaaag


ctcttgggatatttcaaaaatattaggttgcagtgagcgtactgtcactttccatttaaccaatgcgcaaatgaaactcaatacaacaaaccgctgccaaagtatttctaaa


gcaattttaacaggagcaattgattgcccatactttaaaaattgataaggatcctaattggtaacgaatcagacaattgacggctcgagggagtagcatagggtttgcag


aatccctgcttcgtccatttgacaggcacattatgcatcgatgataagctgtcaaacatgagcagatcctctacgccggacgcatcgtggccggcatcaccggcgcca


caggtgcggttgctggcgcctatatcgccgacatcaccgatggggaagatcgggctcgccacttcgggctcatgagcaaatattttatctggctcactcaaaggcggt


aatgacagtaagacgggtaagcctgttgatgataccgctgccttactgggtgcattagccagtctgaatgacctgtcacgggataatccgaagtggtcagactggaaa


atcagagggcaggaactgctgaacagcaaaaagtcagatagcaccacatagcagacccgccataaaacgccctgagaagcccgtgacgggcttttcttgtattatg


ggtagtttccttgcatgaatccataaaaggcgcctgtagtgccatttacccccattcactgccagagccgtgagcgcagcgaactgaatgtcacgaaaaagacagcga


ctcaggtgcctgatggtcggagacaaaaggaatattcagcgatttgcccgagcttgcgagggtgctacttaagcctttagggttttaaggtctgttttgtagaggagcaa


acagcgtttgcgacatccttttgtaatactgcggaactgactaaagtagtgagttatacacagggctgggatctattctttttatctttttttattctttctttattctataaattata


accacttgaatataaacaaaaaaaacacacaaaggtctagcggaatttacagagggtctagcagaatttacaagttttccagcaaaggtctagcagaatttacagatac


ccacaactcaaaggaaaaggactagtaattatcattgactagcccatctcaattggtatagtgattaaaatcacctagaccaattgagatgtatgtctgaattagttgttttc


aaagcaaatgaactagcgattagtcgctatgacttaacggagcatgaaaccaagctaattttatgctgtgtggcactactcaaccccacgattgaaaaccctacaagga


aagaacggacggtatcgttcacttataaccaatacgctcagatgatgaacatcagtagggaaaatgcttatggtgtattagctaaagcaaccagagagctgatgacga


gaactgtggaaatcaggaatcctttggttaaaggctttTGGattttccagtggacaaactatgccaagttctcaagcgaaaaattagaattagtttttagtgaagagatat


tgccttatcttttccagttaaaaaaattcataaaatataatctggaacatgttaagtcttttgaaaacaaatactctatgaggatttatgagtggttattaaaagaactaacaca


aaagaaaactcacaaggcaaatatagagattagccttgatgaatttaagttcatgttaatgcttgaaaataactaccatgagtttaaaaggcttaaccaatgggttttgaaa


ccaataagtaaagatttaaacacttacagcaatatgaaattggtggttgataagcgaggccgcccgactgatacgttgattttccaagttgaactagatagacaaatggat


ctcgtaaccgaacttgagaacaaccagataaaaatgaatggtgacaaaataccaacaaccattacatcagattcctacctacAtaacggactaagaaaaacactacac


gatgctttaactgcaaaaattcagctcaccagttttgaggcaaaatttttgagtgacatgcaaagtaagTatgatctcaatggttcgttctcatggctcacgcaaaaacaa


cgaaccacactagagaacatactggctaaatacggaaggatctgaggttcttatggctcttgtatctatcagtgaagcatcaagactaacaaacaaaagtagaacaact


gttcaccgttaCatatcaaagggaaaactgtccatatgcacagatgaaaacggtgtaaaaaagatagatacatcagagcttttacgagtttttggtgcattCaaagctgt


tcaccatgaacagatcgacaatgtaacagatgaacagcatgtaacacctaatagaacaggtgaaaccagtaaaacaaagcaactagaacatgaaattgaacacctga


gacaacttgttacagctcaacagtcacacatagacagcctgaaacaggcgatgctgcttatcgaatcaaagctgccgacaacacgggagccagtgacgcctcccgt


ggggaaaaaatcatggcaattctggaagaaatagCgctttcagccggcaaacCGGctgaagccggatctgcgattctgataacaaactagcaacaccagaacag


cccgtttgcgggcagcaaaacccgtacCGATTATCAAAAAGGATCTTCACCtagatccttttaaattaaaaatgaagttttaaatcaatctaaagt


atatatgagtaaacttggtctgacagttaccaatgcttaatcagtgaggcacctatctcagcgatctgtctatttcgttcatccatagttgcctgactccccgtcgtgtagata


actacgatacgggagggcttaccatctggccccagtgctgcaatgataccgcgagaAccacgctcaccggctccagatttatcagcaataaaccagccagccgga


agggccgagcgcagaagtggtcctgcaactttatccgcctccatccagtctattaattgttgccgggaagctagagtaagtagttcgccagttaatagtttgcgcaacgt


tgttgccattgctacaggcatcgtggtgtcacgctcgtcgtttggtatggcttcattcagctccggttcccaacgatcaaggcgagttacatgatcccccatgttgtgcaaa


aaagcggttagctccttcggtcctccgatcgttgtcagaagtaagttggccgcagtgttatcactcatggttatggcagcactgcataattctcttactgtcatgccatccgt


aagatgcttttctgtgactggtgagtactcaaccaagtcattctgagaatagtgtatgcggcgaccgagttgctcttgcccggcgtcaatacgggataataccgcgccac


atagcagaactttaaaagtgctcatcattggaaaacgttcttcggggcgaaaactctcaaggatcttaccgctgttgagatccagttcgatAtaacccactcgtgcaccc


aactgatcttcagcatcttttactttcaccagcgtttctgggtgagcaaaaacaggaaggcaaaatgccgcaaaaaagggaataagggcgacacggaaatgttgaata


ctcatactcttcctttttcaatattattgaagcatttatcagggttattgtctcatgagcggatacatatttgaatgtatttagaaaaataaacaaataggggttccgcgcacatt


tccccgaaaag (SEQ ID NO: 73)





lbAMK-102 (plasmid encoding microviridin RiPP library N-terminal to sigma-intein):


tgccacctgacgtctaagaaGAATTCGCGGCCGCTTCTAGAGGGAGccaattattgaaggcctccctaacggggggcctttttttgtttctggtc


tcccgcttaacgatcgttggctgacctgtaggatcgtacaggtTTACGcaagaaaatggtttgtTACAGTcgaataaaagctgtcaccggatgtgctttccggt


ctgatgagtccgtgaggacgaaacagcctctacaaataattttgtttaaTCCATCTCTATGGCGGATTTTatgtcatattaccaccatcaccatcatca


catgTATCGACCTTATATTGCCAAGTATGTCGAAGAACAAACTCTGCAGAATTCAACCAACCTGGTAT


ATGACGACATCACGCAGCTGGCGGAGCTTTCTGAGGAGGCTCTGGTGAAAAAAATTAATCTGNNKC


CCVANACTACGNNKNNKACTNNKDYKNTTGAGNNKNNKGACNNKGATGAGNNKNNKNNKCGAggag


gtAAGggaggaCCTggaggtCGGggaggtGTTggaggtGGTggaggaATTggaggtGGTTTTATCGCTTCCAACTGCTGG


CTGGATACCCGTCCGGCACCGGATGAACAGCTGGAAGCAAGCGCACAGAGCCGTCGTATGGCACAG


GCACTGGATCAGCTGCCGGATCGTCAGCGTGAAGCAATTGTTCTGCAGTATTATCAAGAACTGAGCA


ATACCGAAGCAGCAGCACTGATGCAAATTAGCGTTGAAGCCCTGGAAAGCCTGCTGAGCCGTGCAC


GTCGTAATCTGCGTAGCCATCTGGCCGAAGCACCGGGTGCAGATCTGAGCGGTCGTCGCAAACCGtaa


aggtgatactttcagccaaaaaacttaagaccgccggtcttgtccactaccttgcagtaatgcggtggacaggatcggcggttttcttttctcttctcaaAGACCgT


CCAATGGCGGCGCgccatcgaatggcgcaaaacctttcgcggtatggcatgatagcgcccggaagagagtcaattcagggtggtgaatatgaaaaacat


aaatgccgacgacacatacagaataattaataaaattaaagcttgtagaagcaataatgatattaatcaatgcttatctgatatgactaaaatggtacattgtgaatattattt


actcgcgatcatttatcctcattctatggttaaatctgatatttcaatcctagataattaccctaaaaaatggaggcaatattatgatgacgctaatttaataaaatatgatccta


tagtagattattctaactccaatcattcaccaattaattggaatatatttgaaaacaatgctgtaaataaaaaatctccaaatgtaattaaagaagcgaaaacatcaggtctta


tcactgggtttagtttccctattcatacggctaacaatggcttcggaatgcttagttttgcacattcagaaaaagacaactatatagatagtttatttttacatgcgtgtatgaa


cataccattaattgttccttctctagttgataattatcgaaaaataaatatagcaaataataaatcaaacaacgatttaaccaaaagagaaaaagaatgtttagcgtgggcat


gcgaaggaaaaagctcttgggatatttcaaaaatattaggttgcagtgagcgtactgtcactttccatttaaccaatgcgcaaatgaaactcaatacaacaaaccgctgc


caaagtatttctaaagcaattttaacaggagcaattgattgcccatactttaaaaattgataaggatcctaattggtaacgaatcagacaattgacggctcgagggagtag


catagggtttgcagaatccctgcttcgtccatttgacaggcacattatgcatcgatgataagctgtcaaacatgagcagatcctctacgccggacgcatcgtggccggc


atcaccggcgccacaggtgcggttgctggcgcctatatcgccgacatcaccgatggggaagatcgggctcgccacttcgggctcatgagcaaatattttatctggctc


actcaaaggcggtaatgacagtaagacgggtaagcctgttgatgataccgctgccttactgggtgcattagccagtctgaatgacctgtcacgggataatccgaagtg


gtcagactggaaaatcagagggcaggaactgctgaacagcaaaaagtcagatagcaccacatagcagacccgccataaaacgccctgagaagcccgtgacggg


cttttcttgtattatgggtagtttccttgcatgaatccataaaaggcgcctgtagtgccatttacccccattcactgccagagccgtgagcgcagcgaactgaatgtcacga


aaaagacagcgactcaggtgcctgatggtcggagacaaaaggaatattcagcgatttgcccgagcttgcgagggtgctacttaagcctttagggttttaaggtctgtttt


gtagaggagcaaacagcgtttgcgacatccttttgtaatactgcggaactgactaaagtagtgagttatacacagggctgggatctattctttttatctttttttattctttcttta


ttctataaattataaccacttgaatataaacaaaaaaaacacacaaaggtctagcggaatttacagagggtctagcagaatttacaagttttccagcaaaggtctagcaga


atttacagatacccacaactcaaaggaaaaggactagtaattatcattgactagcccatctcaattggtatagtgattaaaatcacctagaccaattgagatgtatgtctga


attagttgttttcaaagcaaatgaactagcgattagtcgctatgacttaacggagcatgaaaccaagctaattttatgctgtgtggcactactcaaccccacgattgaaaac


cctacaaggaaagaacggacggtatcgttcacttataaccaatacgctcagatgatgaacatcagtagggaaaatgcttatggtgtattagctaaagcaaccagagag


ctgatgacgagaactgtggaaatcaggaatcctttggttaaaggctttTGGattttccagtggacaaactatgccaagttctcaagcgaaaaattagaattagtttttagt


gaagagatattgccttatcttttccagttaaaaaaattcataaaatataatctggaacatgttaagtcttttgaaaacaaatactctatgaggatttatgagtggttattaaaag


aactaacacaaaagaaaactcacaaggcaaatatagagattagccttgatgaatttaagttcatgttaatgcttgaaaataactaccatgagtttaaaaggcttaaccaatg


ggttttgaaaccaataagtaaagatttaaacacttacagcaatatgaaattggtggttgataagcgaggccgcccgactgatacgttgattttccaagttgaactagatag


acaaatggatctcgtaaccgaacttgagaacaaccagataaaaatgaatggtgacaaaataccaacaaccattacatcagattcctacctacAtaacggactaagaaa


aacactacacgatgctttaactgcaaaaattcagctcaccagttttgaggcaaaatttttgagtgacatgcaaagtaagTatgatctcaatggttcgttctcatggctcacg


caaaaacaacgaaccacactagagaacatactggctaaatacggaaggatctgaggttcttatggctcttgtatctatcagtgaagcatcaagactaacaaacaaaagt


agaacaactgttcaccgttaCatatcaaagggaaaactgtccatatgcacagatgaaaacggtgtaaaaaagatagatacatcagagcttttacgagtttttggtgcatt


Caaagctgttcaccatgaacagatcgacaatgtaacagatgaacagcatgtaacacctaatagaacaggtgaaaccagtaaaacaaagcaactagaacatgaaattg


aacacctgagacaacttgttacagctcaacagtcacacatagacagcctgaaacaggcgatgctgcttatcgaatcaaagctgccgacaacacgggagccagtgac


gcctcccgtggggaaaaaatcatggcaattctggaagaaatagCgctttcagccggcaaacCGGctgaagccggatctgcgattctgataacaaactagcaacac


cagaacagcccgtttgcgggcagcaaaacccgtacCGATTATCAAAAAGGATCTTCACCtagatccttttaaattaaaaatgaagttttaaatca


atctaaagtatatatgagtaaacttggtctgacagttaccaatgcttaatcagtgaggcacctatctcagcgatctgtctatttcgttcatccatagttgcctgactccccgtc


gtgtagataactacgatacgggagggcttaccatctggccccagtgctgcaatgataccgcgagaAccacgctcaccggctccagatttatcagcaataaaccagc


cagccggaagggccgagcgcagaagtggtcctgcaactttatccgcctccatccagtctattaattgttgccgggaagctagagtaagtagttcgccagttaatagttt


gcgcaacgttgttgccattgctacaggcatcgtggtgtcacgctcgtcgtttggtatggcttcattcagctccggttcccaacgatcaaggcgagttacatgatcccccat


gttgtgcaaaaaagcggttagctccttcggtcctccgatcgttgtcagaagtaagttggccgcagtgttatcactcatggttatggcagcactgcataattctcttactgtc


atgccatccgtaagatgcttttctgtgactggtgagtactcaaccaagtcattctgagaatagtgtatgcggcgaccgagttgctcttgcccggcgtcaatacgggataat


accgcgccacatagcagaactttaaaagtgctcatcattggaaaacgttcttcggggcgaaaactctcaaggatcttaccgctgttgagatccagttcgatAtaaccca


ctcgtgcacccaactgatcttcagcatcttttactttcaccagcgtttctgggtgagcaaaaacaggaaggcaaaatgccgcaaaaaagggaataagggcgacacgg


aaatgttgaatactcatactcttcctttttcaatattattgaagcatttatcagggttattgtctcatgagcggatacatatttgaatgtatttagaaaaataaacaaataggggtt


ccgcgcacatttccccgaaaag (SEQ ID NO: 74)





lbAMK-103 (plasmid encoding ranthipeptide RiPP library v1 N-terminal to sigma-intein):


tgccacctgacgtctaagaaGAATTCGCGGCCGCTTCTAGAGGGAGccaattattgaaggcctccctaacggggggcctttttttgtttctggtc


tcccgcttaacgatcgttggctgacctgtaggatcgtacaggtTTACGcaagaaaatggtttgtTACAGTcgaataaaagctgtcaccggatgtgctttccggt


ctgatgagtccgtgaggacgaaacagcctctacaaataattttgtttaaTCCATCTCTATGGCGGATTTTatgtcatattaccaccatcaccatcatca


cATGTTGAAACAGATCAATGTGATTGCTGGCGTAAAAGAGCCTATTCGCGCCTATNNKTGTNNKNNK


NNKGAWNNKTGCNNKNNKNNKGAWNNKCGAggaggtAAGggaggaCCTggaggtCGGggaggtGTTggaggtGG


TggaggaATTggaggtGGTTTTATCGCTTCCAACTGCTGGCTGGATACCCGTCCGGCACCGGATGAACAGC


TGGAAGCAAGCGCACAGAGCCGTCGTATGGCACAGGCACTGGATCAGCTGCCGGATCGTCAGCGTG


AAGCAATTGTTCTGCAGTATTATCAAGAACTGAGCAATACCGAAGCAGCAGCACTGATGCAAATTA


GCGTTGAAGCCCTGGAAAGCCTGCTGAGCCGTGCACGTCGTAATCTGCGTAGCCATCTGGCCGAAGC


ACCGGGTGCAGATCTGAGCGGTCGTCGCAAACCGtaaaggtgatactttcagccaaaaaacttaagaccgccggtcttgtccactacc


ttgcagtaatgcggtggacaggatcggcggttttcttttctcttctcaaAGACCgTCCAATGGCGGCGCgccatcgaatggcgcaaaacctttcgcgg


tatggcatgatagcgcccggaagagagtcaattcagggtggtgaatatgaaaaacataaatgccgacgacacatacagaataattaataaaattaaagcttgtagaag


caataatgatattaatcaatgcttatctgatatgactaaaatggtacattgtgaatattatttactcgcgatcatttatcctcattctatggttaaatctgatatttcaatcctagata


attaccctaaaaaatggaggcaatattatgatgacgctaatttaataaaatatgatcctatagtagattattctaactccaatcattcaccaattaattggaatatatttgaaaa


caatgctgtaaataaaaaatctccaaatgtaattaaagaagcgaaaacatcaggtcttatcactgggtttagtttccctattcatacggctaacaatggcttcggaatgctta


gttttgcacattcagaaaaagacaactatatagatagtttatttttacatgcgtgtatgaacataccattaattgttccttctctagttgataattatcgaaaaataaatatagcaa


ataataaatcaaacaacgatttaaccaaaagagaaaaagaatgtttagcgtgggcatgcgaaggaaaaagctcttgggatatttcaaaaatattaggttgcagtgagcg


tactgtcactttccatttaaccaatgcgcaaatgaaactcaatacaacaaaccgctgccaaagtatttctaaagcaattttaacaggagcaattgattgcccatactttaaaa


attgataaggatcctaattggtaacgaatcagacaattgacggctcgagggagtagcatagggtttgcagaatccctgcttcgtccatttgacaggcacattatgcatcg


atgataagctgtcaaacatgagcagatcctctacgccggacgcatcgtggccggcatcaccggcgccacaggtgcggttgctggcgcctatatcgccgacatcacc


gatggggaagatcgggctcgccacttcgggctcatgagcaaatattttatctggctcactcaaaggcggtaatgacagtaagacgggtaagcctgttgatgataccgc


tgccttactgggtgcattagccagtctgaatgacctgtcacgggataatccgaagtggtcagactggaaaatcagagggcaggaactgctgaacagcaaaaagtcag


atagcaccacatagcagacccgccataaaacgccctgagaagcccgtgacgggcttttcttgtattatgggtagtttccttgcatgaatccataaaaggcgcctgtagtg


ccatttacccccattcactgccagagccgtgagcgcagcgaactgaatgtcacgaaaaagacagcgactcaggtgcctgatggtcggagacaaaaggaatattcag


cgatttgcccgagcttgcgagggtgctacttaagcctttagggttttaaggtctgttttgtagaggagcaaacagcgtttgcgacatccttttgtaatactgcggaactgac


taaagtagtgagttatacacagggctgggatctattctttttatctttttttattctttctttattctataaattataaccacttgaatataaacaaaaaaaacacacaaaggtctag


cggaatttacagagggtctagcagaatttacaagttttccagcaaaggtctagcagaatttacagatacccacaactcaaaggaaaaggactagtaattatcattgacta


gcccatctcaattggtatagtgattaaaatcacctagaccaattgagatgtatgtctgaattagttgttttcaaagcaaatgaactagcgattagtcgctatgacttaacgga


gcatgaaaccaagctaattttatgctgtgtggcactactcaaccccacgattgaaaaccctacaaggaaagaacggacggtatcgttcacttataaccaatacgctcag


atgatgaacatcagtagggaaaatgcttatggtgtattagctaaagcaaccagagagctgatgacgagaactgtggaaatcaggaatcctttggttaaaggctttTGG


attttccagtggacaaactatgccaagttctcaagcgaaaaattagaattagtttttagtgaagagatattgccttatcttttccagttaaaaaaattcataaaatataatctgg


aacatgttaagtcttttgaaaacaaatactctatgaggatttatgagtggttattaaaagaactaacacaaaagaaaactcacaaggcaaatatagagattagccttgatga


atttaagttcatgttaatgcttgaaaataactaccatgagtttaaaaggcttaaccaatgggttttgaaaccaataagtaaagatttaaacacttacagcaatatgaaattggt


ggttgataagcgaggccgcccgactgatacgttgattttccaagttgaactagatagacaaatggatctcgtaaccgaacttgagaacaaccagataaaaatgaatggt


gacaaaataccaacaaccattacatcagattcctacctacAtaacggactaagaaaaacactacacgatgctttaactgcaaaaattcagctcaccagttttgaggcaa


aatttttgagtgacatgcaaagtaagTatgatctcaatggttcgttctcatggctcacgcaaaaacaacgaaccacactagagaacatactggctaaatacggaaggat


ctgaggttcttatggctcttgtatctatcagtgaagcatcaagactaacaaacaaaagtagaacaactgttcaccgttaCatatcaaagggaaaactgtccatatgcaca


gatgaaaacggtgtaaaaaagatagatacatcagagcttttacgagtttttggtgcattCaaagctgttcaccatgaacagatcgacaatgtaacagatgaacagcatgt


aacacctaatagaacaggtgaaaccagtaaaacaaagcaactagaacatgaaattgaacacctgagacaacttgttacagctcaacagtcacacatagacagcctga


aacaggcgatgctgcttatcgaatcaaagctgccgacaacacgggagccagtgacgcctcccgtggggaaaaaatcatggcaattctggaagaaatagCgctttca


gccggcaaacCGGctgaagccggatctgcgattctgataacaaactagcaacaccagaacagcccgtttgcgggcagcaaaacccgtacCGATTATCA


AAAAGGATCTTCACCtagatccttttaaattaaaaatgaagttttaaatcaatctaaagtatatatgagtaaacttggtctgacagttaccaatgcttaatcagt


gaggcacctatctcagcgatctgtctatttcgttcatccatagttgcctgactccccgtcgtgtagataactacgatacgggagggcttaccatctggccccagtgctgca


atgataccgcgagaAccacgctcaccggctccagatttatcagcaataaaccagccagccggaagggccgagcgcagaagtggtcctgcaactttatccgcctcc


atccagtctattaattgttgccgggaagctagagtaagtagttcgccagttaatagtttgcgcaacgttgttgccattgctacaggcatcgtggtgtcacgctcgtcgtttg


gtatggcttcattcagctccggttcccaacgatcaaggcgagttacatgatcccccatgttgtgcaaaaaagcggttagctccttcggtcctccgatcgttgtcagaagta


agttggccgcagtgttatcactcatggttatggcagcactgcataattctcttactgtcatgccatccgtaagatgcttttctgtgactggtgagtactcaaccaagtcattct


gagaatagtgtatgcggcgaccgagttgctcttgcccggcgtcaatacgggataataccgcgccacatagcagaactttaaaagtgctcatcattggaaaacgttcttc


ggggcgaaaactctcaaggatcttaccgctgttgagatccagttcgatAtaacccactcgtgcacccaactgatcttcagcatcttttactttcaccagcgtttctgggtg


agcaaaaacaggaaggcaaaatgccgcaaaaaagggaataagggcgacacggaaatgttgaatactcatactcttcctttttcaatattattgaagcatttatcagggtt


attgtctcatgagcggatacatatttgaatgtatttagaaaaataaacaaataggggttccgcgcacatttccccgaaaag (SEQ ID NO: 75)





lbAMK-104 (plasmid encoding ranthipeptide RiPP library v2 N-terminal to sigma-intein):


tgccacctgacgtctaagaaGAATTCGCGGCCGCTTCTAGAGGGAGccaattattgaaggcctccctaacggggggcctttttttgtttctggtc


tcccgcttaacgatcgttggctgacctgtaggatcgtacaggtTTACGcaagaaaatggtttgtTACAGTcgaataaaagctgtcaccggatgtgctttccggt


ctgatgagtccgtgaggacgaaacagcctctacaaataattttgtttaaTCCATCTCTATGGCGGATTTTatgtcatattaccaccatcaccatcatca


cATGTTGAAACAGATCAATGTGATTGCTGGCGTAAAAGAGCCTATTCGCGCCTATNNKTGCNNKNNK


TGCGAWNNKNNKGAWNNKNNKCGAggaggtAAGggaggaCCTggaggtCGGggaggtGTTggaggtGGTggaggaAT


TggaggtGGTTTTATCGCTTCCAACTGCTGGCTGGATACCCGTCCGGCACCGGATGAACAGCTGGAAGC


AAGCGCACAGAGCCGTCGTATGGCACAGGCACTGGATCAGCTGCCGGATCGTCAGCGTGAAGCAAT


TGTTCTGCAGTATTATCAAGAACTGAGCAATACCGAAGCAGCAGCACTGATGCAAATTAGCGTTGA


AGCCCTGGAAAGCCTGCTGAGCCGTGCACGTCGTAATCTGCGTAGCCATCTGGCCGAAGCACCGGG


TGCAGATCTGAGCGGTCGTCGCAAACCGtaaaggtgatactttcagccaaaaaacttaagaccgccggtcttgtccactaccttgcagtaat


gcggtggacaggatcggcggttttcttttctcttctcaaAGACCgTCCAATGGCGGCGCgccatcgaatggcgcaaaacctttcgcggtatggcatga


tagcgcccggaagagagtcaattcagggtggtgaatatgaaaaacataaatgccgacgacacatacagaataattaataaaattaaagcttgtagaagcaataatgat


attaatcaatgcttatctgatatgactaaaatggtacattgtgaatattatttactcgcgatcatttatcctcattctatggttaaatctgatatttcaatcctagataattaccctaa


aaaatggaggcaatattatgatgacgctaatttaataaaatatgatcctatagtagattattctaactccaatcattcaccaattaattggaatatatttgaaaacaatgctgta


aataaaaaatctccaaatgtaattaaagaagcgaaaacatcaggtcttatcactgggtttagtttccctattcatacggctaacaatggcttcggaatgcttagttttgcaca


ttcagaaaaagacaactatatagatagtttatttttacatgcgtgtatgaacataccattaattgttccttctctagttgataattatcgaaaaataaatatagcaaataataaat


caaacaacgatttaaccaaaagagaaaaagaatgtttagcgtgggcatgcgaaggaaaaagctcttgggatatttcaaaaatattaggttgcagtgagcgtactgtcac


tttccatttaaccaatgcgcaaatgaaactcaatacaacaaaccgctgccaaagtatttctaaagcaattttaacaggagcaattgattgcccatactttaaaaattgataag


gatcctaattggtaacgaatcagacaattgacggctcgagggagtagcatagggtttgcagaatccctgcttcgtccatttgacaggcacattatgcatcgatgataagc


tgtcaaacatgagcagatcctctacgccggacgcatcgtggccggcatcaccggcgccacaggtgcggttgctggcgcctatatcgccgacatcaccgatgggga


agatcgggctcgccacttcgggctcatgagcaaatattttatctggctcactcaaaggcggtaatgacagtaagacgggtaagcctgttgatgataccgctgccttactg


ggtgcattagccagtctgaatgacctgtcacgggataatccgaagtggtcagactggaaaatcagagggcaggaactgctgaacagcaaaaagtcagatagcacca


catagcagacccgccataaaacgccctgagaagcccgtgacgggcttttcttgtattatgggtagtttccttgcatgaatccataaaaggcgcctgtagtgccatttacc


cccattcactgccagagccgtgagcgcagcgaactgaatgtcacgaaaaagacagcgactcaggtgcctgatggtcggagacaaaaggaatattcagcgatttgcc


cgagcttgcgagggtgctacttaagcctttagggttttaaggtctgttttgtagaggagcaaacagcgtttgcgacatccttttgtaatactgcggaactgactaaagtagt


gagttatacacagggctgggatctattctttttatctttttttattctttctttattctataaattataaccacttgaatataaacaaaaaaaacacacaaaggtctagcggaattta


cagagggtctagcagaatttacaagttttccagcaaaggtctagcagaatttacagatacccacaactcaaaggaaaaggactagtaattatcattgactagcccatctc


aattggtatagtgattaaaatcacctagaccaattgagatgtatgtctgaattagttgttttcaaagcaaatgaactagcgattagtcgctatgacttaacggagcatgaaac


caagctaattttatgctgtgtggcactactcaaccccacgattgaaaaccctacaaggaaagaacggacggtatcgttcacttataaccaatacgctcagatgatgaaca


tcagtagggaaaatgcttatggtgtattagctaaagcaaccagagagctgatgacgagaactgtggaaatcaggaatcctttggttaaaggctttTGGattttccagtg


gacaaactatgccaagttctcaagcgaaaaattagaattagtttttagtgaagagatattgccttatcttttccagttaaaaaaattcataaaatataatctggaacatgttaa


gtcttttgaaaacaaatactctatgaggatttatgagtggttattaaaagaactaacacaaaagaaaactcacaaggcaaatatagagattagccttgatgaatttaagttc


atgttaatgcttgaaaataactaccatgagtttaaaaggcttaaccaatgggttttgaaaccaataagtaaagatttaaacacttacagcaatatgaaattggtggttgataa


gcgaggccgcccgactgatacgttgattttccaagttgaactagatagacaaatggatctcgtaaccgaacttgagaacaaccagataaaaatgaatggtgacaaaat


accaacaaccattacatcagattcctacctacAtaacggactaagaaaaacactacacgatgctttaactgcaaaaattcagctcaccagttttgaggcaaaatttttgag


tgacatgcaaagtaagTatgatctcaatggttcgttctcatggctcacgcaaaaacaacgaaccacactagagaacatactggctaaatacggaaggatctgaggttc


ttatggctcttgtatctatcagtgaagcatcaagactaacaaacaaaagtagaacaactgttcaccgttaCatatcaaagggaaaactgtccatatgcacagatgaaaac


ggtgtaaaaaagatagatacatcagagcttttacgagtttttggtgcattCaaagctgttcaccatgaacagatcgacaatgtaacagatgaacagcatgtaacacctaa


tagaacaggtgaaaccagtaaaacaaagcaactagaacatgaaattgaacacctgagacaacttgttacagctcaacagtcacacatagacagcctgaaacaggcg


atgctgcttatcgaatcaaagctgccgacaacacgggagccagtgacgcctcccgtggggaaaaaatcatggcaattctggaagaaatagCgctttcagccggcaa


acCGGctgaagccggatctgcgattctgataacaaactagcaacaccagaacagcccgtttgcgggcagcaaaacccgtacCGATTATCAAAAAG


GATCTTCACCtagatccttttaaattaaaaatgaagttttaaatcaatctaaagtatatatgagtaaacttggtctgacagttaccaatgcttaatcagtgaggcacc


tatctcagcgatctgtctatttcgttcatccatagttgcctgactccccgtcgtgtagataactacgatacgggagggcttaccatctggccccagtgctgcaatgataccg


cgagaAccacgctcaccggctccagatttatcagcaataaaccagccagccggaagggccgagcgcagaagtggtcctgcaactttatccgcctccatccagtcta


ttaattgttgccgggaagctagagtaagtagttcgccagttaatagtttgcgcaacgttgttgccattgctacaggcatcgtggtgtcacgctcgtcgtttggtatggcttca


ttcagctccggttcccaacgatcaaggcgagttacatgatcccccatgttgtgcaaaaaagcggttagctccttcggtcctccgatcgttgtcagaagtaagttggccgc


agtgttatcactcatggttatggcagcactgcataattctcttactgtcatgccatccgtaagatgcttttctgtgactggtgagtactcaaccaagtcattctgagaatagtg


tatgcggcgaccgagttgctcttgcccggcgtcaatacgggataataccgcgccacatagcagaactttaaaagtgctcatcattggaaaacgttcttcggggcgaaa


actctcaaggatcttaccgctgttgagatccagttcgatAtaacccactcgtgcacccaactgatcttcagcatcttttactttcaccagcgtttctgggtgagcaaaaaca


ggaaggcaaaatgccgcaaaaaagggaataagggcgacacggaaatgttgaatactcatactcttcctttttcaatattattgaagcatttatcagggttattgtctcatga


gcggatacatatttgaatgtatttagaaaaataaacaaataggggttccgcgcacatttccccgaaaag (SEQ ID NO: 76)





lbAMK-105 (plasmid encoding ranthipeptide RiPP library v3 N-terminal to sigma-intein):


tgccacctgacgtctaagaaGAATTCGCGGCCGCTTCTAGAGGGAGccaattattgaaggcctccctaacggggggcctttttttgtttctggtc


tcccgcttaacgatcgttggctgacctgtaggatcgtacaggtTTACGcaagaaaatggtttgtTACAGTcgaataaaagctgtcaccggatgtgctttccggt


ctgatgagtccgtgaggacgaaacagcctctacaaataattttgtttaaTCCATCTCTATGGCGGATTTTatgtcatattaccaccatcaccatcatca


cATGTTGAAACAGATCAATGTGATTGCTGGCGTAAAAGAGCCTATTCGCGCCTATNNKTGTNNKNNK


NNKGAWNNKTGCNNKNNKTGCGAWNNKNNKGAWNNKCGAggaggtAAGggaggaCCTggaggtCGGggaggt


GTTggaggtGGTggaggaATTggaggtGGTTTTATCGCTTCCAACTGCTGGCTGGATACCCGTCCGGCACCGG


ATGAACAGCTGGAAGCAAGCGCACAGAGCCGTCGTATGGCACAGGCACTGGATCAGCTGCCGGATC


GTCAGCGTGAAGCAATTGTTCTGCAGTATTATCAAGAACTGAGCAATACCGAAGCAGCAGCACTGA


TGCAAATTAGCGTTGAAGCCCTGGAAAGCCTGCTGAGCCGTGCACGTCGTAATCTGCGTAGCCATCT


GGCCGAAGCACCGGGTGCAGATCTGAGCGGTCGTCGCAAACCGtaaaggtgatactttcagccaaaaaacttaagaccgcc


ggtcttgtccactaccttgcagtaatgcggtggacaggatcggcggttttcttttctcttctcaaAGACCgTCCAATGGCGGCGCgccatcgaatggcg


caaaacctttcgcggtatggcatgatagcgcccggaagagagtcaattcagggtggtgaatatgaaaaacataaatgccgacgacacatacagaataattaataaaat


taaagcttgtagaagcaataatgatattaatcaatgcttatctgatatgactaaaatggtacattgtgaatattatttactcgcgatcatttatcctcattctatggttaaatctga


tatttcaatcctagataattaccctaaaaaatggaggcaatattatgatgacgctaatttaataaaatatgatcctatagtagattattctaactccaatcattcaccaattaatt


ggaatatatttgaaaacaatgctgtaaataaaaaatctccaaatgtaattaaagaagcgaaaacatcaggtcttatcactgggtttagtttccctattcatacggctaacaat


ggcttcggaatgcttagttttgcacattcagaaaaagacaactatatagatagtttatttttacatgcgtgtatgaacataccattaattgttccttctctagttgataattatcga


aaaataaatatagcaaataataaatcaaacaacgatttaaccaaaagagaaaaagaatgtttagcgtgggcatgcgaaggaaaaagctcttgggatatttcaaaaatatt


aggttgcagtgagcgtactgtcactttccatttaaccaatgcgcaaatgaaactcaatacaacaaaccgctgccaaagtatttctaaagcaattttaacaggagcaattga


ttgcccatactttaaaaattgataaggatcctaattggtaacgaatcagacaattgacggctcgagggagtagcatagggtttgcagaatccctgcttcgtccatttgaca


ggcacattatgcatcgatgataagctgtcaaacatgagcagatcctctacgccggacgcatcgtggccggcatcaccggcgccacaggtgcggttgctggcgcctat


atcgccgacatcaccgatggggaagatcgggctcgccacttcgggctcatgagcaaatattttatctggctcactcaaaggcggtaatgacagtaagacgggtaagc


ctgttgatgataccgctgccttactgggtgcattagccagtctgaatgacctgtcacgggataatccgaagtggtcagactggaaaatcagagggcaggaactgctga


acagcaaaaagtcagatagcaccacatagcagacccgccataaaacgccctgagaagcccgtgacgggcttttcttgtattatgggtagtttccttgcatgaatccata


aaaggcgcctgtagtgccatttacccccattcactgccagagccgtgagcgcagcgaactgaatgtcacgaaaaagacagcgactcaggtgcctgatggtcggaga


caaaaggaatattcagcgatttgcccgagcttgcgagggtgctacttaagcctttagggttttaaggtctgttttgtagaggagcaaacagcgtttgcgacatccttttgta


atactgcggaactgactaaagtagtgagttatacacagggctgggatctattctttttatctttttttattctttctttattctataaattataaccacttgaatataaacaaaaaaa


acacacaaaggtctagcggaatttacagagggtctagcagaatttacaagttttccagcaaaggtctagcagaatttacagatacccacaactcaaaggaaaaggact


agtaattatcattgactagcccatctcaattggtatagtgattaaaatcacctagaccaattgagatgtatgtctgaattagttgttttcaaagcaaatgaactagcgattagt


cgctatgacttaacggagcatgaaaccaagctaattttatgctgtgtggcactactcaaccccacgattgaaaaccctacaaggaaagaacggacggtatcgttcactt


ataaccaatacgctcagatgatgaacatcagtagggaaaatgcttatggtgtattagctaaagcaaccagagagctgatgacgagaactgtggaaatcaggaatccttt


ggttaaaggctttTGGattttccagtggacaaactatgccaagttctcaagcgaaaaattagaattagtttttagtgaagagatattgccttatcttttccagttaaaaaaat


tcataaaatataatctggaacatgttaagtcttttgaaaacaaatactctatgaggatttatgagtggttattaaaagaactaacacaaaagaaaactcacaaggcaaatat


agagattagccttgatgaatttaagttcatgttaatgcttgaaaataactaccatgagtttaaaaggcttaaccaatgggttttgaaaccaataagtaaagatttaaacactta


cagcaatatgaaattggtggttgataagcgaggccgcccgactgatacgttgattttccaagttgaactagatagacaaatggatctcgtaaccgaacttgagaacaac


cagataaaaatgaatggtgacaaaataccaacaaccattacatcagattcctacctacAtaacggactaagaaaaacactacacgatgctttaactgcaaaaattcagc


tcaccagttttgaggcaaaatttttgagtgacatgcaaagtaagTatgatctcaatggttcgttctcatggctcacgcaaaaacaacgaaccacactagagaacatactg


gctaaatacggaaggatctgaggttcttatggctcttgtatctatcagtgaagcatcaagactaacaaacaaaagtagaacaactgttcaccgttaCatatcaaagggaa


aactgtccatatgcacagatgaaaacggtgtaaaaaagatagatacatcagagcttttacgagtttttggtgcattCaaagctgttcaccatgaacagatcgacaatgta


acagatgaacagcatgtaacacctaatagaacaggtgaaaccagtaaaacaaagcaactagaacatgaaattgaacacctgagacaacttgttacagctcaacagtc


acacatagacagcctgaaacaggcgatgctgcttatcgaatcaaagctgccgacaacacgggagccagtgacgcctcccgtggggaaaaaatcatggcaattctgg


aagaaatagCgctttcagccggcaaacCGGctgaagccggatctgcgattctgataacaaactagcaacaccagaacagcccgtttgcgggcagcaaaacccgt


acCGATTATCAAAAAGGATCTTCACCtagatccttttaaattaaaaatgaagttttaaatcaatctaaagtatatatgagtaaacttggtctgacagtt


accaatgcttaatcagtgaggcacctatctcagcgatctgtctatttcgttcatccatagttgcctgactccccgtcgtgtagataactacgatacgggagggcttaccatc


tggccccagtgctgcaatgataccgcgagaAccacgctcaccggctccagatttatcagcaataaaccagccagccggaagggccgagcgcagaagtggtcctg


caactttatccgcctccatccagtctattaattgttgccgggaagctagagtaagtagttcgccagttaatagtttgcgcaacgttgttgccattgctacaggcatcgtggt


gtcacgctcgtcgtttggtatggcttcattcagctccggttcccaacgatcaaggcgagttacatgatcccccatgttgtgcaaaaaagcggttagctccttcggtcctcc


gatcgttgtcagaagtaagttggccgcagtgttatcactcatggttatggcagcactgcataattctcttactgtcatgccatccgtaagatgcttttctgtgactggtgagt


actcaaccaagtcattctgagaatagtgtatgcggcgaccgagttgctcttgcccggcgtcaatacgggataataccgcgccacatagcagaactttaaaagtgctcat


cattggaaaacgttcttcggggcgaaaactctcaaggatcttaccgctgttgagatccagttcgatAtaacccactcgtgcacccaactgatcttcagcatcttttactttc


accagcgtttctgggtgagcaaaaacaggaaggcaaaatgccgcaaaaaagggaataagggcgacacggaaatgttgaatactcatactcttcctttttcaatattatt


gaagcatttatcagggttattgtctcatgagcggatacatatttgaatgtatttagaaaaataaacaaataggggttccgcgcacatttccccgaaaag (SEQ ID


NO: 77)





pAMK-857 (plasmid encoding ACE2a1 N-terminal to sigma-intein):


tgccacctgacgtctaagaaGAATTCGCGGCCGCTTCTAGAGGGAGccaattattgaaggcctccctaacggggggcctttttttgtttctggtc


tcccgcttaacgatcgttggctgacctgtaggatcgtacaggtTTACGcaagaaaatggtttgtTACAGTcgaataaaagctgtcaccggatgtgctttccggt


ctgatgagtccgtgaggacgaaacagcctctacaaataattttgtttaaTCCATCTCTATGGCGGATTTTatgtcatattaccaccatcaccatcatca


cATGtcaacgatcgaagaacaggctaaaacgttcctggataagttcaatcatgaggcggaggacctgttctaccaaagcagcttggcctcttggaactacaacacg


aacattacggagCGAggaggtAAGggaggaCCTggaggtCGGggaggtGTTggaggtGGTggaggaATTggaggtGGTTTTATCG


CTTCCAACTGCTGGCTGGATACCCGTCCGGCACCGGATGAACAGCTGGAAGCAAGCGCACAGAGCC


GTCGTATGGCACAGGCACTGGATCAGCTGCCGGATCGTCAGCGTGAAGCAATTGTTCTGCAGTATTA


TCAAGAACTGAGCAATACCGAAGCAGCAGCACTGATGCAAATTAGCGTTGAAGCCCTGGAAAGCCT


GCTGAGCCGTGCACGTCGTAATCTGCGTAGCCATCTGGCCGAAGCACCGGGTGCAGATCTGAGCGG


TCGTCGCAAACCGtaaaggtgatactttcagccaaaaaacttaagaccgccggtcttgtccactaccttgcagtaatgcggtggacaggatcggcggttttc


ttttctcttctcaaAGACCgTCCAATGGCGGCGCgccatcgaatggcgcaaaacctttcgcggtatggcatgatagcgcccggaagagagtcaattc


agggtggtgaatatgaaaaacataaatgccgacgacacatacagaataattaataaaattaaagcttgtagaagcaataatgatattaatcaatgcttatctgatatgacta


aaatggtacattgtgaatattatttactcgcgatcatttatcctcattctatggttaaatctgatatttcaatcctagataattaccctaaaaaatggaggcaatattatgatgac


gctaatttaataaaatatgatcctatagtagattattctaactccaatcattcaccaattaattggaatatatttgaaaacaatgctgtaaataaaaaatctccaaatgtaattaa


agaagcgaaaacatcaggtcttatcactgggtttagtttccctattcatacggctaacaatggcttcggaatgcttagttttgcacattcagaaaaagacaactatatagat


agtttatttttacatgcgtgtatgaacataccattaattgttccttctctagttgataattatcgaaaaataaatatagcaaataataaatcaaacaacgatttaaccaaaagag


aaaaagaatgtttagcgtgggcatgcgaaggaaaaagctcttgggatatttcaaaaatattaggttgcagtgagcgtactgtcactttccatttaaccaatgcgcaaatga


aactcaatacaacaaaccgctgccaaagtatttctaaagcaattttaacaggagcaattgattgcccatactttaaaaattgataaggatcctaattggtaacgaatcagac


aattgacggctcgagggagtagcatagggtttgcagaatccctgcttcgtccatttgacaggcacattatgcatcgatgataagctgtcaaacatgagcagatcctctac


gccggacgcatcgtggccggcatcaccggcgccacaggtgcggttgctggcgcctatatcgccgacatcaccgatggggaagatcgggctcgccacttcgggctc


atgagcaaatattttatctggctcactcaaaggcggtaatgacagtaagacgggtaagcctgttgatgataccgctgccttactgggtgcattagccagtctgaatgacc


tgtcacgggataatccgaagtggtcagactggaaaatcagagggcaggaactgctgaacagcaaaaagtcagatagcaccacatagcagacccgccataaaacgc


cctgagaagcccgtgacgggcttttcttgtattatgggtagtttccttgcatgaatccataaaaggcgcctgtagtgccatttacccccattcactgccagagccgtgagc


gcagcgaactgaatgtcacgaaaaagacagcgactcaggtgcctgatggtcggagacaaaaggaatattcagcgatttgcccgagcttgcgagggtgctacttaag


cctttagggttttaaggtctgttttgtagaggagcaaacagcgtttgcgacatccttttgtaatactgcggaactgactaaagtagtgagttatacacagggctgggatcta


ttctttttatctttttttattctttctttattctataaattataaccacttgaatataaacaaaaaaaacacacaaaggtctagcggaatttacagagggtctagcagaatttacaag


ttttccagcaaaggtctagcagaatttacagatacccacaactcaaaggaaaaggactagtaattatcattgactagcccatctcaattggtatagtgattaaaatcaccta


gaccaattgagatgtatgtctgaattagttgttttcaaagcaaatgaactagcgattagtcgctatgacttaacggagcatgaaaccaagctaattttatgctgtgtggcact


actcaaccccacgattgaaaaccctacaaggaaagaacggacggtatcgttcacttataaccaatacgctcagatgatgaacatcagtagggaaaatgcttatggtgta


ttagctaaagcaaccagagagctgatgacgagaactgtggaaatcaggaatcctttggttaaaggctttTGGattttccagtggacaaactatgccaagttctcaagc


gaaaaattagaattagtttttagtgaagagatattgccttatcttttccagttaaaaaaattcataaaatataatctggaacatgttaagtcttttgaaaacaaatactctatgag


gatttatgagtggttattaaaagaactaacacaaaagaaaactcacaaggcaaatatagagattagccttgatgaatttaagttcatgttaatgcttgaaaataactaccat


gagtttaaaaggcttaaccaatgggttttgaaaccaataagtaaagatttaaacacttacagcaatatgaaattggtggttgataagcgaggccgcccgactgatacgtt


gattttccaagttgaactagatagacaaatggatctcgtaaccgaacttgagaacaaccagataaaaatgaatggtgacaaaataccaacaaccattacatcagattcct


acctacAtaacggactaagaaaaacactacacgatgctttaactgcaaaaattcagctcaccagttttgaggcaaaatttttgagtgacatgcaaagtaagTatgatctc


aatggttcgttctcatggctcacgcaaaaacaacgaaccacactagagaacatactggctaaatacggaaggatctgaggttcttatggctcttgtatctatcagtgaag


catcaagactaacaaacaaaagtagaacaactgttcaccgttaCatatcaaagggaaaactgtccatatgcacagatgaaaacggtgtaaaaaagatagatacatcag


agcttttacgagtttttggtgcattCaaagctgttcaccatgaacagatcgacaatgtaacagatgaacagcatgtaacacctaatagaacaggtgaaaccagtaaaac


aaagcaactagaacatgaaattgaacacctgagacaacttgttacagctcaacagtcacacatagacagcctgaaacaggcgatgctgcttatcgaatcaaagctgcc


gacaacacgggagccagtgacgcctcccgtggggaaaaaatcatggcaattctggaagaaatagCgctttcagccggcaaacCGGctgaagccggatctgcg


attctgataacaaactagcaacaccagaacagcccgtttgcgggcagcaaaacccgtacCGATTATCAAAAAGGATCTTCACCtagatcctttt


aaattaaaaatgaagttttaaatcaatctaaagtatatatgagtaaacttggtctgacagttaccaatgcttaatcagtgaggcacctatctcagcgatctgtctatttcgttca


tccatagttgcctgactccccgtcgtgtagataactacgatacgggagggcttaccatctggccccagtgctgcaatgataccgcgagaAccacgctcaccggctcc


agatttatcagcaataaaccagccagccggaagggccgagcgcagaagtggtcctgcaactttatccgcctccatccagtctattaattgttgccgggaagctagagt


aagtagttcgccagttaatagtttgcgcaacgttgttgccattgctacaggcatcgtggtgtcacgctcgtcgtttggtatggcttcattcagctccggttcccaacgatca


aggcgagttacatgatcccccatgttgtgcaaaaaagcggttagctccttcggtcctccgatcgttgtcagaagtaagttggccgcagtgttatcactcatggttatggca


gcactgcataattctcttactgtcatgccatccgtaagatgcttttctgtgactggtgagtactcaaccaagtcattctgagaatagtgtatgcggcgaccgagttgctcttg


cccggcgtcaatacgggataataccgcgccacatagcagaactttaaaagtgctcatcattggaaaacgttcttcggggcgaaaactctcaaggatcttaccgctgttg


agatccagttcgatAtaacccactcgtgcacccaactgatcttcagcatcttttactttcaccagcgtttctgggtgagcaaaaacaggaaggcaaaatgccgcaaaaa


agggaataagggcgacacggaaatgttgaatactcatactcttcctttttcaatattattgaagcatttatcagggttattgtctcatgagcggatacatatttgaatgtattta


gaaaaataaacaaataggggttccgcgcacatttccccgaaaag (SEQ ID NO: 78)





pAMK-876 (plasmid encoding RBD C-terminal to sigma-intein; ECF promoter driving expression of cat-GFP and


hsvtk-RFP):


cgattatcaaaaaggatcttcacctagatccttttaaattaaaaatgaagttttaaatcaatctaaagtatatatgagtaaacttggtctgacagttatcagaagaactcgtca


agaaggcgatagaaggcgatgcgctgcgaatcgggagcggcgataccgtaaagcacgaggaagcggtcagcccattcgccgccaagctcttcagcaatatcacg


ggtagccaacgctatgtcctgatagcggtccgccacacccagccggccacagtcgatgaatccagaaaagcggccattttccaccatgatattcggcaagcaggcat


cgccatgggtcacgacgagatcctcgccgtcgggcatgcgcgccttgagcctggcgaacagttcggctggcgcgagcccctgatgctcttcgtccagatcatcctg


atcgacaagaccggcttccatccgagtacgtgctcgctcgatgcgatgtttcgcttggtggtcgaatgggcaggtagccggatcaagcgtatgcagccgccgcattg


catcagccatgatggatactttctcggcaggagcaaggtgagatgacaggagatcctgccccggcacttcgcccaatagcagccagtcccttcccgcttcagtgaca


acgtcgagcacagctgcgcaaggaacgcccgtcgtggccagccacgatagccgcgctgcctcgtcctgcagttcattcagggcaccggacaggtcggtcttgaca


aaaagaaccgggcgcccctgcgctgacagccggaacacggcggcatcagagcagccgattgtctgttgtgcccagtcatagccgaatagcctctccacccaagcg


gccggagaacctgcgtgcaatccatcttgttcaatcatgcgaaacgatcctcaatattattgaagcatttatcagggttattgtctcatgagcggatacatatttgaatgtatt


tagaaaaataaacaaataggggttccgcgcacatttccccgaaaagtgccacctgacgtctaagaaaccattattatcatgacattaacctataaaaataggcgtatcac


gaggcagaatttcagataaaaaaaatccttagctttcgctaaggatgatttctggaattcgcggccgcttctagagGGAGgcgcggataaaaatttcatttgcccgc


GACGGATtccccgcccatctatCGTTGAAcccatcagctgcgttcatcagcgaAGctgtcaccggatgtgctttccggtctgatgagtccgtgaggacg


aaacagcctctacaaataattttgtttaaTACTtcacacaggaaagtactagATGAGCAAAGGAGAAGAACTTTTCACTGGAGTTG


TCCCAATTCTTGTTGAATTAGATGGTGATGTTAATGGGCACAAATTTTCTGTCCGTGGAGAGGGTGA


AGGTGATGCTACAAACGGAAAACTCACCCTTAAATTTATTTGCACTACTGGAAAACTACCTGTTCCG


TGGCCAACACTTGTCACTACTCTGACCTATGGTGTTCAATGCTTTTCCCGTTATCCGGATCACATGAA


ACGGCATGACTTTTTCAAGAGTGCCATGCCCGAAGGTTATGTACAGGAACGCACTATATCTTTCAAA


GATGACGGGACCTACAAGACGCGTGCTGAAGTCAAGTTTGAAGGTGATACCCTTGTTAATCGTATCG


AGTTAAAGGGTATTGATTTTAAAGAAGATGGAAACATTCTTGGACACAAACTCGAGTACAACTTTAA


CTCACACAATGTATACATCACGGCAGACAAACAAAAGAATGGAATCAAAGCTAACTTCAAAATTCG


CCACAACGTTGAAGATGGTTCCGTTCAACTAGCAGACCATTATCAACAAAATACTCCAATTGGCGAT


GGCCCTGTCCTTTTACCAGACAACCATTACCTGTCGACACAATCTGTCCTTTCGAAAGATCCCAACG


AAAAGCGTGACCACATGGTCCTTCTTGAGTTTGTAACTGCTGCTGGGATTACACATGGCATGGATGA


GCTCTACAAAggaggtgagaaaaaaatcactggatataccaccgttgatatatcccaatggcatcgtaaagaacattttgaggcatttcagtcagttgctcaat


gtacctataaccagaccgttcagctggatattacggcctttttaaagaccgtaaagaaaaataagcacaagttttatccggcctttattcacattcttgcccgcctgatgaat


gctcatccggaatttcgtatggcaatgaaagacggtgagctggtgatatgggatagtgttcacccttgttacaccgttttccatgagcaaactgaaacgttttcatcgctct


ggagtgaataccacgacgatttccggcagtttctacacatatattcgcaagatgtggcgtgttacggtgaaaacctggcctatttccctaaagggtttattgagaatatgtt


tttcgtctcagccaatccctgggtgagtttcaccagttttgatttaaacgtggccaatatggacaacttcttcgcccccgttttcaccatgggcaaatattatacgcaaggcg


acaaggtgctgatgccgctggcgattcaggttcatcatgccgtttgtgatggcttccatgtcggcagaatgcttaatgaattacaacagtactgcgatgagtggcaggg


cggggcgtaaAATGGCGTTAATAAATAAGGAGGTAAGGTAATATGGCGAGCTATCCGTGTCACCAGCATG


CATCTGCTTTCGATCAGGCAGCGCGCAGCCGTGGTCATTCTAATCGTCGTACCGCACTGCGTCCGCG


TCGTCAGCAGGAGGCCACTGAGGTTCGTCTGGAGCAAAAGATGCCGACCCTGTTACGCGTATACATT


GATGGGCCGCATGGTATGGGTAAAACCACCACGACCCAATTACTGGTTGCGCTGGGCAGCCGTGAT


GATATTGTTTATGTGCCTGAACCGATGACGTATTGGCAGGTGCTGGGCGCGAGTGAAACTATTGCTA


ATATCTATACGACCCAGCATCGTCTGGACCAAGGGGAAATCAGCGCCGGTGATGCAGCCGTAGTGA


TGACCAGTGCGCAAATCACGATGGGTATGCCTTACGCAGTAACCGATGCGGTTCTGGCGCCGCATAT


TGGTGGTGAAGCCGGCAGTAGCCATGCGCCGCCGCCTGCCCTGACCCTGATTTTTGATCGTCACCCG


ATTGCGGCTCTGCTGTGCTATCCTGCTGCACGTTATCTGATGGGTTCTATGACCCCACAGGCCGTCCT


GGCATTCGTTGCACTGATTCCGCCTACTCTGCCTGGGACCAATATCGTGCTGGGGGCGCTGCCAGAA


GATCGTCATATCGACCGTCTGGCGAAACGTCAACGTCCTGGTGAACGCCTGGATCTGGCGATGCTGG


CAGCGATTCGTCGTGTATATGGCCTGCTGGCGAACACTGTCCGTTACCTGCAAGGCGGTGGCAGTTG


GCGTGAAGATTGGGGTCAACTGAGCGGTACGGCAGTTCCTCCGCAGGGTGCGGAACCTCAGTCTAA


CGCAGGTCCGCGTCCGCACATTGGTGATACCCTGTTCACCCTGTTCCGTGCGCCGGAGCTGCTGGCA


CCAAATGGGGATCTGTACAATGTTTTCGCGTGGGCGCTGGATGTTCTGGCTAAGCGTCTGCGCCCGA


TGCATGTTTTTATTCTGGATTATGATCAAAGCCCAGCAGGCTGTCGTGATGCGCTGCTTCAACTGACT


AGCGGCATGGTGCAAACGCATGTGACGACGCCTGGGAGTATCCCGACCATCTGTGATCTTGCCCGTA


CCTTCGCACGTGAAATGGGTGAAGCGAATGCCGAAGCTGCAGCAAAGGAGGCCGCAGCTAAAGCG


GCTGCAGCGAAAGCGGTGTCTAAAGGCGAAGCCGTTATTAAAGAATTCATGCGCTTCAAGGTTCAC


ATGGAGGGCTCGATGAATGGTCATGAGTTCGAGATTGAAGGGGAAGGTGAGGGCCGACCATATGAG


GGCACCCAAACTGCAAAACTGAAGGTTACTAAAGGTGGTCCGCTCCCGTTTAGTTGGGATATTCTGA


GCCCGCAGTTCATGTACGGCTCACGCGCTTTTATTAAGCATCCGGCGGACATACCGGACTACTATAA


ACAGTCCTTCCCGGAAGGGTTTAAATGGGAAAGAGTGATGAACTTTGAGGACGGAGGTGCGGTTAC


AGTGACTCAGGATACCAGTCTGGAGGATGGTACGCTGATCTATAAAGTAAAACTGCGTGGTACCAA


TTTTCCCCCAGATGGCCCCGTAATGCAGAAAAAAACCATGGGGTGGGAAGCATCGACCGAACGCCT


TTACCCGGAAGATGGCGTCTTGAAAGGAGACATCAAAATGGCTTTGCGCTTAAAAGATGGCGGCCG


TTATCTGGCGGATTTTAAAACGACCTACAAAGCCAAGAAACCTGTCCAAATGCCTGGTGCCTACAAC


GTGGATCGTAAACTAGACATCACGTCCCATAACGAAGATTATACAGTGGTCGAACAGTATGAACGG


AGCGAAGGCCGTCACAGCACGGGGGGAATGGACGAATTATATAAGTAACATTACTCGCATCCATTC


TCAGGCTctcggtaccaaattccagaaaagaggcctcccgaaaggggggccttttttcgttttggtccTACTGGCGCGCCTTTACgGCTAG


CTCAGTCCTAGGTAcTATGCTAGCaAGgTAGACTGTCGCCGGATGTGTATCCGACCTGACGATGGCCC


AAAAGGGCCGAAACAGTCCTCTACAAATAATTTTGTTTAATACTtcaTGGACgaaagtactagATGAATGAA


ACCGATCCTGATCTGGAACTGCTGAAACGTATTGGTAATAATGATGCACAGGCCGTTAAAGAAATG


GTTACCCGTAAACTGCCTCGTCTGCTGGCACTGGCAAGTCGCCTGCTGGGTGATGCAGATGAAGCAC


GTGATATTGCACAAGAAAGTTTTCTGCGCATTTGGAAACAGGCAGCAAGCTGGCGTAGCGAACAGG


CACGTTTTGATACCTGGCTGCATCGTGTTGCACTGAATCTGTGTTATGATCGTCTGCGTCGTCGTAAA


GAACATGTGCCGGTTGATAGCGAACATGCCTGTGAAGCATGCCTGAGCTACGAAACCGAAATCCTG


ACCGTTGAATATGGTCTGCTGCCGATCGGCAAAATCGTAGAAAAGCGTATCGAATGTACGGTTTACT


CTGTCGATAACAACGGTAACATCTACACCCAGCCGGTAGCGCAGTGGCACGACCGTGGCGAACAAG


AAGTGTTCGAGTACTGCCTGGAGGATGGCTCTCTGATCCGCGCTACTAAAGACCACAAATTTATGAC


CGTGGACGGTCAAATGCTGCCGATCGATGAAATCTTTGAGCGCGAACTGGACCTGATGCGCGTGGA


CAACCTGCCGAACATCAAAATTGCTACCCGCAAGTATCTGGGTAAGCAGAACGTCTATGACATTGGT


GTGGAGCGCGACCACAATTTCGCTCTGAAAAACGGAGGATCTGGTGGAAGTGGTGGTTCTGGAGGTc


gttttccgaatattaccaacttatgcccgtttggtgaggtgttcaacgcgacccgctttgccagcgtatacgcgtggaatcgtaaacgtatctcgaactgcgtagcggatt


actccgtgctttacaactcagcttccttctccacctttaaatgttatggtgtttcaccgaccaagttaaacgatctgtgctttacgaacgtctatgccgattcatttgtgatcag


aggtgatgaggttcgtcaaattgcgcctggacagacaggcaaaattgcagactataactacaaacttcccgacgattttacgggctgtgttattgcgtggaattcgaaca


acctggatagtaaggttggagggaattataactatctgtaccgcctgtttcgtaaatctaacctgaaacctttcgaacgcgacatatcaactgaaatctatcaggcaggta


gcactccctgtaacggtgtcgagggatttaactgctattttcctctgcagagttatggctttcagcctacgaatggagtaggctatcaaccgtaccgggtggtggttcttag


tttcgagctgctgcatgcaccagccacagtatgtggccccaaaaagtcaacgaatctttaaCTCGGTACCAAATTCCAGAAAAGAGACGC


TTTCGAGCGTCTTTTTTCGTTTTGGTCCcgcttactagtagcggccgctgcagtccggcaaaaaagggcaaggtgtcaccaccctgcccttt


ttctttaaaaccgaaaagattacttcgcgttatgcaggcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaaggcgg


taattcatgaccaaaatcccttaacgtgagttttcgttccactgagcgtcagaccccgtagaaaagatcaaaggatcttcttgagatcctttttttctgcgcgtaatctgctgc


ttgcaaacaaaaaaaccaccgctaccaacggtggtttgtttgccggatcaagagctaccaactctttttccgaaggtaactggcttcagcagagcgcagataccaaata


ctgtccttctagtgtagccgtagttaggccaccacttcaagaactctgtagcaccgcctacatacctcgctctgctaatcctgttaccagtggctgctgccagtggcgata


agtcgtgtcttaccgggttggactcaagacgatagttaccggataaggcgcagcggtcgggctgaacggggggttcgtgcacacagcccagcttggagcgaacga


cctacaccgaactgagatacctacagcgtgagctatgagaaagcgccacgcttcccgaagggagaaaggcggacaggtatccggtaagcggcagggtcggaac


aggagagcgcacgagggagcttccagggggaaacgcctggtatctttatagtcctgtcgggtttcgccacctctgacttgagcgtcgatttttgtgatgctcgtcaggg


gggcggagcctatggaaaaacgccagcaacgcggcctttttacggttcctggccttttgctggccttttgctcacatgttctttcctgcgttatcccctgattctgtggataa


ccgt (SEQ ID NO: 79)
















TABLE 8







Protein modifying enzyme and peptide amino acid sequences











SEQ ID


Name
Sequence
NO





EpiA
EAVKEKNDLFNLDVKVNAKESNDSGAEPRIASKFICTPGCAKTGSFNSYCC
173





EpiD
MHGKLLICATASINVININHYIVELKQHFDEVNILFSPSSKNFINTDVLKLFCDNLYDEIKD
174



PLLNHINIVENHEYILVLPASANTINKIANGICDNLLTTVCLTGYQKLFIFPNMNIRMWGNP




FLQKNIDLLKSNDVKVYSPDMNKSFEISSGRYKNNITMPNIENVLNFVLNNEKRPLD






LasA
MDKRVRYEKPSLVKEGTFRKTTAGLRRLFADQLVGRRNI
175





LasF
MSIELTPSLADLVDPLPGHALRAAATLRLADLIAAGADTAPALAAAARIDADAIARLMRYLC
176



SRGIFQAHEGRYALTEFSELLLDEDPSGLRKTLDQDSYGDRFDRAVAELVDVVRSGEPSYPR




LYGSTVYDDLAADPALGEVFADVRGLHSAGYGEDVAAVAGWSSCLRVVDLGGGTGSVLLAVL




ERHPSLSGAVLDLPYVAPQAKKALQASAFAQRCEFIKGSFFDPLPPADRYLLCNVLFNWDDA




QAGAILARCAQAGPVAGVVVAERLIDPDAEVELVAAQDLRLLAVCGGRQRGTAEFEALGAAH




GLALTSVTLTASGMSLLRFDVCRAGSAGGEVVEKS






TruE
MNKKNILPQLGQPVIRLTAGQLSSQLAELSEEALGGVDASTLPVPTLCSYDGVDASTVPTLC
177



SYDD






TruE*
MNKKNILPQLGQPVIRLTAGQLSSQLAELSEEALGGVDASTVPTLCSYDD
178





LynD
MQSTPLLQIQPHFHVEVIEPKQVYLLGEQANHALTGQLYCQILPLLNGQYTLEQIVEKLDGE
179



VPPEYIDYVLERLAEKGYLTEAAPELSSEVAAFWSELGIAPPVAAEALRQPVTLTPVGNISE




VTVAALTTALRDIGISVQTPTEAGSPTALNVVLTDDYLQPELAKINKQALESQQTWLLVKPV




GSVLWLGPVFVPGKTGCWDCLAHRLRGNREVEASVLRQKQAQQQRNGQSGSVIGCLPTARAT




LPSTLQTGLQFAATEIAKWIVKYHVNATAPGTVFFPTLDGKIITLNHSILDLKSHILIKRSQ




CPTCGDPKILQHRGFEPLKLESRPKQFTSDGGHRGTTPEQTVQKYQHLISPVTGVVTELVRI




TDPANPLVHTYRAGHSFGSATSLRGLRNTLKHKSSGKGKTDSQSKASGLCEAVERYSGIFQG




DEPRKRATLAELGDLAIHPEQCLCFSDGQYANRETLNEQATVAHDWIPQRFDASQAIEWTPV




WSLTEQTHKYLPTALCYYHYPLPPEHRFARGDSNGNAAGNTLEEAILQGFMELVERDGVALW




WYNRLRRPAVDLGSFNEPYFVQLQQFYRENDRDLWVLDLTADLGIPAFAGVSNRKTGSSERL




ILGFGAHLDPTIAILRAVTEVNQIGLELDKVPDENLKSDATDWLITEKLADHPYLLPDTTQP




LKTAQDYPKRWSDDIYTDVMTCVNIAQQAGLETLVIDQTRPDIGLNVVKVTVPGMRHFWSRF




GEGRLYDVPVKLGWLDEPLTEAQMNPTPMPF






PaaA
MSLTNVKPLIKESHHIILADDGDICIGEIPGVSQVINDPPSWVRPALAKMDGKRTVPRIFKE
180



LVSEGVQIESEHLEGLVAGLAERKLLQDNSFFSKVLSGEEVERYNRQILQFSLIDADNQHPF




VYQERLKQSKVAIFGMGGWGTWCALQLAMSGIGTLRLIDGDDVELSNINRQVLYRTDDVGKN




KVDAAKDTILAYNENVHVETFFEFASPDRARLEELVGDSTFIILAWAALGYYRKDTAEEIIH




SIAKDKAIPVIELGGDPLEISVGPIYLNDGVHSGFDEVKNSVKDKYYDSNSDIRKFQEARLK




HSFIDGDRKVNAWQSAPSLSIMAGIVTDQVVKTITGYDKPHLVGKKFILSLQDFRSREEEIF




K






PaaP
MIKFSTLSQRISAITEENAMYTKGQVIVLS
181





PadeA
MKKQYSKPSLEVLDVHQTMAGPGTSTPDAFQPDPDEDVHYDS
182





PadeK
MTERAAVRTDHYKAFGFRIESDFVLPELPPAGEREPLDNITVRRTDLQPLWNSSIHFYGNFA
183



ILDHGRTVMFRVPGAAIYAVQDASSILVSPFDQAEENWVRLFILGTCIGIILLQRKIMPLHG




SAVAIDGKAYAIIGESGAGKSTLALHLVSKGYPLLSDDVIPVVMTQGSPWVVPSYPQQKLWV




DTLKHMGMDNANYTPLYERKTKFAVPVGSNFHEEPLPLASIFELVPWDAATHIAPIQGMERF




RVLFHHTYRNFLVQPLGLMEWHFKTLSSFVHQIGMYRLHRPMVGFSTLDLTSHILNITRQGE




NDQ






PalA
MKDLLKELMYEVDLEEMENLQGSGYSAAQCAWMALSCVNYIPGVGFGCGGYSACELYKRYC
184





PalS
MGNLRDFYQLMKDNYADSNLFKDLNLIHNISNDIQIGINCDFSEMLGELVGNYDSLNYPSIT
185



CGILTYNEERCIKRCLESVVNEFDEIIVLDSVSEDNTVKIIKENFNDVKVYVEPWKNDFSFH




RNKIINLATCDWIYFIDADNYYDSKNKGKAMRIAKVMDFLKIEGVVSPTVIEHDNSMSRDTR




KMFRLKDNILFSGKVHEEPVYANGEIPRNIIVDINVFHDGYNPKIINMMEKNERNITLTKEM




MKIEPNNPKWLYFYSRELYQTQRDIALVQSVLFKALELYENSSYTRYYVDTIALLCRVLFES




KNYQKLTECLNILENNTLNCSDIDYYNSALLFYNLLLRIKKISSTLKENIDMYERDYHSFIN




PSHDHIKILILNMLLLLGDYQDAFKVYKEIKSIEIKDEFLVNVNKFKDNLLSFIDSINKI






PlpA2
MSIESAKAFYQRMTDDASFRTPFEAELSKEERQQLIKDSGYDFTAEEWQQAMTEIQAARSNE
186



ELNEEELEAIAGGAVAAMYGVVFPWDNEFPWPRWGG






PlpX
MTKKYRRVSYAVWEITLKCNLACSHCGSRAGQARTKELSTEEAFNLVRQLADVGIKEVTLIG
187



GEAFMRSDWLEIAKAVTEAGMICGMTTGGFGVSLETARKMKEAGIKTVSVSIDGGIPETHDR




QRGKKGAWHSAFRTMSHLKEVGIYFGCNTQINRLSASEFPIIYERIRDAGARAWQIQLTVPM




GNAADNADMLLQPYELLDIYPMLARVAKRAKQEGVRIQAGNNIGYYGPYERLLRGSDEWTFW




QGCGAGLNTLGIEADGKIKGCPSLPTAAYTGGNIRDRPLREIVEQTEELKFNLKAGTEQGTD




HMWGFCKTCEFAELCRGGCSWTAHVFFDRRGNNPYCHHRALKQAQKDIRERFYLKVKAKGNP




FDNGEFVIIEEPFNAPLPENDLLHFNSDHIQWPENWQNSESAYALAK






PlpY
MNSNQIPNKVATAAQKSDDSSSVLPRQGWQDKQAFIKALIKAKQSLEIAEISNFLT
188





TgnA*
MYRPYIAKYVEEQTLQNSTNLVYDDITQISFINKEKNVKKINLGPDTTIVTETIENADPDEY
189



FL






TgnB
MKTILIITNTLDLTVDYIINRYNHTAKFFRLNTDRFFDYDINITNSGTSIRNRKSNLIINIQ
190



EIHSLYYRKITLPNLDGYESKYWTLMQREMMSIVEGIAETAGNFALTRPSVLRKADNKIVQM




KLAEEIGFILPQSLITNSNQAAASFCNKNNTSIVKPLSTGRILGKNKIGIIQTNLVETHENI




QGLELSPAYFQDYIPKDTEIRLTIVGNKLFGANIKSTNQVDWRKNDALLEYKPANIPDKIAK




MCLEMMEKLEINFAAFDFIIRNGDYIFLELNANGQWLWLEDILKFDISNTIINYLLGEPI






ThcoA
MRKKEWQTPELEVLDVRLTAAGPGKAKPDAVQPDEDEIVHYS
191





ThcoK
MTRTNTGYRYRAFGLRIDSDIPLPELGDGTRPDGDADLTVVRCGEAEPEWAEGGGGGRLYAA
192



EGIVSFRVPQTAAFRITNGNRIEVHAYSGADEDRIRLYVLGTCMGALLLQRRILPLHGSVVA




RDGRAYAIVGESGAGKSTMSAALLERGFRLVTDDVAAIVFDERGTPLVMPAYPQQKLWQDSL




DRLQIAGSGLRPLFERETKYAVPADGAFWPEPVPLVHIYELVHSDGQTPELQPIAKLERCYT




LYRHTFRRSLIVPSGLSAWHFETAVKLAEKTGMYRLMRPAKVFAARESARLIETHADGEVSR





*TruE and TgnA peptides used in this study were truncated relative to the wild-type peptides.













TABLE 9







Genetic parts











SEQ


Name
Sequence
ID NO










Promoters









PCymRC
AACAAACAGACAATCTGGTCTGTTTGTATTATGGAAAATTTTTCTGTATAATAGAT
193



TCAACAAACAGACAATCTGGTCTGTTTGTATTAT



PLacI
GCGGCGCGCCATCGAATGGCGCAAAACCTTTCGCGGTATGGCATGATAGCGCCC
194


PLacIQ
GCGGCGCGCCATCGAATGGTGCAAAACCTTTCGCGGTATGGCATGATAGCGCCC
195


PT5LacO
AATCATAAAAAATTTATTTGCTTTGTGAGCGGATAACAATTATAATAGATTCAATT
196



GTGAGCGGATAACAATT











Ribosome Binding Sites









RBSEpiD
ACTGAACTATAAGGTAGGTATATT
197


RBSLacI
GGAAGAGAGTCAATTCAGGGTGGTGAAT
198


RBSLasF
AGAGCCATCAGATTTAAGGAACATAAAAA
199


RBSLynD
CTAAATTCCCCCGAGGTCAATA
200


RBSPaaA
AGATCATTTCCAATAAGGGGGACACT
201


RBSPadeK
AGACACCGAAACCTAAGGAGGGATAT
202


RBSPalS
AGACCAAACAATTAGGAGGACAAAT
203


RBSpeptide
ACCCAACACCACCAGCAAGCCTAAGGAGGAGAAAT
204


RBSPlpxa
AGAGCCACCATTTATAAGGAGAACCTACCG
205


RBSPlpYa
ATATAAAGTTAAGGAGTTGCAC
206


RBSTgnB
AGAAATATTACAACGAGGTAAAGGC
207


RBSTheoK
AGAGCATTCCATAAGGAGAAATTTT
208










Terminators









B0062
CAGATAAAAAAAATCCTTAGCTTTCGCTAAGGATGATTTCT
209


ECK120029600
TTCAGCCAAAAAACTTAAGACCGCCGGTCTTGTCCACTACCTTGCAGTAATGCGGT
210



GGACAGGATCGGCGGTTTTCTTTTCTCTTCTCAA



AraC Terminator
TTGGTAACGAATCAGACAATTGACGGCTCGAGGGAGTAGCATAGGGTTTGCAGAAT
211


w/ 2 SNPs
CCCTGCTTCGTCCATTTGACAGGCACATTATGCATCGATGATAAGCTGTCAAACAT




GAGCA



His operon
TCCGGCAAAAAAGGGCAAGGTGTCACCACCCTGCCCTTTTTCTTTAAAACCGAAAA
212


terminator
GA



L3S3P21
CCAATTATTGAAGGCCTCCCTAACGGGGGGCCTTTTTTTGTTTCTGGTCTCCC
213


L3S3P41b
AAAAAAAAAAAACACCCTAACGGGTGTTTTTTTTTTTTTGGTGTCCC
214


IOT
TTGGTAACGAATCAGACAATTGACGGCTCGAGGGAGTAGCATAGGGTTTGCAGAAT
215



CCCTGCTTCGTCCATTTGACAGGCACATTATGCATCGATGATAAGCTGTCAAACAT




GAGCAGATCCTCTACGCCGGACGCATCGTGGCCGGCATCACCGGCGCCACAGGTGC




GGTTGCTGGCGCCTATATCGCCGACATCACCGATGGGGAAGATCGGGCTCGCCACT




TCGGGCTCATGAGCAAATATTTTATCTG











Ribozymes









RiboJ53
AGCGGTCAACGCATGTGCTTTGCGTTCTGATGAGACAGTGATGTCGAAACCGCCTC
216



TACAAATAATTTTGTTTAA











Linkers/Tags









N-terminal sumo
ATGTCATATTACCACCATCACCATCATCACGGGTCCCTGCAG
217


affinity tag




(ATag-2)




N-terminal sumo
CATCACCATCACCACCATGGATATGATATTAGCACAGGT
218


linker v1 (Link-




1)




N-terminal sumo
TGCATGTCATATTACGACTCCATTCCCACAAGCGAGAACTTGTACTTTCAAGGGTG
219


linker v2 (Link-
C



2)












Genes Miscellaneous









Small Ubiquitin-
GACTCAGAAGTCAATCAAGAAGCTAAGCCAGAGGTCAAGCCAGAAGTCAAGCCTGA
220


like Modifier
GACTCACATCAATTTAAAGGTGTCCGATGGATCTTCAGAGATCTTCTTCAAGATCA



(SUMO)
AAAAGACCACTCCTTTAAGAAGGCTGATGGAAGCGTTCGCTAAAAGACAGGGTAAG




GAAATGGACTCCTTAAGATTCTTGTACGACGGTATTAGAATTCAAGCTGATCAGGC




CCCTGAAGATTTGGACATGGAGGATAACGATATTATTGAGGCTCACCGCGAACAGA




TTGGAGGT



lacI
ATGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGAC
221



CGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAG




TGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAACAACTG




GCGGGCAAACAGTCGTTGCTTATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGC




GCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCG




TGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCAC




AATCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCA




GGATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGATG




TCTCTGACCAGACACCCATCAACAGTATTATTTTCTCCCATGAGGACGGTACGCGA




CTGGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTAGCGGG




CCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCTCA




CTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCC




GGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCT




GGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGC




TGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGATAGCTCA




TGTTATATCCCGCCGTTAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAAC




CAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGC




TGTTGCCAGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACC




GCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCG




ACTGGAAAGCGGGCAGTGATAA



cymR
ATGAGCCCGAAACGTCGTACCCAGGCAGAACGTGCAATGGAAACCCAGGGTAAACT
222



GATTGCAGCAGCACTGGGTGTTCTGCGTGAAAAAGGTTATGCAGGTTTTCGTATTG




CAGATGTTCCGGGTGCAGCCGGTGTTAGCCGTGGTGCACAGAGCCATCATTTTCCG




ACCAAACTGGAACTGCTGCTGGCAACCTTTGAATGGCTGTATGAGCAGATTACCGA




ACGTAGCCGTGCACGTCTGGCAAAACTGAAACCGGAAGATGATGTTATTCAGCAGA




TGCTGGATGATGCAGCAGATTTTTTTCTGGATGATGATTTTAGCATCGGCCTGGAT




CTGATTGTTGCAGCAGATCGTGATCCGGCACTGCGTGAAGGTATTCTGCGTACCGT




TGAACGTAATCGTTTTGTTGTTGAAGATATGTGGCTGGGTGTGCTGGTGAGCCGTG




GTCTGAGCCGTGATGATGCCGAAGATATTCTGTGGCTGATTTTTAACAGCGTTCGT




GGTCTGACAGTTCGTAGCCTGTGGCAGAAAGATAAAGAACGTTTTGAACGTGTGCG




TAATAGCACCCTGGAAATTGCACGTGAACGTTATGCAAAATTCAAACGTTGATAA











Modifying Enzymes









epiD
ATGCACGGTAAACTGCTGATCTGCGCAACTGCTTCGATCAACGTCATCAATATCAA
223



CCATTATATTGTGGAGCTGAAACAGCACTTCGATGAGGTGAATATCCTGTTTTCAC




CTTCCTCGAAGAACTTTATCAACACCGATGTCCTGAAGCTGTTTTGCGATAATCTG




TATGACGAGATCAAAGATCCGCTGCTGAACCACATCAACATAGTGGAGAACCACGA




GTATATCTTGGTGCTGCCTGCCAGTGCCAATACGATCAACAAAATCGCGAACGGTA




TATGCGATAACCTCTTGACGACCGTATGCTTAACCGGGTACCAGAAACTGTTTATC




TTTCCGAATATGAACATCCGCATGTGGGGAAATCCGTTCTTACAGAAAAATATTGA




CCTGCTTAAAAGCAACGACGTGAAGGTGTATTCCCCCGACATGAACAAATCTTTTG




AGATAAGCTCAGGCCGCTACAAAAATAACATCACGATGCCGAATATCGAAAACGTG




CTGAATTTTGTCCTGAACAATGAGAAACGCCCGCTGGATTAATAA



lasF
ATGTCTATCGAACTGACGCCTAGTTTGGCCGATCTGGTCGATCCACTTCCAGGTCA
224



CGCACTGCGCGCTGCGGCGACATTACGTCTGGCAGATCTGATTGCGGCTGGTGCAG




ATACTGCACCGGCATTAGCAGCGGCGGCACGCATTGATGCTGACGCGATCGCGCGT




CTTATGCGGTATCTGTGCAGTCGCGGGATTTTTCAAGCACATGAAGGCCGGTACGC




GTTGACTGAATTTAGCGAATTGCTGCTGGATGAAGATCCATCTGGCCTGCGTAAAA




CCTTAGATCAGGATAGCTATGGGGATCGTTTCGACCGCGCGGTTGCGGAACTGGTG




GACGTTGTACGGTCCGGTGAACCTTCTTATCCTCGCCTTTACGGCTCGACGGTTTA




TGATGACCTGGCAGCCGATCCTGCCCTCGGCGAGGTGTTCGCGGATGTTCGTGGCT




TGCACTCCGCAGGGTATGGGGAAGATGTCGCGGCAGTGGCGGGTTGGTCCTCATGC




CTGCGCGTTGTCGATCTGGGTGGAGGGACTGGCTCCGTCCTGCTTGCTGTGTTAGA




GCGTCACCCGTCCCTGTCAGGCGCAGTACTGGATCTGCCATACGTCGCCCCGCAGG




CAAAGAAAGCTCTGCAGGCCTCAGCGTTTGCCCAACGTTGTGAATTTATCAAAGGG




AGCTTCTTCGATCCGTTACCTCCGGCAGACCGTTACCTGTTGTGTAACGTGCTGTT




CAACTGGGATGACGCGCAAGCAGGCGCTATTTTGGCACGCTGTGCGCAGGCGGGCC




CTGTGGCCGGAGTAGTGGTAGCCGAACGTTTGATCGATCCGGATGCGGAAGTGGAA




CTCGTAGCAGCTCAAGATCTGCGTCTGTTGGCTGTTTGCGGCGGTCGGCAGCGTGG




CACCGCTGAATTCGAAGCGCTTGGGGCAGCCCATGGCCTGGCGTTAACCAGCGTTA




CCCTCACGGCATCTGGTATGAGCCTGCTCCGTTTCGATGTGTGTCGTGCCGGGAGT




GCTGGCGGGGAAGTTGTGGAAAAATCTTAATAA



lynD
ATGCAATCTACACCATTACTGCAAATACAACCACATTTCCATGTAGAGGTCATTGA
225



ACCAAAGCAAGTCTACTTGTTGGGTGAACAAGCTAATCATGCATTGACAGGCCAAT




TATACTGCCAAATTTTGCCATTGTTAAACGGACAATACACATTGGAACAAATCGTT




GAAAAACTAGACGGAGAAGTACCACCTGAATACATTGATTATGTGCTGGAGAGACT




AGCTGAGAAGGGCTATCTGACTGAAGCAGCACCTGAATTATCTAGTGAAGTGGCCG




CTTTCTGGTCTGAGCTGGGGATTGCACCTCCTGTCGCGGCCGAAGCATTACGTCAA




CCTGTGACTTTAACACCTGTTGGAAACATCAGCGAAGTAACAGTAGCAGCCTTAAC




CACAGCCCTACGTGATATCGGTATTTCCGTTCAAACACCTACAGAAGCTGGATCGC




CAACTGCATTGAACGTTGTACTTACCGATGATTATCTCCAACCAGAACTCGCTAAG




ATCAATAAGCAAGCCTTAGAAAGTCAACAAACTTGGCTACTTGTCAAACCAGTTGG




CTCCGTGTTATGGTTGGGTCCGGTATTCGTGCCAGGAAAAACAGGTTGCTGGGATT




GTTTGGCTCACAGATTAAGGGGGAATAGAGAGGTAGAGGCCTCTGTATTGAGACAA




AAACAAGCTCAACAACAACGTAATGGACAAAGCGGGTCTGTAATAGGATGCCTTCC




CACGGCTAGAGCGACACTGCCCTCAACACTCCAAACTGGGCTGCAGTTCGCTGCTA




CCGAAATTGCTAAATGGATAGTTAAGTATCATGTTAATGCCACAGCGCCTGGCACC




GTATTCTTCCCTACATTGGATGGTAAGATAATTACGCTAAATCACTCCATACTGGA




TTTGAAGTCACATATTCTGATCAAGCGTTCTCAATGTCCCACCTGTGGTGACCCAA




AAATCTTACAGCACCGTGGTTTCGAACCTTTAAAACTTGAGTCAAGGCCTAAACAG




TTCACCTCAGACGGCGGACATCGTGGTACTACCCCTGAACAAACTGTCCAGAAATA




TCAACATTTAATCTCGCCTGTTACCGGTGTAGTTACTGAATTGGTCAGGATAACTG




ATCCGGCCAATCCACTAGTTCACACATATAGAGCTGGTCATAGCTTCGGGAGCGCT




ACATCGCTGAGAGGGCTGCGTAATACCTTAAAGCATAAGAGTTCAGGTAAGGGTAA




GACTGATTCTCAAAGTAAAGCCTCGGGCCTGTGTGAGGCGGTAGAACGTTACTCAG




GAATCTTTCAAGGTGACGAACCGAGAAAACGCGCCACATTGGCTGAATTGGGAGAT




TTGGCAATTCACCCTGAGCAATGCTTGTGTTTTTCCGACGGTCAGTACGCTAATAG




AGAAACTTTAAACGAACAGGCAACGGTGGCACATGATTGGATACCTCAACGTTTTG




ATGCATCACAAGCTATTGAATGGACTCCAGTCTGGTCCCTAACTGAACAGACCCAT




AAATATTTGCCCACCGCATTGTGTTACTACCATTATCCTCTACCCCCAGAACACAG




ATTCGCACGTGGAGATTCGAATGGTAATGCTGCCGGAAATACGTTGGAAGAGGCTA




TACTCCAAGGCTTCATGGAATTAGTCGAGAGAGATGGTGTGGCTTTATGGTGGTAT




AACAGGCTACGCAGACCCGCTGTAGACTTAGGCTCATTTAACGAGCCATACTTCGT




TCAGTTGCAACAATTCTACAGAGAAAACGATAGAGATTTGTGGGTTTTGGACTTGA




CAGCTGATTTAGGTATCCCGGCTTTCGCGGGCGTTTCTAATAGAAAAACTGGTAGT




TCGGAGAGGTTGATATTAGGATTCGGTGCACACCTCGATCCTACTATTGCAATTCT




GAGAGCAGTTACAGAAGTTAACCAGATTGGCCTTGAATTAGATAAAGTTCCAGACG




AGAACCTTAAGAGCGACGCAACAGATTGGCTAATTACTGAAAAATTAGCTGACCAC




CCTTATTTGTTACCAGATACAACTCAACCTCTAAAAACTGCTCAAGATTATCCTAA




AAGGTGGTCTGACGATATATACACGGACGTAATGACTTGCGTTAATATTGCTCAAC




AAGCAGGACTTGAAACTCTAGTTATTGATCAAACACGTCCGGACATTGGTTTGAAT




GTTGTTAAGGTGACAGTCCCGGGGATGAGGCACTTTTGGTCAAGATTTGGAGAGGG




GAGGCTTTATGACGTGCCCGTCAAATTAGGTTGGCTTGACGAACCTTTGACCGAAG




CGCAAATGAACCCCACGCCGATGCCTTTTTAATAA



paaA
ATGAGCCTGACGAATGTCAAGCCGTTGATTAAAGAATCCCACCACATCATTTTAGC
226



TGACGATGGTGACATTTGCATTGGGGAAATTCCGGGGGTGTCTCAGGTAATCAATG




ACCCGCCGTCGTGGGTTCGTCCTGCCCTGGCAAAGATGGATGGCAAGCGTACTGTC




CCCCGTATTTTCAAAGAACTGGTCAGTGAAGGCGTACAGATCGAATCCGAACATCT




GGAAGGCCTGGTAGCCGGGCTTGCCGAACGCAAACTTCTCCAGGATAACAGTTTCT




TTTCCAAGGTGTTAAGCGGTGAAGAAGTGGAGCGCTATAACCGCCAGATTCTGCAG




TTCAGCCTTATCGATGCGGATAACCAGCACCCTTTCGTTTACCAAGAGCGGCTGAA




ACAGTCTAAAGTCGCTATCTTCGGTATGGGTGGCTGGGGCACGTGGTGTGCATTGC




AGCTGGCCATGTCAGGCATTGGTACACTGCGGCTGATCGACGGCGATGATGTGGAA




CTGTCGAACATTAACCGCCAAGTTCTGTATCGCACGGATGATGTAGGTAAAAACAA




AGTTGATGCCGCCAAAGACACTATCCTGGCATACAACGAAAACGTGCATGTTGAAA




CCTTCTTTGAATTCGCCAGCCCGGACCGTGCCCGGCTTGAAGAACTTGTGGGTGAT




TCTACCTTTATTATCCTGGCTTGGGCCGCGTTGGGTTACTACCGTAAAGATACGGC




AGAGGAAATTATCCATTCGATTGCGAAAGATAAAGCGATCCCTGTAATTGAACTCG




GCGGTGATCCTTTGGAAATCTCTGTCGGTCCTATTTACCTGAATGATGGCGTACAC




AGCGGCTTCGACGAGGTGAAAAATTCCGTTAAAGATAAATACTACGACAGCAACAG




CGATATCCGCAAATTTCAAGAGGCGCGGTTGAAACACAGCTTCATCGATGGCGATC




GTAAAGTGAACGCGTGGCAATCAGCGCCCAGCCTGAGTATTATGGCTGGTATCGTA




ACGGATCAGGTTGTGAAAACCATTACCGGGTACGACAAGCCACATCTCGTTGGCAA




GAAATTTATCTTGAGTCTGCAAGATTTCCGCAGCCGCGAGGAGGAGATCTTTAAAT




AATAA



padeK
ATGACCGAACGTGCCGCAGTGCGTACCGACCATTATAAAGCCTTTGGGTTTAGAAT
227



TGAAAGCGATTTCGTGCTCCCGGAACTTCCGCCCGCAGGCGAACGCGAACCGCTCG




ATAATATTACGGTTCGTCGTACCGACCTGCAGCCGCTCTGGAATTCTAGTATCCAT




TTTTACGGAAACTTTGCCATTCTGGATCACGGACGCACGGTTATGTTTCGAGTTCC




GGGTGCTGCTATCTATGCGGTACAGGATGCTAGCAGCATATTAGTGTCCCCATTCG




ATCAGGCAGAAGAAAACTGGGTACGTCTTTTTATTCTGGGTACCTGTATTGGGATC




ATCCTGCTGCAGCGTAAGATTATGCCGCTGCACGGTAGCGCCGTTGCCATTGATGG




CAAAGCCTACGCGATTATCGGCGAATCTGGTGCCGGCAAAAGCACTCTTGCACTGC




ATCTTGTCAGTAAGGGTTATCCATTGCTTTCGGATGATGTGATTCCGGTCGTTATG




ACCCAGGGCTCCCCCTGGGTGGTGCCGTCGTACCCGCAACAAAAACTTTGGGTGGA




CACTCTGAAGCACATGGGAATGGATAATGCAAACTATACGCCGCTGTACGAACGTA




AAACGAAGTTCGCGGTGCCCGTGGGCAGTAATTTCCACGAAGAACCGCTGCCGTTA




GCTAGCATTTTCGAGCTTGTCCCGTGGGATGCGGCAACGCACATTGCCCCGATCCA




AGGGATGGAACGCTTTCGTGTCCTGTTCCACCACACTTATCGGAACTTTCTGGTTC




AGCCGCTGGGTCTTATGGAATGGCATTTTAAAACTCTGAGCTCGTTCGTTCACCAA




ATTGGAATGTATCGTCTGCATAGACCTATGGTCGGATTCAGTACCTTAGATTTAAC




GTCGCACATTCTGAATATAACGCGTCAGGGAGAGAACGATCAATAATAA



palS
ATGGGGAATTTGCGTGATTTCTACCAACTGATGAAAGATAACTATGCGGACTCTAA
228



TCTGTTCAAGGATTTGAATCTGATCCACAATATCTCCAACGACATCCAAATTGGAA




TTAATTGCGATTTCTCTGAAATGCTGGGAGAACTGGTAGGTAATTACGATTCCCTG




AACTATCCGTCAATCACCTGTGGTATTCTGACGTATAATGAAGAACGCTGCATTAA




ACGTTGTCTGGAAAGTGTGGTGAACGAATTCGATGAGATTATTGTCTTGGATAGTG




TATCCGAGGACAATACCGTGAAAATTATCAAGGAGAATTTCAACGATGTCAAAGTC




TACGTCGAGCCATGGAAGAACGATTTTTCATTTCACCGCAACAAGATCATTAATCT




CGCAACGTGCGACTGGATCTACTTTATCGACGCGGATAATTATTATGATTCGAAGA




ACAAGGGTAAAGCCATGCGCATCGCTAAGGTTATGGATTTCTTGAAAATCGAAGGC




GTTGTGAGCCCAACGGTCATTGAGCATGACAATAGCATGAGCCGTGATACCCGTAA




GATGTTTCGTCTGAAAGATAACATTCTGTTTAGCGGTAAAGTTCATGAAGAACCGG




TGTATGCCAATGGTGAGATCCCCCGGAACATCATAGTAGACATCAACGTGTTTCAC




GACGGCTATAACCCAAAGATTATCAACATGATGGAAAAGAACGAGCGCAATATCAC




CCTGACTAAAGAGATGATGAAGATCGAACCGAACAATCCGAAATGGCTGTACTTCT




ATAGCCGCGAACTCTATCAGACGCAACGTGACATTGCCCTTGTGCAAAGTGTACTG




TTCAAGGCACTGGAACTGTATGAAAACAGTTCATATACGCGTTATTATGTTGACAC




CATTGCCTTACTGTGCCGAGTGCTGTTCGAATCTAAAAACTACCAGAAACTTACGG




AATGTCTGAACATCCTGGAGAACAATACGCTTAACTGTTCCGATATCGATTACTAT




AATTCAGCGCTGCTGTTCTACAACCTGTTACTGCGCATCAAGAAAATTAGCTCCAC




CCTGAAGGAGAACATTGATATGTACGAACGTGACTATCATAGCTTTATCAACCCCT




CGCATGATCACATTAAGATTCTGATATTAAATATGCTCCTGCTGCTCGGCGATTAC




CAGGATGCCTTTAAGGTTTACAAGGAGATCAAGTCCATTGAGATTAAAGATGAGTT




TCTGGTGAACGTGAACAAATTCAAAGACAATCTTCTGAGCTTCATTGACTCCATTA




ACAAAATTTAATAA



plpXa (Expressed
ATGACCAAAAAGTATCGGCGTGTATCCTACGCAGTGTGGGAAATCACCCTGAAATG
229


as plpXY)
CAATCTGGCATGCTCTCATTGTGGCAGCCGCGCCGGCCAAGCCCGTACGAAAGAGC




TGAGTACCGAAGAAGCGTTCAACCTGGTCCGCCAGCTGGCCGACGTGGGCATTAAG




GAAGTCACCCTGATCGGTGGTGAAGCCTTTATGCGTTCGGATTGGCTGGAAATCGC




GAAAGCCGTCACTGAAGCCGGCATGATCTGTGGCATGACCACAGGGGGCTTCGGGG




TCAGTCTGGAAACGGCGCGTAAAATGAAAGAAGCGGGCATTAAAACGGTGAGCGTT




AGCATTGACGGTGGTATTCCTGAAACCCACGACCGCCAGCGCGGTAAAAAGGGTGC




GTGGCATAGTGCATTCCGGACTATGAGCCATCTGAAAGAAGTCGGGATCTACTTCG




GTTGCAACACTCAAATCAATCGTTTATCGGCGTCAGAATTCCCGATTATCTATGAA




CGTATTCGCGATGCTGGGGCACGTGCGTGGCAAATTCAGCTGACGGTTCCGATGGG




CAACGCCGCGGATAACGCAGATATGCTGCTGCAACCGTATGAATTGCTCGACATCT




ATCCGATGTTAGCCCGCGTTGCCAAACGTGCGAAACAGGAAGGCGTGCGTATTCAG




GCAGGTAACAACATCGGGTACTATGGACCGTATGAGCGTCTGCTGCGTGGCAGCGA




CGAATGGACGTTTTGGCAAGGATGTGGTGCGGGCCTTAACACCCTCGGCATCGAAG




CCGACGGCAAAATCAAAGGCTGTCCATCCCTGCCGACCGCCGCGTACACCGGCGGT




AACATTCGCGATCGCCCGCTGCGGGAAATCGTCGAACAGACCGAAGAACTGAAATT




TAACTTAAAAGCTGGTACAGAACAAGGTACGGACCATATGTGGGGCTTTTGTAAAA




CCTGCGAATTCGCGGAACTCTGTCGCGGCGGATGCAGCTGGACTGCGCATGTGTTC




TTTGACCGGCGCGGCAATAATCCGTACTGCCACCATCGGGCTCTGAAACAAGCCCA




AAAAGACATTCGCGAACGCTTTTATTTAAAAGTGAAAGCAAAGGGCAACCCGTTCG




ACAATGGTGAATTTGTTATCATTGAAGAACCTTTTAACGCTCCGTTACCCGAGAAT




GACCTGCTGCACTTTAACAGTGATCACATTCAATGGCCAGAAAACTGGCAAAATAG




TGAAAGCGCGTACGCATTGGCCAAGTAATAA



plpYa (Expressed
ATGAACAGTAATCAGATCCCTAACAAAGTTGCAACCGCGGCACAGAAATCTGACGA
230


as plpXY)
CAGCAGCAGCGTATTACCGCGCCAGGGGTGGCAAGACAAACAAGCCTTTATTAAGG




CACTCATTAAAGCCAAACAGTCTCTCGAAATTGCCGAAATTAGCAACTTTTTAACC



tgnB
ATGAAAACCATTCTGATTATTACCAATACCCTGGATCTGACCGTGGATTATATTAT
231



TAATCGCTATAATCATACCGCTAAATTTTTTCGTCTGAATACCGATCGTTTTTTTG




ATTATGATATTAATATTACCAATAGCGGTACCAGCATTCGTAATCGTAAATCTAAT




CTGATTATTAATATTCAGGAAATTCATAGCCTGTATTATCGCAAAATTACCCTGCC




GAATCTGGATGGCTATGAAAGTAAATATTGGACCCTGATGCAGCGCGAAATGATGA




GTATTGTTGAAGGCATTGCAGAAACCGCTGGCAATTTTGCACTGACCCGTCCGTCT




GTGCTGCGCAAAGCTGATAATAAAATTGTGCAGATGAAACTGGCAGAAGAAATTGG




TTTTATTCTGCCGCAGAGTCTGATTACCAATTCAAATCAGGCGGCAGCCTCATTTT




GCAATAAAAATAATACCAGCATTGTGAAACCGCTGAGTACCGGCCGCATTCTGGGT




AAAAATAAAATTGGCATTATTCAGACCAATCTGGTTGAAACCCATGAAAATATTCA




GGGCCTGGAACTGTCTCCGGCTTATTTTCAGGATTATATTCCGAAAGATACCGAAA




TTCGTCTGACCATTGTTGGTAATAAACTGTTTGGCGCCAATATTAAATCAACCAAT




CAGGTTGATTGGCGCAAAAATGATGCACTGCTGGAATATAAACCGGCCAATATTCC




GGATAAAATTGCCAAAATGTGTCTGGAAATGATGGAAAAACTGGAAATTAATTTTG




CGGCGTTTGATTTTATTATTCGTAATGGTGATTATATTTTTCTGGAACTGAATGCC




AATGGTCAGTGGCTGTGGCTGGAAGATATTCTGAAATTTGATATTTCAAATACCAT




TATTAATTATCTGCTGGGTGAACCGATTTAATAATAA



thcoK
ATGACGAGAACCAACACCGGCTATCGTTATCGCGCGTTCGGCCTGCGCATAGACTC
232



AGATATTCCGCTGCCAGAATTAGGGGACGGTACGCGCCCTGATGGTGACGCGGATC




TGACGGTCGTCCGGTGTGGGGAAGCGGAGCCGGAATGGGCTGAAGGTGGTGGCGGG




GGTCGTCTGTATGCCGCTGAAGGCATTGTATCTTTTCGCGTGCCGCAGACGGCAGC




GTTCCGTATTACTAATGGAAATCGCATCGAGGTGCATGCCTACTCGGGGGCTGATG




AGGATCGAATACGCCTGTACGTGTTAGGGACCTGTATGGGAGCGCTGTTACTGCAA




CGTAGAATCTTACCGCTTCATGGTTCGGTCGTCGCCCGTGATGGTCGTGCGTATGC




CATAGTTGGCGAAAGCGGAGCGGGCAAATCCACGATGAGTGCAGCACTTCTCGAAC




GTGGATTCCGCCTCGTTACGGATGACGTGGCCGCCATCGTGTTCGATGAGCGTGGG




ACCCCACTGGTTATGCCGGCTTATCCACAGCAAAAACTGTGGCAGGATTCCCTGGA




CCGTCTGCAAATTGCGGGCTCGGGCCTTCGTCCGCTGTTCGAACGCGAAACGAAAT




ACGCTGTACCCGCGGATGGGGCATTCTGGCCCGAACCGGTTCCATTGGTGCACATT




TACGAACTGGTTCATAGCGATGGTCAAACGCCTGAACTGCAGCCGATTGCCAAATT




AGAGCGTTGCTATACCTTGTATCGCCACACATTTCGTAGAAGCCTGATCGTCCCCA




GCGGCTTAAGCGCCTGGCATTTTGAAACGGCAGTGAAACTTGCGGAGAAAACGGGG




ATGTACCGTCTTATGCGCCCGGCCAAAGTTTTCGCGGCTCGCGAATCTGCTCGGCT




GATTGAAACTCACGCCGATGGTGAAGTGTCACGTTAATAA











Wild-type Precursor Peptides









epiA
GAAGCAGTTAAAGAGAAGAACGATCTGTTCAACCTGGATGTTAAAGTCAACGCAAA
233



AGAAAGTAACGATAGTGGCGCAGAACCACGCATAGCGTCGAAATTTATTTGCACAC




CAGGCTGCGCGAAAACGGGTTCGTTTAACAGCTATTGTTGTTAATAA



lasA
ATGGACAAACGTGTGCGTTACGAAAAACCGAGCCTGGTGAAAGAGGGTACGTTTCG
234



CAAAACTACCGCTGGCCTGCGGCGTCTGTTCGCTGACCAGCTGGTTGGCCGCCGTA




ACATTTAATAA



paaP
ATGATTAAATTTTCTACATTGTCTCAGCGCATCAGCGCCATCACGGAAGAAAACGC
235



CATGTACACTAAGGGTCAAGTGATCGTATTGAGCTGATAA



padeA
AAAAAGCAATATAGCAAACCTAGCCTGGAGGTTCTGGACGTCCACCAGACCATGGC
236



TGGCCCGGGCACTAGTACGCCAGACGCGTTTCAGCCAGATCCAGATGAAGATGTTC




ACTATGATTCGTAATAA



palA
AAAGATCTTCTGAAGGAACTGATGTATGAAGTAGACCTCGAAGAGATGGAGAATCT
237



TCAGGGTAGCGGGTACTCAGCCGCCCAGTGTGCCTGGATGGCGCTGAGCTGCGTCA




ATTACATCCCGGGAGTGGGATTCGGTTGTGGCGGCTACAGCGCATGTGAACTCTAC




AAGCGTTATTGTTAATAA



plpA2
ATGTCTATTGAGAGTGCAAAGGCTTTCTACCAGCGTATGACGGATGACGCATCTTT
238



TCGTACCCCTTTTGAAGCGGAACTGTCGAAAGAGGAGCGCCAACAATTAATCAAAG




ATAGCGGATATGACTTTACTGCAGAAGAATGGCAACAGGCTATGACCGAGATCCAG




GCGGCACGCTCAAACGAGGAACTGAATGAGGAAGAACTCGAGGCAATTGCCGGGGG




CGCTGTGGCCGCAATGTATGGTGTGGTTTTCCCATGGGACAACGAGTTCCCGTGGC




CCCGCTGGGGCGGTTAATAA



tgnA*
TATCGACCTTATATTGCCAAGTATGTCGAAGAACAAACTCTGCAGAATTCAACCAA
239



CCTGGTATATGACGACATCACGCAGATCTCTTTTATCAATAAAGAAAAGAACGTGA




AAAAAATTAATCTGGGTCCCGATACTACGATCGTGACTGAAACCATCGAGAATGCG




GACCCCGATGAGTATTTCTTATAATAA



thcoA
CGCAAGAAAGAATGGCAGACACCAGAACTGGAAGTACTCGATGTACGCCTCACCGC
240



AGCGGGCCCGGGTAAAGCTAAACCGGATGCTGTGCAGCCAGACGAAGATGAAATAG




TGCACTACTCATAATAA











Plasmid Origins









pSC101 var2
AGTAAGACGGGTAAGCCTGTTGATGATACCGCTGCCTTACTGGGTGCATTAGCCAG
241



TCTGAATGACCTGTCACGGGATAATCCGAAGTGGTCAGACTGGAAAATCAGAGGGC




AGGAACTGCTGAACAGCAAAAAGTCAGATAGCACCACATAGCAGACCCGCCATAAA




ACGCCCTGAGAAGCCCGTGACGGGCTTTTCTTGTATTATGGGTAGTTTCCTTGCAT




GAATCCATAAAAGGCGCCTGTAGTGCCATTTACCCCCATTCACTGCCAGAGCCGTG




AGCGCAGCGAACTGAATGTCACGAAAAAGACAGCGACTCAGGTGCCTGATGGTCGG




AGACAAAAGGAATATTCAGCGATTTGCCCGAGCTTGCGAGGGTGCTACTTAAGCCT




TTAGGGTTTTAAGGTCTGTTTTGTAGAGGAGCAAACAGCGTTTGCGACATCCTTTT




GTAATACTGCGGAACTGACTAAAGTAGTGAGTTATACACAGGGCTGGGATCTATTC




TTTTTATCTTTTTTTATTCTTTCTTTATTCTATAAATTATAACCACTTGAATATAA




ACAAAAAAAACACACAAAGGTCTAGCGGAATTTACAGAGGGTCTAGCAGAATTTAC




AAGTTTTCCAGCAAAGGTCTAGCAGAATTTACAGATACCCACAACTCAAAGGAAAA




GGACTAGTAATTATCATTGACTAGCCCATCTCAATTGGTATAGTGATTAAAATCAC




CTAGACCAATTGAGATGTATGTCTGAATTAGTTGTTTTCAAAGCAAATGAACTAGC




GATTAGTCGCTATGACTTAACGGAGCATGAAACCAAGCTAATTTTATGCTGTGTGG




CACTACTCAACCCCACGATTGAAAACCCTACAAGGAAAGAACGGACGGTATCGTTC




ACTTATAACCAATACGCTCAGATGATGAACATCAGTAGGGAAAATGCTTATGGTGT




ATTAGCTAAAGCAACCAGAGAGCTGATGACGAGAACTGTGGAAATCAGGAATCCTT




TGGTTAAAGGCTTTTGGATTTTCCAGTGGACAAACTATGCCAAGTTCTCAAGCGAA




AAATTAGAATTAGTTTTTAGTGAAGAGATATTGCCTTATCTTTTCCAGTTAAAAAA




ATTCATAAAATATAATCTGGAACATGTTAAGTCTTTTGAAAACAAATACTCTATGA




GGATTTATGAGTGGTTATTAAAAGAACTAACACAAAAGAAAACTCACAAGGCAAAT




ATAGAGATTAGCCTTGATGAATTTAAGTTCATGTTAATGCTTGAAAATAACTACCA




TGAGTTTAAAAGGCTTAACCAATGGGTTTTGAAACCAATAAGTAAAGATTTAAACA




CTTACAGCAATATGAAATTGGTGGTTGATAAGCGAGGCCGCCCGACTGATACGTTG




ATTTTCCAAGTTGAACTAGATAGACAAATGGATCTCGTAACCGAACTTGAGAACAA




CCAGATAAAAATGAATGGTGACAAAATACCAACAACCATTACATCAGATTCCTACC




TACATAACGGACTAAGAAAAACACTACACGATGCTTTAACTGCAAAAATTCAGCTC




ACCAGTTTTGAGGCAAAATTTTTGAGTGACATGCAAAGTAAGTATGATCTCAATGG




TTCGTTCTCATGGCTCACGCAAAAACAACGAACCACACTAGAGAACATACTGGCTA




AATACGGAAGGATCTGAGGTTCTTATGGCTCTTGTATCTATCAGTGAAGCATCAAG




ACTAACAAACAAAAGTAGAACAACTGTTCACCGTTACATATCAAAGGGAAAACTGT




CCATATGCACAGATGAAAACGGTGTAAAAAAGATAGATACATCAGAGCTTTTACGA




GTTTTTGGTGCATTCAAAGCTGTTCACCATGAACAGATCGACAATGTAACAGATGA




ACAGCATGTAACACCTAATAGAACAGGTGAAACCAGTAAAACAAAGCAACTAGAAC




ATGAAATTGAACACCTGAGACAACTTGTTACAGCTCAACAGTCACACATAGACAGC




CTGAAACAGGCGATGCTGCTTATCGAATCAAAGCTGCCGACAACACGGGAGCCAGT




GACGCCTCCCGTGGGGAAAAAATCATGGCAATTCTGGAAGAAATAGCGCTTTCAGC




CGGCAAACCGGCTGAAGCCGGATCTGCGATTCTGATAACAAACTAGCAACACCAGA




ACAGCCCGTTTGCGGGCAGCAAAACCCGTAC



p15A
TTAATAAGATGATCTTCTTGAGATCGTTTTGGTCTGCGCGTAATCTCTTGCTCTGA
242



AAACGAAAAAACCGCCTTGCAGGGCGGTTTTTCGAAGGTTCTCTGAGCTACCAACT




CTTTGAACCGAGGTAACTGGCTTGGAGGAGCGCAGTCACCAAAACTTGTCCTTTCA




GTTTAGCCTTAACCGGCGCATGACTTCAAGACTAACTCCTCTAAATCAATTACCAG




TGGCTGCTGCCAGTGGTGCTTTTGCATGTCTTTCCGGGTTGGACTCAAGACGATAG




TTACCGGATAAGGCGCAGCGGTCGGACTGAACGGGGGGTTCGTGCATACAGTCCAG




CTTGGAGCGAACTGCCTACCCGGAACTGAGTGTCAGGCGTGGAATGAGACAAACGC




GGCCATAACAGCGGAATGACACCGGTAAACCGAAAGGCAGGAACAGGAGAGCGCAC




GAGGGAGCCGCCAGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCA




CCACTGATTTGAGCGTCAGATTTCGTGATGCTTGTCAGGGGGGCGGAGCCTATGGA




AAAACGGCTTTGCCGCGGCCCTCTCACTTCCCTGTTAAGTATCTTCCTGGCATCTT




CCAGGAAATCTCCGCCCCGTTCGTAAGCCATTTCCGCTCGCCGCAGTCGAACGACC




GAGCGTAGCGAGTCAGTGAGCGAGGAAGCGGAATATATCCTGTATCACATATTCTG




CTGACGCACCGGTGCAGCCTTTTTTCTCCTGCCACATGAAGCACTTCACTGACACC




CTCATCAGTGCCAACATAGTAAGCCAGTATACACTCCGCTA






aPlpXY genes were synthesized/expressed as RBSPLpX + PlpX + RBSPlpY + PlpY.














TABLE 10







Plasmid backbone/chassis sequences.











SEQ




ID


Name
Sequencea
NO





N-term SUMO
CACATTTCCCCGAAAAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGACATTAA
243


Backbone 2
CCTATAAAAATAGGCGTATCACGAGGCAGAATTTCAGATAAAAAAAATCCTTAGCTTTC





GCTAAGGATGATTTCTGGAATTCGCGGCCGCTTCTAGAGGGAGAACGATCGTTGGCTGa





atcataaaaaatttatttgctttgtgagcggataacaattataatagattcaattgtga






embedded image







TTACCACCATCACCATCATCACGGGTCCCTGCAGGACTCAGAAGTCAATCAAGAAGCTA






AGCCAGAGGTCAAGCCAGAAGTCAAGCCTGAGACTCACATCAATTTAAAGGTGTCCGAT






GGATCTTCAGAGATCTTCTTCAAGATCAAAAAGACCACTCCTTTAAGAAGGCTGATGGA






AGCGTTCGCTAAAAGACAGGGTAAGGAAATGGACTCCTTAAGATTCTTGTACGACGGTA






TTAGAATTCAAGCTGATCAGGCCCCTGAAGATTTGGACATGGAGGATAACGATATTATT






GAGGCTCACCGCGAACAGATTGGAGGTTGCATGTCATATTACGACTCCATTCCCACAAG






CGAGAACTTGTACTTTCAAGGGTGC

ATGAGCAAAGGAGAAGAACTTTTCACTGGAGTTG








TCCCAATTCTTGTTGAATTAGATGGTGATGTTAATGGGCACAAATTTTCTGTCCGTGGA








GAGGGTGAAGGTGATGCTACAAACGGAAAACTCACCCTTAAATTTATTTGCACTACTGG








AAAACTACCTGTTCCGTGGCCAACACTTGTCACTACTCTGACCTATGGTGTTCAATGCT








TTTCCCGTTATCCGGATCACATGAAACGGCATGACTTTTTCAAGAGTGCCATGCCCGAA








GGTTATGTACAGGAACGCACTATATCTTTCAAAGATGACGGGACCTACAAGACGCGTGC








TGAAGTCAAGTTTGAAGGTGATACCCTTGTTAATCGTATCGAGTTAAAGGGTATTGATT








TTAAAGAAGATGGAAACATTCTTGGACACAAACTCGAGTACAACTTTAACTCACACAAT








GTATACATCACGGCAGACAAACAAAAGAATGGAATCAAAGCTAACTTCAAAATTCGCCA








CAACGTTGAAGATGGTTCCGTTCAACTAGCAGACCATTATCAACAAAATACTCCAATTG








GCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTCGACACAATCTGTCCTTTCG








AAAGATCCCAACGAAAAGCGTGACCACATGGTCCTTCTTGAGTTTGTAACTGCTGCTGG








GATTACACATGGCATGGATGAGCTCTACAAATAA

TTCAGCCAAAAAACTTAAGACCGCC






GGTCTTGTCCACTACCTTGCAGTAATGCGGTGGACAGGATCGGCGGTTTTCTTTTCTCT






TCTCAACCAATGgcggcgcgccatcgaatggcgcaaaacctttcgcggtatggcatgat







embedded image







GTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAG






CCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACA






TTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTTATTGGCGTTGCC






ACCTCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGC






CGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCT






GTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTAT






CCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTT






ATTTCTTGATGTCTCTGACCAGACACCCATCAACAGTATTATTTTCTCCCATGAGGACG






GTACGCGACTGGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTA






GCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCT






CACTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCCG






GTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTT






GCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGCTGCGCGT






TGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGATAGCTCATGTTATATCC






CGCCGTTAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGC






TTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCAGTCTCACT






GGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGG






CCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGATAA






TTGGTAACGAATCAGACAATTGACGGCTCGAGGGAGTAGCATAGGGTTTGCAGAATCCC






TGCTTCGTCCATTTGACAGGCACATTATGCATCGATGATAAGCTGTCAAACATGAGCAC





GCTTACTAGTAGCGGCCGCTGCAGTCCGGCAAAAAAGGGCAAGGTGTCACCACCCTGCC





CTTTTTCTTTAAAACCGAAAAGATTACTTCGCGTTATGCAGGCTTCCTCGCTCACTGAC





TCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAAT




GACAGTAAGACGGGTAAGCCTGTTGATGATACCGCTGCCTTACTGGGTGCATTAGCCAG




TCTGAATGACCTGTCACGGGATAATCCGAAGTGGTCAGACTGGAAAATCAGAGGGCAGG




AACTGCTGAACAGCAAAAAGTCAGATAGCACCACATAGCAGACCCGCCATAAAACGCCC




TGAGAAGCCCGTGACGGGCTTTTCTTGTATTATGGGTAGTTTCCTTGCATGAATCCATA




AAAGGCGCCTGTAGTGCCATTTACCCCCATTCACTGCCAGAGCCGTGAGCGCAGCGAAC




TGAATGTCACGAAAAAGACAGCGACTCAGGTGCCTGATGGTCGGAGACAAAAGGAATAT




TCAGCGATTTGCCCGAGCTTGCGAGGGTGCTACTTAAGCCTTTAGGGTTTTAAGGTCTG




TTTTGTAGAGGAGCAAACAGCGTTTGCGACATCCTTTTGTAATACTGCGGAACTGACTA




AAGTAGTGAGTTATACACAGGGCTGGGATCTATTCTTTTTATCTTTTTTTATTCTTTCT




TTATTCTATAAATTATAACCACTTGAATATAAACAAAAAAAACACACAAAGGTCTAGCG




GAATTTACAGAGGGTCTAGCAGAATTTACAAGTTTTCCAGCAAAGGTCTAGCAGAATTT




ACAGATACCCACAACTCAAAGGAAAAGGACTAGTAATTATCATTGACTAGCCCATCTCA




ATTGGTATAGTGATTAAAATCACCTAGACCAATTGAGATGTATGTCTGAATTAGTTGTT




TTCAAAGCAAATGAACTAGCGATTAGTCGCTATGACTTAACGGAGCATGAAACCAAGCT




AATTTTATGCTGTGTGGCACTACTCAACCCCACGATTGAAAACCCTACAAGGAAAGAAC




GGACGGTATCGTTCACTTATAACCAATACGCTCAGATGATGAACATCAGTAGGGAAAAT




GCTTATGGTGTATTAGCTAAAGCAACCAGAGAGCTGATGACGAGAACTGTGGAAATCAG




GAATCCTTTGGTTAAAGGCTTTTGGATTTTCCAGTGGACAAACTATGCCAAGTTCTCAA




GCGAAAAATTAGAATTAGTTTTTAGTGAAGAGATATTGCCTTATCTTTTCCAGTTAAAA




AAATTCATAAAATATAATCTGGAACATGTTAAGTCTTTTGAAAACAAATACTCTATGAG




GATTTATGAGTGGTTATTAAAAGAACTAACACAAAAGAAAACTCACAAGGCAAATATAG




AGATTAGCCTTGATGAATTTAAGTTCATGTTAATGCTTGAAAATAACTACCATGAGTTT




AAAAGGCTTAACCAATGGGTTTTGAAACCAATAAGTAAAGATTTAAACACTTACAGCAA




TATGAAATTGGTGGTTGATAAGCGAGGCCGCCCGACTGATACGTTGATTTTCCAAGTTG




AACTAGATAGACAAATGGATCTCGTAACCGAACTTGAGAACAACCAGATAAAAATGAAT




GGTGACAAAATACCAACAACCATTACATCAGATTCCTACCTACATAACGGACTAAGAAA




AACACTACACGATGCTTTAACTGCAAAAATTCAGCTCACCAGTTTTGAGGCAAAATTTT




TGAGTGACATGCAAAGTAAGTATGATCTCAATGGTTCGTTCTCATGGCTCACGCAAAAA




CAACGAACCACACTAGAGAACATACTGGCTAAATACGGAAGGATCTGAGGTTCTTATGG




CTCTTGTATCTATCAGTGAAGCATCAAGACTAACAAACAAAAGTAGAACAACTGTTCAC




CGTTACATATCAAAGGGAAAACTGTCCATATGCACAGATGAAAACGGTGTAAAAAAGAT




AGATACATCAGAGCTTTTACGAGTTTTTGGTGCATTCAAAGCTGTTCACCATGAACAGA




TCGACAATGTAACAGATGAACAGCATGTAACACCTAATAGAACAGGTGAAACCAGTAAA




ACAAAGCAACTAGAACATGAAATTGAACACCTGAGACAACTTGTTACAGCTCAACAGTC




ACACATAGACAGCCTGAAACAGGCGATGCTGCTTATCGAATCAAAGCTGCCGACAACAC




GGGAGCCAGTGACGCCTCCCGTGGGGAAAAAATCATGGCAATTCTGGAAGAAATAGCGC




TTTCAGCCGGCAAACCGGCTGAAGCCGGATCTGCGATTCTGATAACAAACTAGCAACAC




CAGAACAGCCCGTTTGCGGGCAGCAAAACCCGTACCGATTATCAAAAAGGATCTTCACC




TAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAAC




TTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTAT




TTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGC




TTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGAACCACGCTCACCGGCTCCAGA




TTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTT




TATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCA




GTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTC




GTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCC




CCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAG




TTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCAT




GCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAAT




AGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCA




CATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTC




AAGGATCTTACCGCTGTTGAGATCCAGTTCGATATAACCCACTCGTGCACCCAACTGAT




CTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAAT




GCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTT




TCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAAT




GTATTTAGAAAAATAAACAAATAGGGGTTCCGCG






N-term SUMO
CACATTTCCCCGAAAAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGACATTAA
244


Backbone 3
CCTATAAAAATAGGCGTATCACGAGGCAGAATTTCAGATAAAAAAAATCCTTAGCTTTC





GCTAAGGATGATTTCTGGAATTCGCGGCCGCTTCTAGAGGGAGGGTCTCAGTGCAACGA





TCGTTGGCTGaatcataaaaaatttatttgctttgtgagcggataacaattataataga






embedded image








embedded image







TCAAGAAGCTAAGCCAGAGGTCAAGCCAGAAGTCAAGCCTGAGACTCACATCAATTTAA






AGGTGTCCGATGGATCTTCAGAGATCTTCTTCAAGATCAAAAAGACCACTCCTTTAAGA






AGGCTGATGGAAGCGTTCGCTAAAAGACAGGGTAAGGAAATGGACTCCTTAAGATTCTT






GTACGACGGTATTAGAATTCAAGCTGATCAGGCCCCTGAAGATTTGGACATGGAGGATA






ACGATATTATTGAGGCTCACCGCGAACAGATTGGAGGTTGCATGTCATATTACGACTCC






ATTCCCACAAGCGAGAACTTGTACTTTCAAGGGTGC

ATGAGCAAAGGAGAAGAACTTTT








CACTGGAGTTGTCCCAATTCTTGTTGAATTAGATGGTGATGTTAATGGGCACAAATTTT








CTGTCCGTGGAGAGGGTGAAGGTGATGCTACAAACGGAAAACTCACCCTTAAATTTATT








TGCACTACTGGAAAACTACCTGTTCCGTGGCCAACACTTGTCACTACTCTGACCTATGG








TGTTCAATGCTTTTCCCGTTATCCGGATCACATGAAACGGCATGACTTTTTCAAGAGTG








CCATGCCCGAAGGTTATGTACAGGAACGCACTATATCTTTCAAAGATGACGGGACCTAC








AAGACGCGTGCTGAAGTCAAGTTTGAAGGTGATACCCTTGTTAATCGTATCGAGTTAAA








GGGTATTGATTTTAAAGAAGATGGAAACATTCTTGGACACAAACTCGAGTACAACTTTA








ACTCACACAATGTATACATCACGGCAGACAAACAAAAGAATGGAATCAAAGCTAACTTC








AAAATTCGCCACAACGTTGAAGATGGTTCCGTTCAACTAGCAGACCATTATCAACAAAA








TACTCCAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTCGACACAAT








CTGTCCTTTCGAAAGATCCCAACGAAAAGCGTGACCACATGGTCCTTCTTGAGTTTGTA








ACTGCTGCTGGGATTACACATGGCATGGATGAGCTCTACAAATAA

TTCAGCCAAAAAAC






TTAAGACCGCCGGTCTTGTCCACTACCTTGCAGTAATGCGGTGGACAGGATCGGCGGTT






TTCTTTTCTCTTCTCAACAAGTGAGACCATGGgcggcgcgccatcgaatggcgcaaaac







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AACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCC






CGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGC






GATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGT






CGTTGCTTATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGTC






GCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGA






ACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCA






GTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCC






TGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGACACCCATCAACAGTAT






TATTTTCTCCCATGAGGACGGTACGCGACTGGGCGTGGAGCATCTGGTCGCATTGGGTC






ACCAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTG






GCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGG






CGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCG






TTCCCACTGCGATGCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATT






ACCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGA






AGATAGCTCATGTTATATCCCGCCGTTAACCACCATCAAACAGGATTTTCGCCTGCTGG






GGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAAT






CAGCTGTTGCCAGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAAC






CGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGAC






TGGAAAGCGGGCAGTGATAA
TTGGTAACGAATCAGACAATTGACGGCTCGAGGGAGTAG






CATAGGGTTTGCAGAATCCCTGCTTCGTCCATTTGACAGGCACATTATGCATCGATGAT






AAGCTGTCAAACATGAGCACGCTTACTAGTAGCGGCCGCTGCAGTCCGGCAAAAAAGGG






CAAGGTGTCACCACCCTGCCCTTTTTCTTTAAAACCGAAAAGATTACTTCGCGTTATGC





AGGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCA




GCTCACTCAAAGGCGGTAATGACAGTAAGACGGGTAAGCCTGTTGATGATACCGCTGCC




TTACTGGGTGCATTAGCCAGTCTGAATGACCTGTCACGGGATAATCCGAAGTGGTCAGA




CTGGAAAATCAGAGGGCAGGAACTGCTGAACAGCAAAAAGTCAGATAGCACCACATAGC




AGACCCGCCATAAAACGCCCTGAGAAGCCCGTGACGGGCTTTTCTTGTATTATGGGTAG




TTTCCTTGCATGAATCCATAAAAGGCGCCTGTAGTGCCATTTACCCCCATTCACTGCCA




GAGCCGTGAGCGCAGCGAACTGAATGTCACGAAAAAGACAGCGACTCAGGTGCCTGATG




GTCGGAGACAAAAGGAATATTCAGCGATTTGCCCGAGCTTGCGAGGGTGCTACTTAAGC




CTTTAGGGTTTTAAGGTCTGTTTTGTAGAGGAGCAAACAGCGTTTGCGACATCCTTTTG




TAATACTGCGGAACTGACTAAAGTAGTGAGTTATACACAGGGCTGGGATCTATTCTTTT




TATCTTTTTTTATTCTTTCTTTATTCTATAAATTATAACCACTTGAATATAAACAAAAA




AAACACACAAAGGTCTAGCGGAATTTACAGAGGGTCTAGCAGAATTTACAAGTTTTCCA




GCAAAGGTCTAGCAGAATTTACAGATACCCACAACTCAAAGGAAAAGGACTAGTAATTA




TCATTGACTAGCCCATCTCAATTGGTATAGTGATTAAAATCACCTAGACCAATTGAGAT




GTATGTCTGAATTAGTTGTTTTCAAAGCAAATGAACTAGCGATTAGTCGCTATGACTTA




ACGGAGCATGAAACCAAGCTAATTTTATGCTGTGTGGCACTACTCAACCCCACGATTGA




AAACCCTACAAGGAAAGAACGGACGGTATCGTTCACTTATAACCAATACGCTCAGATGA




TGAACATCAGTAGGGAAAATGCTTATGGTGTATTAGCTAAAGCAACCAGAGAGCTGATG




ACGAGAACTGTGGAAATCAGGAATCCTTTGGTTAAAGGCTTTTGGATTTTCCAGTGGAC




AAACTATGCCAAGTTCTCAAGCGAAAAATTAGAATTAGTTTTTAGTGAAGAGATATTGC




CTTATCTTTTCCAGTTAAAAAAATTCATAAAATATAATCTGGAACATGTTAAGTCTTTT




GAAAACAAATACTCTATGAGGATTTATGAGTGGTTATTAAAAGAACTAACACAAAAGAA




AACTCACAAGGCAAATATAGAGATTAGCCTTGATGAATTTAAGTTCATGTTAATGCTTG




AAAATAACTACCATGAGTTTAAAAGGCTTAACCAATGGGTTTTGAAACCAATAAGTAAA




GATTTAAACACTTACAGCAATATGAAATTGGTGGTTGATAAGCGAGGCCGCCCGACTGA




TAGGTTGATTTTCCAAGTTGAACTAGATAGACAAATGGATCTCGTAACCGAACTTGAGA




ACAACCAGATAAAAATGAATGGTGACAAAATACCAACAACCATTACATCAGATTCCTAC




CTACATAACGGACTAAGAAAAACACTACACGATGCTTTAACTGCAAAAATTCAGCTCAC




CAGTTTTGAGGCAAAATTTTTGAGTGACATGCAAAGTAAGTATGATCTCAATGGTTCGT




TCTCATGGCTCACGCAAAAACAACGAACCACACTAGAGAACATACTGGCTAAATACGGA




AGGATCTGAGGTTCTTATGGCTCTTGTATCTATCAGTGAAGCATCAAGACTAACAAACA




AAAGTAGAACAACTGTTCACCGTTACATATCAAAGGGAAAACTGTCCATATGCACAGAT




GAAAACGGTGTAAAAAAGATAGATACATCAGAGCTTTTACGAGTTTTTGGTGCATTCAA




AGCTGTTCACCATGAACAGATCGACAATGTAACAGATGAACAGCATGTAACACCTAATA




GAACAGGTGAAACCAGTAAAACAAAGCAACTAGAACATGAAATTGAACACCTGAGACAA




CTTGTTACAGCTCAACAGTCACACATAGACAGCCTGAAACAGGCGATGCTGCTTATCGA




ATCAAAGCTGCCGACAACACGGGAGCCAGTGACGCCTCCCGTGGGGAAAAAATCATGGC




AATTCTGGAAGAAATAGCGCTTTCAGCCGGCAAACCGGCTGAAGCCGGATCTGCGATTC




TGATAACAAACTAGCAACACCAGAACAGCCCGTTTGCGGGCAGCAAAACCCGTACCGAT




TATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATC




TAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACC




TATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGA




TAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGAA




CCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCG




CAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAG




CTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGC




ATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATC




AAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTC




CGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTG




CATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTC




AACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAA




TACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGT




TCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATATAACC




CACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAG




CAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGA




ATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCAT




GAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCG






Cumate
AACACCCCTTGTATTACTGTTTATGTAAGCAGACAGTTTTATTGTTCATGATGATATAT
245


Modifying
TTTTATCTTGTGCAATGTACATCAGAGATTTTGAGACACAACCAATTATTGAAGGCCTC



Enzyme

CCTAACGGGGGGCCTTTTTTTGTTTCTGGTCTCCCAAGCGCTTAACGATCGTTGGCTGa




Backbone
acaaacagacaatctggtctgtttgtattatggaaaatttttctgtataatagattcaa




caaacagacaatctggtctgtttgtattatCAGCGGTCAACGCATGTGCTTTGCGTTCT






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TGTTGAATTAGATGGTGATGTTAATGGGCACAAATTTTCTGTCCGTGGAGAGGGTGAAG








GTGATGCTACAAACGGAAAACTCACCCTTAAATTTATTTGCACTACTGGAAAACTACCT








GTTCCGTGGCCAACACTTGTCACTACTCTGACCTATGGTGTTCAATGCTTTTCCCGTTA








TCCGGATCACATGAAACGGCATGACTTTTTCAAGAGTGCCATGCCCGAAGGTTATGTAC








AGGAACGCACTATATCTTTCAAAGATGACGGGACCTACAAGACGCGTGCTGAAGTCAAG








TTTGAAGGTGATACCCTTGTTAATCGTATCGAGTTAAAGGGTATTGATTTTAAAGAAGA








TGGAAACATTCTTGGACACAAACTCGAGTACAACTTTAACTCACACAATGTATACATCA








CGGCAGACAAACAAAAGAATGGAATCAAAGCTAACTTCAAAATTCGCCACAACGTTGAA








GATGGTTCCGTTCAACTAGCAGACCATTATCAACAAAATACTCCAATTGGCGATGGCCC








TGTCCTTTTACCAGACAACCATTACCTGTCGACACAATCTGTCCTTTCGAAAGATCCCA








ACGAAAAGCGTGACCACATGGTCCTTCTTGAGTTTGTAACTGCTGCTGGGATTACACAT








GGCATGGATGAGCTCTACAAATAA
TGAAGAGCGCAGAGGTGGTTGTGTTGCGAAAAAAA






AAAAAAACACCCTAACGGGTGTTTTTTTTTTTTTGGTGTCCCCACGTGTGGCGCTGGAG





ACCGTCCAATGgcggcgcgccatcgaatggtgcaaaacctttcgcggtatggcatgata






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CAGAACGTGCAATGGAAACCCAGGGTAAACTGATTGCAGCAGCACTGGGTGTTCTGCGT






GAAAAAGGTTATGCAGGTTTTCGTATTGCAGATGTTCCGGGTGCAGCCGGTGTTAGCCG






TGGTGCACAGAGCCATCATTTTCCGACCAAACTGGAACTGCTGCTGGCAACCTTTGAAT






GGCTGTATGAGCAGATTACCGAACGTAGCCGTGCACGTCTGGCAAAACTGAAACCGGAA






GATGATGTTATTCAGCAGATGCTGGATGATGCAGCAGATTTTTTTCTGGATGATGATTT






TAGCATCGGCCTGGATCTGATTGTTGCAGCAGATCGTGATCCGGCACTGCGTGAAGGTA






TTCTGCGTACCGTTGAACGTAATCGTTTTGTTGTTGAAGATATGTGGCTGGGTGTGCTG






GTGAGCCGTGGTCTGAGCCGTGATGATGCCGAAGATATTCTGTGGCTGATTTTTAACAG






CGTTCGTGGTCTGACAGTTCGTAGCCTGTGGCAGAAAGATAAAGAACGTTTTGAACGTG






TGCGTAATAGCACCCTGGAAATTGCACGTGAACGTTATGCAAAATTCAAACGTTGATAA





GGATCCTAATTGGTAACGAATCAGACAATTGACGGCTCGAGGGAGTAGCATAGGGTTTG





CAGAATCCCTGCTTCGTCCATTTGACAGGCACATTATGCATCGATGATAAGCTGTCAAA






CATGAGCAGATCCTCTACGCCGGACGCATCGTGGCCGGCATCACCGGCGCCACAGGTGC






GGTTGCTGGCGCCTATATCGCCGACATCACCGATGGGGAAGATCGGGCTCGCCACTTCG






GGCTCATGAGCAAATATTTTATCTGAGGTGCTTCCTCGCTCACTGACTCGCTGCACGAG





GCAGACCTCAGCGCTAGCGGAGTGTATACTGGCTTACTATGTTGGCACTGATGAGGGTG




TCAGTGAAGTGCTTCATGTGGCAGGAGAAAAAAGGCTGCACCGGTGCGTCAGCAGAATA




TGTGATACAGGATATATTCCGCTTCCTCGCTCACTGACTCGCTACGCTCGGTCGTTCGA




CTGCGGCGAGCGGAAATGGCTTACGAACGGGGCGGAGATTTCCTGGAAGATGCCAGGAA




GATACTTAACAGGGAAGTGAGAGGGCCGCGGCAAAGCCGTTTTTCCATAGGCTCCGCCC




CCCTGACAAGCATCACGAAATCTGACGCTCAAATCAGTGGTGGCGAAACCCGACAGGAC




TATAAAGATACCAGGCGTTTCCCCTGGCGGCTCCCTCGTGCGCTCTCCTGTTCCTGCCT




TTCGGTTTACCGGTGTCATTCCGCTGTTATGGCCGCGTTTGTCTCATTCCACGCCTGAC




ACTCAGTTCCGGGTAGGCAGTTCGCTCCAAGCTGGACTGTATGCACGAACCCCCCGTTC




AGTCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGAAAGACAT




GCAAAAGCACCACTGGCAGCAGCCACTGGTAATTGATTTAGAGGAGTTAGTCTTGAAGT




CATGCGCCGGTTAAGGCTAAACTGAAAGGACAAGTTTTGGTGACTGCGCTCCTCCAAGC




CAGTTACCTCGGTTCAAAGAGTTGGTAGCTCAGAGAACCTTCGAAAAACCGCCCTGCAA




GGCGGTTTTTTCGTTTTCAGAGCAAGAGATTACGCGCAGACCAAAACGATCTCAAGAAG




ATCATCTTATTAAGGGGTCTGACGCTCAGTGGAACGAAAAATCAATCTAAAGTATATAT




GAGTAAACTTGGTCTGACAGTTACCTTAGAAAAACTCATCGAGCATCAAATGAAACTGC




AATTTATTCATATCAGGATTATCAATACCATATTTTTGAAAAAGCCGTTTCTGTAATGA




AGGAGAAAACTCACCGAGGCAGTTCCATAGGATGGCAAGATCCTGGTATCGGTCTGCGA




TTCCGACTCGTCCAACATCAATACAACCTATTAATTTCCCCTCGTCAAAAATAAGGTTA




TCAAGTGAGAAATCACCATGAGTGACGACTGAATCCGGTGAGAATGGCAAAAGCTTATG




CATTTCTTTCCAGACTTGTTCAACAGGCCAGCCATTACGCTCGTCATCAAAATCACTCG




CATCAACCAAACCGTTATTCATTCGTGATTGCGCCTGAGCGAGACGAAATACGCGATCG




CTGTTAAAAGGACAATTACAAACAGGAATCGAATGCAACCGGCGCAGGAACACTGCCAG




CGCATCAACAATATTTTCACCTGAATCAGGATATTCTTCTAATACCTGGAATGCTGTTT




TCCCGGGGATCGCAGTGGTGAGTAACCATGCATCATCAGGAGTACGGATAAAATGCTTG




ATGGTCGGAAGAGGCATAAATTCCGTCAGCCAGTTTAGTCTGACCATCTCATCTGTAAC




ATCATTGGCAACGCTACCTTTGCCATGTTTCAGAAACAACTCTGGCGCATCGGGCTTCC




CATACAATCGATAGATTGTCGCACCTGATTGCCCGACATTATCGCGAGCCCATTTATAC




CCATATAAATCAGCATCCATGTTGGAATTTAATCGCGGCCTCGAGCAAGACGTTTCCCG




TTGAATATGGCTCAT






Multi-Enzyme
CCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAA
246


Backboneb
ACTTGGTCTGATTATTTGCCGACTACCTTGGTGATCTCGCCTTTCACGTAGTGGACAAA





TTCTTCCAACTGATCTGTGCGCGAGGCCAAGCGATCTTCTTCTTGTCCAAGATAAGCCT






GTCTAGCTTCAAGTATGACGGGCTGATACTGGGCCGGCAGGCGCTCCATTGCCCAGTCG






GCAGCGACATCCTTCGGCGCGATTTTGCCGGTTACTGCGCTGTACCAAATGCGGGACAA






CGTAAGCACTACATTTCGCTCATCGCCAGCCCAGTCGGGCGGCGAGTTCCATAGCGTTA






AGGTTTCATTTAGCGCCTCAAATAGATCCTGTTCAGGAACCGGATCAAAGAGTTCCTCC






GCCGCTGGACCTACCAAGGCAACGCTATGTTCTCTTGCTTTTGTCAGCAAGATAGCCAG






ATCAATGTCGATCGTGGCTGGCTCGAAGATACCTGCAAGAATGTCATTGCGCTGCCATT






CTCCAAATTGCAGTTCGCGCTTAGCTGGATAACGCCACGGAATGATGTCGTCGTGCACA






ACAATGGTGACTTCTACAGCGCGGAGAATCTCGCTCTCTCCAGGGGAAGCCGAAGTTTC






CAAAAGGTCGTTGATCAAAGCTCGCCGCGTTGTTTCATCAAGCCTTACGGTCACCGTAA






CCAGCAAATCAATATCACTGTGTGGCTTCAGGCCGCCATCCACTGCGGAGCCGTACAAA






TGTACGGCCAGCAACGTCGGTTCGAGATGGCGCTCGATGACGCCAACTACCTCTGATAG






TTGAGTCGATACTTCGGCGATCACCGCTTCCCTCATTTTAGCTTCCTTAGCTCCTGAAA





ATCTCGATAACTCAAAAAATACGCCCGGTAGTGATCTTATTTCATTATGGTGAAAGTTG




GAACCTCTTACGTGCCATTTCCCCGAAAAGTGCCACCTGACGTCTAAGAAACCATTATT




ATCATGACATTAACCTATAAAAATAGGCGTATCACGAGGCAGAATTTCAGATAAAAAAA





ATCCTTAGCTTTCGCTAAGGATGATTTCTGGAATTCGCGGCCGCTTCTAGAGCGCGAAG





ACTTACGAAAATCCGCTTAACGATCGTTGGCTGttttcagcaggacgcactgacctccc




tatcagtgatagagattgacatccctatcagtgatagagatactgagcacCAGGGTGTC





TCAAGGTGCGTACCTTGACTGATGAGTCCGAAAGGACGAAACACCCCTCTACAAATAAT







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CTGCAAATACAACCACATTTCCATGTAGAGGTCATTGAACCAAAGCAAGTCTACTTGTT






GGGTGAACAAGCTAATCATGCATTGACAGGCCAATTATACTGCCAAATTTTGCCATTGT






TAAACGGACAATACACATTGGAACAAATCGTTGAAAAACTAGACGGAGAAGTACCACCT






GAATACATTGATTATGTGCTGGAGAGACTAGCTGAGAAGGGCTATCTGACTGAAGCAGC






ACCTGAATTATCTAGTGAAGTGGCCGCTTTCTGGTCTGAGCTGGGGATTGCACCTCCTG






TCGCGGCCGAAGCATTACGTCAACCTGTGACTTTAACACCTGTTGGAAACATCAGCGAA






GTAACAGTAGCAGCCTTAACCACAGCCCTACGTGATATCGGTATTTCCGTTCAAACACC






TACAGAAGCTGGATCGCCAACTGCATTGAACGTTGTACTTACCGATGATTATCTCCAAC






CAGAACTCGCTAAGATCAATAAGCAAGCCTTAGAAAGTCAACAAACTTGGCTACTTGTC






AAACCAGTTGGCTCCGTGTTATGGTTGGGTCCGGTATTCGTGCCAGGAAAAACAGGTTG






CTGGGATTGTTTGGCTCACAGATTAAGGGGGAATAGAGAGGTAGAGGCCTCTGTATTGA






GACAAAAACAAGCTCAACAACAACGTAATGGACAAAGCGGGTCTGTAATAGGATGCCTT






CCCACGGCTAGAGCGACACTGCCCTCAACACTCCAAACTGGGCTGCAGTTCGCTGCTAC






CGAAATTGCTAAATGGATAGTTAAGTATCATGTTAATGCCACAGCGCCTGGCACCGTAT






TCTTCCCTACATTGGATGGTAAGATAATTACGCTAAATCACTCCATACTGGATTTGAAG






TCACATATTCTGATCAAGCGTTCTCAATGTCCCACCTGTGGTGACCCAAAAATCTTACA






GCACCGTGGTTTCGAACCTTTAAAACTTGAGTCAAGGCCTAAACAGTTCACCTCAGACG






GCGGACATCGTGGTACTACCCCTGAACAAACTGTCCAGAAATATCAACATTTAATCTCG






CCTGTTACCGGTGTAGTTACTGAATTGGTCAGGATAACTGATCCGGCCAATCCACTAGT






TCACACATATAGAGCTGGTCATAGCTTCGGGAGCGCTACATCGCTGAGAGGGCTGCGTA






ATACCTTAAAGCATAAGAGTTCAGGTAAGGGTAAGACTGATTCTCAAAGTAAAGCCTCG






GGCCTGTGTGAGGCGGTAGAACGTTACTCAGGAATCTTTCAAGGTGACGAACCGAGAAA






ACGCGCCACATTGGCTGAATTGGGAGATTTGGCAATTCACCCTGAGCAATGCTTGTGTT






TTTCCGACGGTCAGTACGCTAATAGAGAAACTTTAAACGAACAGGCAACGGTGGCACAT






GATTGGATACCTCAACGTTTTGATGCATCACAAGCTATTGAATGGACTCCAGTCTGGTC






CCTAACTGAACAGACCCATAAATATTTGCCCACCGCATTGTGTTACTACCATTATCCTC






TACCCCCAGAACACAGATTCGCACGTGGAGATTCGAATGGTAATGCTGCCGGAAATACG






TTGGAAGAGGCTATACTCCAAGGCTTCATGGAATTAGTCGAGAGAGATGGTGTGGCTTT






ATGGTGGTATAACAGGCTACGCAGACCCGCTGTAGACTTAGGCTCATTTAACGAGCCAT






ACTTCGTTCAGTTGCAACAATTCTACAGAGAAAACGATAGAGATTTGTGGGTTTTGGAC






TTGACAGCTGATTTAGGTATCCCGGCTTTCGCGGGCGTTTCTAATAGAAAAACTGGTAG






TTCGGAGAGGTTGATATTAGGATTCGGTGCACACCTCGATCCTACTATTGCAATTCTGA






GAGCAGTTACAGAAGTTAACCAGATTGGCCTTGAATTAGATAAAGTTCCAGACGAGAAC






CTTAAGAGCGACGCAACAGATTGGCTAATTACTGAAAAATTAGCTGACCACCCTTATTT






GTTACCAGATACAACTCAACCTCTAAAAACTGCTCAAGATTATCCTAAAAGGTGGTCTG






ACGATATATACACGGACGTAATGACTTGCGTTAATATTGCTCAACAAGCAGGACTTGAA






ACTCTAGTTATTGATCAAACACGTCCGGACATTGGTTTGAATGTTGTTAAGGTGACAGT






CCCGGGGATGAGGCACTTTTGGTCAAGATTTGGAGAGGGGAGGCTTTATGACGTGCCCG






TCAAATTAGGTTGGCTTGACGAACCTTTGACCGAAGCGCAAATGAACCCCACGCCGATG






CCTTTTTAATAATGAAGAGCTAAGCGTTGAACGCTACACGGACTCTAACTAAAAAGGCC






TCCCAAATCGGGGGGCCTTTTTTATTGATAACAAAACGGCATGCGCATGGACGACTACG





GATGCGGGCAAGGTGCCGCTTAACGATCGTTGGCTGccctttgtgcgtccaaacggacg




cacggcgctctaaagcgggtcgcgatctttcagattcgctcctcgcgctttcagtcttt




gttttggcgcatgtcgttatcgcaaaaccgctgcacacttttgcgcgacatgctctgat




ccccctcatctgggggggcctatctgagggaatttccgatccggctcgcctgaaccatt




ctgctttccacgaacttgaaaacgctCAGTCATAAGTCTGGGCTAAGCCCACTGATGAG





TCGCTGAAATGCGACGAAACTTATGACCTCTACAAATAATTTTGTTTAAGAGCCACCAG






TTATAAGGAGAACCTACCG
ATGACCAAAAAGTATCGGCGTGTATCCTACGCAGTGTGGG






AAATCACCCTGAAATGCAATCTGGCATGCTCTCATTGTGGCAGCCGCGCCGGCCAAGCC






CGTACGAAAGAGCTGAGTACCGAAGAAGCGTTCAACCTGGTCCGCCAGCTGGCCGACGT






GGGCATTAAGGAAGTCACCCTGATCGGTGGTGAAGCCTTTATGCGTTCGGATTGGCTGG






AAATCGCGAAAGCCGTCACTGAAGCCGGCATGATCTGTGGCATGACCACAGGGGGCTTC






GGGGTCAGTCTGGAAACGGCGCGTAAAATGAAAGAAGCGGGCATTAAAACGGTGAGCGT






TAGCATTGACGGTGGTATTCCTGAAACCCACGACCGCCAGCGCGGTAAAAAGGGTGCGT






GGCATAGTGCATTCCGGACTATGAGCCATCTGAAAGAAGTCGGGATCTACTTCGGTTGC






AACACTCAAATCAATCGTTTATCGGCGTCAGAATTCCCGATTATCTATGAACGTATTCG






CGATGCTGGGGCACGTGCGTGGCAAATTCAGCTGACGGTTCCGATGGGCAACGCCGCGG






ATAACGCAGATATGCTGCTGCAACCGTATGAATTGCTCGACATCTATCCGATGTTAGCC






CGCGTTGCCAAACGTGCGAAACAGGAAGGCGTGCGTATTCAGGCAGGTAACAACATCGG






GTACTATGGACCGTATGAGCGTCTGCTGCGTGGCAGCGACGAATGGACGTTTTGGCAAG






GATGTGGTGCGGGCCTTAACACCCTCGGCATCGAAGCCGACGGCAAAATCAAAGGCTGT






CCATCCCTGCCGACCGCCGCGTACACCGGCGGTAACATTCGCGATCGCCCGCTGCGGGA






AATCGTCGAACAGACCGAAGAACTGAAATTTAACTTAAAAGCTGGTACAGAACAAGGTA






CGGACCATATGTGGGGCTTTTGTAAAACCTGCGAATTCGCGGAACTCTGTCGCGGCGGA






TGCAGCTGGACTGCGCATGTGTTCTTTGACCGGCGCGGCAATAATCCGTACTGCCACCA






TCGGGCTCTGAAACAAGCCCAAAAAGACATTCGCGAACGCTTTTATTTAAAAGTGAAAG






CAAAGGGCAACCCGTTCGACAATGGTGAATTTGTTATCATTGAAGAACCTTTTAACGCT






CCGTTACCCGAGAATGACCTGCTGCACTTTAACAGTGATCACATTCAATGGCCAGAAAA






CTGGCAAAATAGTGAAAGCGCGTACGCATTGGCCAAGTAATAAATATAAAGTTAAGGAG






TTGCACATGAACAGTAATCAGATCCCTAACAAAGTTGCAACCGCGGCACAGAAATCTGA






CGACAGCAGCAGCGTATTACCGCGCCAGGGGTGGCAAGACAAACAAGCCTTTATTAAGG






CACTCATTAAAGCCAAACAGTCTCTCGAAATTGCCGAAATTAGCAACTTTTTAACCTAA





TAAAGAATTACCTACCGCGGTCGCTCGGTACCAAATTTTCGAAAAAAGACGCTGAAAAG





CGTCTTTTTTCGTTTTGGTCCCACGTGGCAAGCGCTTAACGATCGTTGGCTGaacaaac





agacaatctggtctgtttgtattatggaaaatttttctgtataatagattcaacaaaca




gacaatctggtctgtttgtattatCAGCGGTCAACGCATGTGCTTTGCGTTCTGATGAG





ACAGTGATGTCGAAACCGCCTCTACAAATAATTTTGTTTAAGCTCTTCAAGAGCATTCC






ATAAGGAGAAATTTT
ATGACGAGAACCAACACCGGCTATCGTTATCGCGCGTTCGGCCT






GCGCATAGACTCAGATATTCCGCTGCCAGAATTAGGGGACGGTACGCGCCCTGATGGTG






ACGCGGATCTGACGGTCGTCCGGTGTGGGGAAGCGGAGCCGGAATGGGCTGAAGGTGGT






GGCGGGGGTCGTCTGTATGCCGCTGAAGGCATTGTATCTTTTCGCGTGCCGCAGACGGC






AGCGTTCCGTATTACTAATGGAAATCGCATCGAGGTGCATGCCTACTCGGGGGCTGATG






AGGATCGAATACGCCTGTACGTGTTAGGGACCTGTATGGGAGCGCTGTTACTGCAACGT






AGAATCTTACCGCTTCATGGTTCGGTCGTCGCCCGTGATGGTCGTGCGTATGCCATAGT






TGGCGAAAGCGGAGCGGGCAAATCCACGATGAGTGCAGCACTTCTCGAACGTGGATTCC






GCCTCGTTACGGATGACGTGGCCGCCATCGTGTTCGATGAGCGTGGGACCCCACTGGTT






ATGCCGGCTTATCCACAGCAAAAACTGTGGCAGGATTCCCTGGACCGTCTGCAAATTGC






GGGCTCGGGCCTTCGTCCGCTGTTCGAACGCGAAACGAAATACGCTGTACCCGCGGATG






GGGCATTCTGGCCCGAACCGGTTCCATTGGTGCACATTTACGAACTGGTTCATAGCGAT






GGTCAAACGCCTGAACTGCAGCCGATTGCCAAATTAGAGCGTTGCTATACCTTGTATCG






CCACACATTTCGTAGAAGCCTGATCGTCCCCAGCGGCTTAAGCGCCTGGCATTTTGAAA






CGGCAGTGAAACTTGCGGAGAAAACGGGGATGTACCGTCTTATGCGCCCGGCCAAAGTT






TTCGCGGCTCGCGAATCTGCTCGGCTGATTGAAACTCACGCCGATGGTGAAGTGTCACG






TTAATAATGAAGAGCGGATGAGCTCTACAAATAAGCAGAGGTGGTTGTGTTGCGAAAAA





AAAAAAAAAACACCCTAACGGGTGTTTTTTTTTTTTTGGTGTCCCCACGTGTGGCGCTT




TACAAAGTCTTCCTGTACTAGTAGCGGCCGCTGCAGTCCGGCAAAAAAGGGCAAGGTGT




CACCACCCTGCCCTTTTTCTTTAAAACCGAAAAGATTACTTCGCGTTATGCAGGCTTCC




TCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTC




AAAGGCGGTAATTTAATAAGATGATCTTCTTGAGATCGTTTTGGTCTGCGCGTAATCTC




TTGCTCTGAAAACGAAAAAACCGCCTTGCAGGGCGGTTTTTCGAAGGTTCTCTGAGCTA




CCAACTCTTTGAACCGAGGTAACTGGCTTGGAGGAGCGCAGTCACCAAAACTTGTCCTT




TCAGTTTAGCCTTAACCGGCGCATGACTTCAAGACTAACTCCTCTAAATCAATTACCAG




TGGCTGCTGCCAGTGGTGCTTTTGCATGTCTTTCCGGGTTGGACTCAAGACGATAGTTA




CCGGATAAGGCGCAGCGGTCGGACTGAACGGGGGGTTCGTGCATACAGTCCAGCTTGGA




GCGAACTGCCTACCCGGAACTGAGTGTCAGGCGTGGAATGAGACAAACGCGGCCATAAC




AGCGGAATGACACCGGTAAACCGAAAGGCAGGAACAGGAGAGCGCACGAGGGAGCCGCC




AGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCACTGATTTGAGC




GTCAGATTTCGTGATGCTTGTCAGGGGGGCGGAGCCTATGGAAAAACGGCTTTGCCGCG




GCCCTCTCACTTCCCTGTTAAGTATCTTCCTGGCATCTTCCAGGAAATCTCCGCCCCGT




TCGTAAGCCATTTCCGCTCGCCGCAGTCGAACGACCGAGCGTAGCGAGTCAGTGAGCGA




GGAAGCGGAATATATCCTGTATCACATATTCTGCTGACGCACCGGTGCAGCCTTTTTTC




TCCTGCCACATGAAGCACTTCACTGACACCCTCATCAGTGCCAACATAGTAAGCCAGTA




TACACTCCGCTACGATTATCAAAAAGGATCTTCA






aText formatting correspond to sequence features/components: promoters (lowercase),





embedded image

terminators (UNDERLINED), and plasmid backbone and spacers (REGULAR ALL CAPS). Each backbone plasmid sequence except for the multi-enzyme backbone includes a coding sequence for GFP. The portion of the sequence that is double underlined can be replaced with a peptide coding sequence or an RBS + enzyme coding sequence, for example chosen from Table 9, to generate a plasmid encoding a sequence of interest (e.g., a peptide or enzyme).




bThe multi-enzyme backbone shown is the sequence of the 6048 plasmid. To generate an alternative multi-enzyme plasmid, the protein coding sequences (shown in bold) can be replaced with coding sequences for alternative enzymes (e.g., one chosen from Table 9)














TABLE 17







Enzyme and peptide amino acid sequences










SEQ




ID



Name
NO
Sequence





AlbA
247
MFIEQMFPFINESVRVHQLPEGGVLEIDYLRDNVSISDFEYLDLNKTAYELCMRMDGQKTA


enzyme

EQILAEQCAVYDESPEDHKDWYYDMLNMLQNKQVIQLGNRASRHTITTSGSNEFPMPLHAT




FELTHRCNLKCAHCYLESSPEALGTVSIEQFKKTADMLFDNGVLTCEITGGEIFVHPNANE




ILDYVCKKFKKVAVLTNGTLMRKESLELLKTYKQKIIVGISLDSVNSEVHDSFRGRKGSFA




QTCKTIKLLSDHGIFVRVAMSVFEKNMWEIHDMAQKVRDLGAKAFSYNWVDDFGRGRDIVH




PTKDAEQHRKFMEYEQHVIDEFKDLIPIIPYERKRAANCGAGWKSIVISPFGEVRPCALFP




KEFSLGNIFHDSYESIFNSPLVHKLWQAQAPRFSEHCMKDKCPFSGYCGGCYLKGLNSNKY




HRKNICSWAKNEQLEDVVQLI





AlbsA
248
MDSLLSTETVISDDELLPIEVGGTAELTEGQGGGQSEDKRRAYNC





AlbsB
249
MPELPRFATAPRHVRALDFGHVLVLIDYRSNHVQCLLPAAAAHWTATARTGRLDTMPAALA


enzyme

TQLLTSALLVPRPTATPWTAPVAAPPAPPSWGGSEHPAGTSRPRARHRHSTTAAAALACVL




AIKAAGPTRYAMQRLTTVVKAAASTCRRPATPAQATAAALAVRQACWYSPARTACLEESAA




TVILLATRRLSSTWCHGVAPDPIRLHAWVETEDGTPVAEPASTLAYTPALTIGGHHQHQP





AlbsC
250
MIFGGFSTTREVRQRPGNAEFIATDSPIWRLGRSPARCVAADHGQRRLVVLGECGATDGEL


enzyme

SRLATAGLPTDITWRWPGVYVVVEEQPERTVLHTDPAAALPVYATPWQGGWAWSTSARILA




RLTEAPIDGQRLACSVLAPSVPALSGTRTFFAGIEQLALGSRIELPVDGSRLRVTVRWRPD




PVPGEPYHRLRTALTEAVALRVNRAPDLSCDLSGGLDSTSLAVLAAVCLPESHHLNAITIH




PEGDESGADLRYARLAAAHHGRIRHHLLPLAAEHLPYTEITAVPPTTEPAPSTLTRARLAW




QLDWMRQHLGSRTHMTGDGGDSVLFQPPAHLADLLRHRQWRRTLSESLGWARLRHTSVLPL




LRGAATLARTSRRSGLQDLARALAGAGQQGDGRGNVSWFAPLPLPGWATPTARRLLLDAAD




EAISTADPLPGLDTSLRVLIDEIREVARTAAADAELADAHGTTLHNPFLDPRTIDAVLRTP




IAHRPAVHSYKPALGHAMQDLLPGAVARRSTKGSFNADHYAGMRANLPALTALADGHLADL




GLLEPTRFRSHLRQAAAGIPMPLAAIEQALSAEAWCHAHHATPSPAWTTQPPEHPHA





AlbsT
251
MSTSPEQTLWISTDTCGLGPYRADLVDTYWQWEQDPTLLVGYGRQSPQSLEARTEGMAHQL


enzyme

RGDNIRFTIYDLCSSTPTPAGVATLLPDHSVRTAEYVIMLAPEARGRGLGTTATQLTLDYA




FHITNLRMVWLKVLAPNTAGIRAYEKAGFRTVGALREAGYWLGKVCDEVLMDALAKDFTGP




SAVHAALTGASGRQLRRAP





AMdnA
252
MPENRQEDLNAQAVPFFARFLEGQNCEDLTDEESEAVSGGKRGQTRKYPSDCEDGNGVTGK




LRDEDIAVTLKYPSDNEDNGGGEIVTLKFPSDDDDQPVG





AMdnC
253
MNVLIITHSHDNESISLVTQAIESQGGKAFRFDTDRFPTEVQLDIYYSNTEKCVLVADDQK


enzyme

LDLNEVTAVWYRRIAIGGKIPPTMDKQLRQASIQESRATIQGMIASIRGFHLDPVPNIRRA




ENKQLQLQVARKIGLDTPRTLTTNNPQAVKEFAAECQQDVITKMLSSFAIYDEKGGEQVVF




TNPVKSEDLENLEGLRFCPMTFQEKIAKVLELRITIVGKSILTAAVNSQALDKSRYDWRKQ




GVALLDAWQTHTLPQDVADKLLQLMAHFGLNYGAIDVILTPDNRYVFLEVNPVGEFFWLER




CPGLPISQAIAKVLLSHI





AtxA1
254
MHTPIISETVQPKTAGLIVLGKASAETRGLSQGVEPDIGQTYFEESRINQD





AtxB
255
MYELNDGVGLALVDQHPIFLDLKTDRYLSLSPDGAAVLLGAAPATKESPLFLGLESIGLVK


enzyme

NGPSGLKPCQIAVATGSAPPRKVQFESLSLLLLRLIRARLDQRALLKRVTDLKKAGTIAQT




KNRDCALSLLGSVETEAKACRTLLSSTDKCLPDAFAIATHLRRRGVDAKLVFGVRLPFAAH




AWVQVDDIVVGDRPDRILAFTPILVV





AtxC
256
MRYVASFFVRGHVSTPALRHPEPKGFAYAKVSGGLSVWSDAPIRHRAPLITVGAVFDRASF


enzyme

KGLDCDLSGLRQDGLNTLKAETFGPYLALEVADNGTLRVYRDPSGGAPCYYLQTEDGFWLA




SDADLLFTHSGVHPSVSLPGLIEHLRRPEFQNEGTCLNVKQVRPGEQVDLSLSGEVRACLF




PPASSLRPPELHRAYDDIKAELRALILRSIKAYASDFPHVVVSFSGGLDSSVVAAGLAQTS




TKVLLHTFKGPDAKGDETAFAAECAAYLGLSLEIDTLSIDDVDLSATISPHLPRPSTSFFL




PSLLRGFSTSSQTRTGGAIFSGNGGDSVFCFMHSATPLADLMCRPSGLTPFMQTWADVQKL




TRASATEVLRRALKTAMARGYIWPESNLLLSRDTSSSRLTPDSVLSSLEGILPGRLRHLAL




IRRAHNTFEPFAPWRTPPVVHPLMAKPIQAFCLSLPSWMWVSGGKDRSLVRDAFEGLLPDS




VRLRKSKGSPAGFLHALYRAKGRQMIERIRHGYLRREGIIDISTGPDALFSEGFRNPRVMH




RFFELAATEVWIDHWRNWRRPRT





BamA
257
LKIRKVKIVRAQNGHYTN





BamB
258
MEGLYQLKVHSRIHKLQNNIAIGSMPPHALIIEDAPEYLSNVLRFFSSKKTIKEAEVYLSD


enzyme

NTNLSSNEINLLLGDLIENEIIVKQNYDSNNRYSRHSLYYEMIDANAENAQKILAEKTVGL




VGMGGIGSNVAMNLAAAGVGKLIFSDGDTIELSNLTRQYLYKEDQVGLSKVESAKEQLQLL




NSEVELIPVCESISGEELFDNHFSECDFVVLSADSPFFVHEWINNAALKYGFSYSNAGYIE




TYGAIGPLVIPGETACYECYKDKGDLYLYSDNKEEFSVNLNESFQAPSYGPLNAMVSSIQA




NEVIRHLLGLKTKTSGKRLLINSEIYKIHEENFEKKNNCLCSDIKGEKLSKNTLNSDKELH




EVYIEERESDSFNSILLDKTMSKLVKINKEETKILDIGCATGEQALYFANKGAKVTAVDIS




DDMLKVLDKKASNINAGSIKTMRGNIESIEVNDTFNYIVCNNILDYLPEIDRTLRKLNMFL




KNDGTLIVTIPHPVKDGGGWRKDYYNGKWNYEEFILKDYFNEGLIEKSREDKNGETVIKSI




KTYHRTTETYFNSFTDAGFKVVSLLEPQPLSTVSETHPILFEKCSRIPYFQVFVLKKEDRH




AI





BmbC
259
MGPVVVFDCMTADFLNDDPNNAELSALEMEELESWGAWDGEATS





BsjA2
260
MTNEEIIVAWKNPKVRGKNMPSHPSGVGFQELSINEMAQVTGGAVEQRATPTLATPLTPHT




PYATYVVSGGVVSAISGIFSNNKTCLG





BsjA3
261
MTNEEIIVAWKNPKVRGKNMPSHPSGVGFQELSINEMAQVTGGAVEQRATPATPATPWLIK




ASYVVSGAGVSFVASYITVN





BsjM
262
MIKNVNLKEAIKGLTVSERYDTLKNSGVNLNLNISALEEWRNRKNLLADEDFTEMLTVLEY


enzyme

DPVYFSHAINENIEEHIDIYKSKILGENWFIVLNDILDELDNPIEYKKEMNHSYLLRPFLL




YAEKEMNKYIVNRKELLPVEPQVIQQIMENLASKLFAVSVKSFVLELNISKLKDELAGETP




DERFHSFIRLMGEKTRLVDFYNEYIVLSRILVNITILFVNNIIELFERLQESKLDIVKKLG




VQEEFKISNISIGEGDTHQQGRSVIVLTFVSGKKVVYKPKNLKVVSAYNSLIDWINNKNNI




LKMPSYNTLIYDDFVIEEFVEKRDCKSIEEVKKYYIRYGQILGIMYILNGNDFHMENLIAS




GEYPIIVDLETLLQNIINFKNKPSADLITTKKMLNLVNSTLLLPEKLLKGDITDEGIDMSA




LAGKEQHLERREYQLKNLFTDNMVFDLEKVKIEGANNIPKLNGENVDYSTYIDEIVVGFEN




ICNLFIQYRDELLHSGILEEFKDVKVRHVLRNTVVYAKMLANTYHPDYLRDSLNREQVLEN




IWVHPFERKEFIKSEMEDILNNDIPIFFSYASSKDIIDSNGKLHKNVMEISGYERFTTKLK




ELNPFLIEQQVSVINIKTGRYGDKKFEKNYSVRDVATEKKDNPIDFLQEAMNIGDKILEHA




IICDETKTISWLTINNHHDKNWEIGPISGEFYDGLAGISLFYHYLYKKSHNVEYKKIRDYA




FNMAKVKALSLKYDSGLTGYASLLYTAHKIVQDEPRKQYKDVINEVFKYIDESKVVTAKYN




WLHGTASIIHVLLNLYEDSRDMAYLTKCIQYGKYLVKQIKEHKDMLAPGFSQGISSVIMVL




VRLSKKCEVEEFLELALELMEMERNKLGNLSESNWLNGLVGIGLSRIKLKGLDSNLQVDND




IELVLDGVMNSLYSKDDTLSCGNSGTVELFLSLFEQTKKKEYLDMAKAICGKMIEESRISF




EYQTKSLPGLELVGLYSGLAGIGYQFLRISDVEDIASIATLD





CapA
263
MVRFLAKLLRSTIHGSNGVSLDAVSSTHGTPGFQTPDARVISRFGFN





CapB
264
MQPDLEVVDVRRGESFKAWSHGYPYRTVRWHFHPEFEVHLIVETTGQMFVGDYVGGFGPGN


enzyme

LVLMGPNLPHNWVSDVPEGKTVAERNLVVQFGQAFVSRCEDSLTEWRHVETLLADARRGVQ




FGPRTSEAIKPLFAELIHARGLRRIVLFLSMLQILVDATDRELLASPAYQADPSTFASTRI




NHALAYIGKNLANELRETDLARLAGQSVSAFSHYFRRHTGLPFVQYVNRMRINLACQLLMD




GDASVTDICFRSGFNNLSNFNRQFLAVKGMSPSRFRRYQALNDASRDASEAAAKRGAGIAG




APAIVPAAQARGEARPIPEVLLSG





CapC
265
MMLTASSTPASGNPAARALRAAAFALALGGACVAHAAPLRIGMTFQELNNPYFVTMQKALN


enzyme

EAAASIGAQVIVTDAHHDVSKQVSDVEDMLQKKIDILLVNPTDSTGIQSAIVSAKKAGAVV




VAVDANANGPVDSFVGSKNFDAGAMSCEYLAKAINGGGEVAILDGIPVVPILERVRGCRAA




LAKFPNVKIVDVQNGKQERATALTVTENMIQAHPKLKGVFSVNDGGSMGALSAIEASGKDI




RLTSVDGAPEAVAAIQKPNSKFIETSAQFPRDQIRLAIGIGLAKKWGANVPKAIPVDVKLI




DKGNAKTFSW





CinA
266
MTASILQSVVDADFRAALIENPAAFGASTAVLPTPVEQQDQASLDFWTKDIAATEAFACKQ




SGSFGPFTFVCDGNTK





CinX
267
MALKTCEEFLRDALDPDRFGREMKAVTEIPEIVKLGHRHGYGFTAEEFLTKAMSFGAPPAG


enzyme

AAAPGESASVPGQNGSSPGHAARAAMAGPEAGATSFAHYEYRLDELPEFAPVVAELPKLKV




MPPSVGPDRFAARYRDEDMRTISMSPADPAYQAWHQELAGRGWRDAEDTAAAPDAPRRDFH




LLNLDEHVDYPGYEEYFAAKTRVVAALENLFGGDVRCSGSMWYPPSSYRLWHTNADQPGWR




MYLVDVDRPFADPDRTSFFRYLHPRTREIVTLRESPRIVRFFKVEQDPEKLFWHCIANPTD




RHRWSFGYVVPENWMDALRHHG





Cln1A1
268
MTPIQSKFCLLRVGSAKRLTQSFDVGTIKEGLVSQYYFA





Cln1A2
269
MTQVSPSPLRLIRVGRALDLTRSIGDSGLRESMSSQTYWP





Cln1B
270
MPLWLAQDVHAVALDEDIVVLDAVSDAYLCLVGASALISLGSERSVSADPVAAETLREAGL


enzyme

VGPHPSGATRPIPPKPTIDLPDAARQAQGRELRAAAWAGAATAIDFRRRSFRQLLARAGQR




PPGQAAAPADEVLAAAAVFMRLRPWSPVGGACLMRSYYLLRHLRILGFDADWIIGVRTWPF




MAHCWLQVGAVALDDDVERLTAYTPILAV





Cln1C
271
MGDYLALYWPRGMPGVAADAMRAAIEAEGAWTLAFEAYQLVVYVKGPRAPKVRALPDQGGV


enzyme

VIGELFDTAATREGRVQDFPIALIKDVAAQDAARILATHAWGRYVAVLKAGDRPPWIFRDP




SGAVECLAWVRDEVTIISSDVAAQRAWSPDRLAIDWSGLGRVLARGNLWGEICPLAGVTAI




APGTARCDLGDAALSLWRPGDHARRSRHDVSPRDLARVVDASVAALARDRSAILVEISGGL




DSAIVATSLARGGAPVVAGINHYWPEPEGDERRWAQDIADRCGFRLIAGQRQRLLLDEAKL




LRHAQGPRPGLNAQDPDLDHDLAEQAKALGADALFSGQGGDGVFYQMANAALAADILMGKP




APMGRAASLAAVARRARATVWSLCGQAMFPSRAFAAGMPPPSFLSAGLAPPPVHPWIADQR




GVSPAKRIQIRGLTNIQCAFGDSLRGRAADLLYPLMAQPVMELCLSIPAPLLAVGALDRPF




ARAAFADRLPPRSLVRRSKGDVTVFFSKSLAASLPALRPFLLDGRLAEQGLIDRAKLEPLL




HPEPMIWRDSVGEVMLAAYLEAWVRAWEAKLRVS





Cln2A1
272
MNTLKTRLIRFGSAKRLTRAGTGVLLPETNQIKRYDPA





Cln2A2
273
MTTPKFRLIRLGSAKRLTRSGIGDVFPEPNMVRRWD





Cln2B
274
MTLTWRPGVHAVMVEDDLVLLDEAADAYVCLLDGAKVVSVRADGALSFNPPHAAEDMIAGG


enzyme

LVEPSSSAAASANPPAKLPCTPLARLSRPRHVKVRPAEAALFLIQAWGVARAVRRWPMARL




LEALRGDRAAEPAKGRRSMAEACAVFDALLAWSPFDGECLFRSVLRRRFLMALGHSPDLVI




GVRTWPFRAHCWLQSGVDALDDWPERLCAYRPILAASASQGR





Cln2C
275
MSYLLMTWPPGQPSVEADALHAAFNGQGGWSLVLERFCLRVYVRGAAAPAVTLTPKGGVLI


enzyme

GEMFDRAATETGAVAAYDLSRLGDDDGMAVARRVVDEAWGRYVLVLPVKERRPVVLREPLG




ALDALIWRKGDVWCVGADVPPGLEPKDLGVEETRLTHLIAEPDLASASLPLTGVAAVMPGT




AVDETGQVHRLWTPARFARSPRTDAWTAAERIPLVTRACIAALSANRSGILCEISGGLDSA




IVATSLKAEGAKISSGINFHWPQAEADERPYARAVAKSVRTRLQVVASRVAPVDPETFDEI




VVARPSFNAIDPVYDTVLAQRLIQGGEGALFTGQGGDAVFYQMPAPQLSLDLLARGPRRRG




LMGLSRRTNRSVWSLLRMGLRAPVRATFPYGARGADRPPMHPWLEDARGVGAAKRIQIEAL




VANQAVFEASRRGAAAHLVHPLLSQPLVELCLSTPAAVLAGAEQDRAFVRSAFRAQLPRLV




LDRQSKGDLSVFFAKGVARSLPGLRPRLLEGRLAARGLIDVEALSQAMQPEAMIWRDGSAE




ILCLAVLESWLRSWEARGA





Cln3A1
276
MQRIIDETTDGLIELGAASVQTQGDVLFAPEPGVGRPPMGLSED





Cln3A2
277
MERIEDHIDDELIDLGAASVETQGDVLNAPEPGIGREPTGLSRD





Cln3A3
278
MEFEGIPSPDARIDLGLASEETCGQIYDHPEVGIGAYGCEGLQR





Cln3B
279
MRVAVPDHLAYCVKQGGVTFLDVRGDRYFGLPPVLEHAFVAIAEADFLLKEPNSLLEPLEA


enzyme

LGVLVRGQARRADLTIPSANLSWVDEVSPTPPRLDPASLVATVTSVIRTRLSQKSKSLQAL




LEEVRTRRPGSPAHNWQLMRRLTAGFRASRAWAPIEPICLLDSLALLDFLHRRGLYPHIVF




GVIRQPFAAHCWVQADDVVLNDRLDHVGEYTPILVV





Cln3C
280
MEDYVVLIWPALAEAPARDLIRRLPKLKTVIETSGLVVLRPENGAGLRVGGNGVVLGSVFR


enzyme

TGGDRETVAEFSESEASAIATSRGQQLVTEFWGGYLAVLGDASRSEVMVLRDPSGAMPAYC




LVHGEVQIICSRLEVLEDAGLGQQALNWDVVAQLLAFPNLRGRSTGLKGVEELLPGCRLTF




TGGLKTETLTWNPWLFARPSAQAPERGVAATAVRQAVEVSVRKWADQSSPVLLELSGGLDS




SIIACCLDEPRTAATFVNFVTPTAEGDERGYARLVAKAADKQLIEQDIRADEVDVTRPRPG




RHPRPASQALLQPLEQACAELAPQLGARSFFSGLGGDNVFCSIATASPAADALLTSGLGRQ




FWAAIGDLCARHNCTVWAALSATLKKLLRSDRRLVIKPNLDFLSFREDAIDRPDHPWLEVA




ADRLPGKREHVASILLAQGFLDRYEHAQVAAVRFPLLTQPVMEACLRVPTWMANHQGRNRA




VARDAFFDRLPPRVRDRQTKGGLNAFMGVAFERNRQALARHLLDGRLVQRGLIDAVAIKSA




LASPVLEGGAMNRLLYLADVESWVRSWEDV





ComQ
281
MKEIVKQNISNKDLSQLLCSFIDSKETFSFAESAILHYVVFGGENLDVATWLGAGIEILIL


enzyme

SSDIMDDLEDEDNHHALWMKINRSESLNAALSLYTVGLTSIYSLNTNPLIFKYVLRYVNEA




MQGQHDDITNKSKTEDESLEVIRLKCGSLIALANVAGVLLATGEYNETVERYSYYKGIVAQ




ISGDYHVLLSGNRSDIEKNKQTLIYLYLKRLFNNASEELLYLFSHKDLYYKALLDREKFEE




KLIQAGVTQYISVLLEIYKQKCFSTIEQLNLDKEKKELIKESLLSYKKGDTRCKT





ComX
282
MQDLINYFLNYPEALKKLKNKEACLIGFDVQETETIIKAYNDYYRADPITRQWGD





CrnA1
283
MSELSMEKVVGETFEDLSIAEMTMVQGSGDINGEFTTSPACVYSVMVVSKASSAKCAAGAS




AVSGAILSAIRC





CrnA2
284
MSESNMKKVVGETFEDLSIAEMTKVQGSGDVMPESTPICAGFATLMSSIGLVKTIKGNVKS




FSVLI





CrnM
285
MNDINKNKTKTINEKIKIFTKEEVIDISYFEEWRSVRTLLNENYFKIMLEEMNISKNQFSY


enzyme

ALQPLNDEFKLHTNVKNEEWIKCFNRVINNFNYKNINYKVGLYLPIQPFSVYLQEKLKEIL




KKLNNIKINDKIIDAFIEAHLIEMFDLVGKVIALKFEDYKQINFLKNTNNGTRLEEFLRST




FYSRKSFLKLFNEFPVLARVCTVRTIYLINNFSAIIQNINSDYLEIQEFLNVDFLNLTNIT




LSTGDSHEQGKSVSILYFDEKKLIYKPKNLKISEIFESFIDWYTNVSNHKLLDLKIPKGIF




KDDYTYNEFIEPNYCENKREIENYYNRYGYLIAICYLFNLNDLHVENVIAHGEYPVIVDIE




TSFQVPVQMEDDTLYVKLLRELELESVSSSFLLPTNLSFGMDDKVDLSALSGTMVELNQQI




LAPVNINMDNFHYEKSPSYFPGGNNIPKNNKSVTVDYKKYLLNIVTGFDEFMKYTQENQLE




FIEFLKKFSDKKIRVLVKGTEKYASMIRYSNHPNYNKEMKYRERLMMNLWAYPYKDKRIVN




SEVQDLLFNDIPIFYSFPNSRDLIDSRGLVYKDYLPVTGLQKAIDRVKDTSVKSLFDQKLI




LQSSLGLWDEILNKPVQKKELLFEKQNFNYVKEAINIAELLIGYLIETDDQSTMLSIDCSE




DKHWKIVPLDESLYGGLSGIALFFLDIYKITKDEKYFNYYDKIISTAIKQCKATIFSSSFT




GWLSPIYPLILEKKYFGTMKDKKFFDYTMEKLSNMTEEQINNMDGMDYISGKAGIVKLLIS




AYRESKNNENIGLALSKFSNDLIQNIGTGKVSELQNVGLAHGISGIMVVVASLDTFKSEYI




REQLAIEYEMFCLREDSYKWCWGISGMIQARLEILKLSPECVDKKELNLLIKRFKNILNQM




INEDSLCHGNGSIITTMKMIYMYTQDTEWNSLINLWLSNVSIYSTLQGYSIPKLGDVTIKG




LFDGICGIGWLYLYSNFSIENVLLLEV





CsegA1
286
MTKKNATQAPRLVRVGDAHRLTQGAFVGQPEAVNPLGREIQG





CsegA2
287
MTKTHRLIRLGDAQRLTQGTLTPGLPEDFLPGHYMPG





CsegA3
288
MTSRFQLLRLGKADRLTRGALVGLLIEDITVARYDPM





CsegB
289
MDLWLSAGVYAVMIDDDVVFLDVATNAYFCLPAVGSVLALEGRSLRVAARELAEDLIQAGL


enzyme

ASAAAAIEPPPSTRAPVRTARAVLEALPARERPRPRLAHWRQAIMAGLASRAAERRPFAQR




LPPPSTGVSPPASEGLLADLDAFRRLQPWLPFDGACLFRSQMLRDYLLALGHRVDWIFGVR




TWPFGAHCWLQAGDLVLDDEAERLIAYHPIMVR





CsegC
290
MGYAALTYPGGLAAAAFDEMVEALIDAGWTLALRAFRLAVLTDGQAPAVSPLMGRGGVAGV


enzyme

LIGEAFDRRATLGGAVARAALDGLADIDPLEAGRHLIETAWGGYVGMWIGRAEAGPTLLRD




PSGALEALAWRRDGVTVMSARPLTGRAGPADLAIDWPRIVQILADPISAALGPPPLTGLAT




IDPGAAVHGADGQERSVLWTPAAVVRGARHRPWPSRQDLRRTIDATVAALASDAGPIVCEI




SGGLDSAIVATSLAASGLGPQLTVNFYGDQPEADERGYAQAVAERIGAPLRTLRREPFAFD




ETVLAAAGQAARPNFNALDPGYDAGLVGALEAIDARALFTGHGGDTVFYQVAASALAADLL




GGAPCEGSRRARLEEVARRTRRSIWSLAWEAFSGRPSTVSIEGQLLRQEAERIRRVGLTHP




WVGGLSSVTPAKRQQIRALVSNLNAHGATGRAERARIVHPLLAQPVVEACLAIPAPILSAG




EGERSFAREAFADRLPPSIVGRRSKGEISVFLNRSLAASAPFLRGFLLEGRLAARGLIDRD




ELAAALEPEAIVWKDASRDLLTAAALEAWVRHWEARIGEGEAAEGERAAGRGTAATGPRTS




ARKANTR





EpiA
291
EAVKEKNDLFNLDVKVNAKESNDSGAEPRIASKFICTPGCAKTGSFNSYCC





EpiD
292
MHGKLLICATASINVININHYIVELKQHFDEVNILFSPSSKNFINTDVLKLFCDNLYDEIK


enzyme

DPLLNHINIVENHEYILVLPASANTINKIANGICDNLLTTVCLTGYQKLFIFPNMNIRMWG




NPFLQKNIDLLKSNDVKVYSPDMNKSFEISSGRYKNNITMPNIENVLNFVLNNEKRPLD





HalA1
293
MTNLLKEWKMPLERTHNNSNPAGDIFQELEDQDILAGVNGAENLYFQGCAWYNISCRLGNK




GAYCTLTVECMPSCN





HalA2
294
MVNSKDLRNPEFRKAQGLQFVDEVNEKELSSLAGSENLYFQGTTWPCATVGVSVALCPTTK




CTSQC





HalM1
295
MRELQNALYFSEVVFGPNLEKIVGEKRLNFWLKLIGEDPENLKEFLSRKGNSFEEQTLPEK


enzyme

EAIVPNRLGEEALEKVREELEFLNTYSTKHVRRVKELGVQIPFEGILLPFISMYIEKFQQQ




QLRKKIGPIHEEIWTQIVQDITSKLNAILHRTLILELNVARVTSQLKGDTPEERFAYYSKT




YLGKREVTHRLYSEYPVVLRLLFTTISHHISFITEILERVANDREAIETEFSPCSPIGTLA




SLHLNSGDAHHKQRTVTILEFSSSLKLVYKPRSLKVDGVFNGLLAFLNDRTGEVIKDQYCP




KVLQRDGYGYVEFVTHQSCQSLEEVSDFYERLGSLMSLSYVLNSSDFHFENIIAHGPYPVL




IDLETIIHNTADSSEETSTAMDRAFRMLNDSVLSTGMLPSSIYYRDQPNMKGLNVGGVSKS




EGQKTPFKVNQIANRNTDEMRIEKDHVTLSSQKNLPIFQSAAMESVHFLDQIQKGFTSMYQ




WIEKNKQEFKEQVRKFEGVPVRAVLRSTTRYTELLKSSYHPDLLRSALDREVLLNRLTVDS




VMTPYLKEIIPLEVEDLLNGDVPYFYTLPEERALYQEASAINSTFFTTSIFHKIDQKIDKL




GIEDHTQQMKILHMSMLASNANHYADVADLDIQKGHTIKNEQYVEMAKDIGDYLMELSVEG




ENQGEPDLCWISTVLEGSSEIIWDISPVGEDLYNGSAGVALFYAYLFKITGEKRYQEIAYK




ALVPVRRSVAQFQHHPNWSIGAFNGASGYLYAMGTIAALFNDERLKHEVTRSIPHIEPMIH




EDKIYDFIGGSAGALKVFLSLSGLFDEPKFLELAIACSEHLMKNAIKTDQGIGWKPPWEVT




PLTGFSHGVSGVMASFIELYQQTGDERLLSYIDQSLAYERSFFSEQEENWLTPNKETPVVA




WCHGAPGILVSRLLLKKCGYLDEKVEKEIEVALSTTIRKGLGNNRSLCHGDFGQLEILRFA




AEVLGDSYLQEVVNNLSGELYNLFKTEGYQSGTSRGTESVGLMVGLSGFGYGLLSAAYPSA




VPSILTLDGEIQKYREPHEA





HalM2
296
MKTPLTSEHPSVPTTLPHTNDTDWLEQLHDILSIPVTEEIQKYFHAENDLFSFFYTPFLQF


enzyme

TYQSMSDYFMTFKTDMALIERQSLLQSTLTAVHHRLFHLTHRTLISEMHIDKLTVGLNGST




PHERYMDFNHKFNKTSKSKNLFNIYPILGKLVVNETLRTINFVKKIIQHYMKDYLLLSDFF




KEKDLRLTNLQLGVGDTHVNGQCVTILTFASGQKVVYKPRSLSIDKQFGEFIEWVNSKGFQ




PSLRIPIAIDRQTYGWYEFIPHQEATSEDEIERYYSRIGGYLAIAYLFGATDLHLDNLIAC




GEHPMLIDLETLFTNDLDCYDSAFPFPALARELTQSVFGTLMLPITIASGKLLDIDLSAVG




GGKGVQSEKIKTWVIVNQKTDEMKLVEQPYVTESSQNKPTVNGKEANIGNYIPHVTDGFRK




MYRLFLNEIDELMDHNGPIFAFESCQIRHVFRATHVYAKFLEASTHPDYLQEPTRRNKLFE




SFWNITSLMAPFKKIVPHEIAELENHDIPYFVLTCGGTIVKDGYGRDIADLFQSSCIERVT




HRLQQLGSEDEARQIRYIKSSLATLTNGDWTPSHEKTPMSPASADREDGYFLREAQAIGDD




ILAQLIWEDDRHAAYLIGVSVGMNEAVTVSPLTPGIYDGTLGIVLFFDQLAQQTGETHYRH




AADALLEGMFKQLKPELMPSSAYFGLGSLFYGLMVLGLQRSDSHIIQKAYEYLKHLEECVQ




HEETPDFVSGLSGVLYMLTKIYQLTNEPRVFEVAKTTASRLSVLLDSKQPDTVLTGLSHGA




AGFALALLTYGTAANDEQLLKQGHSYLVYERNRFNKQENNWVDLRKGNAYQTFWCHGAPGI




GISRLLLAQFYDDELLHEELNAALNKTISDGFGHNHSLCHGDFGNLDLLLLYAQYTNNPEP




KELARKLAISSIDQAHTYGWKLGLNHSDQLQGMMLGVTGIGYQLLRHINPTVPSILALELP




SSTLTEKELRIHDR





KgpE
297
MKNPTLLPKLTAPVERPAVTSSDLKQASSVDAAWLNGDNNWSTPFAGVNAAWLNGDNNWST




PFAGVNAAWLNGDNNWSTPFAADGAE





KgpF
298
MINYANAQLHKSKNLMYMKAHENIFEIEALYPLELFERFMQSQTDCSIDCACKIDGDELYP


enzyme

ARFSLALYNNQYAEKQIRETIDFFHQVEGRTEVKLNYQQLQHFLGADFDFSKVIRNLVGVD




ARRELADSRVKLYIWMNDYPEKMATAMAWCDDKKELSTLIVNQEFLVGFDFYFDGRTAIEL




YISLSSEEFQQTQVWERLAKVVCAPALRLVNDCQAIQIGVSRANDSKIMYYHTLNPNSFID




NLGNEMASRVHAYYRHQPVRSLVVCIPEQELTARSIQRLNMYYCMN





LasA
299
MDKRVRYEKPSLVKEGTFRKTTAGLRRLFADQLVGRRNI





LasB
300
MKGEEMLGHPQTGFVVLPDNDATGDVTGRLLPWGDVVTVYPSGRPWIIGNCWDRPVLVHDG


enzyme

VIVLGHTSVTRDQIARHGNDPHRLLDEADGAFHAAVLIGHEVHVRGSAYGVCRLYTCVVDG




VTLVSDRTDVLQRLAGTDVDVDVLAGHLLEPIPHWLGEQPLLTSVEPVPPTHHVILTPDAR




SRLRPSRRRRPEPSLGLRDGAELVRERLAAAVATRVDSPALITSELSGGYDSTSVSYLAAR




GKAEVVLVTAAGRDSTSEDLWWAERAAAGLPELDHVVLPADELPFTYAGLTEPGALLDEPC




TAVAGRERVLALVRKAAARGSTLHLTGHGGDHLFTSLPTPFHDLFRTRPVAALRQLRAFGA




LAAWPTRKLMRELADRRDHSTWWRAHARPQNGQPDPHSPMLGWAIPPTVPAWVTADGVRAI




ELGILEMAERAEPLGHARGEHAELDSIFEGARMARGLNRMATHAGVPLAAPFHDDRVVEAC




LSIRPEERISAWQYKPLLNAAMQGVVPSTVLDRSAKDDGSIDVAYGLQEHRDELVALWESS




RLAETGLIDAGMLRRLCAQPSSHELEHGSLYATIACELWLRGLDQDRTQRY





LasC
301
MPVQLRRHVSFTATEYGGVLLDETKGAYWRLNTTGAEVVRAMGEAERDEIVRHVVATFDVD


enzyme

AQTAAQDVDVLLAELRDAGLVAS





LasD
302
MSVNMALRGHGMSGRRRRLDATRARLAVVVARVLNLLPPRLIRRCLRVLSRGARPASIEAA


enzyme

EAARRTVVAVSPAAAGAYGCLIRSIATTLVLRSRGQWPTWCVGVRAEPPFGAHAWIEAEER




LVDEPGTMHTYRRLITVGPLSRKVR





LasF
303
MSIELTPSLADLVDPLPGHALRAAATLRLADLIAAGADTAPALAAAARIDADAIARLMRYL


enzyme

CSRGIFQAHEGRYALTEFSELLLDEDPSGLRKTLDQDSYGDRFDRAVAELVDVVRSGEPSY




PRLYGSTVYDDLAADPALGEVFADVRGLHSAGYGEDVAAVAGWSSCLRVVDLGGGTGSVLL




AVLERHPSLSGAVLDLPYVAPQAKKALQASAFAQRCEFIKGSFFDPLPPADRYLLCNVLFN




WDDAQAGAILARCAQAGPVAGVVVAERLIDPDAEVELVAAQDLRLLAVCGGRQRGTAEFEA




LGAAHGLALTSVTLTASGMSLLRFDVCRAGSAGGEVVEKS





LcnA
304
MTKGLDKMLLTKKKKDSMGLLNEIDVTTLDEQLGGKMSKAWCRSMVVSCVYNLVDFSSSSD




GKKTCALYRKYC





LcnG
305
MDGTNKRLEDKWFDINFLEMYTRSCLKTFGYFDEILIVKKRIEVLKNVLEKQYLSTNDYAE


enzyme

EFFELNTTLESIKEYIKLNLVIEKEP1SICIMVKNEERCIKRCIDSVEILAEEIIIIDTGS




TDNTINIIEECANDKIKVFSKEWRNDFSEIRNYAIEKASSEWLVFIDADEYLDEASVLNLL




STLNIFNNHKLKDSIVLCPMINEANNTIHFRTGKFFRKDSGIKFFGTCHEEPRIKGMPNST




LLIPIKVDYLHDGYLAKVQSNKDKKTRNIELLEGMVELEPDNPRWAYMFVRDGFAILDNEY




IEKTCLRFLLLDKNVRICVNNLQDHKFTLSLLTILGRLYLRECEFEKSNLIIRILDELIPN




SLDGKFLAFMERFSKLKIEINTLLTEVIEYRRNHEVDETSLINTQGYHIDYVLSILLFETG




NYAQSKKYFDFLQENHFLEELFQDSSYSIILKMLESVED





LtnA1
306
MNKNEIETQPVTWLEEVSDQNFDEDVFGACSTNTFSLSDYWGNNGAWCTLTHECMAWCK





LtnA2
307
MKEKNMKKNDTIELQLGKYLEDDMIELAEGDESHGGTTPATPAISILSAYISTNTCPTTKC




TRAC





LtnM1
308
MKFNKNVFPEINETDFDNNIKPLLDELESRITIPQEELSFSSINDDLFRELTRNEEYPYQS


enzyme

ICTIVANIVMDDGSEIWRKDIFVDSNSVREAVCDILSQTLFLYFIRCFSEQIKDIRKTDED




KESTYNRYINLLFSSNFKIFSDEYPVLWYRTIRIIKNRWYSIKKSLLLTQKHRVEIDKQLD




IPHKMKIKGLKIGGDTHNGGATVTTIFFEKGYKLIYKPRSTSGEFSYKKFIEKINPYLKKD




MGAIKAIDFGEYGFSEYIECNTDEEDMKQVGQLAFFMYLLNASDMHYSNVIWTKQGPVPID




LETLFQPDRIRKGLKQSETNAYHKMEKSVYGTGIIPISLSVKGKKGEVDVGFSGIRDERSS




SPFRVLEILDGFSSDIKIVWKKQQKSSSSKNNLIVDHKKEREILQRAQSVVEGFQETSKIF




MKHREEFISIILDSFENIKIRYIHNMTFRYEQLLRTLTDAEPAQKIELDRLLLSRTGILSI




SSSPYISLSECQQMWQGDVPYFYSKFSSKSIFDTNGFVDEIELTPRQAFIIKAESITNDEV




DFQSKIIKLAFMARLSDPHTTNDNKLNKKVIIESNQQSNSSESGNKAILFLSDLLKNNVLE




DRYSHLPKTWIGPVARDGGLGWAPGVLGYDLYSGRTGPALALAAAGRVLKDKDSIELSADI




FNKSSQILQEKTYDFRNLFASGIGGFSGITGLFWALNAAGNILNNDDWIKTSNQSMLLLNE




NMLKVDKNFFDLISGNSGAIGMMYLTNPNFYLSRSKINDILLTTDCLITEMEKDETSGLAH




GVSQILWFLSIMMQRQPSSEIKIRATIVDNIIKKKYTNSYGEIECYYPTDGHSKSTSWCNG




TSGILVAYIEGYKANIVDKSSVYHIINQINVEQLQHDNIPIMCHGSLGVYESLKYASKYFE




IETKYLLDVMRNGGCSSQEVLKYYGKGNGRYPLSPGLMAGQSGALLHCCKLEDNDISVSPI




SLMT





LtM2
309
MDPSIKKLVDSIIEFYKKDIYLAYKELEREIKNIDKTIYNTSNDEILRIFKESLISIITDD


enzyme

IYRLSIKTFIYEFHKFRIDNGFPAVKDSESAFNYYISTFDVKTIARWFEKFPMLESIISSS




IKNDCTFMVDVCVNFILDLSECEKINLISEDSRLITISSSNSDPHNGGTRVLFFRFHNGDT




ILYKPRSLTVDKLISNIFEEVFEFDATNSKNPIPKVLDRGTYGWQEFIEKKSISSSEIKQA




YYNLGIFSSIFTVLGSTDIHDENLIFKGTTPYFIDLETALSPRIRYEGNEENLFYRMSSSL




FTSIVGTTIIPAKLAVHSQEIMIGAINTPAKQKTKKDGFNIINFGTDAVDIAKQNIEVERI




ANPMRIKNNIVNDPLPYQNIFTRGFKEGIKSIILKKGSIISILNNFNSPIRYIMRPTAKYY




LILDAAVFPENLYSEQTLNKTLNYLKPPKIVENSLISKQLFLAEKRILSEGDIPSFYVLGK




EKNIRAQNFISEQIFEETAVDNAIQILESISQDWVNFNERLIAEGFSYIREQSRGYLSSDF




ENSDIFKSSLTETKKSGYTAMLKTIISMSVKTSENKKIGWLPGIYDDYPISYMSAAFCSFH




DSGGIITLLEHHFGHCSPEYNEMKRGLLELGKMLKINNSNLSIISGSESLEFLYTHREVEC




LELEYILNNSAEIMGDVFLGKLGLYLILASYLKTDLKIFQDFSIICQKNLEFKKFGIAHGE




LGYLWTIFRIQNKLKNKNACLSIYHEVLNIYKGKRIESVGWCNGLSGILMILSEMSTVLEK




NQDYLFKLANLSTKLNEESVDLSVCHGASGVLQTLLFVYSNTNDKRYLSLANKYWKKVLDN




SIKYGFYNGERDKDYLLGYFQGWSGFTDSALLLDKYNNNEQVWIPINLSSDIYQHNLNNCK




EKNYEGDGCHKS





LynD
310
MQSTPLLQIQPHFHVEVIEPKQVYLLGEQANHALTGQLYCQILPLLNGQYTLEQIVEKLDG


enzyme

EVPPEYIDYVLERLAEKGYLTEAAPELSSEVAAFWSELGIAPPVAAEALRQPVTLTPVGNI




SEVTVAALTTALRDIGISVQTPTEAGSPTALNVVLTDDYLQPELAKINKQALESQQTWLLV




KPVGSVLWLGPVFVPGKTGCWDCLAHRLRGNREVEASVLRQKQAQQQRNGQSGSVIGCLPT




ARATLPSTLQTGLQFAATEIAKWIVKYHVNATAPGTVFFPTLDGKIITLNHSILDLKSHIL




IKRSQCPTCGDPKILQHRGFEPLKLESRPKQFTSDGGHRGTTPEQTVQKYQHLISPVTGVV




TELVRITDPANPLVHTYRAGHSFGSATSLRGLRNTLKHKSSGKGKTDSQSKASGLCEAVER




YSGIFQGDEPRKRATLAELGDLAIHPEQCLCFSDGQYANRETLNEQATVAHDWIPQRFDAS




QAIEWTPVWSLTEQTHKYLPTALCYYHYPLPPEHRFARGDSNGNAAGNTLEEAILQGFMEL




VERDGVALWWYNRLRRPAVDLGSFNEPYFVQLQQFYRENDRDLWVLDLTADLGIPAFAGVS




NRKTGSSERLILGFGAHLDPTIAILRAVTEVNQIGLELDKVPDENLKSDATDWLITEKLAD




HPYLLPDTTQPLKTAQDYPKRWSDDIYTDVMTCVNIAQQAGLETLVIDQTRPDIGLNVVKV




TVPGMRHFWSRFGEGRLYDVPVKLGWLDEPLTEAQMNPTPMPF





McbA
311
MELKASEFGVVLSVDALKLSRQSPLGVGIGGGGGGGGGGGSCGGQGGGCGGCSNGCSGGNG




GSGGSGSHI





McbC
312
MSKHELSLVEVTHYTDPEVLAIVKDFHVRGNFASLPEFAERTFVSAVPLAHLEKFENKEVL


enzyme

FRPGFSSVINISSSHNFSRERLPSGINFCDKNKLSIRTIEKLLVNAFSSPDPGSVRRPYPS




GGALYPIEVFLCRLSENTENWQAGTNVYHYLPLSQALEPVATCNTQSLYRSLSGGDSERLG




KPHFALVYCIIFEKALFKYRYRGYRMALMETGSMYQNAVLVADQIGLKNRVWAGYTDSYVA




KTMNLDQRTVAPLIVQFFGDVNDDKCLQ





McbD
313
MINVYSNLMSAWPATMAMSPKLNRNMPTFSQIWDYERITPASAAGETLKSIQGAIGEYFER


enzyme

RHFFNEIVTGGQKTLYEMMPPSAAKAFTEAFFQISSLTRDEIITHKFKTVRAFNLFSLEQQ




EIPAVIIALDNITAADDLKFYPDRDTCGCSFHGSLNDAIEGSLCEFMERQSLLLYWLQGKA




NTEISSEIVTGINHIDEILLALRSEGDIRIFDITLPGAPGHAVLTLYGTKNKISRIKYSTG




LSYANSLKKALCKSVVELWQSYICLHNFLIGGYTDDDIIDSYQRHFMSCNKYESFTDLCEN




TVLLSDDVKLTFEENITSDTNLLNYLQQISDNIFVYYARERVSNSLVWYTKIVSPDFFLHM




NNSGAININNKIYHTGDGIKVRESKMVPFP





MdnA
314
MAYPNDQQGKALPFFARFLSVSKEESSIKSPSPEPTYGGTFKYPSDWEDY





MdnA*
315
MALPFFARFLSVSKEESSIKSPSPEPTYGGTFKYPSDWEDY





MdnC
316
MTVLIVTFSHDNESIPLVIKAIEAMGKKAFRFDTDRFPTEVKVDLYSGGQKGGIITDGEQK


enzyme

LELKEVSSVWYRRMRYGLKLPDGMDSQFREASLKECRLSIRGMIASLSGFHLDPIAKVDHA




NHKQLQLQVAQQLGLLIPGTLTSNNPEAVKQFAREFEATGIVTKMLSQFAIYGDKQEEMVV




FTSPVTKEDLDNLEGLQFCPMTFQENIPKALELRITIVGEQIFTAAINSQQLDGAIYDWRK




EGRALHQQWQPYDLPKTIEKQLLELVKYFGLNYGAIDMIVTPDERYIFLEINPVGEFFWLE




LYPPYFPISQAIAEILVNS





MibA
317
MPADILETRTSETEDLLDLDLSIGVEEITAGPA





MibD
318
MTAHSDAGGDPRPPERLLLGVSGSVAALNLPAYIYAFRAAGVARLAVVLTPAAEGFLPAGA


enzyme

LRPIVDAVHTEHDQGKGHVALSRWAQHLLVLPATANLLGCAASGLAPNFLATVLLAADCP1




TFVPAMNPVMWRKPAVRRNVATLRADGHHVVDPLPGAVYEAASRSIVEGLAMPRPEALVRL




LGGGDDGSPAGPAGPVGRAEHVGAVEAVEAVEAVEAVEAAEALA





MibH
319
MARSEESNTLARLFDVLGDDAAAAREWVTEPHRLIASNERLGTAPEAPADDDPEAIRTVGV


enzyme

IGGGTAGYLTALALKAKRPWLDVALVESADIPIIGVGEATVSYMVMFLHHYLGIDPAEFYQ




HVRPTWKLGIRFEWGSRPEGFVAPFDWGTGSVGLVGSLRETGNVNEATLQAMLMTEDRVPV




YRGEGGHVSLMKYLPFAYHMDNARLVRYLTELATRRGVHHVDATVAEVRLDGPDHVGDLIT




TDGRRLHYDFYVDCTGFRSLLLEKALGIPFESYASSLFTDAAITGTLAHGGHLKPYTTATT




MNAGWCWTIPTPESDHLGYVFSSAAIDPDDAAAEMARRFPGVTREALVRFRSGRHREAWRG




NVIAVGNSYAFVEPLESSGLLMIATAVQILVSLLPSSRRDPLPSNVANQALAHRWDAIRWF




LSIHYRFNGRLDTPFWKEARAETDISGIEPLLRLFSAGAPLTGRDSFARYLADGAAPLFYG




LEGVDTLLLGQEVPARLLPPRESPEQWRARAAAARSLASRGLRQSEALDAYAADPCLNAEL




LSDSDSWAGERVAVRAGLR





MibO
320
MIFGPDFHRDPYPVYRRLRDEAPCHHEPALGLYALSRYEDVLAALRQPTVFSSAARAVASS


enzyme

AAGAGPYRGADTVSPERETAAEGPARSLLFLDPPEHQVLRQAVSRGFTPQAVLRLEPAVRD




IAAGLADRIPDRGGGEFVTEFAAPLAIAVILRLLGVPEADRARVSELLSASALSGAEAELR




SYWLGLSALLRDREDAGEGDGEDRGVVAALVRPDAGLRDADVAAGPAVRAPLTDEQVAAFC




ALVGQAGTESVAMALSNALVLFGRHHDQWRTLCARPDAIPAAFEEVLRYWAPTQHQGRTLT




AAVRLHGRLLPAGAHVLLLTGSAGRDERAYPDPDVFDIGRFHPDRRPSTALGFGLGAHFCL




GAALARLQARVALRELTRRFPRYRTDEERTVRSEVMNGFGHSRVPFST





MibS
321
MTTGTTVAHAVEPDGFRAVMATLPAAVAIVTAAAADGRPWGMTCSSVCSVTLTPPTLLVCL


enzyme

RTASPTLAAVVSGRAFSVNLLCARAYPVAELFASAAADRFDRVRWRRPPGTGGPHLADDAR




AVLDCRLSESAEVGDHVVVFGQVRAIRRLSDEPPLMYGYRRYAPWPADRGPGAAGG





PaaA
322
MSLTNVKPLIKESHHIILADDGDICIGEIPGVSQVINDPPSWVRPALAKMDGKRTVPRIFK


enzyme

ELVSEGVQIESEHLEGLVAGLAERKLLQDNSFFSKVLSGEEVERYNRQILQFSLIDADNQH




PFVYQERLKQSKVAIFGMGGWGTWCALQLAMSGIGTLRLIDGDDVELSNINRQVLYRTDDV




GKNKVDAAKDTILAYNENVHVETFFEFASPDRARLEELVGDSTFIILAWAALGYYRKDTAE




EIIHSIAKDKAIPVIELGGDPLEISVGPIYLNDGVHSGFDEVKNSVKDKYYDSNSDIRKFQ




EARLKHSFIDGDRKVNAWQSAPSLSIMAGIVTDQVVKTITGYDKPHLVGKKFILSLQDFRS




REEEIFK





PaaP
323
MIKFSTLSQRISAITEENAMYTKGQVIVLS





PadeA
324
MKKQYSKPSLEVLDVHQTMAGPGTSTPDAFQPDPDEDVHYDS





PadeK
325
MTERAAVRTDHYKAFGFRIESDFVLPELPPAGEREPLDNITVRRTDLQPLWNSSIHFYGNF


enzyme

AILDHGRTVMFRVPGAAIYAVQDASSILVSPFDQAEENWVRLFILGTCIGIILLQRKIMPL




HGSAVAIDGKAYAIIGESGAGKSTLALHLVSKGYPLLSDDVIPVVMTQGSPWVVPSYPQQK




LWVDTLKHMGMDNANYTPLYERKTKFAVPVGSNFHEEPLPLASIFELVPWDAATHIAPIQG




MERFRVLFHHTYRNFLVQPLGLMEWHFKTLSSFVHQIGMYRLHRPMVGFSTLDLTSHILNI




TRQGENDQ





PalA
326
MKDLLKELMYEVDLEEMENLQGSGYSAAQCAWMALSCVNYIPGVGFGCGGYSACELYKRYC





PalS
327
MGNLRDFYQLMKDNYADSNLFKDLNLIHNISNDIQIGINCDFSEMLGELVGNYDSLNYPSI


enzyme

TCGILTYNEERCIKRCLESVVNEFDEIIVLDSVSEDNTVKIIKENFNDVKVYVEPWKNDFS




FHRNKIINLATCDWIYFIDADNYYDSKNKGKAMRIAKVMDFLKIEGVVSPTVIEHDNSMSR




DTRKMFRLKDNILFSGKVHEEPVYANGEIPRNIIVDINVFHDGYNPKIINMMEKNERNITL




TKEMMKIEPNNPKWLYFYSRELYQTQRDIALVQSVLFKALELYENSSYTRYYVDTIALLCR




VLFESKNYQKLTECLNILENNTLNCSDIDYYNSALLFYNLLLRIKKISSTLKENIDMYERD




YHSFINPSHDHIKILILNMLLLLGDYQDAFKVYKEIKSIEIKDEFLVNVNKFKDNLLSFID




SINKI





PapA
328
MLKQINVIAGVKEPIRAYGCSANDACYFCDTRDNCKACDASDFCIKSDT





PapA_tev
329
LKQINVIAGVKEPIRAYENLYFQGCSANDACYFCDTRDNCKACDASDFCIKSDT





PapB
330
MANLIQDREDELIHFHPYKLFEVDSKTFFYNVVTNAIFEIDSLIIDILHSKGKNEEHVVKD


enzyme

LAERYELSQVREAIQNMKEAYIIATDANISDVEKMGILDNSQRVFKLSSLTLFMVQECNLR




CTYCYGEEGEYNQKGKMTSEIARSAVDFLIQQSGEIEQLNITFFGGEPLLNFPLIQETVQY




VHEQSEIHNKKFSFSITTNGTLITPKIKNFFYKHHFAVQTSIDGDEKTHNFNRFFKGGQGS




YDLLLKRTEEMRNDRKIGARGTVTPAELDLSKSFDHLVKLGFRKIYLSPALYSLSDDHYDT




LSKEMVKLVEQFRELLEREDYVTAKKMSNVLGMLSKIHSGGPRIHFCGAGTNAAAVDVRGN




LFPCHRFVGEDECSIGNLFDEDPLSKQYNFIENSTVRNRTTCSKCWAKNLCGGGCHQENFA




ENGNVNQPVGKLCKVTKNFINATINLYLQLTQEQRSILFG





PapoA
331
SKKEWQEPTIEVLDINQTMAGKGWKQIDWVSDHDADLHNPS





PapoK
332
MHDRSANVSWTKYIAFGLRIASELNLPELILAAPEAVEDVVIRQADLTAWSGQLEQANFVM


enzyme

LDERFMFQIPGTAIYAVREGKEIEVSIFSGADPDTVRLFVLGTCMGVLLMQRRILPIHGSA




VVIGGRAYAFVGESGTGKSTLAAAFRQAGYQMVSDDVIAVKATASSAIVYPAYPQQKLGLD




SLLQLEALRENKHARKRNNIRSLTDGNSVMPQYSDLRMLAGELNKYAVPAVDEFFNDPLPL




GGVFELVADSPIRALMREGELVAVTEQPLNVLECLHTLLQHTYRRVIIPRMGLSEWSFDTA




ARMARKVEGWRLLRDSSVFTASEVVQRVLDIIRKEEKSYGSH





PbtA
333
MNLNDLPMDVFEMADSGMEVESLTAGHGMPEVGASCNCVCGFCCSCSPSA





PbtM1
334
MLSSALEVDIDEAAVAADLRELAAALDRSGYGEILTCFLPQKAQAHIWAQTAAKIDGPLRT


enzyme

LMELFLLGRAVPQDDLPPRIAAVIPGLVSAGLVKTGQGAVWLPNLILLRPMGQWLWCQRPH




PSPTMYFGDDSLALVHRMVTYRGGRALDLCAGPGVQALTAALRSEHVTAVEINPVAAALCR




TNIAMNGLSDRMEVRLGSLYDVVRGEVFDDIVSNPPLLPVPEDVQFAFVGDGGRDGFDISW




TILDGLPEHLSDRGACRIVGCVLSDGYVPVVMEGLGEWAAKHDFDVLLTVTAHVEAHKDSS




FLRSMSLMSSAISGRPAEELQERYAADYAELGGSHVAFYELCARRGGGSARLADVSATKRS




AEVWFV





PbtO
335
MTQYPLSRPEPLGVHPDYRRLRETCPVARVGSPYGPAWLVTRYADVAAVLTDARFSRAAAP


enzyme

EDDGGILLNTDPPEHDRLRKLIVAHTGTARVERLRPRAEEIAVALARRIPGEGEFISAFAE




PFSHRVLSLFVGHLVGLPAQDLGPLATVVTLAPVPDRERGAAFAELCRRLGRQVDRETLAV




VLNVVFGGHAAVVAALGYCLLAALDAPLPRLAGDPEGIAELVEETLRLAPPGDRTLLRRTT




EPVELGGRTLPAGALVIPSIAAANRDPDRPVGRRMPRHLAFGRGAHACLGMALARMELQAA




LKALAEHAPDVRLPAGTGALVRTHEELSVSPLAGIPIQR





PcpA
336
MSSNILEKVKEFFVRLVKDDAFQSQLQNNSIDEVRNILQEAGYIFSKEEFETATIELLDLK




ERDEFHELTEEELVTAVGGVTGGSGIYGPIQAMYGAVVGDPKPGKDWGWRFPSPLPKPSPI




PSPWKPPVDVQPMYGVVVSNDS





PcpX
337
MTYRRTSYAVWEITLKCNLACSHCGSRAGHTRAKELSTQEALDLVRQMADVGIIEVTLIGG


enzyme

EAFLRPDWLQIAEAITKAGMLCSMTTGGYGISLETARKMKAAGIASVSVSIDGLEETHDRL




RGRKGSWQAAFKTMSHLREVGIFFGCNTQINRLSAPEFPLIYERIRDAGARAWQIQLTVPM




GRAADNANILLQPYELLDLYPMIARVARRARQEGVQIQPGNNIGYYGPYERLLRGRGSDSE




WAFWQGCAAGLSTLGIEADGAIKGCPSLPTSAYTGGNIREHSLREIVEESEQLRFNLGAGT




SQGTAHLWGFCQTCEFSELCRGGCTWTAHVFFNRRGNNPYCHHRALFQAEQGIRERVVPKV




EAQGLPFDNGEFELIEEPIDAPLPENDPLHFTSDLVQWSASWQEESESIGAVVD





PcpY
338
MVENIDNEREKSANEIEPESLLLPRQAWQSQIAYLKAILKAKQALDRIEKRYLR


enzyme







Pgm2
339
MEREIVWTEIEESDLAAVVSASNVKDGPTVSSSNVKDR





PlpA1
340
MSIENAKSFYERVSTDKQFRTQLENTASAEERQKIIQAAGFEFTNQEWEIAKEQILATSES




NNGELSEAELTAVSGGVDLSIFELLDEEPLFPIRPLYGLP1





PlpA2
341
MSIESAKAFYQRMTDDASFRTPFEAELSKEERQQLIKDSGYDFTAEEWQQAMTEIQAARSN




EELNEEELEAIAGGAVAAMYGVVFPWDNEFPWPRWGG





PlpX
342
MTKKYRRVSYAVWEITLKCNLACSHCGSRAGQARTKELSTEEAFNLVRQLADVGIKEVTLI


enzyme

GGEAFMRSDWLEIAKAVTEAGMICGMTTGGFGVSLETARKMKEAGIKTVSVSIDGGIPETH




DRQRGKKGAWHSAFRTMSHLKEVGIYFGCNTQINRLSASEFPIIYERIRDAGARAWQIQLT




VPMGNAADNADMLLQPYELLDIYPMLARVAKRAKQEGVRIQAGNNIGYYGPYERLLRGSDE




WTFWQGCGAGLNTLGIEADGKIKGCPSLPTAAYTGGNIRDRPLREIVEQTEELKFNLKAGT




EQGTDHMWGFCKTCEFAELCRGGCSWTAHVFFDRRGNNPYCHHRALKQAQKDIRERFYLKV




KAKGNPFDNGEFVIIEEPFNAPLPENDLLHFNSDHIQWPENWQNSESAYALAK





PlpY
343
MNSNQIPNKVATAAQKSDDSSSVLPRQGWQDKQAFIKALIKAKQSLEIAEISNFLT


enzyme







ProcA*
344
MSEEQLKAFIAKVQADTSLQEQLKVEGADVVAIAKASGFAITTEDLNSHRQNLSDDELEGV




AGGFFCVQGTANRFTINVC





ProcA1.7
345
MSEEQLKAFIAKVQADTSLQEQLKVEGADVVAIAKASGFAITTEDLKAHQANSQKNLSDAE




LEGVAGGTIGGTIGGTIVSITCETCDLLVGKMC





ProcM
346
MESPSSWKTSWLAAIAPDEPHKFDRRLEWDELSEENFFAALNSEPASLEEDDPCFEEALQD


enzyme

ALEALKAAWDLPLLPVDNNLNRPFVDVWWPIRCHSAESLRQSFVSDSAGLADEIFDQLADS




LLDRLCALGDQVLWEAFNKERTPGTMLLAHLGAAGDGSGPPVREHYERFIQSHRRNGLAPL




LKEFPVLGRLIGTVLSLWFQGSVEMLQRICADRTVLQQCFAIPCGHHLKTVKQGLSDPHRG




GRAVAVLEFADPNSTANSSMHVVYKPKDMAVDAAYQATLADLNTHSDLSPLRTLAIHNGNG




YGYMEHVVHHLCANDKELTNFYFNAGRLTALLHLLGCTDCHHENLIACGDQLLLIDTETLL




EADLPDHISDASSTTAQPKPSSLQKQFQRSVLRSGLLPQWMFLGESKLAIDISALGMSPPN




KPERIALGWLGFNSDGMMPGRVSQPVEIPTSLPVGIGEVNPFDRFLEDFCDGFSMQSEALI




KLRNRWLDVNGVLAHFAGLPRRIVLRATRVYFTIQRQQLEPTALRSPLAQALKLEQLTRSF




LLAESKPLHWPIFAAEVKQMQHLDIPFFTHLIDADALQLGGLEQELPGFIQTSGLAAAYER




LRNLDTDEIAFQLRLIRGAVEARELHTTPESSPTLPPPATPEALMSSSAETSLEAAKRIAH




RLLELAIRDSQGQVEWLGMDLGADGESFSFGPVGLSLYGGSIGIAHLLQRLQAQQVSLMDA




DAIQTAILQPLVGLVDQPSDDGRRRWWRDQPLGLSGCGGTLLALTLQGEQAMANSLLAAAL




PRFIEADQQLDLIGGCAGLIGSLVQLGTESALQLALRAGDHLIAQQNEEGAWSSSSSQPGL




LGFSHGTAGYAAALAHLHAFSADERYRTAAAAALAYERARFNKDAGNWPDYRSIGRDSDSD




EPSFMASWCHGAPGIALGRACLWGTALWDEECTKEIGIGLQTTAAVSSVSTDHLCCGSLGL




MVLLEMLSAGPWPIDNQLRSHCQDVAFQYRLQALQRCSAEPIKLRCFGTKEGLLVLPGFFT




GLSGMGLALLEDDPSRAVVSQLISAGLWPTE





PsnA2
347
MSKNENNKKQLRDLFIEDLGKVTGGKGGPYTTLAIGEEDPITTLAIGEEDPDPTTLALGEE




DPTTLAIGEE





PsnA2_
348
MSKNENNKKQLRDLFIEDLGKVTGENLYFQGKGGPYTTLAIGEEDPITTLAIGEEDPDPTT


tev

LALGEEDPTTLAIGEE





PsnB
349
MTNLDTSIVVVGSPDDLHVQSVTEGLRARGHEPYVFDTQRFPEEMTVSLGEQGASIFVDGQ


enzyme

QIARPAAVYLRSLYQSPGAYGVDADKAMQDNWRRTLLAFRERSTLMSAVLLRWEEAGTAVY




NSPRASANITKPFQLALLRDAGLPVPRSLWTNDPEAVRRFHAEVGDCIYKPVAGGARTRKL




EAKDLEADRIERLSAAPVCFQELLTGDDVRVYVIDDQVICALRIVTDEIDFRQAEERIEAI




EISDEVKDQCVRAAKLVGLRYTGMDIKAGADGNYRVLELNASAMFRGFEGRANVDICGPLC




DALIAQTKR





RaxST
350
MDYHFISGLPRAGSSLLAALLRQNPQLHADVTSPVARLYAAMLMGMSEEHPSNVQIDDAQR


enzyme

VRLLRAVFDAYYQNRQELGTVFDTNRAWCSRLTGLARLFPRSRMICCVRDVGWIVDSFERL




AQSQPLRLSALFGYDPEDSVSMHADLLTAPRGVVGYALDGLRQAFYGDHADRLLLLRYDTL




AQRPAQAMEQVYAFLQLPAFAHDYAGVQAEAERFDAALQMPGLHRVRRGVHYVPRRSVLPP




ALFDQLQELAFWESAPSHGALLV





RaxX
351
MNHSKKSPAKGAASLQRPAGAKGRPEPLDQRLWKHVGGGDYPPPGANPKHDPPPRNPGHH





SboA
352
MKKAVIVENKGCATCSIGAACLVDGPIPDFEIAGATGLFGLWG





SgbA
353
MENQDLELLARLHALPETEPVGVDGLPYGETCECVGLLTLLNTVCIGISCA





SgbL
354
MTSHATEVEWEDLLRQALHATGTGARWAVEADEMWCRVAPVPGTRREQGWKLHVSATTASA


enzyme

PEVLTRALGVLLREKSGFKFARSLEQVSALNSRATPRGSSGKFITVYPRSDAEAVALARDL




HAATAGLAGPRILSDQPYAAHSLVHYRYGAFVGRRRLSDDGLLVWFIEDPDGNPVEDKRTG




RYAPPPWAVCPFPASVPVAPHDGEATSRPVVLGGRFAVREAIRQTNKGGVYRGSDTRTGTG




VVIKEARPHVEGDASGGDVRDWLRAEARTLEKLKGTGLAPEAVALFEHAGHLFLAQDEVPG




VTLRTWVAEHFRDVGGERYRADALAQVARLVDLVAAAHARGLVLRDFTPGNVMVRPDGELR




LIDLELAVLEDEAALPTHVGTPGFSAPERLADAPVRPTADYYSLGATACFVLAGKVPNLLP




EEPVGRPSEERLAAWLTACTRPLRLPDGVVDMILGLMRDDPAERWDPSRAREALRKADPTA




RPGDADRTAVRRTGSSAVAGPVPDSRTADGRTADGRSADEVVAGLVDHLVDSMTPADDRLW




PVSTLTGESDPCTVQQGAAGVLAVLTRYFELTGDPRLPGLLSTAGRWIADRTDVRSPRPGL




HFGGRGTAWALYDAGRAVDDRRLVEHALDLALAPPQATPHHDVTHGTAGSGLAALHLWQRT




GDTRFADLAVEAADRLTAAARREPSGVGWAVPAEADSPEGGKRYLGFAHGAAGIGCFLLAA




AELSRQPDHRATALEVGEGLVADAVRIGEAAQWPAQSGDLPTAPYWCHGAAGIGTFLVRLW




QATGDDRFGDLARGSAHAVAERASRAPLAQCHGLAGNGDFLLDLADATGDPVHRDTAEELA




GLILAEGTRRQGHVVFPNEYGEVSSSWSDGSAGILAFLLRTRHTGPRHWMVEQRG





StspA
355
MKKFYEAPALIERGAFAAATAGFGRLLADQLVGRLIP





StspM
356
MADHIAAGHDTVLSLAERTGTDPDLLGRVLRFLACRGVFAEPRPGTYALTPLSLTLLEGHP


enzyme

SGLREWLDASGAGARMDAAVGDLLGALRSGEPSYPRLHGRPFYEDLALHSRGPAFDGLRHT




HAESYVADLLAAYPWERVRRVVDVGGGTGVLVEALMRTHATLRTVLVDLPGAVATATARIA




AAGFGNRYTPVTGSFFDPLPAGADVYTLVNVVHNWNDERASALLRRCADAGRRDSTFVIVE




RLADDADPRAITAMDLRMFLFLGGKERTAAQIREVASAAGMAHQSTIKTPSGLHLLVFRKK




RFAARGHGRRMVT





TbtA
357
MDLNDLPMDVFELADSGVAVESLTAGHGMTEVGASCNCFCYICCSCSSA





TfxA
358
MDNKVAKNVEVKKGSIKATFKAAVLKSKTKVDIGGSRQGCVA





TgnA*
359
MYRPYIAKYVEEQTLQNSTNLVYDDITQISFINKEKNVKKINLGPDTTIVTETIENADPDE




YFL





TgnB
360
MKTILIITNTLDLTVDYIINRYNHTAKFFRLNTDRFFDYDINITNSGTSIRNRKSNLIINI


enzyme

QEIHSLYYRKITLPNLDGYESKYWTLMQREMMSIVEGIAETAGNFALTRPSVLRKADNKIV




QMKLAEEIGFILPQSLITNSNQAAASFCNKNNTSIVKPLSTGRILGKNKIGIIQTNLVETH




ENIQGLELSPAYFQDYIPKDTEIRLTIVGNKLFGANIKSTNQVDWRKNDALLEYKPANIPD




KIAKMCLEMMEKLEINFAAFDFIIRNGDYIFLELNANGQWLWLEDILKFDISNTIINYLLG




EPI





ThcoA
361
MRKKEWQTPELEVLDVRLTAAGPGKAKPDAVQPDEDEIVHYS





ThcoK
362
MTRTNTGYRYRAFGLRIDSDIPLPELGDGTRPDGDADLTVVRCGEAEPEWAEGGGGGRLYA


enzyme

AEGIVSFRVPQTAAFRITNGNRIEVHAYSGADEDRIRLYVLGTCMGALLLQRRILPLHGSV




VARDGRAYAIVGESGAGKSTMSAALLERGFRLVTDDVAAIVFDERGTPLVMPAYPQQKLWQ




DSLDRLQIAGSGLRPLFERETKYAVPADGAFWPEPVPLVHIYELVHSDGQTPELQPIAKLE




RCYTLYRHTFRRSLIVPSGLSAWHFETAVKLAEKTGMYRLMRPAKVFAARESARLIETHAD




GEVSR





TruD
363
MQPTALQIKPHFHVEIIEPKQVYLLGEQGNHALTGQLYCQILPFLNGEYTREQIVEKLDGQ


enzyme

VPEEYIDFVLSRLVEKGYLTEVAPELSLEVAAFWSELGIAPSVVAEGLKQPVTVTTAGKGI




REGIVANLAAALEEAGIQVSDPRDPKAPKAGDSTAQLQVVLTDDYLQPELAAINKEALERQ




QPWLLVKPVGSILWLGPLFVPGETGCWHCLAQRLQGNREVEASVLQQKRALQERNGQNKNG




AVSCLPTARATLPSTLQTGLQWAATEIAKWMVKRHLNAIAPGTARFPTLAGKIFTFNQTTL




ELKAHPLSRRPQCPTCGDRETLQRRGFEPLKLESRPKHFTSDGGHRAMTPEQTVQKYQHLI




GPITGVVTELVRISDPANPLVHTYRAGHSFGSATSLRGLRNVLRHKSSGKGKTDSQSRASG




LCEAIERYSGIFQGDEPRKRATLAELGDLAIHPEQCLHFSDRQYDNRESSNERATVTHDWI




PQRFDASKAHDWTPVWSLTEQTHKYLPTALCYYRYPFPPEHRFCRSDSNGNAAGNTLEEAI




LQGFMELVERDSVCLWWYNRVSRPAVDLSSEDERYFLQLQQFYQTQNRDLWVLDLTADLGI




PAFVGVSNRKAGSSERIILGFGAHLDPTVAILRALTEVNQIGLELDKVSDESLKNDATDWL




VNATLAASPYLVADASQPLKTAKDYPRRWSDDIYTDVMTCVEIAKQAGLETLVLDQTRPDI




GLNVVKVIVPGMRFWSRFGSGRLYDVPVKLGWREQPLAEAQMNPTPMPF





TruE*
364
MNKKNILPQLGQPVIRLTAGQLSSQLAELSEEALGGVDASYAVFWPICSYDD





TruE
365
MNKKNILPQLGQPVIRLTAGQLSSQLAELSEEALGGVDASTLPVPTLCSYDGVDASTVPTL




CSYDD
















TABLE 18





Genetic Parts







Promoters











SEQ


Name
Sequence
ID NO





PCymRC
AACAAACAGACAATCTGGTCTGTTTGTATTATGGAAAATTTTTCTGTATAATAGATTC
366



AACAAACAGACAATCTGGTCTGTTTGTATTAT






PLacI
GCGGCGCGCCATCGAATGGCGCAAAACCTTTCGCGGTATGGCATGATAGCGCCC
367





PLacIQ
GCGGCGCGCCATCGAATGGTGCAAAACCTTTCGCGGTATGGCATGATAGCGCCC
368





PLuxB
ACCTGTAGGATCGTACAGGTTTACGCAAGAAAATGGTTTGTTACAGTCGAATAAA
369





PT5LacO
AATCATAAAAAATTTATTTGCTTTGTGAGCGGATAACAATTATAATAGATTCAATTGT
370



GAGCGGATAACAATT






PT7A1
ATCCCGAAAATTTATCAAAAAGAGTATTGACTTAAAGTCTAACCTATAGGATACTTAC
371



AGCCATCGAGAGCTGCG










Ribosom binding sites (RBSs)













SEQ ID


Name
Gene
Sequence
NO:





lac1
LacI
GGAAGAGAGTCAATTCAGGGTGGTGAAT
372





lux1
LuxR
GGAAGAGAGTCAATTCAGGGTGGTGAAT
373





PP_1
peptide
ACCCAACACCACCAGCAAGCCTAAGGAGGAGAAAT
374





PP_2
MBP-TruE*
TTCCACCATCAAAACACGGAGAGTAGCCCAC
375





ME_1
AlbA
AGAATCAAGCAAGTCAAAGGAGTTAACCCGA
376





ME_2
AlbsBb
AGAGTTTAGGAGAAAGACATAAGGAAATATTAA
377





ME_3
AlbsCb
GGAAGCAGCCGTAAAAGGTAGGTTTTTTTT
378





ME_4
AlbsT
AGACGCTTGAACCAGCAATAAGGAGAGTAATT
379





ME_5
AMdnC
AGAGGCTATATAGGATAGGGGGGTCCCC
380





ME_6
AtxBb
AGAGCTGTTAGTCGCTGCCAGGAGGTCCCGT
381





ME_7
AtxCb
CTTTTAACATCCCTTCTCATAAGGAGGTTTTA
382





ME_8
BamB
GCCCCGTCAGACACCTTCTAAGGAGGACATAT
383





ME_9
BsjM
AGAGACGGGCGGCCACCAGGAGGAACGAGA
384





ME_10
CapBb
AGAGGCCTACAGATATTCCAGACTAACACTAAGGAGGAAAACG
385





ME_11
CapCb
TGGCTTCCGTTTTTCACCACTTGTTAAGGAGTACTTT
386





ME_12
CinX
AGAAATTTTTCATACCGAGGGAGGAAAAT
387





ME_13
Cln1Bb
AGACAGTAGTATAAAGGAGGGTTCAAGT
388





ME_14
Cln1Cb
TTCAATAAATTAAGGAATTTTG
389





ME_15
Cln2Bb
AGAACCACTATAAGGAACGATTT
390





ME_16
Cln2Cb
CAGTATAACTAGAACAACAAGGAGTCAGATA
391





ME_17
Cln3Bb
AGATCCCGATAAAGGAGGTCCTA
392





ME_18
Cln3Cb
TAACATAAGGAGGGTTTCTAA
393





ME_19
ComQ
AGAGGAACGAGAAATAAGGACACAGATAT
394





ME_20
CrnM
AGATCACCCATACCAAGTATAACGAGAACCTCC
395





ME_21
CsegBb
AGATCACTGCAATAGTAAGGAGGTATATA
396





ME_22
CsegCb
AGCACCGAGGGGTCAATAATAAGGAGGTAAAC
397





ME_23
EpiD
ACTGAACTATAAGGTAGGTATATT
398





ME_24
HalM1
CCAATCAAGGAGGTAGAAAACATA
399





ME_25
HalM2
TAAAACCGCTCGTAAGGAGGTCTT
400





ME_26
KgpF
AGAACGCAGACAATTTCATAGGAGGTCCCG
401





ME_27
LasBb
AGACAATTCATAAGGAGGTTAAGGT
402





ME_28
LasCb
CCTACTACTCTGATCCCCATAAGGAGGTTTTTT
403





ME_29
LasDb
CAACCTAATCTTAGGCGAGGTCATTTTTT
404





ME_30
LasF
AGAGCCATCAGATTTAAGGAACATAAAAA
405





ME_31
LcnG
AGACTATCGATAATAGGAGGTAGACC
406





ME_32
LtnM1
AGACAATTGAAGCAGGCTAGCCAGGAGTTCCAT
407





ME_33
LtnM2
AGAATTCCACCCCCCACTAAGGAGGTTTTTT
408





ME_34
LynD
CTAAATTCCCCCGAGGTCAATA
409





ME_35
McbC
AGAGCTTCACCCTACAAGGAGGATATAGA
410





ME_36
MdnC
AGACGCCCGCAACATTTTATTTTAAGGACGACCCA
411





ME_37
MibD
AGATAACCCAATCCGTAAGGACACACGTCAAGGAGGCGATTT
412





ME_38
MibHb
AGAGCACATCAGACCTAAGGAAAATATAA
413





ME_39
MibO
AGAGTTCATCAGTTTATTAGGAAAAT
414





ME_40
MibSb
ACCCTGCCATTTTTTTAGCCCAAAGAACACGGAGCATCTTT
415





ME_41
PaaA
AGATCATTTCCAATAAGGGGGACACT
416





ME_42
PadeK
AGACACCGAAACCTAAGGAGGGATAT
417





ME_43
PalS
AGACCAAACAATTAGGAGGACAAAT
418





ME_44
PapB
AGAACTAAGGAGGTTAGAGG
419





ME_45
PapoK
TTCAATCGTTAAGGAGGTACATAA
420





ME_47
PbtM1
AGAGGAACGGATAAGGAGGTCAATAT
421





ME_48
PbtO
AGACGTCACTATCAAACACACTAATACCACATAAGGAGCGAACA
422





ME_49
PcpXb
AGACACAGGGAGGTCTTTAT
423





ME_50
PcpYb
CACAAGGGGGTAGTAGT
424





ME_51
PlpXb
AGAGCCACCATTTATAAGGAGAACCTACCG
425





ME_52
PlpYb
ATATAAAGTTAAGGAGTTGCAC
426





ME_53
ProcM
AGAAATCACATTACGCATAGGGGGAGGTAGACAC
427





ME_54
PsnB
AGACGAATATAAGGAATAAAATA
428





ME_55
RaxST
AGAGCCTTCCACAAACTAAGGAGCACAATT
429





ME_56
SgbL
AGAAAAACGAGGAGGTAATAG
430





ME_57
StspM
AGAGGCGGTATTAAGGGGGCCAGAG
431





ME_58
TgnB
AGAAATATTACAACGAGGTAAAGGC
432





ME_59
ThcoK
AGAGCATTCCATAAGGAGAAATTTT
433





ME_60
TruD
AGACACACTCGAATTACTCAAAGGACCTCTAGCA
434





ME_61
TruD
AGCCACACTCGAATTACTCAAAGGACCTCTAGCA
435










Terminators













SEQ


Name
Details
Sequence
ID NO:





B0062

CAGATAAAAAAAATCCTTAGCTTTCGCTAAGGATGATTTCT
436





ECK120029600

TTCAGCCAAAAAACTTAAGACCGCCGGTCTTGTCCACTACCTTGCA
438




GTAATGCGGTGGACAGGATCGGCGGTTTTCTTTTCTCTTCTCAA






AraC
Includes 2
TTGGTAACGAATCAGACAATTGACGGCTCGAGGGAGTAGCATAGGG
438



SNPs
TTTGCAGAATCCCTGCTTCGTCCATTTGACAGGCACATTATGCATC





GATGATAAGCTGTCAAACATGAGCA






B0053
aka His
TCCGGCAAAAAAGGGCAAGGTGTCACCACCCTGCCCTTTTTCTTTA
439



Operon
AAACCGAAAAGATTACTTCGCGTT




Terminator







L3S3P21

CCAATTATTGAAGGCCTCCCTAACGGGGGGCCTTTTTTTGTTTCTG
440




GTCTCCC






L3S2P41

CTCGGTACCAAAAAAAAAAAAAAAGACGCTGAAAAGCGTCTTTTTT
441




TTTTTTGGTCC






L3S3P41
g →c SNP to
AAAAAAAAAAAACACCCTAACGGGTGTTTTTTTTTTTTTGGTGTCC
442



remove BsaI
C




site.







IOT

TTGGTAACGAATCAGACAATTGACGGCTCGAGGGAGTAGCATAGGG
443




TTTGCAGAATCCCTGCTTCGTCCATTTGACAGGCACATTATGCATC





GATGATAAGCTGTCAAACATGAGCAGATCCTCTACGCCGGACGCAT





CGTGGCCGGCATCACCGGCGCCACAGGTGCGGTTGCTGGCGCCTAT





ATCGCCGACATCACCGATGGGGAAGATCGGGCTCGCCACTTCGGGC





TCATGAGCAAATATTTTATCTG










Ribozymes













SEQ


Name
Details
Sequence
ID NO:





RiboJ53

AGCGGTCAACGCATGTGCTTTGCGTTCTGATGAGACAGTGATGTCG
444




AAACCGCCTCTACAAATAATTTTGTTTAA






ElvJ

AGCCCCATAGGGTGGTGTGTACCACCCCTGATGAGTCCAAAAGGAC
445




GAAATGGGGCCTCTACAAATAATTTTGTTTAA










Linkers/Tags













SEQ


Name
Details
Sequence
ID NO:





ATag-1
Affinity tag
ATGTCATATTACCACCATCACCATCATCACGACTATGATATTCCCA
446




CAAGCGAGAACTTGTACTTTCAAGGG






ATag-2
N-terminal
ATGTCATATTACCACCATCACCATCATCACGGGTCCCTGCAG
447



SUMO affinity





tag







ATag-3
C-terminal
ATGTCATATTACCACCATCACCATCATCAC
448



sumo affinity





tag (N-





terminal to the





peptide)







ATag-4
C-terminal
TCCATTACAAGCCACCATCACCATCATCACGGT
449



sumo affinity





tag (C-





terminal to





SUMO)







Link-1
N-terminal
CATCACCATCACCACCATGGATATGATATTAGCACAGGT
450



SUMO linker





v1







Link-2
N-terminal
TGCATGTCATATTACGACTCCATTCCCACAAGCGAGAACTTGTACT
451



SUMO linker
TTCAAGGGTGC




v2







Link-3
C-terminal
CGACTGGTTCCGCGTGGTAGCTATTACGACTCCATTCCCACAAGCG
452



sumo linker
AGAAC






RSTN*
Concatenation
ATGTCATATTACCACCATCACCATCATCACGGGTCCCTGCAGGACT
453



of: ATag-2,
CAGAAGTCAATCAAGAAGCTAAGCCAGAGGTCAAGCCAGAAGTCAA




SUMO, and
GCCTGAGACTCACATCAATTTAAAGGTGTCCGATGGATCTTCAGAG




Link-1
ATCTTCTTCAAGATCAAAAAGACCACTCCTTTAAGAAGGCTGATGG





AAGCGTTCGCTAAAAGACAGGGTAAGGAAATGGACTCCTTAAGATT





CTTGTACGACGGTATTAGAATTCAAGCTGATCAGGCCCCTGAAGAT





TTGGACATGGAGGATAACGATATTATTGAGGCTCACCGCGAACAGA





TTGGAGGTCATCACCATCACCACCATGGATATGATATTAGCACAGG





T






RSTN
Concatenation
ATGTCATATTACCACCATCACCATCATCACGGGTCCCTGCAGGACT
454



of: ATag-2,
CAGAAGTCAATCAAGAAGCTAAGCCAGAGGTCAAGCCAGAAGTCAA




SUMO, and
GCCTGAGACTCACATCAATTTAAAGGTGTCCGATGGATCTTCAGAG




Link-2
ATCTTCTTCAAGATCAAAAAGACCACTCCTTTAAGAAGGCTGATGG





AAGCGTTCGCTAAAAGACAGGGTAAGGAAATGGACTCCTTAAGATT





CTTGTACGACGGTATTAGAATTCAAGCTGATCAGGCCCCTGAAGAT





TTGGACATGGAGGATAACGATATTATTGAGGCTCACCGCGAACAGA





TTGGAGGTTGCATGTCATATTACGACTCCATTCCCACAAGCGAGAA





CTTGTACTTTCAAGGGTGC






RSTc
Concatenation
ATGTCATATTACCACCATCACCATCATCAC[]CGACTGGTTCCGCG
455



of: ATag-3,
TGGTAGCTATTACGACTCCATTCCCACAAGCGAGAACGACTCAGAA




peptide insert,
GTCAATCAAGAAGCTAAGCCAGAGGTCAAGCCAGAAGTCAAGCCTG




Link-3,
AGACTCACATCAATTTAAAGGTGTCCGATGGATCTTCAGAGATCTT




SUMO, ATag-
4CTTCAAGATCAAAAAGACCACTCCTTTAAGAAGGCTGATGGAAGC




4. Site for
GTTCGCTAAAAGACAGGGTAAGGAAATGGACTCCTTAAGATTCTTG




peptide
TACGACGGTATTAGAATTCAAGCTGATCAGGCCCCTGAAGATTTGG




insertion is
ACATGGAGGATAACGATATTATTGAGGCTCACCGCGAACAGATTGG




indicated by [].
AGGCTCCATTACAAGCCACCATCACCATCATCACGGT










Genes













SEQ


Name
Details
Sequence
ID NO:





SUMO
sequence from
GACTCAGAAGTCAATCAAGAAGCTAAGCCAGAGGTCAAGCCAGAAG
456



pE-SUMO
TCAAGCCTGAGACTCACATCAATTTAAAGGTGTCCGATGGATCTTC





AGAGATCTTCTTCAAGATCAAAAAGACCACTCCTTTAAGAAGGCTG





ATGGAAGCGTTCGCTAAAAGACAGGGTAAGGAAATGGACTCCTTAA





GATTCTTGTACGACGGTATTAGAATTCAAGCTGATCAGGCCCCTGA





AGATTTGGACATGGAGGATAACGATATTATTGAGGCTCACCGCGAA





CAGATTGGAGGT






lacI

ATGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCT
457




CTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTC





TGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAAT





TACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGT





TGCTTATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTC





GCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCC





AGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTA





AAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTGAT





CATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCT





GCCTGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGA





CACCCATCAACAGTATTATTTTCTCCCATGAGGACGGTACGCGACT





GGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTG





TTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTG





GCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGA





ACGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATG





CAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTTGCCA





ACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGG





GCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACC





GAAGATAGCTCATGTTATATCCCGCCGTTAACCACCATCAAACAGG





ATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACT





CTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCAGTCTCA





CTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCT





CTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGT





TTCCCGACTGGAAAGCGGGCAG






HIS6-MBP

ATGTCATATTACCACCATCACCATCATCACGACTATGATATTCCCA
458




CAAGCATGAAAATCGAAGAAGGTAAACTGGTAATCTGGATTAACGG





CGATAAAGGCTATAACGGATTGGCTGAAGTCGGTAAGAAATTCGAG





AAAGATACCGGAATTAAAGTCACCGTTGAGCATCCGGATAAACTGG





AAGAGAAATTCCCACAGGTTGCGGCAACTGGCGATGGCCCTGACAT





TATCTTCTGGGCACACGACCGCTTTGGTGGCTACGCTCAATCTGGC





CTGTTGGCTGAAATCACCCCGGACAAAGCGTTCCAGGACAAGCTGT





ATCCGTTTACCTGGGATGCCGTACGTTACAACGGCAAGCTGATTGC





TTACCCGATCGCTGTTGAAGCGTTATCGCTGATTTATAACAAAGAT





CTGCTGCCGAACCCGCCAAAAACCTGGGAAGAGATCCCGGCGCTGG





ATAAAGAACTGAAAGCGAAAGGTAAGAGCGCGCTGATGTTCAACCT





GCAAGAACCGTACTTCACCTGGCCGCTGATTGCTGCTGACGGGGGT





TATGCGTTCAAGTATGAAAACGGCAAGTACGACATTAAAGACGTGG





GCGTGGATAACGCTGGCGCGAAAGCGGGTCTGACCTTCCTGGTTGA





CCTGATTAAAAACAAACACATGAATGCAGACACCGATTACTCCATC





GCAGAAGCTGCCTTTAATAAAGGCGAAACAGCGATGACCATCAACG





GCCCGTGGGCATGGTCCAACATCGACACCAGCAAAGTGAATTATGG





TGTAACGGTACTGCCGACCTTCAAGGGTCAACCATCCAAACCGTTC





GTTGGCGTGCTGAGCGCAGGTATTAACGCCGCCAGTCCGAACAAAG





AGCTGGCGAAAGAGTTCCTCGAAAACTATCTGCTGACTGATGAAGG





TCTGGAAGCGGTTAATAAAGACAAACCGCTGGGTGCCGTAGCGCTG





AAGTCTTACGAGGAAGAGTTGGCGAAAGATCCACGTATTGCCGCCA





CCATGGAAAACGCCCAGAAAGGTGAAATCATGCCGAACATCCCGCA





GATGTCCGCTTTCTGGTATGCCGTGCGTACTGCGGTGATCAACGCC





GCCAGCGGTCGTCAGACTGTCGATGAAGCCCTGAAAGACGCGCAGA





CTCGTATCACCAAGTCGTACTACCATCACCATCACCATCACGGCGG





TAGTGGCGAAAACCTGTATTTTCAGGGT






luxR

ATGAAAAACATAAATGCCGACGACACATACAGAATAATTAATAAAA
459




TTAAAGCTTGTAGAAGCAATAATGATATTAATCAATGCTTATCTGA





TATGACTAAAATGGTACATTGTGAATATTATTTACTCGCGATCATT





TATCCTCATTCTATGGTTAAATCTGATATTTCAATCCTAGATAATT





ACCCTAAAAAATGGAGGCAATATTATGATGACGCTAATTTAATAAA





ATATGATCCTATAGTAGATTATTCTAACTCCAATCATTCACCAATT





AATTGGAATATATTTGAAAACAATGCTGTAAATAAAAAATCTCCAA





ATGTAATTAAAGAAGCGAAAACATCAGGTCTTATCACTGGGTTTAG





TTTCCCTATTCATACGGCTAACAATGGCTTCGGAATGCTTAGTTTT





GCACATTCAGAAAAAGACAACTATATAGATAGTTTATTTTTACATG





CGTGTATGAACATACCATTAATTGTTCCTTCTCTAGTTGATAATTA





TCGAAAAATAAATATAGCAAATAATAAATCAAACAACGATTTAACC





AAAAGAGAAAAAGAATGTTTAGCGTGGGCATGCGAAGGAAAAAGCT





CTTGGGATATTTCAAAAATATTAGGTTGCAGTGAGCGTACTGTCAC





TTTCCATTTAACCAATGCGCAAATGAAACTCAATACAACAAACCGC





TGCCAAAGTATTTCTAAAGCAATTTTAACAGGAGCAATTGATTGCC





CATACTTTAAAAATTGATAA






cymR

ATGAGCCCGAAACGTCGTACCCAGGCAGAACGTGCAATGGAAACCC
460




AGGGTAAACTGATTGCAGCAGCACTGGGTGTTCTGCGTGAAAAAGG





TTATGCAGGTTTTCGTATTGCAGATGTTCCGGGTGCAGCCGGTGTT





AGCCGTGGTGCACAGAGCCATCATTTTCCGACCAAACTGGAACTGC





TGCTGGCAACCTTTGAATGGCTGTATGAGCAGATTACCGAACGTAG





CCGTGCACGTCTGGCAAAACTGAAACCGGAAGATGATGTTATTCAG





CAGATGCTGGATGATGCAGCAGATTTTTTTCTGGATGATGATTTTA





GCATCGGCCTGGATCTGATTGTTGCAGCAGATCGTGATCCGGCACT





GCGTGAAGGTATTCTGCGTACCGTTGAACGTAATCGTTTTGTTGTT





GAAGATATGTGGCTGGGTGTGCTGGTGAGCCGTGGTCTGAGCCGTG





ATGATGCCGAAGATATTCTGTGGCTGATTTTTAACAGCGTTCGTGG





TCTGACAGTTCGTAGCCTGTGGCAGAAAGATAAAGAACGTTTTGAA





CGTGTGCGTAATAGCACCCTGGAAATTGCACGTGAACGTTATGCAA





AATTCAAACGT










Modifying Enzymes













SEQ


Name
Details
Sequence
ID NO:





albA
Amplified
ATGTTTATAGAGCAGATGTTTCCATTTATTAATGAAAGTGTAAGAG
461



from genome
TTCACCAGCTTCCTGAGGGCGGCGTGTTAGAAATCGACTACTTGCG





CGATAATGTCTCCATTTCTGACTTTGAGTATTTGGATCTCAACAAA





ACGGCTTACGAGCTCTGCATGCGCATGGATGGCCAAAAAACAGCTG





AGCAGATTTTAGCTGAGCAATGTGCAGTGTATGATGAATCACCGGA





AGATCATAAAGATTGGTATTACGACATGCTCAACATGCTCCAGAAC





AAGCAGGTTATTCAGCTTGGAAACCGGGCCAGCCGCCATACAATCA





CCACGAGCGGAAGCAATGAATTTCCGATGCCCCTGCACGCCACCTT





TGAACTGACGCACCGCTGTAATTTGAAATGCGCCCACTGTTATTTG





GAAAGCTCACCTGAAGCGCTCGGCACCGTGTCGATTGAGCAATTCA





AAAAAACGGCTGATATGCTGTTTGATAACGGTGTATTGACATGCGA





AATCACAGGTGGAGAAATTTTTGTCCATCCAAACGCCAATGAGATT





CTTGACTATGTGTGTAAAAAGTTCAAAAAAGTCGCTGTCTTAACAA





ACGGAACACTCATGCGAAAAGAGAGCCTGGAGCTTTTGAAAACTTA





CAAGCAAAAAATCATCGTCGGCATTTCTCTAGATAGTGTCAATTCC





GAGGTCCATGACTCCTTTAGAGGGAGAAAAGGCTCTTTTGCCCAAA





CTTGTAAAACGATAAAATTGTTGAGTGACCACGGTATATTTGTCAG





AGTCGCTATGTCTGTATTCGAAAAAAACATGTGGGAAATCCACGAT





ATGGCCCAAAAGGTTCGGGATCTCGGGGCGAAGGCGTTTTCTTACA





ATTGGGTTGACGATTTCGGAAGAGGCAGGGATATTGTCCATCCAAC





GAAAGACGCCGAGCAGCACCGCAAGTTTATGGAATACGAGCAACAT





GTGATTGATGAGTTTAAAGATCTGATTCCGATTATTCCCTATGAGA





GAAAACGCGCGGCAAATTGCGGCGCTGGCTGGAAGTCCATTGTGAT





CAGTCCGTTCGGCGAAGTACGTCCTTGCGCCCTCTTTCCAAAGGAA





TTTTCATTGGGAAATATTTTTCATGATTCCTATGAAAGCATCTTTA





ACTCCCCTCTCGTCCATAAACTGTGGCAAGCGCAAGCGCCGCGGTT





CAGCGAACATTGCATGAAAGACAAATGCCCGTTCAGCGGCTATTGC





GGAGGCTGTTACTTAAAAGGGCTGAACTCTAACAAATATCACCGGA





AAAACATTTGCTCTTGGGCGAAAAATGAACAATTAGAAGATGTGGT





CCAGCTTATT






albsB
Codon
ATGCCTGAGCTTCCCCGTTTCGCGACGGCCCCTCGTCACGTGCGTG
462



optimized
CCCTGGATTTCGGTCATGTTCTGGTCCTGATCGATTACCGTTCCAA





TCACGTCCAGTGCCTGCTTCCGGCAGCCGCAGCCCATTGGACAGCC





ACAGCGCGTACCGGCCGCTTGGACACCATGCCGGCAGCGCTGGCCA





CCCAGTTACTGACATCGGCGTTATTAGTACCGCGGCCGACCGCAAC





ACCGTGGACGGCACCTGTAGCGGCACCACCTGCTCCACCGTCATGG





GGTGGATCCGAGCATCCTGCCGGGACATCACGCCCTCGGGCACGTC





ATCGGCACTCAACCACGGCTGCGGCGGCGCTGGCATGTGTGCTGGC





GATTAAGGCAGCAGGCCCAACCCGCTATGCTATGCAGCGCTTGACC





ACGGTCGTGAAGGCAGCCGCTTCTACGTGCCGTCGCCCGGCAACGC





CAGCACAAGCGACGGCTGCTGCGCTTGCGGTCCGTCAGGCATGCTG





GTACTCGCCAGCGCGTACAGCCTGTCTGGAAGAATCCGCCGCGACT





GTCATTTTACTCGCTACCCGGCGTTTGAGTTCGACATGGTGCCATG





GAGTAGCTCCCGATCCGATTCGCCTCCATGCCTGGGTGGAAACTGA





GGATGGGACACCTGTAGCAGAGCCAGCCTCGACCCTTGCGTACACC





CCGGCCTTAACCATTGGAGGCCACCATCAACACCAGCCT






albsC
Codon
ATGATCTTTGGTGGATTTTCGACGACCCGTGAAGTTCGTCAACGCC
463



optimized
CTGGTAATGCCGAGTTTATTGCTACGGACTCGCCTATTTGGCGCCT





CGGTCGTAGTCCAGCTCGTTGCGTGGCTGCGGACCATGGACAGCGT





CGCCTGGTAGTGTTGGGAGAATGCGGGGCAACGGATGGCGAATTAT





CTCGCCTGGCGACCGCGGGGCTGCCCACGGATATTACCTGGCGCTG





GCCAGGCGTGTACGTGGTGGTCGAAGAACAACCGGAACGTACGGTG





CTGCACACTGATCCAGCAGCTGCACTCCCGGTATACGCAACCCCTT





GGCAAGGCGGCTGGGCATGGTCAACCAGCGCGCGCATCCTGGCACG





TTTAACAGAAGCTCCAATTGATGGTCAACGCCTGGCATGTTCAGTG





CTGGCCCCGTCTGTTCCGGCTCTGAGCGGTACCCGCACATTCTTTG





CGGGTATCGAACAATTGGCCCTGGGTTCGCGTATTGAACTGCCGGT





GGATGGGTCCCGTCTGCGTGTTACGGTACGTTGGCGCCCGGATCCA





GTCCCGGGAGAACCATATCATCGCTTGCGCACAGCGTTGACCGAGG





CGGTCGCCCTGCGTGTCAACCGCGCACCAGACCTGTCATGCGACCT





CTCGGGCGGCCTCGATTCCACGTCACTGGCAGTCCTGGCGGCTGTG





TGCTTACCGGAGTCCCACCATCTGAATGCTATCACGATTCATCCGG





AGGGCGATGAAAGTGGCGCGGACTTACGGTATGCGCGCTTGGCAGC





TGCGCACCACGGGCGTATTCGCCACCACCTTCTCCCCCTTGCGGCA





GAACACCTGCCGTATACTGAAATTACGGCGGTGCCCCCTACCACCG





AACCGGCACCTTCAACATTAACGCGTGCACGCCTCGCGTGGCAGTT





AGATTGGATGCGCCAGCACTTAGGCAGCCGCACCCATATGACTGGC





GATGGAGGCGACAGCGTACTGTTCCAACCGCCGGCACATCTGGCGG





ATCTCCTGCGGCATCGGCAGTGGCGTCGGACTTTGTCGGAAAGTTT





GGGATGGGCACGCCTTCGCCATACGTCTGTTTTACCCTTACTGCGT





GGAGCAGCAACTCTTGCACGTACATCACGTCGGTCGGGCCTCCAGG





ATCTCGCACGCGCATTGGCGGGTGCAGGTCAGCAGGGCGATGGTCG





TGGCAATGTGAGCTGGTTCGCACCATTACCGCTGCCTGGCTGGGCG





ACCCCAACCGCTCGTCGCTTACTGCTTGATGCAGCCGATGAAGCTA





TCTCGACCGCGGATCCGTTACCGGGACTGGATACGTCGCTGCGCGT





ACTGATCGATGAAATTCGCGAAGTCGCCCGCACGGCAGCGGCAGAT





GCCGAACTGGCGGATGCTCACGGAACGACTCTGCATAACCCATTTC





TCGATCCGCGCACTATTGATGCAGTCCTGCGCACGCCAATCGCACA





TCGCCCGGCGGTCCACTCGTATAAGCCAGCGCTGGGGCATGCAATG





CAGGATTTGCTCCCGGGTGCAGTCGCTCGGCGCTCAACTAAAGGCT





CTTTTAACGCCGATCATTATGCGGGGATGCGTGCAAATCTGCCAGC





ATTGACAGCGCTGGCAGATGGCCACCTGGCCGACCTGGGTTTGTTG





GAGCCGACGCGCTTCCGCAGTCATCTTCGCCAAGCCGCCGCGGGCA





TTCCGATGCCGCTTGCGGCGATCGAACAGGCGCTGTCTGCCGAAGC





ATGGTGTCATGCACATCACGCCACCCCAAGCCCTGCCTGGACAACG





CAGCCACCGGAACACCCGCATGCC






albsT
Codon
ATGAGCACGTCCCCCGAACAGACCCTCTGGATCTCAACTGATACCT
464



optimized
GTGGTCTGGGGCCGTATCGCGCTGACTTGGTGGATACCTATTGGCA





GTGGGAACAAGACCCAACATTGCTTGTAGGCTACGGTCGTCAGTCA





CCGCAGTCACTGGAGGCCCGCACGGAAGGTATGGCCCACCAATTGC





GTGGCGATAACATCCGTTTCACTATCTATGATCTGTGCAGCAGTAC





ACCTACCCCGGCGGGCGTGGCAACGCTGCTGCCCGATCATAGCGTC





CGTACTGCCGAGTATGTTATTATGCTTGCGCCTGAAGCACGTGGGC





GTGGCTTAGGAACCACCGCCACGCAGCTGACGTTAGATTATGCGTT





TCACATCACCAATCTGCGGATGGTCTGGTTGAAAGTACTGGCGCCG





AACACCGCGGGCATCCGTGCGTATGAGAAAGCTGGCTTTCGTACAG





TTGGAGCGCTTCGCGAAGCCGGCTATTGGCTGGGGAAGGTCTGCGA





TGAGGTACTGATGGATGCCTTAGCGAAAGACTTCACGGGTCCAAGT





GCAGTCCACGCAGCATTAACTGGCGCCAGCGGTCGCCAGCTGCGCC





GTGCACCT






amdnC
Codon
ATGAACGTTCTGATTATAACGCATTCCCACGATAACGAGAGCATTT
465



optimized
CATTGGTAACCCAAGCCATTGAATCCCAGGGTGGTAAAGCATTTCG





CTTCGATACCGATCGTTTTCCGACGGAAGTCCAGCTGGACATCTAT





TACTCAAATACAGAGAAATGCGTGCTGGTGGCTGACGATCAAAAAC





TGGATTTAAATGAAGTAACCGCGGTCTGGTATCGCCGCATTGCGAT





CGGTGGCAAAATCCCGCCCACGATGGATAAGCAACTTCGTCAGGCC





TCGATTCAGGAGAGTCGTGCTACAATTCAAGGCATGATAGCGAGCA





TTCGCGGCTTTCACCTTGACCCAGTGCCGAACATTCGTCGCGCTGA





AAATAAGCAACTGCAGCTGCAGGTTGCCCGCAAAATCGGACTGGAT





ACCCCACGCACTCTCACCACTAATAATCCGCAGGCCGTGAAGGAAT





TTGCGGCAGAATGCCAGCAGGACGTAATCACCAAAATGCTGAGTAG





TTTTGCGATTTATGATGAGAAAGGCGGAGAACAGGTGGTTTTCACC





AATCCCGTGAAATCTGAGGATCTGGAAAATTTAGAAGGTCTGCGCT





TTTGCCCTATGACGTTTCAAGAGAAAATCGCAAAGGTTCTGGAGCT





CCGGATCACCATCGTGGGTAAGTCAATTTTAACGGCTGCGGTGAAT





TCACAGGCCCTGGACAAATCCCGTTATGATTGGCGCAAGCAGGGCG





TAGCATTACTGGATGCATGGCAGACCCATACGTTACCCCAGGACGT





GGCTGATAAATTGCTTCAACTGATGGCCCATTTCGGGTTAAACTAT





GGAGCCATTGACGTGATTCTGACCCCGGATAATCGCTATGTGTTCT





TGGAGGTCAATCCGGTGGGCGAATTCTTTTGGCTTGAGCGTTGCCC





AGGTCTGCCGATTAGTCAAGCTATTGCTAAAGTGCTGCTTTCTCAT





ATA






atxB
Codon
ATGTACGAGCTGAATGATGGCGTAGGTTTGGCCCTCGTGGATCAGC
466



optimized
ATCCGATTTTTCTGGACCTGAAAACAGACCGTTACCTGTCGTTGAG





TCCAGATGGGGCAGCAGTCCTGCTGGGAGCAGCGCCAGCCACCAAA





GAGAGTCCACTGTTTCTCGGATTAGAATCCATTGGCTTGGTCAAAA





ACGGTCCGTCAGGCCTTAAGCCTTGCCAAATTGCCGTAGCCACTGG





GTCTGCACCGCCCCGTAAGGTGCAATTCGAGTCGTTGTCACTCCTG





CTTTTGCGCTTAATTCGTGCACGTCTGGATCAACGTGCTCTTTTGA





AGCGTGTGACCGACTTAAAGAAGGCCGGCACCATTGCCCAGACGAA





GAACCGTGACTGCGCCTTGTCATTATTAGGTAGCGTGGAGACTGAG





GCAAAGGCTTGTCGTACCCTTTTAAGTAGTACAGACAAATGCCTGC





CCGACGCATTCGCAATTGCAACGCACCTGCGCCGTCGCGGAGTAGA





CGCCAAGTTAGTTTTCGGTGTGCGCCTGCCATTCGCGGCACATGCC





TGGGTCCAGGTAGATGATATTGTAGTGGGTGATCGTCCCGACCGTA





TCCTTGCGTTCACCCCCATCTTAGTCGTT






atxC
Codon
ATGCGCTATGTCGCGTCTTTCTTTGTTCGCGGACATGTCAGCACAC
467



optimized
CAGCACTGCGTCACCCAGAGCCAAAGGGTTTCGCTTATGCAAAAGT





CAGTGGCGGACTGAGCGTATGGAGCGATGCGCCGATTCGTCACCGT





GCGCCCCTTATTACAGTGGGCGCGGTGTTCGATCGCGCGTCTTTTA





AAGGGCTGGATTGCGACTTATCAGGTCTGCGTCAGGATGGTCTTAA





TACATTGAAAGCGGAAACGTTCGGACCCTACCTGGCGTTAGAGGTT





GCCGATAACGGCACCCTTCGCGTTTATCGCGATCCGTCAGGCGGCG





CGCCTTGCTATTACCTGCAGACCGAGGACGGCTTCTGGCTTGCAAG





CGATGCTGATTTGTTATTCACTCATTCGGGCGTACATCCATCAGTA





AGCTTACCGGGACTGATTGAACACTTGCGTCGTCCAGAGTTCCAAA





ATGAGGGCACATGCTTAAACGTCAAGCAAGTACGCCCTGGGGAGCA





GGTTGATTTATCGCTCTCGGGCGAGGTCCGTGCCTGTTTGTTCCCG





CCTGCATCATCCCTGCGCCCGCCTGAGTTGCACCGCGCATACGATG





ACATTAAGGCTGAGCTGCGCGCTCTGATTTTACGCAGCATTAAGGC





CTATGCCAGTGATTTCCCTCACGTTGTTGTTAGCTTCAGCGGTGGT





CTGGATAGCAGTGTTGTTGCGGCCGGCTTAGCGCAAACTTCCACTA





AGGTCCTGCTTCACACCTTTAAGGGCCCAGATGCCAAAGGGGACGA





GACTGCCTTCGCCGCAGAATGCGCGGCATATCTGGGTTTAAGCTTA





GAGATTGATACTCTCAGTATCGATGACGTTGATCTGTCGGCAACTA





TTTCCCCGCACCTGCCGCGCCCCAGCACATCATTCTTCTTGCCATC





ACTGCTGCGCGGTTTCTCTACCTCGAGCCAAACGCGCACAGGCGGG





GCAATCTTTTCGGGAAACGGCGGTGACTCGGTCTTTTGTTTCATGC





ATAGCGCGACCCCGCTGGCCGATTTGATGTGTCGTCCGTCAGGTCT





TACGCCGTTCATGCAAACATGGGCCGACGTGCAAAAGCTTACCCGT





GCCTCAGCGACCGAAGTGCTGCGTCGCGCGTTAAAGACAGCCATGG





CGCGTGGCTACATCTGGCCTGAATCCAATCTCCTCTTGTCCCGCGA





CACAAGCTCGAGCCGTTTAACACCTGACTCCGTTCTGTCGAGCCTT





GAGGGGATTCTGCCCGGTCGCTTGCGTCACCTCGCCCTGATTCGTC





GTGCTCACAACACCTTCGAGCCATTCGCCCCTTGGCGTACGCCGCC





AGTCGTTCACCCTCTCATGGCCAAGCCGATTCAAGCCTTCTGCCTT





TCTCTTCCTTCATGGATGTGGGTCAGCGGTGGTAAAGACCGCTCGC





TCGTGCGTGACGCGTTCGAAGGATTACTTCCAGATTCAGTGCGCCT





TCGTAAATCAAAGGGAAGTCCTGCAGGCTTTCTGCATGCGCTGTAC





CGCGCCAAGGGTCGTCAAATGATTGAGCGTATCCGTCACGGTTACC





TGCGTCGTGAGGGGATCATCGATATCTCTACTGGCCCGGACGCATT





GTTCTCGGAAGGGTTCCGCAATCCGCGTGTAATGCACCGTTTCTTT





GAGCTCGCCGCAACTGAGGTGTGGATCGATCACTGGCGCAACTGGC





GCCGCCCCCGCACA






bamB
Codon
ATGGAAGGGTTGTATCAGCTGAAAGTGCATAGTCGTATACACAAAC
468



optimized
TGCAAAATAATATCGCAATAGGTAGCATGCCGCCTCACGCGCTGAT





CATCGAGGATGCCCCCGAATATTTGTCAAACGTTCTGCGCTTCTTT





AGTAGCAAAAAGACTATAAAAGAAGCTGAAGTGTACCTGTCGGATA





ATACGAATCTGAGCTCCAATGAGATCAACCTGTTGTTAGGTGATCT





GATTGAGAACGAGATTATCGTAAAGCAAAACTACGACTCGAATAAT





CGGTACAGTCGACACAGTCTGTATTACGAGATGATTGATGCCAACG





CTGAAAACGCGCAGAAAATTCTGGCAGAGAAAACAGTGGGCCTCGT





TGGGATGGGCGGGATTGGTTCCAATGTAGCCATGAATCTCGCAGCC





GCCGGTGTTGGCAAACTGATCTTTAGTGATGGCGATACCATAGAAC





TGTCTAATTTAACGCGACAGTATCTTTACAAAGAGGATCAGGTGGG





CTTGAGCAAAGTAGAGAGCGCCAAAGAACAACTGCAATTACTGAAT





AGCGAAGTCGAGCTTATCCCGGTTTGCGAAAGTATCTCTGGTGAGG





AACTGTTCGACAACCATTTCTCCGAATGCGATTTCGTCGTACTGTC





CGCCGACTCTCCGTTCTTTGTTCACGAATGGATTAACAATGCCGCG





TTGAAATATGGCTTCTCCTACTCTAACGCAGGATATATCGAAACCT





ATGGCGCGATCGGTCCACTGGTGATACCTGGGGAAACTGCCTGCTA





CGAATGCTATAAAGACAAGGGCGATCTTTACTTGTACTCCGACAAC





AAGGAAGAATTTTCTGTGAACCTGAATGAATCATTCCAAGCACCGA





GCTATGGACCGCTTAATGCGATGGTTAGTTCCATTCAGGCGAATGA





AGTGATACGCCACCTCCTCGGACTTAAAACCAAAACGTCCGGCAAA





CGGCTGCTGATCAACAGTGAAATCTACAAAATCCACGAAGAGAACT





TCGAGAAGAAGAACAACTGCCTGTGCTCGGATATTAAGGGCGAGAA





GCTGTCGAAGAACACCCTTAACTCCGATAAAGAGCTGCACGAAGTG





TATATCGAAGAACGCGAATCGGATTCTTTCAACTCCATTCTCTTGG





ATAAAACCATGAGCAAGCTGGTAAAAATTAACAAAGAGGAGACAAA





AATCCTCGACATTGGTTGCGCTACCGGCGAACAGGCTCTGTATTTC





GCGAATAAAGGTGCTAAGGTGACCGCTGTCGACATTTCAGACGATA





TGTTGAAGGTGCTGGACAAGAAAGCAAGCAACATTAACGCGGGGAG





TATCAAAACCATGCGTGGTAATATCGAATCCATCGAGGTGAATGAC





ACTTTTAATTACATCGTCTGTAACAACATCCTTGATTACCTGCCGG





AGATCGACCGCACGCTGAGAAAACTTAACATGTTTTTGAAAAATGA





CGGGACGCTGATTGTGACGATTCCCCACCCCGTGAAGGATGGTGGA





GGGTGGCGGAAAGATTATTATAACGGCAAATGGAACTACGAAGAGT





TTATCCTGAAGGATTACTTCAACGAGGGTCTGATCGAAAAGAGCCG





CGAGGACAAAAATGGGGAAACGGTGATCAAAAGCATTAAAACGTAC





CACAGAACCACCGAAACCTATTTCAATAGCTTTACTGACGCTGGCT





TCAAGGTAGTATCTCTGCTGGAACCGCAACCGCTTTCAACTGTTTC





AGAGACTCATCCAATTCTGTTCGAAAAGTGTTCGCGCATTCCGTAC





TTTCAAGTTTTTGTGCTCAAGAAAGAGGATCGCCACGCCATT






bsjM
Codon
ATGATCAAAAATGTAAACCTCAAAGAGGCCATTAAAGGTTTGACCG
469



optimized
TATCAGAACGTTATGACACTCTGAAAAATTCGGGAGTCAACCTGAA





TCTGAACATTTCGGCTTTGGAAGAGTGGCGCAACCGTAAGAATCTT





TTAGCCGATGAGGACTTTACGGAGATGCTGACGGTGCTGGAATATG





ACCCGGTGTATTTTAGCCACGCGATTAACGAGAACATCGAAGAACA





TATCGATATCTACAAGAGCAAAATTCTGGGGGAAAACTGGTTTATC





GTGCTGAACGATATTCTGGACGAGCTCGATAATCCCATCGAATACA





AGAAAGAGATGAATCACAGCTACCTCCTGCGTCCGTTCTTGCTCTA





CGCCGAAAAGGAGATGAACAAATACATTGTCAATCGTAAGGAGTTA





CTTCCGGTGGAACCCCAGGTCATCCAACAGATCATGGAAAATTTGG





CCTCCAAACTGTTCGCCGTTTCTGTGAAAAGCTTTGTCCTGGAGCT





GAATATTTCGAAATTGAAGGACGAACTGGCCGGCGAAACACCGGAC





GAACGCTTTCACTCATTTATTCGTTTGATGGGTGAGAAAACGCGCC





TGGTGGACTTTTACAACGAATATATCGTTCTGAGTCGTATTCTGGT





GAACATCACGATCTTATTCGTCAACAACATTATTGAGCTGTTTGAG





CGCCTGCAGGAATCCAAGCTGGATATTGTTAAGAAACTTGGCGTGC





AGGAGGAGTTCAAAATCAGTAATATTAGCATTGGCGAAGGTGATAC





ACATCAGCAAGGACGCTCGGTTATCGTTCTTACGTTCGTGAGTGGA





AAGAAAGTGGTGTATAAACCAAAAAATCTGAAAGTTGTTTCTGCTT





ATAATTCTTTAATTGACTGGATCAACAATAAAAATAATATTCTGAA





AATGCCTTCGTATAACACATTGATTTATGATGATTTCGTGATCGAG





GAGTTTGTCGAGAAACGTGACTGCAAAAGTATCGAGGAGGTCAAAA





AATATTATATTCGTTATGGGCAAATTTTGGGGATTATGTATATCTT





AAATGGGAACGATTTTCATATGGAAAACCTGATTGCCTCGGGTGAA





TATCCGATCATTGTTGACTTGGAAACGCTGCTTCAGAACATTATCA





ATTTTAAAAACAAACCATCAGCGGACTTGATCACCACCAAAAAGAT





GCTTAACCTGGTAAACAGTACTCTGCTGCTCCCTGAAAAACTTCTG





AAGGGCGACATCACGGACGAAGGAATCGACATGTCAGCCTTGGCAG





GGAAAGAACAACACTTGGAACGCCGCGAATACCAGTTGAAAAACCT





GTTCACCGACAACATGGTTTTTGATCTCGAAAAAGTGAAAATCGAA





GGTGCGAACAACATCCCGAAATTAAACGGTGAAAACGTTGACTACA





GCACCTATATTGATGAGATTGTGGTTGGGTTCGAAAATATCTGTAA





CCTGTTCATTCAATATCGCGACGAGTTACTGCATTCCGGCATCCTG





GAGGAGTTTAAAGATGTGAAGGTTCGTCATGTGCTTCGCAATACGG





TTGTTTATGCTAAGATGCTGGCGAATACATATCATCCAGATTACCT





GCGTGATTCGTTGAATCGCGAACAGGTTCTTGAAAACATTTGGGTG





CATCCGTTTGAGCGCAAAGAATTCATTAAGAGCGAGATGGAAGATA





TCCTCAACAACGACATCCCGATCTTTTTCTCATACGCGTCGTCTAA





GGATATTATCGATTCGAATGGCAAACTGCACAAAAACGTTATGGAA





ATTTCGGGTTACGAACGTTTTACCACCAAACTGAAGGAACTGAATC





CCTTTCTGATTGAACAGCAGGTGAGCGTTATTAATATTAAAACCGG





CCGCTATGGGGATAAGAAATTCGAAAAAAATTATAGCGTGCGCGAC





GTTGCAACGGAGAAAAAAGATAATCCGATTGATTTCCTGCAGGAGG





CAATGAATATCGGCGATAAAATTTTGGAACATGCTATCATCTGTGA





TGAGACCAAAACGATTTCGTGGCTTACCATTAACAACCATCATGAT





AAAAATTGGGAAATTGGGCCTATTTCCGGTGAATTTTATGATGGTC





TGGCGGGAATTTCACTCTTCTACCACTACCTCTATAAAAAATCCCA





CAATGTCGAGTATAAAAAAATTCGTGATTACGCGTTCAACATGGCG





AAAGTCAAAGCCCTGTCACTGAAATACGATAGTGGCTTGACCGGTT





ACGCTTCCTTGCTGTATACGGCACACAAGATTGTTCAGGATGAACC





GCGGAAGCAATACAAAGACGTGATCAACGAAGTGTTCAAGTACATT





GATGAGAGCAAAGTCGTGACCGCTAAGTATAACTGGTTGCATGGCA





CTGCCTCTATTATTCATGTGTTATTGAACCTCTACGAGGACTCTCG





TGATATGGCGTACCTGACTAAATGTATTCAGTACGGCAAATATTTG





GTCAAGCAAATCAAAGAACACAAGGATATGCTTGCGCCTGGCTTTA





GCCAGGGCATCTCTTCGGTCATTATGGTTCTGGTGCGCTTAAGTAA





AAAGTGTGAAGTCGAAGAATTTCTCGAATTAGCTCTGGAATTAATG





GAAATGGAACGCAACAAACTGGGAAACCTTTCTGAATCAAACTGGC





TGAACGGCTTGGTGGGCATTGGCTTATCACGTATCAAACTGAAAGG





ACTGGATTCCAACTTACAGGTCGACAACGACATCGAACTCGTCCTG





GATGGCGTCATGAACAGCTTGTACTCAAAAGATGATACTTTGAGCT





GTGGTAACTCTGGCACAGTGGAATTGTTCCTGAGTCTGTTTGAACA





GACGAAAAAGAAAGAGTATCTGGATATGGCGAAAGCAATCTGCGGG





AAAATGATCGAAGAGAGTCGCATCTCCTTTGAGTATCAGACAAAGA





GTCTGCCGGGTTTAGAACTGGTGGGCCTCTACTCTGGCTTAGCCGG





AATTGGTTATCAATTCTTACGTATCTCGGACGTTGAGGATATTGCG





AGCATTGCTACCTTAGAT






capB
Codon
ATGCAGCCAGACCTGGAGGTTGTTGATGTTCGTCGCGGCGAGTCGT
470



optimized
TCAAGGCATGGTCGCATGGGTACCCATATCGCACTGTTCGCTGGCA





CTTCCATCCTGAGTTTGAAGTACATCTGATCGTGGAAACCACCGGC





CAGATGTTTGTGGGTGATTATGTCGGAGGCTTTGGTCCGGGTAATC





TGGTCCTGATGGGTCCCAATCTGCCTCATAATTGGGTGTCTGACGT





TCCTGAGGGTAAAACCGTTGCAGAGCGTAACCTTGTTGTTCAATTT





GGGCAAGCGTTCGTTTCCCGTTGCGAGGATTCCTTAACGGAGTGGC





GTCACGTGGAAACGTTACTGGCGGATGCGCGGCGTGGCGTGCAATT





TGGGCCGCGCACCTCTGAGGCCATTAAACCTCTGTTCGCGGAACTG





ATTCACGCGCGCGGCCTGCGTCGCATTGTGCTGTTTCTGTCTATGC





TGCAAATCCTCGTCGATGCAACGGATCGCGAACTGCTGGCATCTCC





AGCTTATCAGGCGGATCCTTCGACATTTGCAAGCACGCGCATTAAT





CATGCGCTGGCCTACATTGGAAAGAATCTGGCGAACGAGCTTCGTG





AAACAGATTTAGCACGGCTGGCCGGACAGTCTGTTTCCGCCTTCTC





TCATTATTTTCGTCGTCATACCGGCCTGCCTTTCGTGCAGTACGTT





AATCGCATGCGTATCAACCTGGCCTGTCAGCTTCTGATGGACGGGG





ACGCATCGGTGACAGATATTTGTTTCCGTAGCGGTTTTAACAACCT





GTCCAATTTTAACCGTCAGTTTCTGGCAGTGAAAGGTATGTCACCC





AGTCGGTTCCGTCGCTACCAGGCTCTCAACGACGCGTCACGTGATG





CGAGTGAAGCGGCTGCAAAACGCGGCGCAGGTATTGCAGGTGCACC





GGCAATCGTTCCAGCGGCTCAAGCACGTGGCGAGGCACGCCCAATT





CCTGAAGTGCTGCTTAGCGGC






capC
Codon
ATGATGCTGACGGCGAGCTCCACACCGGCATCCGGTAATCCAGCTG
471



optimized
CCCGTGCATTGCGCGCCGCTGCCTTTGCACTGGCCTTAGGCGGAGC





ATGCGTTGCGCATGCCGCACCTCTGCGGATTGGCATGACATTCCAA





GAATTGAATAACCCGTATTTTGTGACCATGCAGAAAGCACTGAACG





AAGCCGCGGCGAGCATTGGCGCGCAAGTGATTGTAACAGACGCACA





TCACGACGTGTCAAAACAGGTATCAGACGTTGAGGATATGCTGCAG





AAGAAAATTGATATTTTACTGGTGAATCCAACCGACTCCACGGGCA





TCCAGAGTGCGATTGTTTCCGCAAAGAAGGCTGGCGCCGTGGTCGT





GGCGGTCGATGCCAATGCCAATGGCCCGGTGGATTCCTTCGTAGGG





TCCAAGAATTTTGATGCCGGCGCTATGTCATGCGAGTACCTTGCGA





AAGCGATCAACGGCGGCGGCGAAGTGGCCATTCTGGATGGCATCCC





GGTCGTCCCAATCCTGGAACGTGTCCGCGGCTGCCGCGCGGCACTG





GCCAAATTCCCGAATGTGAAAATTGTCGACGTTCAGAATGGAAAAC





AGGAACGTGCGACAGCGTTAACGGTAACCGAGAATATGATCCAGGC





GCACCCGAAACTGAAAGGTGTGTTTAGTGTAAACGACGGCGGGTCA





ATGGGCGCTTTGAGCGCCATTGAAGCGAGCGGCAAAGATATCCGCC





TCACGTCCGTAGATGGTGCCCCAGAGGCGGTGGCGGCGATTCAAAA





GCCGAACTCCAAATTTATTGAAACAAGCGCTCAATTTCCGCGCGAC





CAGATCCGTTTAGCGATTGGTATTGGCCTGGCCAAGAAATGGGGCG





CGAACGTGCCAAAAGCGATTCCAGTCGACGTGAAACTGATTGACAA





AGGGAACGCGAAAACCTTTAGTTGG






cinX
Codon
ATGGCTCTCAAAACCTGCGAAGAATTTCTGCGCGATGCGTTAGATC
472



optimized
CGGATCGCTTCGGCCGCGAGATGAAGGCAGTAACAGAAATTCCCGA





GATCGTTAAACTCGGCCATCGTCATGGTTATGGATTTACTGCCGAA





GAATTTCTGACCAAAGCTATGAGTTTTGGTGCTCCGCCGGCAGGAG





CAGCAGCACCTGGCGAATCAGCCAGCGTTCCTGGCCAGAACGGTTC





CTCCCCCGGACACGCTGCGCGTGCAGCTATGGCTGGTCCAGAAGCA





GGGGCCACCAGCTTTGCCCACTATGAATACCGTCTGGATGAGCTGC





CGGAATTCGCCCCCGTTGTGGCCGAGCTTCCGAAACTGAAAGTCAT





GCCGCCTTCCGTGGGACCTGATCGGTTTGCAGCACGCTACCGTGAT





GAAGATATGCGCACAATTTCAATGAGTCCGGCGGATCCGGCTTACC





AGGCTTGGCACCAGGAACTGGCGGGTCGTGGTTGGCGCGATGCAGA





AGATACGGCTGCTGCTCCAGATGCCCCACGGCGCGATTTTCATCTG





CTGAACCTCGATGAGCATGTAGATTACCCAGGTTATGAAGAATATT





TTGCGGCCAAGACCCGTGTCGTCGCGGCACTCGAAAACCTGTTTGG





TGGTGACGTGCGTTGCTCAGGCTCTATGTGGTATCCGCCGTCGAGC





TATCGCTTATGGCATACAAATGCCGATCAACCGGGGTGGCGTATGT





ACCTGGTAGATGTAGATCGCCCATTCGCGGACCCCGACCGTACCTC





CTTCTTTCGCTACCTGCATCCACGTACCCGTGAAATCGTCACGCTG





CGCGAAAGCCCTCGTATTGTCCGTTTCTTTAAAGTCGAACAGGATC





CCGAGAAGCTGTTCTGGCACTGTATCGCGAACCCCACCGATCGCCA





TCGCTGGTCGTTTGGTTACGTTGTTCCGGAAAACTGGATGGACGCC





CTCCGTCACCATGGC






cln1B
Codon
ATGCCTTTATGGTTAGCGCAGGACGTCCACGCGGTCGCTCTGGACG
473



optimized
AAGATATCGTGGTGCTGGATGCGGTGAGCGACGCATACCTGTGTTT





AGTTGGTGCCAGCGCTCTGATCAGCTTGGGCAGCGAGCGTTCCGTC





AGTGCAGATCCGGTGGCCGCTGAGACACTTCGTGAGGCTGGTCTGG





TGGGTCCACATCCTAGCGGCGCCACCCGACCAATACCTCCGAAGCC





GACGATTGACTTACCTGATGCAGCCCGTCAGGCGCAAGGTCGTGAA





TTACGTGCCGCCGCGTGGGCTGGCGCGGCAACCGCAATCGATTTCC





GCCGGCGTTCATTTAGACAACTCCTCGCGAGAGCAGGGCAACGCCC





GCCGGGTCAAGCAGCTGCTCCGGCTGATGAGGTATTGGCAGCAGCC





GCAGTGTTCATGCGGTTACGTCCATGGTCACCCGTTGGAGGCGCGT





GCCTTATGCGTTCGTATTACTTATTACGGCATTTGCGCATCCTCGG





TTTCGATGCCGATTGGATCATTGGTGTGCGTACGTGGCCATTTATG





GCCCATTGCTGGCTGCAGGTCGGTGCCGTCGCACTCGACGATGACG





TCGAGAGATTAACAGCATACACACCGATTCTGGCGGTG






cln1C
Codon
ATGGGCGACTACCTGGCTCTGTACTGGCCGCGCGGCATGCCCGGTG
474



optimized
TAGCTGCAGACGCAATGCGGGCCGCCATCGAAGCTGAGGGCGCCTG





GACCCTGGCGTTCGAGGCCTACCAGCTGGTAGTGTATGTCAAAGGG





CCCCGAGCACCTAAAGTGCGTGCCCTGCCGGATCAGGGCGGGGTGG





TCATTGGGGAACTGTTTGATACTGCAGCAACCCGCGAAGGACGCGT





GCAGGACTTTCCTATAGCGCTGATCAAAGACGTCGCAGCTCAGGAT





GCCGCACGTATTCTTGCTACCCATGCGTGGGGTCGTTATGTGGCTG





TATTAAAAGCCGGTGATCGTCCGCCATGGATCTTTCGCGATCCAAG





CGGGGCGGTGGAATGTCTGGCGTGGGTCCGCGATGAAGTGACCATC





ATTAGCAGCGATGTTGCAGCGCAACGAGCTTGGTCCCCTGATCGGC





TGGCGATTGACTGGTCGGGACTGGGACGTGTACTGGCACGCGGAAA





CTTATGGGGAGAAATTTGCCCGCTGGCTGGCGTCACGGCGATTGCG





CCAGGTACCGCACGGTGTGATCTCGGTGATGCAGCTCTGAGCCTGT





GGCGCCCAGGAGATCATGCACGTCGTAGTCGTCATGATGTTTCCCC





ACGTGATTTGGCAAGAGTGGTGGATGCTAGCGTTGCAGCCCTGGCT





AGAGATCGCAGCGCTATTCTGGTCGAAATCAGCGGGGGACTGGATT





CCGCTATCGTTGCCACGTCGCTGGCTCGTTGTGGAGCCCCAGTTGT





TGCTGGAATTAACCATTACTGGCCCGAACCGGAGGGTGATGAACGT





CGCTGGGCCCAGGACATCGCAGATCGGTGCGGTTTTCGCCTGATCG





CGGGCCAACGTCAGCGGCTGTTGCTGGACGAGGCAAAGCTGCTGAG





ACATGCACAGGGCCCGCGACCTGGTCTGAATGCGCAGGACCCGGAC





CTCGATCACGATCTGGCGGAACAGGCTAAAGCGTTGGGTGCCGATG





CACTGTTCTCAGGGCAAGGTGGCGATGGTGTGTTCTATCAAATGGC





AAATGCTGCACTGGCAGCCGATATCCTCATGGGGAAACCTGCTCCT





ATGGGTAGAGCCGCGTCTTTAGCCGCTGTGGCTCGTCGGGCACGAG





CCACGGTCTGGAGTTTGTGCGGCCAGGCTATGTTTCCGTCGCGCGC





ATTTGCCGCTGGTATGCCGCCGCCAAGTTTCTTGAGCGCCGGTTTG





GCGCCGCCACCCGTGCACCCGTGGATTGCAGACCAGCGCGGTGTTT





CACCGGCGAAACGTATTCAAATTCGGGGGCTGACCAATATTCAATG





TGCTTTCGGCGATAGCTTACGGGGCCGAGCAGCAGATCTTTTATAT





CCGCTTATGGCCCAACCGGTCATGGAACTGTGTCTGTCTATCCCTG





CACCGCTGTTGGCAGTAGGCGCATTGGATCGCCCTTTCGCACGTGC





GGCGTTCGCAGATCGATTACCTCCTCGTTCACTCGTTCGACGCTCA





AAAGGTGATGTTACCGTGTTTTTCAGCAAAAGCCTTGCAGCAAGCC





TGCCGGCCCTTCGTCCTTTCCTGCTGGACGGGCGCCTTGCAGAACA





GGGTCTGATCGATCGAGCAAAACTGGAACCTCTGCTGCACCCCGAA





CCGATGATTTGGCGCGACTCAGTCGGCGAGGTAATGCTGGCAGCGT





ATCTTGAAGCCTGGGTGCGCGCATGGGAAGCCAAGTTGCGTGTTAG





C






cln2B
Codon
ATGACTCTGACCTGGCGCCCGGGTGTTCACGCGGTAATGGTCGAAG
475



optimized
ATGATCTGGTTCTGCTGGATGAAGCAGCGGACGCTTATGTCTGTTT





GTTGGATGGCGCCAAAGTGGTTAGCGTCCGGGCTGACGGTGCTCTG





AGCTTCAATCCCCCACATGCAGCAGAAGATATGATCGCGGGTGGCC





TCGTCGAACCTTCATCAAGTGCCGCGGCGTCAGCAAACCCGCCGGC





AAAACTCCCATGTACTCCGCTGGCGCGCTTATCGCGCCCGCGGCAT





GTAAAAGTGCGTCCGGCTGAAGCGGCCTTGTTCCTGATCCAAGCCT





GGGGTGTTGCGCGTGCGGTACGTCGTTGGCCAATGGCTAGATTATT





AGAAGCATTACGTGGAGATCGTGCCGCAGAACCGGCGAAAGGCCGC





CGATCGATGGCGGAGGCGTGCGCTGTTTTTGATGCGCTTCTGGCCT





GGAGCCCTTTTGACGGTGAATGTTTGTTTCGCTCAGTATTACGACG





TAGATTTTTAATGGCACTGGGCCATTCGCCGGACTTGGTGATAGGC





GTGCGTACCTGGCCGTTCCGCGCACATTGCTGGCTGCAGAGCGGAG





TGGATGCCCTGGATGATTGGCCGGAACGGCTCTGCGCATATCGCCC





GATTCTGGCAGCTTCTGCAAGCCAGGGTAGA






cln2C
Codon
ATGAGTTACCTGCTGATGACCTGGCCGCCGGGGCAGCCGAGCGTAG
476



optimized
AAGCTGATGCACTTCACGCAGCCTTTAACGGGCAGGGTGGATGGAG





CCTGGTTTTGGAACGATTCTGCCTGCGCGTATACGTGCGTGGCGCG





GCAGCCCCTGCAGTTACCCTTACCCCGAAAGGAGGCGTGCTCATTG





GTGAGATGTTTGATCGGGCTGCCACAGAAACGGGCGCCGTTGCCGC





TTATGATCTGAGCCGCCTGGGAGATGACGACGGTATGGCCGTAGCC





CGGCGTGTGGTGGACGAAGCGTGGGGGAGATATGTGTTGGTGCTGC





CAGTTAAAGAACGCCGTCCAGTGGTTTTGCGAGAACCACTGGGCGC





GCTGGATGCGCTGATCTGGCGCAAAGGCGATGTCTGGTGCGTGGGG





GCAGACGTACCCCCGGGTCTTGAACCAAAAGATCTGGGTGTGGAAG





AGACTAGACTGACGCACCTGATCGCGGAACCGGATCTGGCATCTGC





GAGCCTGCCCTTAACCGGCGTCGCGGCAGTGATGCCAGGTACTGCG





GTCGATGAAACCGGCCAGGTGCACCGTCTGTGGACCCCCGCGCGTT





TTGCTCGCTCCCCTCGCACTGACGCGTGGACTGCAGCCGAACGTAT





TCCGCTGGTTACCCGTGCGTGCATCGCGGCGCTGTCTGCGAATCGA





AGTGGTATTCTGTGCGAGATTTCGGGCGGCCTGGATAGCGCTATTG





TTGCGACCTCTCTGAAAGCGGAAGGTGCGAAGATTAGTAGCGGGAT





CAACTTCCATTGGCCCCAGGCTGAAGCAGATGAGCGCCCGTACGCA





CGCGCTGTTGCGAAAAGCGTGCGAACCCGGTTACAGGTGGTAGCGA





GTCGTGTAGCGCCCGTTGACCCGGAAACGTTTGATGAGATCGTGGT





CGCGCGACCAAGTTTTAATGCCATTGATCCAGTCTATGATACCGTA





CTGGCCCAACGTCTGATTCAGGGCGGTGAAGGAGCCCTGTTTACCG





GACAAGGTGGTGACGCAGTTTTCTATCAGATGCCAGCACCACAACT





TTCGTTGGATTTGTTGGCTCGTGGCCCCCGCCGCCGCGGTCTTATG





GGATTATCACGCCGCACCAACCGCAGTGTCTGGTCGTTGCTGCGCA





TGGGCTTACGTGCACCCGTACGAGCAACCTTTCCCTACGGTGCGAG





AGGTGCCGATCGTCCTCCGATGCACCCGTGGCTGGAGGACGCGCGT





GGTGTTGGGGCCGCGAAACGGATTCAGATCGAAGCGCTGGTTGCTA





ACCAGGCCGTGTTTGAAGCATCTCGTCGCGGTGCGGCGGCTCATTT





GGTGCACCCACTGCTGTCGCAACCGCTTGTGGAGCTGTGCCTTTCA





ACCCCAGCGGCCGTGCTGGCGGGTGCCGAACAAGATAGAGCATTCG





TGCGTAGCGCTTTTCGTGCGCAACTGCCACGCCTGGTCTTAGATCG





TCAAAGCAAAGGAGATCTGAGCGTTTTCTTTGCTAAAGGTGTGGCG





CGGAGCTTGCCGGGCTTGCGTCCGCGTCTGCTCGAAGGACGCTTAG





CGGCACGTGGCCTGATCGACGTGGAAGCGTTATCACAAGCGATGCA





GCCAGAAGCGATGATTTGGCGTGACGGTTCGGCCGAAATCCTGTGC





CTTGCTGTTCTGGAATCATGGCTCCGCTCTTGGGAGGCTCGTGGTG





CA






cln3B
Codon
ATGCGCGTTGCAGTGCCGGATCATTTAGCGTATTGCGTAAAACAAG
477



optimized
GTGGAGTTACGTTTCTGGACGTCCGCGGGGATCGTTACTTCGGCCT





GCCGCCGGTGCTGGAACACGCGTTCGTTGCCATTGCCGAGGCGGAT





TTTCTGCTGAAAGAACCAAATTCACTTCTGGAGCCACTCGAAGCAC





TGGGTGTCTTAGTGCGAGGCCAAGCCCGCCGTGCCGATCTGACAAT





TCCGTCTGCAAATCTGTCATGGGTGGATGAGGTCAGCCCGACCCCA





CCACGTCTTGACCCTGCGTCACTCGTCGCAACCGTCACGTCTGTTA





TTCGAACGCGTCTGAGCCAAAAGAGTAAGTCCTTGCAGGCTCTCTT





GGAAGAGGTCCGTACCCGCCGTCCGGGATCGCCGGCCCATAATTGG





CAGCTGATGCGTCGTCTGACGGCTGGATTCCGTGCATCGCGTGCTT





GGGCGCCGATAGAACCCATCTGCCTCCTGGACAGCTTGGCGTTACT





GGATTTTCTGCATCGCCGTGGCCTGTATCCGCATATTGTTTTCGGT





GTGATCCGCCAACCGTTTGCCGCTCATTGTTGGGTGCAAGCTGATG





ATGTAGTCCTGAATGACCGGCTGGATCATGTCGGTGAATATACACC





GATCCTGGTGGTC






cln3C
Codon
ATGGAAGATTACGTGGTCCTCATTTGGCCGGCACTCGCTGAAGCTC
478



optimized
CTGCACGCGACTTGATTCGTCGCCTGCCGAAACTCAAAACCGTCAT





TGAAACTAGCGGATTGGTGGTACTGCGCCCCGAAAATGGTGCGGGT





CTGCGGGTAGGCGGGAACGGTGTGGTCCTGGGTAGCGTCTTTCGCA





CCGGCGGTGATCGCGAAACTGTTGCGGAATTTTCGGAATCGGAAGC





ATCCGCGATCGCCACGAGTCGTGGTCAGCAGTTAGTGACAGAGTTC





TGGGGTGGCTACCTGGCTGTTCTTGGAGATGCTTCGCGTTCCGAAG





TGATGGTCCTGCGAGATCCTTCAGGTGCAATGCCGGCTTATTGTTT





AGTTCATGGCGAAGTCCAGATCATCTGCTCTCGCTTGGAGGTCCTG





GAGGACGCAGGACTGGGGCAGCAGGCGCTGAACTGGGACGTGGTGG





CGCAATTACTGGCCTTCCCAAACCTTCGAGGTCGCTCAACGGGTCT





TAAAGGCGTGGAAGAATTACTTCCCGGTTGCCGTCTGACATTTACG





GGAGGACTGAAAACCGAAACGCTGACCTGGAACCCGTGGCTTTTTG





CCCGCCCATCTGCGCAAGCGCCTGAACGTGGAGTTGCGGCGACCGC





CGTGCGTCAGGCGGTGGAAGTAAGCGTTCGAAAATGGGCTGATCAG





AGTTCACCGGTACTTTTGGAATTGTCAGGCGGGCTGGATAGTAGTA





TCATCGCCTGCTGTCTGGACGAACCGCGCACCGCGGCCACCTTCGT





GAACTTTGTCACACCGACGGCCGAAGGCGATGAACGAGGATATGCA





CGTCTGGTTGCCAAGGCAGCAGATAAACAACTGATCGAGCAGGACA





TCCGGGCTGACGAAGTAGATGTTACCCGTCCAAGACCTGGCCGCCA





TCCTCGTCCGGCCAGTCAGGCGCTGTTACAGCCGCTGGAACAGGCT





TGCGCTGAACTGGCACCTCAGTTGGGTGCGAGAAGTTTCTTCTCCG





GTCTGGGAGGAGACAACGTGTTTTGTAGCATTGCAACCGCAAGCCC





GGCTGCGGATGCACTTTTGACTAGCGGTCTGGGCCGACAGTTCTGG





GCCGCAATCGGGGACCTGTGTGCACGTCATAACTGCACCGTATGGG





CAGCCTTAAGCGCCACGCTGAAGAAACTGCTCCGCTCAGATCGTCG





TCTGGTGATCAAACCAAACCTGGATTTTCTGTCCTTTCGGGAGGAC





GCCATAGACCGTCCGGATCACCCATGGCTTGAAGTGGCCGCCGATC





GTCTGCCGGGGAAACGCGAACATGTCGCAAGCATTCTGTTGGCGCA





AGGCTTCCTGGATCGTTATGAGCACGCTCAGGTTGCTGCCGTCCGC





TTTCCCTTGTTAACGCAACCGGTTATGGAGGCTTGTCTGCGCGTGC





CGACCTGGATGGCAAACCACCAGGGTCGCAATCGGGCGGTCGCACG





CGATGCCTTCTTTGATCGCTTGCCCCCGAGAGTACGTGATCGGCAG





ACAAAAGGAGGTTTGAACGCGTTTATGGGTGTTGCGTTCGAACGCA





ACCGTCAGGCCTTAGCTCGTCATCTGTTAGACGGGCGCCTGGTACA





GCGTGGCCTGATAGATGCAGTGGCAATAAAATCGGCGCTGGCCTCA





CCAGTCCTGGAAGGAGGAGCCATGAACCGCTTACTGTACCTGGCCG





ATGTCGAATCCTGGGTACGCTCATGGGAAGATGTG






comQ
Codon
ATGAAGGAAATCGTGAAACAGAATATCAGTAACAAAGACCTGTCGC
479



optimized
AACTCCTGTGTTCCTTCATTGATTCAAAGGAAACTTTCAGTTTTGC





CGAGAGCGCTATACTGCATTATGTAGTATTCGGCGGTGAGAACCTG





GACGTAGCTACCTGGCTGGGCGCCGGAATTGAAATTCTGATCCTGA





GCAGCGATATCATGGACGACCTGGAGGACGAGGATAACCATCATGC





GTTGTGGATGAAAATTAACCGCAGCGAGAGCTTGAATGCGGCCCTG





TCCTTATACACCGTCGGCTTAACGAGCATCTATTCCCTGAACACAA





ATCCGTTGATATTTAAGTATGTGCTGCGCTACGTCAATGAGGCCAT





GCAGGGTCAGCATGATGATATAACCAATAAAAGCAAAACCGAAGAT





GAATCGCTTGAAGTGATTCGCCTTAAATGCGGCAGCCTGATCGCCC





TGGCAAATGTCGCGGGCGTGCTGTTAGCCACGGGCGAGTACAATGA





AACAGTTGAACGTTACTCTTATTACAAAGGCATCGTGGCGCAAATT





TCCGGCGACTATCACGTGCTGCTGTCAGGAAACCGGAGCGATATCG





AGAAAAACAAACAGACACTGATTTACCTGTATCTGAAACGCCTGTT





TAACAACGCGAGCGAGGAATTGCTGTATCTGTTCTCCCATAAAGAT





TTGTACTATAAAGCCCTGCTCGACCGTGAAAAGTTTGAAGAAAAAC





TGATCCAGGCCGGGGTGACGCAGTACATCAGCGTTCTGCTCGAAAT





ATATAAGCAGAAGTGCTTCTCCACCATAGAACAGCTGAACTTAGAT





AAAGAAAAGAAAGAGCTGATCAAGGAGAGCCTGCTGTCATATAAGA





AAGGCGACACCCGTTGCAAGACC






crnM
Codon
ATGAATGATATCAACAAAAACAAAACTAAAACCATTAACGAAAAGA
480



optimized
TTAAAATTTTCACCAAAGAAGAGGTGATTGATATCAGTTACTTTGA





AGAATGGCGCAGCGTTCGTACTCTGCTTAACGAAAACTACTTTAAA





ATTATGCTCGAGGAAATGAATATTTCCAAAAACCAATTTTCGTATG





CGCTGCAACCGTTAAACGACGAGTTCAAACTGCATACTAACGTTAA





AAATGAAGAATGGATCAAATGCTTTAATCGCGTCATTAACAATTTT





AACTATAAAAATATTAACTATAAAGTTGGTTTGTACCTGCCTATTC





AGCCTTTCTCCGTTTATTTACAGGAGAAACTGAAAGAGATCCTGAA





GAAGCTGAACAACATTAAGATTAATGATAAAATTATCGACGCCTTT





ATCGAAGCTCACCTGATCGAAATGTTCGACCTCGTCGGTAAAGTAA





TCGCCCTTAAATTTGAAGATTATAAACAGATCAACTTCCTGAAAAA





CACAAATAATGGCACCCGCTTGGAGGAATTCTTGCGTAGCACCTTT





TATTCTCGGAAGTCATTTCTGAAACTGTTTAACGAGTTTCCGGTAC





TCGCGCGGGTTTGCACCGTACGTACGATCTATTTGATCAATAACTT





TAGTGCTATCATCCAGAACATCAATAGCGACTACCTGGAAATCCAG





GAATTTCTGAACGTCGATTTCCTGAACTTGACAAACATCACTCTTT





CGACGGGTGATTCCCACGAACAGGGTAAAAGTGTGTCCATCCTCTA





TTTTGATGAAAAAAAGCTGATTTATAAACCGAAAAATCTGAAGATT





TCAGAAATTTTCGAGAGCTTCATCGACTGGTACACCAACGTCTCTA





ACCATAAGCTGCTCGACCTGAAAATCCCGAAAGGAATTTTTAAAGA





CGATTACACTTATAACGAATTTATTGAGCCAAACTACTGCGAGAAT





AAGCGCGAAATTGAAAATTACTATAACCGTTATGGGTACCTGATCG





CAATCTGTTATCTGTTCAACCTGAATGACCTGCATGTAGAAAATGT





GATCGCCCATGGCGAGTACCCGGTTATTGTTGATATTGAAACGAGC





TTTCAAGTCCCTGTGCAAATGGAGGACGATACTTTATATGTGAAGC





TGTTGCGCGAGCTGGAATTGGAAAGCGTTTCATCGTCGTTTCTGTT





ACCTACCAATCTGTCGTTTGGTATGGACGATAAAGTGGACCTGTCC





GCGCTGAGCGGAACCATGGTCGAGCTGAATCAGCAAATTCTGGCGC





CTGTCAACATTAATATGGACAACTTTCATTACGAGAAATCACCGAG





CTATTTTCCAGGCGGAAACAATATCCCTAAAAACAACAAATCAGTG





ACTGTTGATTATAAAAAATACTTGCTCAATATTGTGACTGGTTTCG





ACGAATTTATGAAGTATACCCAAGAAAATCAGCTGGAATTTATTGA





GTTCCTGAAAAAATTCTCAGATAAAAAAATCCGGGTGCTGGTGAAG





GGTACGGAAAAATATGCGTCCATGATTCGCTACAGCAACCATCCGA





ACTACAACAAAGAAATGAAATATCGCGAGCGTCTCATGATGAACTT





GTGGGCGTACCCTTACAAAGACAAGCGTATTGTTAATAGCGAAGTA





CAGGACCTGTTATTTAACGATATCCCGATCTTTTACTCCTTTCCAA





ATAGCCGTGACCTCATTGATAGTCGCGGCTTGGTGTATAAAGATTA





CCTTCCTGTGACAGGACTGCAGAAAGCAATTGATCGCGTGAAAGAT





ACCTCGGTAAAAAGCTTGTTCGACCAGAAGCTGATTCTTCAGAGTA





GCTTAGGTCTGTGGGATGAGATTCTCAACAAGCCGGTCCAGAAAAA





GGAACTGCTCTTTGAAAAGCAGAACTTTAACTATGTGAAAGAGGCG





ATCAATATTGCGGAATTGCTGATTGGCTATTTAATCGAAACGGACG





ACCAGAGCACCATGCTGAGCATTGATTGTTCTGAAGATAAACACTG





GAAGATTGTTCCTTTAGACGAATCCCTGTATGGTGGGCTGTCCGGC





ATTGCATTATTTTTTCTCGATATTTATAAAATTACCAAAGATGAAA





AATATTTTAATTACTATGATAAAATCATTTCCACGGCCATTAAACA





ATGTAAAGCGACCATCTTCTCGTCAAGCTTCACGGGTTGGCTGAGT





CCCATTTATCCGTTGATTCTGGAAAAGAAATACTTTGGTACCATGA





AAGATAAGAAATTCTTTGACTACACGATGGAAAAGCTGTCGAATAT





GACTGAAGAACAAATTAACAACATGGATGGTATGGACTATATCAGT





GGCAAGGCGGGTATTGTCAAACTGCTGATTAGCGCGTACCGGGAAT





CGAAGAACAATGAAAACATCGGACTGGCCCTGAGTAAATTCAGCAA





CGATCTGATTCAAAATATTGGCACCGGCAAAGTCAGTGAATTACAA





AACGTGGGCCTGGCGCACGGCATTTCTGGTATTATGGTCGTAGTAG





CCTCACTGGACACGTTTAAAAGTGAATATATTCGCGAGCAGCTGGC





AATTGAATATGAGATGTTCTGTTTGCGTGAAGATTCATACAAATGG





TGTTGGGGCATCTCTGGAATGATTCAAGCCCGTCTCGAAATTCTGA





AACTGAGCCCGGAGTGTGTGGATAAAAAAGAGCTGAACTTGCTTAT





TAAGCGTTTTAAAAACATCTTGAATCAGATGATTAACGAAGATTCC





CTTTGTCACGGCAACGGTTCGATCATTACTACGATGAAGATGATCT





ATATGTACACCCAAGACACCGAGTGGAACTCTCTGATTAATCTGTG





GTTATCAAATGTAAGTATCTATTCGACCTTACAAGGCTATAGCATT





CCAAAGCTGGGCGATGTAACAATTAAGGGGTTGTTTGATGGCATTT





GTGGTATTGGCTGGTTATACCTGTATTCGAACTTTAGCATTGAAAA





CGTGCTGCTCCTCGAGGTC






csegB
Codon
ATGGACCTGTGGTTGAGCGCCGGGGTCTATGCTGTCATGATCGATG
481



optimized
ATGATGTAGTTTTCCTGGACGTCGCCACCAATGCATACTTCTGCCT





CCCAGCCGTTGGGAGCGTGTTGGCACTCGAAGGTCGTTCGCTGCGT





GTGGCGGCTCGCGAACTGGCAGAAGATCTTATTCAGGCAGGCTTAG





CATCCGCGGCTGCGGCAATCGAACCCCCACCGAGCACACCAGCCCC





AGTTCGCACTGCGCGTGCGGTATTGGAAGCTCTGCCGGCGCGTGAA





AGACCACGTCCACGTCTTGCCCACTGGCGTCAGGCGATTATGGCTG





GCTTGGCGTCCCGTGCCGCTGAACGTCGACCATTCGCGCAGAGACT





GCCGCCGCCTTCAACGGGGGTTTCACCTCCGGCATCAGAAGGCCTG





CTTGCCGATCTGGATGCGTTCCGTCGACTTCAGCCATGGTTGCCGT





TCGACGGTGCTTGTCTGTTCCGTAGCCAAATGCTGCGCGATTATCT





CCTTGCGCTGGGTCACCGCGTTGACTGGATTTTCGGTGTACGTACG





TGGCCGTTTGGTGCCCACTGTTGGTTGCAGGCCGGCGACCTGGTGC





TGGATGATGAGGCCGAACGTCTGATTGCGTATCACCCCATTATGGT





AGGT






csegC
Codon
ATGGGGTATGCCGCATTGACTTATCCGGGTGGTTTAGCGGCAGCAG
482



optimized
CGTTTGATGAGATGGTAGAAGCACTGATCGATGCTGGATGGACCTT





GGCGTTGCGTGCGTTCAGACTCGCCGTTCTCACCGATGGTCAGGCT





CCAGCCGTGTCGCCGCTGATGGGCAGAGGCGGCGTAGCAGGCGTTC





TCATCGGCGAAGCGTTTGATCGTCGCGCCACATTAGGTGGCGCGGT





CGCACGTGCCGCGCTGGATGGTTTGGCTGACATCGATCCGCTGGAA





GCAGGTCGCCATCTGATTGAAACCGCGTGGGGCGGCTACGTGGGTA





TGTGGATTGGTCGGGCCGAAGCTGGTCCGACACTGCTGCGCGATCC





TAGTGGCGCGCTCGAAGCCTTAGCGTGGCGCCGTGACGGTGTAACC





GTTATGTCAGCGCGCCCGTTGACGGGGCGCGCAGGCCCAGCTGATT





TAGCAATCGATTGGCCACGTATCGTGCAGATTCTGGCCGATCCCAT





TTCCGCGGCTCTCGGCCCGCCCCCTCTGACTGGCTTAGCGACCATA





GACCCGGGCGCGGCGGTTCATGGCGCGGATGGCCAAGAACGCTCAG





TGCTGTGGACCCCAGCTGCAGTTGTCCGTGGTGCTCGTCACCGTCC





TTGGCCAAGCCGTCAGGATCTGCGTCGCACCATCGATGCGACTGTC





GCGGCACTGGCCTCGGATGCGGGCCCGATTGTCTGCGAAATTTCAG





GAGGTCTGGACTCGGCCATAGTTGCGACTAGCCTTGCGGCGTCCGG





TCTGGGTCCGCAGCTGACAGTGAATTTTTACGGTGACCAGCCTGAA





GCTGATGAACGCGGATACGCTCAAGCCGTCGCCGAACGTATCGGTG





CGCCTCTGCGGACCCTTCGTCGAGAGCCGTTCGCGTTCGATGAAAC





CGTGCTGGCAGCCGCTGGACAGGCCGCACGTCCGAATTTTAACGCC





CTCGATCCTGGATACGATGCCGGGCTCGTGGGTGCCCTGGAAGCTA





TCGATGCTCGTGCATTATTTACGGGCCATGGCGGTGATACCGTGTT





TTATCAAGTGGCGGCCAGTGCCTTGGCCGCAGACTTACTGGGCGGC





GCACCATGTGAAGGTAGCCGCCGTGCACGTTTAGAGGAAGTAGCTC





GGCGGACCCGACGCTCGATTTGGAGTCTTGCATGGGAAGCGTTTTC





TGGTCGACCCAGCACTGTAAGCATTGAAGGTCAGTTGCTTCGACAG





GAAGCAGAGAGAATTCGGCGCGTCGGCCTGACCCATCCGTGGGTTG





GAGGCCTGTCGTCTGTGACCCCTGCGAAACGCCAGCAAATCCGCGC





GCTGGTCAGTAACCTGAACGCGCATGGCGCCACTGGTCGCGCCGAA





CGCGCTAGAATCGTGCACCCGCTTTTAGCTCAGCCGGTGGTTGAAG





CCTGCCTGGCGATTCCTGCCCCTATCCTCAGTGCGGGCGAAGGAGA





ACGCTCATTTGCGAGAGAAGCCTTTGCAGACCGTTTGCCACCGAGC





ATTGTGGGCCGCCGAAGCAAAGGGGAAATTAGTGTGTTTCTTAACA





GATCTTTAGCAGCCAGCGCCCCCTTTCTGCGTGGCTTTTTACTTGA





AGGACGGCTGGCGGCTCGCGGGCTGATTGATCGTGACGAACTTGCA





GCCGCGCTGGAACCGGAAGCAATCGTCTGGAAGGATGCGTCACGCG





ACCTGCTTACTGCGGCGGCCCTGGAGGCGTGGGTCAGACATTGGGA





AGCACGTATTGGCGAGGGGGAAGCAGCGGAAGGTGAGCGTGCTGCC





GGTCGTGGTACCGCAGCGACGGGACCGCGTACAAGCGCGCGGAAGG





CGAACACCGGT






epiD
Codon
ATGCACGGTAAACTGCTGATCTGCGCAACTGCTTCGATCAACGTCA
483



optimized
TCAATATCAACCATTATATTGTGGAGCTGAAACAGCACTTCGATGA





GGTGAATATCCTGTTTTCACCTTCCTCGAAGAACTTTATCAACACC





GATGTCCTGAAGCTGTTTTGCGATAATCTGTATGACGAGATCAAAG





ATCCGCTGCTGAACCACATCAACATAGTGGAGAACCACGAGTATAT





CTTGGTGCTGCCTGCCAGTGCCAATACGATCAACAAAATCGCGAAC





GGTATATGCGATAACCTCTTGACGACCGTATGCTTAACCGGGTACC





AGAAACTGTTTATCTTTCCGAATATGAACATCCGCATGTGGGGAAA





TCCGTTCTTACAGAAAAATATTGACCTGCTTAAAAGCAACGACGTG





AAGGTGTATTCCCCCGACATGAACAAATCTTTTGAGATAAGCTCAG





GCCGCTACAAAAATAACATCACGATGCCGAATATCGAAAACGTGCT





GAATTTTGTCCTGAACAATGAGAAACGCCCGCTGGAT






halM1
Codon
ATGCGCGAACTCCAAAATGCGCTTTACTTTAGCGAAGTGGTTTTTG
484



optimized
GACCGAATCTTGAGAAGATTGTAGGAGAAAAGCGCCTCAATTTTTG





GCTCAAACTTATAGGTGAGGACCCGGAAAACCTGAAGGAGTTTCTC





TCGAGAAAGGGCAATTCTTTCGAAGAACAAACCTTACCGGAAAAGG





AAGCTATCGTTCCGAACCGCTTAGGTGAAGAGGCGCTGGAAAAAGT





CCGCGAAGAACTTGAGTTCCTCAATACTTACAGCACTAAACATGTG





CGTCGCGTTAAAGAGTTGGGAGTGCAGATCCCTTTCGAAGGGATTC





TGCTGCCATTCATTAGCATGTATATCGAAAAATTTCAGCAGCAGCA





ACTTCGCAAAAAGATAGGGCCGATTCACGAAGAGATCTGGACGCAG





ATTGTTCAAGATATCACCTCCAAATTAAATGCGATTCTGCACCGTA





CCCTGATCCTGGAACTGAATGTAGCTCGTGTTACCTCCCAACTTAA





AGGTGATACTCCGGAAGAAAGATTCGCCTACTACTCGAAAACCTAT





TTAGGCAAACGTGAAGTAACTCACCGTCTGTATAGCGAATATCCGG





TGGTTCTGCGGTTGCTGTTCACCACCATTTCACACCACATTTCGTT





CATTACGGAAATCCTTGAACGCGTTGCAAATGACCGTGAAGCCATT





GAAACCGAATTTTCACCGTGTTCCCCGATTGGTACCCTCGCCTCTC





TCCACTTAAACTCGGGAGATGCTCACCATAAACAGCGTACTGTGAC





GATTTTGGAATTCTCCTCCTCGCTGAAACTTGTCTACAAACCTCGC





TCCCTCAAAGTTGATGGGGTGTTCAACGGTTTACTCGCTTTCCTGA





ACGATAGAACGGGGGAAGTCATTAAGGACCAGTATTGCCCTAAGGT





GTTACAGCGCGATGGCTACGGCTATGTGGAATTTGTCACTCACCAG





TCTTGTCAATCCCTTGAGGAAGTGTCAGACTTCTACGAGAGACTCG





GCTCTCTGATGAGTCTGTCCTACGTACTGAATAGTTCTGACTTTCA





TTTCGAGAACATTATAGCTCATGGTCCCTATCCTGTCCTGATCGAT





CTTGAAACCATCATTCATAATACAGCGGATAGCAGCGAGGAAACGT





CTACCGCTATGGATCGCGCGTTCCGTATGTTGAACGATTCGGTGCT





GTCCACTGGTATGCTTCCCTCCTCTATTTATTATCGCGATCAGCCG





AATATGAAGGGTCTGAACGTCGGAGGTGTGAGCAAATCAGAAGGTC





AGAAAACACCGTTCAAAGTTAATCAAATCGCCAATCGCAACACCGA





TGAGATGCGTATCGAAAAAGATCACGTTACCCTGAGCAGCCAGAAA





AATCTGCCCATTTTTCAGTCTGCCGCAATGGAGAGCGTACATTTCT





TAGATCAGATCCAGAAAGGCTTTACCTCCATGTATCAGTGGATCGA





GAAGAACAAACAAGAATTTAAAGAACAGGTGCGTAAGTTTGAAGGT





GTGCCGGTTCGTGCTGTTCTTCGGAGCACGACTCGCTATACCGAAC





TGCTGAAATCTTCCTACCACCCTGACCTGCTCCGCAGCGCGTTGGA





CCGTGAAGTACTGCTGAACCGTTTGACTGTTGACTCGGTAATGACC





CCGTATCTCAAAGAGATTATTCCACTCGAGGTGGAAGATCTGCTGA





ACGGTGACGTGCCATACTTCTACACCCTGCCGGAAGAACGCGCCCT





GTATCAGGAAGCGTCTGCGATCAATAGTACGTTCTTTACCACTTCG





ATTTTCCATAAGATTGACCAGAAAATCGATAAGCTGGGTATCGAGG





ACCATACCCAGCAAATGAAGATCTTACACATGAGTATGCTTGCCTC





TAACGCTAACCATTACGCCGATGTTGCCGACTTGGATATTCAGAAA





GGACACACCATTAAAAACGAACAGTACGTTGAGATGGCCAAAGACA





TCGGTGATTACCTGATGGAGTTATCGGTCGAGGGTGAAAATCAAGG





GGAACCAGATCTGTGTTGGATTTCGACCGTCCTGGAAGGGAGCTCT





GAAATCATTTGGGACATCAGCCCAGTGGGCGAAGATTTATACAACG





GCAGCGCTGGCGTCGCTCTCTTTTATGCGTACCTGTTCAAAATTAC





AGGTGAAAAGCGTTACCAAGAGATCGCATACAAAGCCCTGGTTCCG





GTTCGCCGCAGTGTGGCCCAATTCCAGCACCATCCGAATTGGAGCA





TTGGTGCGTTTAACGGAGCGTCAGGCTATCTGTACGCGATGGGTAC





GATAGCGGCCCTGTTTAATGATGAACGTTTGAAGCATGAAGTAACC





CGCAGCATTCCGCACATTGAACCGATGATCCACGAGGATAAGATCT





ATGATTTCATTGGCGGTTCCGCAGGGGCGCTGAAGGTGTTCCTGAG





CCTGTCGGGGCTGTTTGACGAGCCGAAGTTTTTGGAACTTGCCATT





GCATGCAGCGAACATCTGATGAAAAACGCCATTAAAACGGATCAAG





GTATCGGCTGGAAACCACCGTGGGAGGTCACCCCACTGACCGGTTT





CAGCCATGGGGTTAGCGGCGTCATGGCATCCTTCATCGAACTGTAC





CAGCAAACCGGTGATGAGCGCTTGCTCAGTTACATTGATCAGAGTT





TAGCCTATGAACGTTCCTTCTTCAGCGAACAAGAGGAGAACTGGCT





GACTCCGAACAAAGAAACACCCGTGGTAGCTTGGTGCCACGGCGCG





CCGGGAATTTTGGTATCACGACTGCTTCTGAAGAAATGCGGCTATT





TGGATGAAAAAGTCGAAAAAGAAATTGAGGTGGCATTATCCACAAC





TATCCGTAAAGGCCTTGGTAACAATCGCAGTCTTTGCCATGGTGAT





TTCGGCCAGCTGGAAATTCTTCGCTTTGCGGCGGAAGTGTTAGGCG





ATAGCTATCTCCAGGAAGTTGTCAACAATCTGTCCGGCGAGTTGTA





TAATCTTTTCAAAACGGAGGGATATCAGAGCGGAACCAGCCGCGGT





ACTGAATCCGTGGGCCTGATGGTAGGTCTGTCCGGGTTTGGGTATG





GTTTACTTTCAGCGGCATATCCATCTGCTGTCCCCTCAATCTTAAC





ATTGGATGGTGAGATCCAGAAGTACCGGGAGCCTCATGAAGCC






halM2
Codon
ATGAAAACGCCGCTGACCTCGGAACATCCTTCAGTGCCGACGACGC
485



optimized
TGCCGCATACTAACGACACCGATTGGCTCGAGCAATTACATGACAT





TTTGTCCATTCCTGTTACGGAAGAAATCCAGAAATATTTCCACGCC





GAAAATGATCTGTTCTCGTTTTTCTATACACCGTTCCTGCAGTTTA





CGTACCAGAGCATGTCGGACTACTTTATGACCTTCAAGACCGATAT





GGCCCTGATCGAAAGACAGAGCCTCCTGCAAAGCACGCTGACCGCG





GTACATCACCGACTCTTCCACTTAACGCATCGCACCCTTATTAGTG





AAATGCATATTGATAAACTTACCGTTGGCCTGAATGGCTCTACGCC





GCACGAGCGCTACATGGATTTCAACCACAAATTCAACAAAACCTCG





AAGTCGAAGAACCTGTTTAACATCTACCCAATTTTGGGAAAATTGG





TCGTTAACGAAACTCTGCGCACTATTAACTTCGTCAAGAAAATCAT





TCAGCACTACATGAAGGACTACCTGCTCCTGTCGGACTTCTTCAAA





GAGAAGGACTTGCGTCTTACCAACCTGCAATTAGGCGTGGGGGATA





CACACGTTAATGGGCAATGCGTCACCATTCTGACGTTTGCATCAGG





CCAAAAAGTGGTATACAAACCTAGATCATTGTCGATAGATAAACAG





TTCGGAGAATTCATCGAGTGGGTAAACTCGAAAGGTTTTCAGCCTT





CCTTGCGTATCCCTATTGCGATTGATCGTCAAACCTATGGTTGGTA





TGAATTCATCCCTCATCAAGAGGCCACCAGCGAAGATGAAATAGAA





CGCTACTATTCTCGCATCGGTGGTTATCTGGCGATCGCCTACTTGT





TCGGGGCAACCGACCTGCACCTGGATAACCTGATCGCCTGCGGCGA





ACATCCGATGCTTATTGATTTGGAAACACTCTTTACCAACGATCTC





GACTGCTATGACAGTGCGTTTCCGTTCCCGGCGCTGGCCCGCGAAT





TAACCCAATCCGTTTTTGGCACCCTTATGCTTCCCATCACCATCGC





GTCGGGGAAACTGCTGGATATAGACCTGTCAGCAGTAGGAGGCGGT





AAAGGTGTGCAGTCCGAAAAGATCAAAACCTGGGTCATCGTGAATC





AGAAAACTGATGAGATGAAGCTGGTCGAGCAGCCGTATGTTACCGA





GAGTTCCCAGAATAAACCAACAGTTAATGGGAAAGAGGCGAACATT





GGCAATTATATTCCTCATGTCACAGATGGCTTTCGTAAAATGTACC





GCCTGTTTCTGAATGAAATTGATGAGTTAATGGATCATAACGGGCC





AATCTTTGCGTTTGAGAGTTGTCAGATTCGTCATGTTTTTCGAGCT





ACCCACGTGTATGCGAAATTTTTGGAGGCAAGTACCCACCCAGATT





ACTTGCAAGAACCTACCAGACGTAATAAACTGTTCGAGTCCTTTTG





GAACATCACGTCGCTGATGGCACCGTTCAAGAAAATTGTACCGCAC





GAAATCGCGGAGTTGGAGAACCATGATATTCCGTACTTCGTCCTGA





CTTGTGGCGGCACCATTGTTAAAGATGGATACGGCCGGGATATCGC





AGACCTGTTTCAAAGTAGCTGCATCGAACGTGTAACTCATCGTCTG





CAGCAGCTGGGAAGCGAGGATGAGGCGCGTCAAATTCGCTACATTA





AAAGCAGCCTGGCGACGTTGACCAACGGTGATTGGACCCCATCCCA





TGAGAAAACCCCGATGTCTCCGGCCTCGGCCGACCGTGAAGATGGT





TACTTCCTGCGCGAGGCTCAGGCCATCGGCGACGACATTTTGGCGC





AGCTGATTTGGGAGGATGACCGTCACGCCGCTTACCTTATTGGCGT





AAGCGTGGGCATGAACGAAGCCGTCACTGTGTCACCCCTGACGCCT





GGCATCTACGACGGCACACTTGGCATAGTGCTGTTCTTCGATCAGC





TGGCCCAGCAGACCGGCGAAACCCATTATCGCCACGCCGCCGACGC





TTTACTGGAAGGAATGTTCAAACAGCTGAAACCTGAACTGATGCCG





TCTAGCGCTTACTTCGGACTGGGTAGCCTGTTCTATGGCCTGATGG





TGTTGGGCCTCCAGCGTTCCGACTCGCATATCATTCAGAAAGCGTA





TGAGTATCTGAAACATTTGGAAGAGTGTGTGCAGCATGAGGAAACG





CCAGATTTTGTCTCGGGTTTGTCTGGTGTACTGTATATGCTCACGA





AAATTTATCAGCTCACGAATGAACCGAGAGTTTTCGAAGTGGCCAA





AACCACAGCTTCGCGTCTGTCTGTGCTGCTTGACAGCAAGCAGCCC





GACACTGTGCTCACCGGGTTATCCCATGGCGCCGCAGGATTCGCCC





TTGCATTACTGACCTACGGAACCGCTGCAAATGATGAACAGTTGCT





GAAACAGGGCCACTCCTATCTGGTGTACGAACGTAATCGGTTTAAC





AAACAGGAAAACAACTGGGTTGATTTACGTAAAGGCAACGCGTATC





AAACATTTTGGTGCCATGGCGCCCCGGGTATTGGCATCTCACGCCT





CCTGTTAGCGCAATTTTACGATGACGAACTGCTGCATGAAGAGTTA





AACGCAGCACTGAACAAGACTATTTCGGACGGCTTCGGCCACAATC





ACTCACTGTGTCATGGCGATTTCGGCAACCTCGATCTGTTATTGCT





TTATGCCCAATATACGAATAACCCAGAACCAAAGGAACTCGCTCGC





AAACTGGCCATAAGCAGTATCGATCAAGCGCACACGTATGGCTGGA





AACTCGGGCTCAATCATAGCGATCAACTGCAGGGTATGATGTTAGG





GGTGACTGGTATCGGCTATCAGCTCCTTCGTCATATAAATCCGACA





GTCCCCAGCATTTTGGCACTGGAACTGCCCAGCTCCACGTTAACTG





AAAAAGAGCTGAGAATCCATGATCGT






kgpF
Codon
ATGATCAATTATGCTAATGCGCAGCTCCATAAGAGTAAAAACTTGA
486



optimized
TGTATATGAAAGCCCACGAAAACATCTTCGAAATCGAGGCGCTGTA





CCCGCTGGAATTGTTCGAGCGTTTTATGCAGTCCCAAACCGATTGC





TCCATCGATTGTGCCTGTAAAATTGATGGTGACGAATTGTATCCCG





CCCGTTTTAGTCTGGCCCTGTATAACAACCAGTATGCCGAAAAGCA





AATTCGCGAAACCATCGACTTCTTCCATCAGGTAGAGGGTCGGACC





GAGGTGAAACTGAACTATCAGCAACTGCAGCACTTCCTGGGTGCTG





ACTTCGATTTTAGCAAAGTGATTCGAAACCTGGTGGGTGTGGATGC





ACGCCGCGAACTGGCTGATTCCCGGGTTAAACTGTATATTTGGATG





AACGATTACCCAGAGAAAATGGCGACCGCCATGGCATGGTGCGATG





ATAAGAAGGAATTGTCGACGTTGATAGTAAATCAGGAGTTTCTGGT





CGGGTTCGATTTTTATTTCGATGGTCGCACGGCAATAGAATTATAC





ATTAGTCTGTCATCCGAAGAATTTCAGCAGACACAAGTTTGGGAAC





GCCTCGCAAAGGTAGTGTGCGCCCCAGCGCTGCGCCTTGTTAATGA





TTGCCAGGCGATCCAGATTGGCGTGAGCCGTGCCAATGATAGTAAG





ATCATGTATTACCATACCCTTAATCCGAACTCGTTTATCGACAATC





TGGGCAATGAAATGGCAAGCAGAGTTCACGCGTATTACCGACATCA





ACCGGTTCGCTCTCTGGTAGTATGCATACCAGAACAGGAGTTGACC





GCCCGGTCCATACAGCGCTTAAACATGTATTACTGTATGAAC






lasB
Codon
ATGAAAGGCGAGGAAATGTTGGGACATCCACAGACCGGTTTTGTTG
487



optimized
TACTGCCAGACAACGATGCCACCGGCGACGTGACGGGCCGCCTGTT





ACCTTGGGGTGATGTAGTTACAGTGTATCCGTCTGGCCGTCCATGG





ATCATCGGCAACTGCTGGGATCGCCCAGTCCTCGTCCATGATGGCG





TGATCGTCTTGGGTCATACCAGCGTCACGCGTGATCAAATTGCCCG





TCATGGGAACGATCCGCATCGCTTACTGGACGAGGCCGACGGCGCA





TTTCATGCGGCGGTCCTGATCGGACACGAAGTTCATGTTCGCGGCT





CCGCCTACGGTGTCTGTCGTCTGTATACATGCGTTGTTGACGGTGT





GACCTTAGTGAGTGATCGTACAGACGTCCTGCAGCGTCTGGCAGGT





ACTGATGTGGACGTCGACGTGCTGGCTGGCCACTTGTTAGAGCCGA





TCCCGCACTGGTTAGGCGAACAACCGTTATTGACGTCCGTGGAGCC





CGTGCCACCGACACATCACGTTATTTTAACTCCGGACGCACGTAGT





CGTTTACGGCCATCACGTCGTCGTCGGCCTGAACCGTCGCTGGGTT





TGCGGGACGGTGCGGAACTTGTCCGGGAGCGTCTGGCCGCAGCTGT





GGCTACCCGTGTGGACAGTCCAGCGTTAATTACCAGTGAACTGAGT





GGCGGCTATGATTCCACTAGTGTGTCATACTTGGCAGCGCGCGGTA





AAGCCGAGGTGGTGCTGGTCACGGCCGCGGGACGTGACAGCACAAG





CGAGGATCTGTGGTGGGCTGAACGCGCAGCCGCAGGGCTCCCGGAA





CTCGATCACGTAGTGTTACCTGCGGATGAATTACCGTTTACGTACG





CCGGCCTGACGGAGCCTGGTGCACTTTTGGATGAACCGTGTACGGC





TGTTGCCGGCCGTGAGCGTGTACTGGCGCTGGTACGTAAAGCCGCG





GCCCGCGGCTCTACACTTCATCTGACTGGCCATGGTGGCGATCACC





TGTTTACTTCACTGCCGACACCGTTTCATGACCTGTTTCGTACGCG





TCCAGTCGCCGCGCTCCGCCAGTTGCGTGCATTTGGCGCGTTGGCT





GCGTGGCCGACCCGTAAGCTGATGCGCGAACTCGCGGACCGCCGCG





ATCATAGCACCTGGTGGCGCGCGCACGCACGTCCTCAGAATGGCCA





GCCGGATCCGCACAGCCCCATGTTAGGCTGGGCAATTCCCCCGACT





GTCCCGGCGTGGGTTACTGCTGACGGCGTGCGCGCGATCGAACTTG





GGATTTTAGAAATGGCAGAACGCGCGGAGCCCCTTGGTCATGCGCG





CGGAGAACACGCTGAGCTGGATTCAATCTTTGAAGGGGCGCGTATG





GCCCGTGGCCTCAATCGTATGGCTACGCATGCCGGAGTCCCGCTTG





CAGCCCCGTTCCATGACGATCGGGTCGTGGAAGCGTGTCTGTCGAT





CCGGCCGGAGGAACGCATTTCTGCATGGCAGTACAAACCCTTACTG





AACGCCGCAATGCAGGGTGTGGTGCCGAGCACCGTTCTTGATCGTA





GCGCTAAAGATGACGGGAGTATTGATGTGGCCTATGGGCTGCAGGA





ACACCGTGATGAACTGGTAGCGCTGTGGGAATCATCACGTCTGGCG





GAAACCGGTCTGATTGATGCGGGTATGCTGCGGCGTTTATGCGCGC





AGCCGTCCTCCCACGAGCTCGAGCATGGATCCTTGTACGCTACTAT





CGCTTGTGAGTTGTGGCTGCGTGGTTTAGATCAGGATCGTACCCAA





CGCTAC






lasC
Codon
ATGCCGGTGCAGCTGCGTCGGCATGTGTCTTTTACGGCTACGGAAT
488



optimized
ACGGCGGCGTGCTGCTGGATGAAACCAAAGGCGCATACTGGCGTCT





GAACACCACAGGCGCCGAAGTTGTTCGCGCCATGGGGGAAGCCGAG





CGGGATGAGATTGTACGGCATGTGGTGGCGACCTTCGATGTTGATG





CGCAAACCGCAGCCCAGGATGTCGATGTCCTGCTGGCAGAACTTCG





TGATGCCGGCCTTGTGGCCTCG






lasD
Codon
ATGTCTGTGAATATGGCTCTCCGTGGCCATGGTATGTCCGGTCGCC
489



optimized
GTCGTCGCTTAGATGCCACGCGTGCTCGCCTGGCCGTTGTGGTTGC





CCGTGTCCTGAATCTCTTACCGCCGCGCTTAATCCGTCGTTGTTTG





CGTGTACTGAGTCGCGGAGCCCGCCCTGCCTCGATTGAGGCAGCAG





AAGCTGCTCGTCGTACTGTGGTTGCGGTGAGTCCAGCTGCCGCCGG





TGCGTACGGCTGTTTAATCCGCAGCATTGCCACCACCCTGGTTCTT





CGTTCACGCGGGCAATGGCCAACCTGGTGTGTTGGTGTACGTGCGG





AGCCTCCTTTTGGTGCCCATGCCTGGATTGAAGCAGAGGAGCGGCT





GGTGGATGAACCTGGTACTATGCATACTTACCGTCGTCTTATCACC





GTTGGTCCACTGTCTCGCAAAGTTCGT






lasF
Codon
ATGTCTATCGAACTGACGCCTAGTTTGGCCGATCTGGTCGATCCAC
490



optimized
TTCCAGGTCACGCACTGCGCGCTGCGGCGACATTACGTCTGGCAGA





TCTGATTGCGGCTGGTGCAGATACTGCACCGGCATTAGCAGCGGCG





GCACGCATTGATGCTGACGCGATCGCGCGTCTTATGCGGTATCTGT





GCAGTCGCGGGATTTTTCAAGCACATGAAGGCCGGTACGCGTTGAC





TGAATTTAGCGAATTGCTGCTGGATGAAGATCCATCTGGCCTGCGT





AAAACCTTAGATCAGGATAGCTATGGGGATCGTTTCGACCGCGCGG





TTGCGGAACTGGTGGACGTTGTACGGTCCGGTGAACCTTCTTATCC





TCGCCTTTACGGCTCGACGGTTTATGATGACCTGGCAGCCGATCCT





GCCCTCGGCGAGGTGTTCGCGGATGTTCGTGGCTTGCACTCCGCAG





GGTATGGGGAAGATGTCGCGGCAGTGGCGGGTTGGTCCTCATGCCT





GCGCGTTGTCGATCTGGGTGGAGGGACTGGCTCCGTCCTGCTTGCT





GTGTTAGAGCGTCACCCGTCCCTGTCAGGCGCAGTACTGGATCTGC





CATACGTCGCCCCGCAGGCAAAGAAAGCTCTGCAGGCCTCAGCGTT





TGCCCAACGTTGTGAATTTATCAAAGGGAGCTTCTTCGATCCGTTA





CCTCCGGCAGACCGTTACCTGTTGTGTAACGTGCTGTTCAACTGGG





ATGACGCGCAAGCAGGCGCTATTTTGGCACGCTGTGCGCAGGCGGG





CCCTGTGGCCGGAGTAGTGGTAGCCGAACGTTTGATCGATCCGGAT





GCGGAAGTGGAACTCGTAGCAGCTCAAGATCTGCGTCTGTTGGCTG





TTTGCGGCGGTCGGCAGCGTGGCACCGCTGAATTCGAAGCGCTTGG





GGCAGCCCATGGCCTGGCGTTAACCAGCGTTACCCTCACGGCATCT





GGTATGAGCCTGCTCCGTTTCGATGTGTGTCGTGCCGGGAGTGCTG





GCGGGGAAGTTGTGGAAAAATCT






IcnG
Codon
ATGGACGGAACCAACAAGCGCCTGGAGGACAAGTGGTTTGATATTA
491



optimized
ACTTCCTGGAAATGTATACACGCAGCTGCCTGAAAACTTTTGGCTA





CTTCGACGAAATTCTGATCGTGAAGAAACGCATCGAGGTCCTGAAG





AACGTGCTTGAAAAACAGTACTTGTCTACCAATGATTATGCTGAGG





AGTTTTTCGAGCTGAATACCACCTTGGAGAGCATAAAAGAATACAT





CAAACTGAATCTGGTCATCGAGAAAGAACCGATCTCAATTTGCATT





ATGGTCAAAAACGAAGAACGTTGCATCAAGCGCTGCATTGATAGCG





TTGAAATCCTCGCCGAGGAGATAATCATTATCGATACCGGCTCTAC





GGATAATACCATTAACATTATTGAGGAATGCGCAAACGACAAAATT





AAAGTGTTCTCAAAAGAATGGCGTAACGATTTTTCCGAAATTCGGA





ACTATGCCATCGAGAAAGCGAGTAGCGAATGGCTGGTGTTTATAGA





TGCCGATGAATATCTGGACGAAGCCTCGGTGCTCAACCTGCTCAGT





ACGCTCAACATCTTTAACAATCATAAGCTCAAAGACTCTATTGTCC





TGTGCCCCATGATCAACGAAGCCAATAACACCATCCATTTCCGTAC





CGGGAAATTTTTCAGAAAAGACTCCGGGATTAAATTCTTTGGTACC





TGCCATGAGGAGCCCCGCATTAAAGGCATGCCGAATTCTACCCTGC





TGATTCCGATCAAGGTTGATTATCTGCATGACGGCTACCTGGCAAA





AGTACAATCAAATAAAGACAAGAAAACCCGTAACATCGAACTGTTA





GAAGGTATGGTGGAACTGGAACCGGATAATCCTCGTTGGGCGTATA





TGTTTGTGCGCGACGGATTTGCAATCCTCGATAACGAATACATTGA





GAAAACTTGTTTGCGGTTTTTACTGCTGGACAAAAACGTACGCATC





TGCGTCAACAACCTGCAAGACCATAAATTCACTTTGTCACTCCTGA





CGATCCTGGGCCGCCTCTATCTGCGCGAGTGCGAATTCGAGAAAAG





CAATCTGATAATTCGCATTCTTGACGAACTCATCCCTAATAGTCTG





GATGGTAAATTTCTGGCATTCATGGAGCGATTCAGCAAACTGAAAA





TTGAGATTAATACGCTGTTAACGGAGGTCATCGAATATCGTCGTAA





CCACGAAGTAGATGAAACCAGTTTAATCAACACACAAGGCTACCAT





ATCGACTATGTTCTGTCGATTTTGCTGTTCGAAACGGGTAATTACG





CGCAAAGTAAGAAATACTTCGATTTCCTGCAGGAGAACCATTTTCT





GGAAGAACTGTTTCAAGACAGCTCTTATTCTATCATACTGAAAATG





CTCGAGTCAGTAGAAGAT






ItnMI
Codon
ATGAAGTTTAACAAGAACGTGTTCCCAGAGATCAATGAAACGGATT
492



optimized
TCGATAACAATATCAAGCCCCTGCTGGATGAACTGGAATCTCGTAT





TACCATTCCGCAGGAGGAACTGAGCTTTTCAAGCATTAACGATGAT





TTATTTCGCGAGTTAACCCGCAACGAGGAGTACCCTTACCAGAGCA





TTTGTACGATCGTTGCAAACATCGTGATGGATGACGGCAGTGAGAT





TTGGCGCAAAGATATTTTTGTTGATTCCAATAGTGTGCGCGAAGCC





GTATGCGACATTCTGAGCCAAACGTTATTCCTCTATTTCATCCGCT





GCTTCTCCGAACAAATTAAAGACATTCGCAAAACTGATGAGGATAA





AGAGTCCACCTACAACCGCTACATTAACCTCCTGTTCAGCTCCAAC





TTCAAAATCTTCTCCGACGAATACCCTGTCCTGTGGTATCGGACCA





TTCGCATCATCAAAAATCGCTGGTATTCTATCAAGAAATCGTTACT





GCTGACTCAAAAACACCGTGTGGAGATCGATAAGCAGTTGGACATC





CCGCACAAGATGAAGATTAAAGGCCTGAAAATCGGGGGAGACACGC





ATAACGGCGGTGCCACAGTGACCACGATCTTCTTTGAGAAAGGGTA





TAAACTGATTTATAAGCCGCGGAGCACATCCGGCGAATTCTCGTAC





AAGAAATTTATCGAAAAGATTAACCCGTACCTGAAGAAAGACATGG





GAGCGATTAAAGCGATCGATTTCGGTGAATACGGCTTTTCTGAGTA





TATTGAGTGTAACACGGATGAAGAGGACATGAAACAGGTCGGTCAG





CTTGCATTTTTCATGTACCTGTTGAATGCATCAGATATGCATTATA





GCAATGTCATTTGGACCAAACAGGGCCCTGTGCCGATTGATTTAGA





AACCTTGTTCCAGCCGGATCGTATTCGCAAAGGCCTGAAGCAGTCG





GAAACTAACGCGTACCACAAAATGGAGAAAAGTGTATACGGAACGG





GAATTATTCCAATTTCCCTGAGCGTTAAAGGCAAAAAGGGTGAGGT





CGACGTCGGCTTTAGTGGAATCCGTGATGAGCGCTCTAGTTCGCCG





TTTCGCGTTCTGGAAATTTTGGATGGGTTTTCGAGCGACATCAAAA





TCGTGTGGAAAAAGCAGCAGAAGTCTAGCTCCAGCAAAAACAATCT





GATTGTCGATCACAAAAAGGAGCGCGAAATCCTTCAGCGTGCCCAG





TCCGTCGTAGAAGGTTTCCAGGAAACCTCTAAAATCTTCATGAAAC





ATCGTGAGGAATTCATCTCCATTATCTTAGACTCATTCGAGAACAT





CAAAATTCGCTACATCCATAACATGACGTTTCGCTACGAACAGTTG





CTGCGCACTCTGACGGATGCCGAGCCGGCCCAGAAGATTGAGTTAG





ACCGTCTGCTGCTGAGTCGTACCGGAATTCTGTCCATCTCGTCTAG





TCCCTACATCTCGCTCTCCGAATGTCAACAGATGTGGCAGGGTGAC





GTGCCGTACTTCTACTCGAAGTTTTCGAGCAAAAGTATCTTTGATA





CCAATGGCTTCGTTGATGAAATCGAGCTGACGCCCCGCCAGGCATT





TATCATCAAAGCCGAAAGTATCACCAACGATGAAGTCGATTTTCAG





TCCAAGATCATTAAACTGGCGTTCATGGCACGCTTAAGTGACCCGC





ACACAACCAACGACAACAAACTGAATAAAAAGGTGATTATCGAAAG





CAACCAGCAGAGCAACAGCAGTGAATCAGGTAACAAAGCCATTTTG





TTCCTGAGCGATCTGCTGAAAAATAACGTACTGGAAGATCGTTATA





GTCATCTGCCGAAAACTTGGATTGGCCCTGTAGCACGTGATGGCGG





TTTGGGTTGGGCGCCGGGCGTGCTGGGATACGATCTGTACTCGGGC





CGTACAGGACCTGCGTTAGCATTGGCTGCGGCCGGGCGCGTTTTGA





AAGATAAAGACAGTATCGAACTTAGCGCCGACATTTTTAATAAATC





GTCCCAGATTCTGCAGGAAAAGACTTACGACTTTCGTAACCTGTTC





GCATCAGGTATCGGCGGTTTTAGCGGGATTACCGGTCTGTTTTGGG





CGCTGAACGCGGCAGGGAATATTCTGAACAATGATGACTGGATTAA





AACCTCGAATCAGAGTATGCTGCTGCTGAATGAGAACATGCTGAAA





GTGGACAAAAATTTCTTTGACCTGATTAGCGGCAACTCGGGAGCGA





TCGGTATGATGTACCTGACCAATCCAAATTTCTATTTGTCTCGCTC





GAAAATTAACGACATTCTGCTGACCACGGACTGCTTGATTACTGAA





ATGGAAAAAGACGAAACGAGCGGACTGGCCCATGGCGTGTCTCAGA





TCCTGTGGTTCCTTAGCATTATGATGCAACGTCAGCCCTCAAGTGA





AATCAAAATCCGCGCGACGATTGTCGACAACATCATCAAGAAGAAG





TATACGAATTCCTATGGCGAAATCGAATGCTACTATCCGACTGATG





GGCACTCCAAATCCACCTCGTGGTGCAACGGGACAAGTGGGATTCT





GGTCGCCTATATTGAGGGGTATAAAGCTAATATCGTGGACAAATCC





TCGGTGTATCATATTATTAATCAGATCAACGTCGAACAACTTCAGC





ATGATAACATTCCGATCATGTGCCATGGTAGCCTTGGTGTGTATGA





ATCGCTTAAATATGCGTCAAAGTACTTTGAAATCGAAACCAAGTAC





CTTCTGGATGTGATGCGCAATGGCGGCTGCTCCTCCCAAGAAGTAT





TAAAGTACTATGGCAAGGGTAACGGCCGTTACCCGCTGTCACCAGG





TTTAATGGCGGGTCAGTCGGGCGCGTTGCTGCACTGTTGCAAACTG





GAGGATAACGATATCAGCGTGAGCCCCATTTCACTGATGACG






ltnM2
Codon
ATGGATCCGAGTATCAAAAAGCTCGTGGATTCTATCATCGAATTCT
493



optimized
ACAAAAAGGACATCTACCTGGCATACAAAGAGCTGGAACGCGAAAT





CAAAAACATCGATAAGACCATCTACAACACTTCAAATGACGAGATC





TTGCGGATTTTTAAAGAGAGCCTGATCAGCATCATCACCGATGATA





TTTACCGCCTCTCGATTAAAACCTTCATCTATGAGTTTCACAAGTT





TCGTATCGATAACGGGTTTCCGGCTGTCAAAGATAGCGAAAGCGCC





TTCAATTATTACATCAGTACCTTTGACGTGAAAACGATCGCTCGCT





GGTTTGAGAAATTCCCAATGCTGGAATCCATCATCTCCAGTAGCAT





CAAAAACGATTGCACATTTATGGTGGATGTATGTGTCAATTTCATC





TTAGACCTGTCGGAATGCGAGAAGATTAATCTGATCTCAGAGGATA





GCCGGCTCATCACGATCTCATCCAGCAACTCTGACCCGCACAACGG





TGGCACGCGTGTCTTGTTCTTTCGTTTCCACAACGGTGATACCATT





CTTTACAAACCCCGCAGCCTGACCGTGGACAAGCTGATCTCTAATA





TTTTCGAAGAGGTATTCGAATTCGATGCGACGAACTCGAAAAATCC





TATTCCCAAGGTGCTGGATCGGGGTACCTATGGCTGGCAGGAATTC





ATTGAGAAGAAATCGATCTCTTCCTCAGAGATTAAGCAGGCCTACT





ATAACCTGGGTATCTTTAGCAGTATCTTTACAGTGTTAGGGTCTAC





TGATATCCACGATGAAAACTTGATTTTTAAAGGTACGACCCCGTAT





TTCATCGATCTGGAAACAGCCCTCTCTCCGCGTATCCGGTATGAAG





GTAATGAGGAAAACCTGTTCTATCGGATGAGCTCATCGTTGTTCAC





TTCTATCGTGGGGACGACTATTATTCCTGCAAAACTTGCTGTCCAT





TCCCAGGAAATTATGATCGGCGCAATTAACACCCCTGCGAAACAGA





AAACCAAGAAGGATGGCTTTAACATCATCAACTTCGGCACGGATGC





CGTCGATATCGCAAAACAGAATATTGAGGTGGAGCGTATTGCTAAC





CCTATGCGCATTAAAAATAACATCGTGAACGATCCGCTGCCGTACC





AGAACATCTTTACGCGCGGCTTCAAAGAGGGGATCAAATCCATCAT





CCTGAAGAAAGGCTCGATCATTTCCATTCTGAACAACTTCAACAGC





CCGATTCGTTACATCATGCGGCCGACGGCAAAATATTATTTGATTC





TGGATGCCGCGGTATTTCCCGAAAACCTGTATTCGGAACAGACACT





GAACAAAACCCTGAATTAGTTAAAGCCGCCAAAAATCGTGGAAAAT





TCCCTGATTTCTAAACAGCTCTTTCTTGCCGAAAAACGCATTCTGT





CCGAAGGCGATATTCCGAGCTTCTATGTGCTGGGCAAAGAGAAAAA





TATCCGTGCGCAGAACTTCATTAGCGAACAGATCTTCGAGGAAACC





GCGGTCGATAACGCGATTCAAATTCTGGAATCCATTTCGCAAGACT





GGGTGAATTTTAATGAGCGCCTGATTGCGGAGGGCTTCTCCTATAT





TCGTGAACAGAGTCGTGGCTATCTGTCCAGTGATTTTGAGAACTCT





GATATTTTCAAAAGCTCACTGACCGAAACAAAGAAGTCCGGTTATA





CCGCAATGCTGAAAACAATTATCTCCATGTCGGTCAAGACCTCGGA





AAACAAAAAGATCGGTTGGCTGCCAGGCATTTATGATGATTATCCG





ATCAGCTATATGAGTGCCGCGTTTTGTTCGTTCCATGATTCCGGCG





GTATCATCACTTTGCTTGAACACCACTTTGGGCACTGCTCCCCCGA





ATATAACGAGATGAAGCGCGGGCTGCTGGAACTGGGCAAAATGTTG





AAAATTAACAATAGTAACCTGAGCATCATCTCCGGCTCAGAGTCTC





TGGAATTTCTGTATACGCACCGCGAAGTCGAATGCCTGGAACTGGA





ATACATTTTAAACAATTCAGCGGAAATCATGGGCGACGTGTTCCTG





GGGAAATTAGGCCTTTATCTTATCCTGGCGAGCTACCTGAAAACAG





ACCTGAAAATTTTCCAAGATTTCAGTATCATCTGCCAGAAAAACCT





CGAGTTTAAAAAGTTCGGGATCGCGCACGGTGAATTAGGGTATCTG





TGGACCATCTTCCGTATTCAAAACAAACTGAAGAACAAAAATGCGT





GTCTGAGCATCTATCATGAAGTGTTGAACATTTATAAAGGTAAGCG





CATTGAATCCGTGGGATGGTGCAACGGTTTATCGGGTATTCTGATG





ATTTTGTCAGAAATGAGCACCGTATTAGAGAAAAATCAAGACTATC





TGTTCAAGCTGGCAAATCTGAGCACTAAACTGAATGAGGAATCCGT





TGACCTGAGTGTGTGCCACGGCGCCAGCGGGGTGCTTCAAACACTG





CTTTTCGTCTATAGCAACACGAACGATAAACGTTATCTCAGCCTGG





CCAATAAGTATTGGAAGAAAGTGCTGGATAACAGCATTAAGTACGG





TTTCTACAATGGAGAACGCGATAAGGATTATCTGTTGGGATATTTC





CAGGGTTGGTCAGGCTTCACGGACAGCGCACTCCTGCTGGATAAAT





ACAATAACAATGAGCAAGTGTGGATTCCGATCAACCTGAGCTCCGA





TATCTATCAGCATAATCTGAACAACTGCAAAGAGAAGAATTATGAG





GGCGATGGCTGCCATAAATCT






lynD
Codon
ATGCAATCTACACCATTACTGCAAATACAACCACATTTCCATGTAG
494



optimized
AGGTCATTGAACCAAAGCAAGTCTACTTGTTGGGTGAACAAGCTAA





TCATGCATTGACAGGCCAATTATACTGCCAAATTTTGCCATTGTTA





AACGGACAATACACATTGGAACAAATCGTTGAAAAACTAGACGGAG





AAGTACCACCTGAATACATTGATTATGTGCTGGAGAGACTAGCTGA





GAAGGGCTATCTGACTGAAGCAGCACCTGAATTATCTAGTGAAGTG





GCCGCTTTCTGGTCTGAGCTGGGGATTGCACCTCCTGTCGCGGCCG





AAGCATTACGTCAACCTGTGACTTTAACACCTGTTGGAAACATCAG





CGAAGTAACAGTAGCAGCCTTAACCACAGCCCTACGTGATATCGGT





ATTTCCGTTCAAACACCTACAGAAGCTGGATCGCCAACTGCATTGA





ACGTTGTACTTACCGATGATTATCTCCAACCAGAACTCGCTAAGAT





CAATAAGCAAGCCTTAGAAAGTCAACAAACTTGGCTACTTGTCAAA





CCAGTTGGCTCCGTGTTATGGTTGGGTCCGGTATTCGTGCCAGGAA





AAACAGGTTGCTGGGATTGTTTGGCTCACAGATTAAGGGGGAATAG





AGAGGTAGAGGCCTCTGTATTGAGACAAAAACAAGCTCAACAACAA





CGTAATGGACAAAGCGGGTCTGTAATAGGATGCCTTCCCACGGCTA





GAGCGACACTGCCCTCAACACTCCAAACTGGGCTGCAGTTCGCTGC





TACCGAAATTGCTAAATGGATAGTTAAGTATCATGTTAATGCCACA





GCGCCTGGCACCGTATTCTTCCCTACATTGGATGGTAAGATAATTA





CGCTAAATCACTCCATACTGGATTTGAAGTCACATATTCTGATCAA





GCGTTCTCAATGTCCCACCTGTGGTGACCCAAAAATCTTACAGCAC





CGTGGTTTCGAACCTTTAAAACTTGAGTCAAGGCCTAAACAGTTCA





CCTCAGACGGCGGACATCGTGGTACTACCCCTGAACAAACTGTCCA





GAAATATCAACATTTAATCTCGCCTGTTACCGGTGTAGTTACTGAA





TTGGTCAGGATAACTGATCCGGCCAATCCACTAGTTCACACATATA





GAGCTGGTCATAGCTTCGGGAGCGCTACATCGCTGAGAGGGCTGCG





TAATACCTTAAAGCATAAGAGTTCAGGTAAGGGTAAGACTGATTCT





CAAAGTAAAGCCTCGGGCCTGTGTGAGGCGGTAGAACGTTACTCAG





GAATCTTTCAAGGTGACGAACCGAGAAAACGCGCCACATTGGCTGA





ATTGGGAGATTTGGCAATTCACCCTGAGCAATGCTTGTGTTTTTCC





GACGGTCAGTACGCTAATAGAGAAACTTTAAACGAACAGGCAACGG





TGGCACATGATTGGATACCTCAACGTTTTGATGCATCACAAGCTAT





TGAATGGACTCCAGTCTGGTCCCTAACTGAACAGACCCATAAATAT





TTGCCCACCGCATTGTGTTACTACCATTATCCTCTACCCCCAGAAC





ACAGATTCGCACGTGGAGATTCGAATGGTAATGCTGCCGGAAATAC





GTTGGAAGAGGCTATACTCCAAGGCTTCATGGAATTAGTCGAGAGA





GATGGTGTGGCTTTATGGTGGTATAACAGGCTACGCAGACCCGCTG





TAGACTTAGGCTCATTTAACGAGCCATACTTCGTTCAGTTGCAACA





ATTCTACAGAGAAAACGATAGAGATTTGTGGGTTTTGGACTTGACA





GCTGATTTAGGTATCCCGGCTTTCGCGGGCGTTTCTAATAGAAAAA





CTGGTAGTTCGGAGAGGTTGATATTAGGATTCGGTGCACACCTCGA





TCCTACTATTGCAATTCTGAGAGCAGTTACAGAAGTTAACCAGATT





GGCCTTGAATTAGATAAAGTTCCAGACGAGAACCTTAAGAGCGACG





CAACAGATTGGCTAATTACTGAAAAATTAGCTGACCACCCTTATTT





GTTACCAGATACAACTCAACCTCTAAAAACTGCTCAAGATTATCCT





AAAAGGTGGTCTGACGATATATACACGGACGTAATGACTTGCGTTA





ATATTGCTCAACAAGCAGGACTTGAAACTCTAGTTATTGATCAAAC





ACGTCCGGACATTGGTTTGAATGTTGTTAAGGTGACAGTCCCGGGG





ATGAGGCACTTTTGGTCAAGATTTGGAGAGGGGAGGCTTTATGACG





TGCCCGTCAAATTAGGTTGGCTTGACGAACCTTTGACCGAAGCGCA





AATGAACCCCACGCCGATGCCTTTT






mcbCD
Synthesized
ATGTCAAAACACGAACTCTCTTTAGTGGAAGTAACGCATTACACAG
495



without codon
ATCCTGAAGTTCTGGCCATTGTTAAAGATTTTCATGTCAGAGGTAA




optimization
CTTTGCTTCCCTCCCCGAATTTGCTGAACGAACTTTCGTGTCCGCG




as overlapping
GTACCTCTTGCCCATCTGGAGAAATTTGAAAATAAAGAAGTTCTCT




reading frames
TCAGGCCAGGTTTCAGCTCCGTAATAAACATATCCTCATCACATAA




(same as
TTTTAGTCGTGAAAGGCTCCCATCAGGAATAAACTTTTGCGACAAA




native E. coli
AATAAACTTTCCATTCGTACTATTGAAAAGTTATTAGTCAATGCAT




cluster)
TCAGCTCACCTGATCCTGGCTCTGTAAGGCGGCCTTATCCTTCTGG





GGGGGCATTGTACCCGATTGAAGTTTTTTTATGCAGATTATCTGAA





AATACAGAAAACTGGCAGGCAGGAACTAATGTTTATCACTACCTGC





CGCTAAGTCAGGCACTAGAACCTGTTGCTACATGTAATACTCAGTC





ACTCTACCGAAGCCTGTCCGGTGGGGATTCGGAACGTCTTGGTAAA





CCCCATTTTGCTCTCGTCTATTGCATTATTTTTGAAAAAGCTTTGT





TCAAATATCGCTACAGAGGATACCGGATGGCCTTAATGGAAACAGG





TTCGATGTATCAGAACGCAGTATTGGTTGCAGATCAAATAGGACTG





AAAAACCGGGTATGGGCGGGATATACCGATTCATACGTAGCAAAAA





CAATGAATCTGGATCAGAGGACTGTAGCGCCACTGATCGTTCAGTT





TTTTGGAGATGTAAACGATGATAAATGTCTACAGTAACCTTATGTC





CGCATGGCCGGCCACAATGGCCATGAGTCCAAAACTGAACAGAAAT





ATGCCAACGTTTTCTCAGATATGGGACTATGAGCGTATTACACCAG





CCAGCGCGGCCGGTGAAACTCTGAAGTCAATTCAGGGGGCAATAGG





TGAATATTTTGAACGCCGTCATTTTTTTAATGAGATAGTCACCGGT





GGTCAGAAAACATTATATGAGATGATGCCTCCATCTGCTGCAAAGG





CTTTTACCGAAGCATTTTTTCAGATCTCATCACTGACCCGCGATGA





AATCATAACCCATAAATTTAAAACGGTCAGAGCCTTTAATCTGTTT





AGCCTTGAACAACAAGAAATACCTGCAGTCATAATTGCACTCGACA





ATATAACCGCTGCAGATGATCTGAAATTTTATCCTGACAGAGATAC





ATGCGGATGTAGCTTTCATGGTAGTTTGAACGATGCCATAGAAGGT





TCCTTGTGTGAATTTATGGAGAGACAGTCCCTCCTTCTTTACTGGT





TACAGGGAAAAGCCAATACTGAAATATCCAGTGAAATAGTAACAGG





CATAAATCATATAGATGAGATTTTACTGGCTCTCAGGTCAGAAGGA





GATATCAGGATTTTCGATATCACCCTGCCCGGAGCTCCTGGACACG





CAGTACTAACCCTGTATGGCACAAAAAACAAAATCAGTCGAATAAA





ATACAGTACCGGATTATCCTATGCTAATAGTCTGAAAAAAGCACTT





TGTAAATCCGTAGTGGAATTGTGGCAATCGTATATATGCCTGCACA





ACTTTCTTATTGGCGGTTATACTGATGATGACATTATTGATAGTTA





CCAGCGTCACTTTATGTCATGCAACAAGTACGAGTCGTTTACGGAT





TTGTGTGAAAATACGGTACTACTGTCTGATGATGTCAAGTTAACGT





TTGAGGAAAATATTACGTCAGACACAAATTTATTAAACTATCTTCA





ACAAATTTCTGATAATATTTTTGTTTACTATGCCAGGGAAAGAGTA





AGTAACAGCCTTGTCTGGTACACAAAAATAGTAAGCCCTGATTTTT





TCCTTCATATGAATAACTCAGGTGCAATAAACATTAATAATAAAAT





TTACCATACCGGGGACGGTATTAAAGTCAGAGAATCAAAGATGGTA





CCATTCCCA






mdnC
Amplified
ATGACCGTTTTAATTGTTACTTTTAGCCACGATAATGAAAGTATTC
496



from
CTCTGGTAATCAAAGCCATAGAAGCCATGGGTAAAAAAGCCTTCCG




pARW071
TTTTGATACTGATCGCTTCCCTACAGAGGTGAAAGTTGATCTTTAC





TCAGGCGGTCAAAAAGGCGGAATTATTACCGATGGAGAACAAAAAT





TAGAGCTAAAAGAAGTTTCTTCTGTCTGGTATCGACGCATGAGATA





CGGACTAAAATTACCCGATGGGATGGATAGTCAATTTCGCGAAGCT





TCTCTTAAGGAATGTCGGTTAAGTATTCGAGGAATGATTGCTAGTT





TATCTGGCTTTCATCTTGATCCAATTGCTAAGGTAGATCATGCTAA





TCATAAACAATTGCAGTTACAAGTGGCGCAACAATTAGGTTTATTA





ATTCCGGGGACTTTAACTTCTAATAATCCTGAAGCTGTCAAGCAAT





TTGCTCGGGAGTTTGAAGCGACGGGAATTGTGACTAAAATGCTTTC





TCAATTTGCTATTTATGGAGACAAGCAAGAGGAAATGGTTGTTTTT





ACCAGTCCTGTTACAAAGGAAGATCTAGATAATTTGGAAGGTTTGC





AATTTTGTCCAATGACTTTTCAGGAAAACATTCCTAAAGCTTTGGA





ATTACGCATCACTATCGTCGGTGAACAAATATTTACGGCGGCGATT





AATTCCCAACAATTAGACGGTGCTATCTACGATTGGCGAAAAGAGG





GACGCGCGCTCCATCAACAATGGCAACCCTACGATTTACCGAAAAC





TATTGAAAAACAACTACTAGAATTAGTGAAATATTTCGGTCTTAAT





TATGGTGCAATTGATATGATTGTCACACCAGATGAACGTTATATCT





TTTTAGAAATTAATCCCGTTGGCGAGTTTTTCTGGCTAGAACTTTA





TCCTCCTTATTTTCCTATCTCCCAGGCGATCGCTGAAATCCTAGTT





AACTCA






mibD
Codon
ATGACGGCACACAGCGACGCAGGAGGTGACCCACGCCCGCCTGAAC
497



optimized
GCTTACTGTTGGGGGTGTCAGGAAGTGTCGCTGCACTGAACTTACC





GGCGTACATTTATGCCTTTCGGGCAGCCGGTGTGGCACGTCTTGCG





GTCGTGCTGACACCAGCGGCTGAAGGGTTCCTTCCAGCGGGTGCGT





TACGCCCGATTGTGGATGCCGTTCATACGGAACATGACCAAGGCAA





AGGTCACGTAGCGCTGTCACGCTGGGCGCAACACTTACTCGTGCTG





CCGGCAACAGCGAATTTGCTTGGCTGTGCAGCGTCAGGACTTGCGC





CGAACTTTTTAGCGACCGTTCTGCTCGCGGCAGATTGCCCAATCAC





ATTCGTCCCGGCGATGAATCCGGTCATGTGGCGTAAACCAGCCGTA





CGCCGGAACGTTGCAACCTTACGCGCAGATGGTCATCACGTGGTGG





ATCCTCTGCCGGGCGCTGTGTACGAAGCTGCCTCACGTTCTATCGT





GGAAGGTCTTGCTATGCCGCGCCCTGAAGCGTTAGTCCGTTTACTG





GGTGGCGGTGATGACGGTTCTCCAGCAGGACCGGCAGGTCCGGTTG





GACGCGCAGAGCATGTTGGGGCTGTTGAGGCTGTTGAAGCCGTGGA





AGCAGTTGAGGCCGTTGAGGCTGCGGAAGCACTTGCG






mibH
Codon
ATGGCACGTAGTGAGGAATCGAACACTCTGGCACGTCTGTTTGACG
498



optimized
TGTTGGGTGACGATGCCGCTGCCGCACGTGAATGGGTAACGGAACC





CCATCGTCTGATCGCTAGCAATGAGCGCCTGGGCACAGCTCCGGAA





GCCCCGGCGGATGACGATCCGGAGGCCATTCGGACGGTTGGAGTGA





TCGGAGGGGGCACAGCCGGGTATTTAACGGCGTTGGCTCTGAAGGC





TAAACGCCCTTGGTTGGATGTGGCGCTCGTCGAAAGTGCGGATATC





CCGATCATTGGGGTAGGAGAGGCGACGGTGTCTTATATGGTGATGT





TTCTGCACCATTATCTGGGCATTGATCCGGCGGAGTTTTACCAACA





TGTGCGCCCTACTTGGAAACTGGGCATCCGTTTTGAATGGGGGTCA





CGTCCGGAGGGCTTTGTTGCGCCATTCGATTGGGGGACCGGATCTG





TTGGCCTGGTTGGGAGCCTGCGTGAAACGGGCAATGTCAACGAAGC





TACGTTACAGGCGATGCTCATGACGGAGGATCGCGTTCCGGTATAT





CGTGGCGAAGGTGGGCATGTTAGTCTGATGAAATATCTGCCATTCG





CATATCATATGGATAACGCTCGCCTGGTTCGCTACCTGACGGAACT





CGCCACTCGTCGTGGCGTGCATCATGTCGATGCGACTGTAGCTGAA





GTTCGCCTGGATGGTCCTGACCACGTTGGGGACCTGATTACTACGG





ACGGTCGTCGCCTGCACTATGACTTTTACGTCGATTGTACTGGATT





TCGTTCCCTGCTGCTGGAAAAAGCCCTGGGTATCCCGTTCGAATCT





TATGCGTCAAGCCTGTTTACCGACGCGGCAATTACCGGTACCCTTG





CACATGGGGGTCATCTTAAACCTTACACTACGGCAACTACCATGAA





TGCGGGCTGGTGTTGGACGATCCCTACTCCTGAGTCCGATCACCTG





GGGTACGTTTTCAGTAGTGCCGCGATCGATCCAGACGATGCAGCAG





CAGAAATGGCCCGCCGTTTCCCGGGCGTTACCCGCGAAGCATTAGT





TCGCTTTCGCTCCGGCCGTCACCGTGAAGCTTGGCGCGGCAATGTC





ATCGCGGTAGGAAACAGCTATGCTTTCGTGGAACCTCTGGAGAGTT





CGGGACTCCTGATGATTGCTACCGCAGTCCAGATCCTGGTGAGTTT





GCTGCCGAGTAGTCGTCGTGACCCGCTGCCTAGCAATGTGGCGAAT





CAGGCGTTAGCTCACCGGTGGGACGCGATTCGTTGGTTTCTGAGTA





TTCATTACCGTTTCAACGGCCGCCTCGATACTCCGTTCTGGAAGGA





AGCCCGTGCCGAAACAGATATTAGCGGTATTGAACCGTTGCTTCGT





CTGTTCAGTGCCGGTGCCCCTCTGACCGGTCGCGATAGCTTTGCGC





GCTATTTGGCCGACGGAGCAGCCCCGTTGTTCTATGGCCTGGAGGG





TGTTGATACCTTACTGCTGGGACAGGAAGTGCCTGCGCGTCTGTTA





CCACCGCGTGAATCTCCTGAGCAGTGGCGTGCCCGTGCTGCAGCAG





CCCGCTCATTAGCCTCGCGTGGCTTACGTCAGAGCGAAGCTCTGGA





TGCTTACGCTGCGGACCCCTGTCTCAATGCGGAACTGCTGTCTGAT





AGCGACTCATGGGCGGGTGAACGCGTCGCGGTACGTGCAGGTCTGC





GT






mibO
Codon
ATGATTTTTGGCCCGGATTTTCATCGCGATCCGTATCCAGTGTATC
499



optimized
GTCGTCTGCGTGATGAGGCTCCGTGCCACCATGAACCAGCGTTAGG





TCTGTATGCGTTGAGCCGCTACGAGGACGTTCTGGCTGCCCTTCGT





CAGCCCACCGTGTTCAGCTCAGCAGCGCGTGCGGTAGCCTCCAGTG





CAGCGGGAGCAGGTCCATACCGCGGTGCCGACACCGTTAGTCCGGA





GCGGGAAACTGCGGCTGAAGGGCCCGCCCGTAGCCTGTTGTTCCTG





GATCCGCCAGAGCACCAGGTGCTGCGTCAGGCGGTGTCCCGTGGCT





TTACGCCGCAGGCAGTATTGCGCCTTGAGCCGGCCGTCCGCGACAT





TGCGGCGGGTCTTGCTGATCGTATCCCCGATCGCGGTGGTGGCGAG





TTCGTTACCGAATTTGCGGCTCCGCTGGCAATCGCAGTGATTCTGC





GGTTACTTGGTGTACCGGAAGCAGATCGTGCCCGCGTAAGCGAACT





TTTATCGGCATCAGCCCTGTCGGGGGCGGAAGCAGAACTGCGCTCC





TATTGGCTGGGCCTTTCGGCACTCCTCCGCGATCGTGAAGATGCAG





GCGAAGGTGACGGAGAGGATCGTGGTGTGGTGGCGGCTCTGGTCCG





TCCTGATGCTGGACTGCGCGACGCGGATGTTGCCGCAGGACCTGCC





GTGCGTGCACCGCTGACGGATGAGCAGGTTGCAGCATTCTGCGCCT





TAGTGGGGCAAGCCGGCACTGAAAGTGTGGCAATGGCGCTCTCCAA





CGCATTGGTCCTGTTCGGGCGTCACCATGACCAGTGGCGCACACTG





TGTGCGCGTCCGGATGCGATTCCAGCAGCATTCGAAGAGGTCCTCC





GCTATTGGGCACCTACGCAGCATCAAGGTCGGACGTTAACCGCGGC





GGTACGTTTACATGGCCGTCTGCTGCCGGCCGGTGCGCATGTACTG





CTGCTGACCGGTTCAGCCGGCCGGGATGAACGTGCGTACCCAGACC





CCGATGTATTTGACATCGGTCGCTTCCACCCGGATCGTCGTCCGTC





GACCGCGCTGGGTTTTGGTCTGGGCGCACACTTTTGTTTAGGCGCT





GCTCTCGCTCGTCTGCAGGCACGCGTAGCGCTGCGCGAACTGACAC





GCCGGTTCCCGCGTTATCGTACGGACGAGGAACGCACTGTGCGTTC





GGAAGTGATGAACGGGTTCGGCCACAGCCGTGTACCATTTTCCACG






mibS
Codon
ATGACGACTGGCACCACGGTAGCGCATGCTGTAGAACCAGACGGTT
500



optimized
TCCGCGCCGTGATGGCCACACTGCCGGCCGCTGTGGCGATCGTTAC





GGCAGCTGCGGCAGATGGGCGCCCGTGGGGTATGACCTGCAGTTCG





GTTTGCTCAGTGACCTTGACCCCGCCGACCCTTCTGGTCTGCCTTC





GGACGGCGTCCCCGACTCTGGCCGCAGTCGTGTCAGGTCGTGCATT





TAGCGTGAACCTTCTGTGTGCGCGGGCCTATCCTGTGGCGGAATTG





TTTGCATCTGCGGCAGCAGACCGGTTTGATCGCGTTCGTTGGCGTC





GCCCGCCGGGTACAGGCGGTCCACATCTTGCCGATGATGCACGTGC





AGTGTTAGACTGTCGCCTGAGCGAAAGCGCAGAAGTAGGCGACCAT





GTGGTCGTATTTGGCCAAGTCCGGGCGATTCGTCGCCTGAGTGATG





AACCACCACTGATGTATGGTTATCGTCGTTACGCACCTTGGCCGGC





AGATCGTGGTCCGGGTGCGGCAGGCGGC






paaA
Codon
ATGAGCCTGACGAATGTCAAGCCGTTGATTAAAGAATCCCACCACA
501



optimized
TCATTTTAGCTGACGATGGTGACATTTGCATTGGGGAAATTCCGGG





GGTGTCTCAGGTAATCAATGACCCGCCGTCGTGGGTTCGTCCTGCC





CTGGCAAAGATGGATGGCAAGCGTACTGTCCCCCGTATTTTCAAAG





AACTGGTCAGTGAAGGCGTACAGATCGAATCCGAACATCTGGAAGG





CCTGGTAGCCGGGCTTGCCGAACGCAAACTTCTCCAGGATAACAGT





TTCTTTTCCAAGGTGTTAAGCGGTGAAGAAGTGGAGCGCTATAACC





GCCAGATTCTGCAGTTCAGCCTTATCGATGCGGATAACCAGCACCC





TTTCGTTTACCAAGAGCGGCTGAAACAGTCTAAAGTCGCTATCTTC





GGTATGGGTGGCTGGGGCACGTGGTGTGCATTGCAGCTGGCCATGT





CAGGCATTGGTACACTGCGGCTGATCGACGGCGATGATGTGGAACT





GTCGAACATTAACCGCCAAGTTCTGTATCGCACGGATGATGTAGGT





AAAAACAAAGTTGATGCCGCCAAAGACACTATCCTGGCATACAACG





AAAACGTGCATGTTGAAACCTTCTTTGAATTCGCCAGCCCGGACCG





TGCCCGGCTTGAAGAACTTGTGGGTGATTCTACCTTTATTATCCTG





GCTTGGGCCGCGTTGGGTTACTACCGTAAAGATACGGCAGAGGAAA





TTATCCATTCGATTGCGAAAGATAAAGCGATCCCTGTAATTGAACT





CGGCGGTGATCCTTTGGAAATCTCTGTCGGTCCTATTTACCTGAAT





GATGGCGTACACAGCGGCTTCGACGAGGTGAAAAATTCCGTTAAAG





ATAAATACTACGACAGCAACAGCGATATCCGCAAATTTCAAGAGGC





GCGGTTGAAACACAGCTTCATCGATGGCGATCGTAAAGTGAACGCG





TGGCAATCAGCGCCCAGCCTGAGTATTATGGCTGGTATCGTAACGG





ATCAGGTTGTGAAAACCATTACCGGGTACGACAAGCCACATCTCGT





TGGCAAGAAATTTATCTTGAGTCTGCAAGATTTCCGCAGCCGCGAG





GAGGAGATCTTTAAA






padeK
Codon
ATGACCGAACGTGCCGCAGTGCGTACCGACCATTATAAAGCCTTTG
502



optimized
GGTTTAGAATTGAAAGCGATTTCGTGCTCCCGGAACTTCCGCCCGC





AGGCGAACGCGAACCGCTCGATAATATTACGGTTCGTCGTACCGAC





CTGCAGCCGCTCTGGAATTCTAGTATCCATTTTTACGGAAACTTTG





CCATTCTGGATCACGGACGCACGGTTATGTTTCGAGTTCCGGGTGC





TGCTATCTATGCGGTACAGGATGCTAGCAGCATATTAGTGTCCCCA





TTCGATCAGGCAGAAGAAAACTGGGTACGTCTTTTTATTCTGGGTA





CCTGTATTGGGATCATCCTGCTGCAGCGTAAGATTATGCCGCTGCA





CGGTAGCGCCGTTGCCATTGATGGCAAAGCCTACGCGATTATCGGC





GAATCTGGTGCCGGCAAAAGCACTCTTGCACTGCATCTTGTCAGTA





AGGGTTATCCATTGCTTTCGGATGATGTGATTCCGGTCGTTATGAC





CCAGGGCTCCCCCTGGGTGGTGCCGTCGTACCCGCAACAAAAACTT





TGGGTGGACACTCTGAAGCACATGGGAATGGATAATGCAAACTATA





CGCCGCTGTACGAACGTAAAACGAAGTTCGCGGTGCCCGTGGGCAG





TAATTTCCACGAAGAACCGCTGCCGTTAGCTAGCATTTTCGAGCTT





GTCCCGTGGGATGCGGCAACGCACATTGCCCCGATCCAAGGGATGG





AACGCTTTCGTGTCCTGTTCCACCACACTTATCGGAACTTTCTGGT





TCAGCCGCTGGGTCTTATGGAATGGCATTTTAAAACTCTGAGCTCG





TTCGTTCACCAAATTGGAATGTATCGTCTGCATAGACCTATGGTCG





GATTCAGTACCTTAGATTTAACGTCGCACATTCTGAATATAACGCG





TCAGGGAGAGAACGATCAA






palS
Codon
ATGGGGAATTTGCGTGATTTCTACCAACTGATGAAAGATAACTATG
503



optimized
CGGACTCTAATCTGTTCAAGGATTTGAATCTGATCCACAATATCTC





CAACGACATCCAAATTGGAATTAATTGCGATTTCTCTGAAATGCTG





GGAGAACTGGTAGGTAATTACGATTCCCTGAACTATCCGTCAATCA





CCTGTGGTATTCTGACGTATAATGAAGAACGCTGCATTAAACGTTG





TCTGGAAAGTGTGGTGAACGAATTCGATGAGATTATTGTCTTGGAT





AGTGTATCCGAGGACAATACCGTGAAAATTATCAAGGAGAATTTCA





ACGATGTCAAAGTCTACGTCGAGCCATGGAAGAACGATTTTTCATT





TCACCGCAACAAGATCATTAATCTCGCAACGTGCGACTGGATCTAC





TTTATCGACGCGGATAATTATTATGATTCGAAGAACAAGGGTAAAG





CCATGCGCATCGCTAAGGTTATGGATTTCTTGAAAATCGAAGGCGT





TGTGAGCCCAACGGTCATTGAGCATGACAATAGCATGAGCCGTGAT





ACCCGTAAGATGTTTCGTCTGAAAGATAACATTCTGTTTAGCGGTA





AAGTTCATGAAGAACCGGTGTATGCCAATGGTGAGATCCCCCGGAA





CATCATAGTAGACATCAACGTGTTTCACGACGGCTATAACCCAAAG





ATTATCAACATGATGGAAAAGAACGAGCGCAATATCACCCTGACTA





AAGAGATGATGAAGATCGAACCGAACAATCCGAAATGGCTGTACTT





CTATAGCCGCGAACTCTATCAGACGCAACGTGACATTGCCCTTGTG





CAAAGTGTACTGTTCAAGGCACTGGAACTGTATGAAAACAGTTCAT





ATACGCGTTATTATGTTGACACCATTGCCTTACTGTGCCGAGTGCT





GTTCGAATCTAAAAACTACCAGAAACTTACGGAATGTCTGAACATC





CTGGAGAACAATACGCTTAACTGTTCCGATATCGATTACTATAATT





CAGCGCTGCTGTTCTACAACCTGTTACTGCGCATCAAGAAAATTAG





CTCCACCCTGAAGGAGAACATTGATATGTACGAACGTGACTATCAT





AGCTTTATCAACCCCTCGCATGATCACATTAAGATTCTGATATTAA





ATATGCTCCTGCTGCTCGGCGATTACCAGGATGCCTTTAAGGTTTA





CAAGGAGATCAAGTCCATTGAGATTAAAGATGAGTTTCTGGTGAAC





GTGAACAAATTCAAAGACAATCTTCTGAGCTTCATTGACTCCATTA





ACAAAATT






papB
Codon
ATGGCAAACCTGATCCAGGACCGCGAGGACGAACTGATTCATTTCC
504



optimized
ATCCGTACAAACTGTTCGAGGTGGATTCAAAAACCTTCTTCTATAA





CGTAGTCACCAACGCGATTTTTGAAATTGATAGCCTGATAATCGAC





ATTCTTCACTCAAAAGGTAAAAATGAGGAGCACGTTGTGAAAGATT





TGGCTGAACGCTATGAGCTGTCTCAGGTTCGCGAAGCGATCCAGAA





CATGAAAGAGGCATACATTATAGCAACCGATGCTAACATCTCCGAC





GTAGAGAAGATGGGTATCTTAGATAACTCGCAGCGCGTTTTTAAAC





TGTCTAGCCTGACGCTCTTTATGGTGCAGGAATGCAACCTGCGGTG





TACGTATTGTTACGGCGAAGAAGGAGAATACAACCAGAAAGGTAAA





ATGACGTCCGAAATCGCCCGGAGCGCAGTGGATTTTCTGATTCAAC





AGAGTGGTGAAATCGAACAGTTGAACATCACATTCTTTGGAGGCGA





ACCGCTGCTCAACTTTCCATTAATACAAGAAACCGTGCAGTATGTG





CACGAACAGAGCGAGATCCATAACAAGAAATTTAGCTTTTCCATCA





CCACCAATGGCACGCTCATTACCCCCAAAATCAAAAACTTCTTCTA





TAAACACCACTTTGCAGTCCAGACTTCTATCGATGGTGATGAAAAG





ACGCACAATTTCAATCGCTTCTTCAAAGGAGGCCAGGGCTCTTATG





ATCTGCTGTTAAAGCGGACGGAAGAAATGCGCAATGACCGTAAAAT





TGGTGCACGTGGAACCGTGACCCCTGCCGAGCTGGACCTCTCAAAA





TCATTTGACCACTTAGTTAAACTCGGCTTTCGCAAAATCTACTTAT





CACCCGCTTTATATAGTCTCTCTGACGATCACTACGACACCCTGAG





CAAAGAGATGGTCAAACTTGTTGAACAATTCCGTGAGCTGCTGGAG





CGTGAAGATTACGTCACCGCGAAGAAAATGTCTAATGTTCTGGGTA





TGTTATCGAAGATTCACTCCGGTGGCCCGCGCATTCATTTTTGCGG





TGCCGGCACTAATGCTGCCGCTGTCGATGTCCGCGGCAACCTTTTC





CCGTGTCATCGTTTCGTGGGTGAAGATGAATGTTCAATCGGTAACC





TGTTCGACGAGGACCCGCTGTCAAAACAGTACAACTTTATAGAGAA





TTCTACAGTACGCAACCGTACTACGTGTTCGAAATGCTGGGCGAAG





AATCTGTGCGGCGGTGGTTGTCACCAAGAAAATTTCGCCGAGAATG





GTAATGTGAACCAGCCAGTGGGCAAATTATGCAAAGTGACCAAAAA





CTTCATCAACGCGACCATCAATCTGTACTTGCAACTTACTCAAGAA





CAACGCAGCATTCTGTTCGGC






papoK
Codon
ATGCACGATCGTAGCGCGAATGTTAGCTGGACCAAATACATCGCGT
505



optimized
TTGGTCTGCGCATTGCCAGCGAACTCAACTTACCGGAACTGATATT





GGCGGCTCCCGAAGCCGTTGAGGATGTTGTCATACGCCAGGCAGAT





CTCACGGCCTGGTCTGGCCAACTTGAACAGGCAAATTTTGTCATGT





TGGACGAACGTTTCATGTTTCAGATCCCGGGGACCGCCATTTATGC





GGTACGCGAAGGCAAAGAGATTGAAGTGAGCATCTTCTCTGGGGCC





GACCCGGACACCGTGCGCCTTTTCGTGCTGGGGACGTGCATGGGCG





TGCTCTTGATGCAGCGCCGCATTCTGCCTATCCACGGCTCCGCCGT





CGTTATCGGTGGCCGCGCGTATGCCTTTGTTGGTGAATCAGGCACA





GGTAAATCGACCTTAGCTGCAGCATTTCGGCAGGCCGGTTACCAAA





TGGTTAGCGATGATGTCATTGCCGTCAAAGCGACCGCATCTAGCGC





TATTGTTTACCCTGCGTATCCACAGCAAAAACTGGGTTTAGATTCG





CTGTTGCAGCTTGAAGCGCTCCGTGAGAATAAGCACGCCCGCAAGC





GTAACAACATCCGTTCTCTGACGGATGGCAATAGTGTGATGCCGCA





GTACAGCGATCTGCGCATGCTGGCGGGGGAACTGAATAAATATGCA





GTTCCAGCCGTCGATGAATTCTTTAATGACCCGCTGCCGTTGGGCG





GTGTTTTCGAACTGGTAGCAGACAGTCCGATTCGAGCATTAATGCG





CGAAGGCGAACTCGTCGCTGTGACCGAGCAACCGCTGAACGTTCTG





GAATGTTTACATACTCTTCTGCAACACACGTACCGTCGGGTAATCA





TCCCTCGAATGGGACTGAGCGAGTGGAGCTTCGATACTGCGGCCCG





AATGGCACGCAAGGTCGAGGGCTGGCGACTCCTCCGTGATAGCTCC





GTGTTCACGGCTAGTGAAGTCGTCCAGCGCGTCCTCGACATCATCC





GTAAGGAGGAAAAGAGCTACGGATCACAC






pbtM1
Codon
ATGCTGTCTAGCGCGCTGGAGGTGGATATCGATGAAGCTGCGGTGG
506



optimized
CGGCGGACTTACGCGAATTGGCCGCAGCTCTGGATCGCAGTGGTTA





TGGTGAAATCCTCACCTGTTTTCTGCCTCAGAAGGCACAGGCGCAT





ATCTGGGCTCAGACCGCTGCAAAAATTGATGGGCCGTTGCGTACCC





TGATGGAATTATTCCTTCTGGGTCGGGCGGTTCCCCAGGATGATCT





CCCGCCTCGCATCGCGGCCGTGATTCCCGGTTTAGTTAGCGCAGGT





CTGGTTAAGACTGGACAGGGCGCGGTTTGGCTGCCGAACTTGATTC





TGCTGCGTCCTATGGGCCAGTGGTTATGGTGTCAGCGGCCTCACCC





CTCACCGACCATGTACTTTGGTGACGATAGCCTGGCGCTGGTTCAC





CGGATGGTAACATATCGTGGCGGCCGTGCCCTGGATTTATGTGCAG





GTCCGGGTGTTCAGGCCCTTACCGCAGCCCTCCGCTCAGAGCACGT





TACCGCGGTTGAGATCAATCCGGTCGCGGCAGCCCTTTGCCGCACC





AACATTGCCATGAACGGTCTGTCCGACCGCATGGAGGTTCGCCTGG





GCTCACTGTACGACGTCGTGCGCGGTGAGGTTTTTGATGATATTGT





ATCAAACCCGCCGCTGCTGCCTGTTCCGGAGGATGTGCAATTCGCC





TTTGTGGGAGATGGCGGACGCGATGGTTTCGATATTTCTTGGACGA





TTCTGGATGGCCTGCCTGAACATCTGTCCGACCGTGGTGCGTGTCG





CATCGTTGGTTGTGTTCTGTCCGATGGCTATGTGCCTGTTGTGATG





GAAGGCTTGGGAGAATGGGCCGCTAAACACGATTTCGACGTGCTTC





TTACAGTGACCGCACATGTCGAGGCGCATAAAGATAGTAGTTTTCT





GCGTTCAATGAGCCTGATGAGTTCGGCGATCTCAGGCCGCCCAGCG





GAGGAGCTGCAAGAACGGTACGCAGCTGATTATGCCGAACTGGGCG





GTTCCCACGTTGCGTTCTATGAACTGTGTGCCCGCCGTGGTGGGGG





TTCTGCACGTCTGGCCGACGTGAGCGCTACAAAACGCAGTGCGGAA





GTGTGGTTTGTT






pbtO
Codon
ATGACCCAGTATCCCCTGTCGCGTCCAGAACCGCTGGGCGTGCACC
507



optimized
CAGATTATCGTCGCCTGCGTGAGACTTGCCCGGTTGCACGTGTGGG





TAGCCCGTATGGCCCAGCGTGGCTTGTCACCCGTTACGCCGATGTG





GCCGCAGTTCTGACCGATGCCCGTTTTAGTCGTGCAGCCGCTCCGG





AAGATGATGGTGGCATCCTGCTGAACACCGATCCGCCGGAACATGA





TCGTCTGCGTAAACTGATTGTAGCACACACAGGCACCGCTCGCGTG





GAACGGCTGCGTCCGCGTGCTGAAGAGATCGCTGTTGCGTTAGCGC





GCCGTATCCCGGGCGAAGGCGAATTCATTAGTGCATTTGCCGAGCC





CTTCAGCCATCGCGTTTTGTCTTTATTTGTTGGCCATCTTGTTGGG





TTACCAGCGCAGGACCTGGGCCCCTTAGCGACCGTAGTGACTCTGG





CACCCGTTCCCGACCGCGAACGTGGCGCGGCATTTGCAGAGCTGTG





TCGTCGGCTGGGTCGTCAGGTGGATCGCGAAACGCTTGCAGTAGTT





TTAAACGTGGTCTTTGGCGGACATGCGGCTGTAGTGGCCGCGCTGG





GTTATTGCCTGTTAGCTGCATTAGATGCGCCACTGCCACGTCTGGC





CGGTGACCCAGAGGGCATTGCCGAACTGGTGGAAGAAACCCTTCGT





TTGGCTCCACCGGGAGATCGTACACTGTTGCGTCGTACTACAGAAC





CTGTGGAACTTGGCGGTCGCACATTACCAGCGGGTGCGCTTGTAAT





CCCGTCCATTGCAGCCGCAAACCGTGATCCGGATCGCCCTGTGGGC





CGTCGTATGCCACGTCATCTTGCATTTGGACGTGGAGCGCATGCCT





GTTTAGGCATGGCGCTGGCGCGCATGGAACTCCAGGCAGCACTGAA





AGCGTTAGCGGAACACGCGCCAGACGTACGGTTGCCGGCTGGTACA





GGCGCGCTGGTCCGCACACACGAAGAACTCTCGGTGAGCCCGCTCG





CAGGAATCCCAATTCAACGC






pcpX
Codon
ATGACATACCGTCGCACCTCCTATGCGGTATGGGAGATCACGCTGA
508



optimized
AATGCAATCTGGCATGTTCGCACTGTGGAAGTCGTGCCGGGCACAC





GCGAGCAAAAGAACTGTCCACACAGGAAGCGCTGGATCTGGTCCGT





CAGATGGCTGATGTCGGCATTATCGAAGTTACTCTGATTGGGGGTG





AAGCGTTCCTGCGTCCAGACTGGCTGCAGATTGCCGAGGCGATAAC





GAAAGCCGGGATGCTGTGCAGCATGACTACGGGCGGTTATGGCATA





TCGCTGGAAACCGCCCGCAAAATGAAAGCGGCAGGAATCGCGAGCG





TGAGCGTTAGCATCGATGGCTTGGAGGAAACCCATGATCGCTTACG





CGGTCGCAAAGGCTCTTGGCAGGCTGCGTTTAAAACAATGAGCCAT





TTGAGAGAAGTGGGCATCTTCTTTGGCTGTAACACCCAGATTAACC





GTCTGTCGGCCCCTGAATTTCCGCTGATATATGAACGCATCCGTGA





CGCCGGGGCACGTGCCTGGCAGATCCAGCTTACGGTGCCGATGGGC





CGCGCTGCCGATAACGCAAATATCCTTCTGCAACCGTACGAACTGC





TTGATCTGTATCCGATGATTGCTCGAGTGGCCCGCCGGGCCCGTCA





AGAGGGCGTGCAAATCCAGCCAGGTAATAATATTGGGTATTACGGC





CCTTACGAACGTCTTTTACGTGGCCGGGGGAGCGATAGTGAGTGGG





CATTTTGGCAGGGCTGTGCCGCGGGCTTAAGTACCCTGGGTATTGA





AGCGGATGGTGCTATAAAAGGTTGTCCCTCACTGCCAACGAGCGCG





TATACCGGCGGTAACATTCGCGAACATAGTCTGCGAGAAATAGTGG





AAGAATCGGAACAGCTGCGTTTTAACCTCGGTGCAGGGACGAGCCA





AGGGACCGCCCACTTGTGGGGCTTTTGCCAGACGTGTGAATTTAGT





GAATTGTGCAGAGGTGGTTGTACGTGGACAGCTCACGTGTTCTTTA





ACCGCCGTGGGAATAACCCGTATTGTCATCATCGGGCGCTTTTCCA





AGCGGAGCAGGGTATCAGAGAACGTGTCGTGCCAAAGGTCGAAGCT





CAGGGCCTGCCGTTTGACAACGGTGAATTTGAACTTATCGAAGAAC





CTATTGACGCGCCTCTGCCCGAAAATGATCCACTGCACTTTACCAG





CGACTTAGTGCAGTGGTCAGCGAGTTGGCAGGAAGAATCGGAATCT





ATAGGCGCAGTGGTAGAC






pcpY
Codon
ATGGTGGAAAACATTGATAATGAACGTGAGAAAAGTGCGAACGAAA
509



optimized
TTGAACCGGAAAGCCTGCTTCTGCCGCGCCAGGCTTGGCAGTCGCA





GATCGCCTATCTTAAAGCGATTCTGAAAGCCAAACAGGCGCTTGAC





CGGATCGAAAAACGTTATCTGCGG






plpX
Codon
ATGACCAAAAAGTATCGGCGTGTATCCTACGCAGTGTGGGAAATCA
510



optimized
CCCTGAAATGCAATCTGGCATGCTCTCATTGTGGCAGCCGCGCCGG





CCAAGCCCGTACGAAAGAGCTGAGTACCGAAGAAGCGTTCAACCTG





GTCCGCCAGCTGGCCGACGTGGGCATTAAGGAAGTCACCCTGATCG





GTGGTGAAGCCTTTATGCGTTCGGATTGGCTGGAAATCGCGAAAGC





CGTCACTGAAGCCGGCATGATCTGTGGCATGACCACAGGGGGCTTC





GGGGTCAGTCTGGAAACGGCGCGTAAAATGAAAGAAGCGGGCATTA





AAACGGTGAGCGTTAGCATTGACGGTGGTATTCCTGAAACCCACGA





CCGCCAGCGCGGTAAAAAGGGTGCGTGGCATAGTGCATTCCGGACT





ATGAGCCATCTGAAAGAAGTCGGGATCTACTTCGGTTGCAACACTC





AAATCAATCGTTTATCGGCGTCAGAATTCCCGATTATCTATGAACG





TATTCGCGATGCTGGGGCACGTGCGTGGCAAATTCAGCTGACGGTT





CCGATGGGCAACGCCGCGGATAACGCAGATATGCTGCTGCAACCGT





ATGAATTGCTCGACATCTATCCGATGTTAGCCCGCGTTGCCAAACG





TGCGAAACAGGAAGGCGTGCGTATTCAGGCAGGTAACAACATCGGG





TACTATGGACCGTATGAGCGTCTGCTGCGTGGCAGCGACGAATGGA





CGTTTTGGCAAGGATGTGGTGCGGGCCTTAACACCCTCGGCATCGA





AGCCGACGGCAAAATCAAAGGCTGTCCATCCCTGCCGACCGCCGCG





TACACCGGCGGTAACATTCGCGATCGCCCGCTGCGGGAAATCGTCG





AACAGACCGAAGAACTGAAATTTAACTTAAAAGCTGGTACAGAACA





AGGTACGGACCATATGTGGGGCTTTTGTAAAACCTGCGAATTCGCG





GAACTCTGTCGCGGCGGATGCAGCTGGACTGCGCATGTGTTCTTTG





ACCGGCGCGGCAATAATCCGTACTGCCACCATCGGGCTCTGAAACA





AGCCCAAAAAGACATTCGCGAACGCTTTTATTTAAAAGTGAAAGCA





AAGGGCAACCCGTTCGACAATGGTGAATTTGTTATCATTGAAGAAC





CTTTTAACGCTCCGTTACCCGAGAATGACCTGCTGCACTTTAACAG





TGATCACATTCAATGGCCAGAAAACTGGCAAAATAGTGAAAGCGCG





TACGCATTGGCCAAG






plpY
Codon
ATGAACAGTAATCAGATCCCTAACAAAGTTGCAACCGCGGCACAGA
511



optimized
AATCTGACGACAGCAGCAGCGTATTACCGCGCCAGGGGTGGCAAGA





CAAACAAGCCTTTATTAAGGCACTCATTAAAGCCAAACAGTCTCTC





GAAATTGCCGAAATTAGCAACTTTTTAACC






procM
Codon
ATGGAGAGTCCTAGCTCATGGAAAACATCGTGGCTGGCCGCCATCG
512



optimized
CTCCGGATGAACCCCACAAATTCGACCGCCGCTTAGAATGGGACGA





GCTTTCAGAGGAGAACTTCTTCGCAGCACTGAACTCAGAACCTGCA





TCGTTGGAAGAGGATGATCCATGTTTTGAAGAAGCACTGCAAGACG





CCCTGGAGGCCTTGAAGGCAGCATGGGATTTACCCCTTCTTCCCGT





CGATAATAATCTTAATCGTCCCTTCGTAGATGTCTGGTGGCCCATT





CGCTGTCACTCTGCGGAGAGCTTGCGTCAAAGCTTCGTCAGTGATA





GTGCTGGACTTGCGGACGAGATTTTTGATCAGCTGGCCGATTCGTT





ACTGGACCGTCTGTGCGCCCTGGGAGATCAGGTGTTGTGGGAGGCG





TTTAACAAGGAGCGTACACCAGGAACGATGTTGTTAGCCCACTTAG





GAGCCGCAGGCGACGGCTCCGGACCCCCTGTACGTGAGCATTACGA





ACGTTTTATTCAGTCTCACCGCCGTAATGGATTAGCGCCTTTGCTT





AAGGAATTCCCTGTACTGGGCCGCCTTATTGGAACAGTTTTGTCCC





TTTGGTTCCAAGGGAGCGTGGAAATGCTGCAACGTATCTGCGCTGA





CCGCACCGTTCTGCAACAGTGTTTCGCTATCCCTTGCGGGCATCAC





CTGAAAACTGTAAAGCAGGGACTTTCTGATCCACACCGCGGCGGTC





GCGCTGTGGCAGTTTTGGAATTTGCGGACCCAAATTCCACCGCTAA





TTCAAGTATGCACGTAGTGTATAAACCGAAGGATATGGCTGTGGAT





GCAGCTTACCAGGCCACCTTAGCAGATCTTAATACTCATAGCGACC





TTTCCCCGTTGCGCACGCTTGCCATTCATAACGGCAACGGATATGG





TTACATGGAACATGTGGTTCACCATCTTTGCGCTAACGACAAAGAG





CTGACAAATTTCTATTTCAACGCTGGGCGTTTAACCGCGCTTCTGC





ATCTTCTTGGATGTACTGACTGTCACCATGAAAATTTGATTGCATG





TGGTGATCAATTACTGTTGATCGATACAGAAACATTATTGGAGGCG





GATTTACCCGATCACATTTCGGATGCTTCGAGCACCACGGCGCAAC





CAAAGCCTAGTAGCCTTCAAAAGCAATTTCAGCGTTCTGTTTTGCG





TAGCGGGTTACTTCCTCAATGGATGTTCCTGGGGGAGTCGAAGTTG





GCCATCGACATCTCGGCTCTGGGAATGTCCCCACCCAATAAGCCTG





AGCGTATTGCACTTGGCTGGTTAGGATTCAATTCTGACGGGATGAT





GCCTGGGCGTGTATCCCAACCAGTTGAGATTCCTACATCCTTGCCC





GTTGGGATTGGTGAGGTTAATCCCTTTGATCGTTTTTTAGAGGATT





TTTGTGATGGCTTTTCCATGCAATCAGAGGCCCTTATTAAGCTTCG





CAACCGTTGGCTGGACGTTAATGGGGTTCTTGCTCATTTCGCGGGT





CTGCCCCGCCGTATCGTTCTTCGCGCGACTCGCGTATACTTCACTA





TCCAGCGTCAGCAGTTAGAGCCTACGGCACTGCGCTCTCCACTTGC





ACAGGCCTTGAAACTTGAGCAGCTTACTCGTTCTTTCTTGTTGGCA





GAGTCAAAGCCTCTTCACTGGCCCATTTTCGCAGCTGAAGTAAAGC





AGATGCAGCACCTTGACATTCCTTTCTTCACACACTTAATCGACGC





TGACGCTCTGCAGCTGGGCGGCCTGGAACAAGAATTACCAGGCTTC





ATCCAGACTAGTGGCTTGGCAGCTGCTTACGAGCGTTTGCGTAATT





TAGATACGGACGAGATTGCTTTCCAACTTCGTCTGATCCGCGGTGC





AGTAGAGGCTCGCGAGTTGCATACTACGCCGGAGTCGAGCCCGACG





TTGCCGCCGCCTGCCACCCCCGAGGCTCTTATGTCCTCTTCAGCCG





AGACTAGTTTAGAAGCTGCTAAGCGCATCGCTCACCGCTTACTGGA





GTTGGCAATTCGTGATTCTCAAGGGCAAGTAGAATGGCTGGGCATG





GATCTGGGGGCAGATGGAGAGAGCTTCTCCTTTGGCCCAGTTGGCT





TGAGCCTTTATGGGGGCTCAATCGGTATCGCTCACCTTCTGCAACG





TTTGCAGGCGCAGCAAGTTTCCTTGATGGACGCAGACGCTATCCAA





ACGGCAATTTTACAGCCCCTTGTGGGACTGGTTGATCAACCTAGCG





ACGACGGACGTCGCCGTTGGTGGCGTGATCAGCCGCTGGGCTTAAG





TGGATGTGGCGGTACCTTGCTTGCACTTACACTTCAAGGTGAACAA





GCGATGGCTAATTCCCTGCTGGCCGCTGCTTTGCCCCGTTTTATCG





AGGCTGATCAGCAACTTGACCTGATTGGTGGCTGCGCTGGACTGAT





CGGTTCGTTGGTACAATTAGGTACTGAAAGTGCCTTACAATTAGCT





TTGCGTGCGGGCGACCATCTTATTGCGCAACAGAATGAAGAGGGGG





CGTGGTCTAGCTCGTCATCACAGCCCGGTTTGTTGGGCTTTAGTCA





TGGTACTGCAGGTTACGCAGCAGCCTTAGCACACTTACATGCATTT





TCCGCTGATGAGCGTTACCGCACCGCAGCCGCTGCCGCTTTAGCAT





ACGAACGCGCACGTTTTAATAAAGATGCCGGCAACTGGCCAGACTA





CCGCTCGATCGGACGTGACTCTGATTCAGATGAACCGTCCTTTATG





GCTTCCTGGTGTCACGGCGCACCCGGCATTGCCCTGGGCCGCGCCT





GTTTGTGGGGTACGGCGCTTTGGGACGAAGAATGCACCAAGGAGAT





CGGAATTGGGTTACAGACCACAGCTGCTGTTTCGTCTGTTAGTACT





GACCACCTGTGTTGTGGTTCACTTGGCCTTATGGTATTATTAGAGA





TGCTGTCAGCAGGACCCTGGCCCATCGACAATCAATTACGTTCCCA





TTGCCAGGACGTAGCATTCCAGTACCGCCTGCAGGCTTTGCAGCGC





TGTTCAGCCGAGCCGATTAAGCTTCGTTGCTTCGGTACAAAAGAGG





GCCTTTTAGTCCTGCCTGGATTTTTCACTGGCTTATCAGGAATGGG





TTTAGCACTGCTTGAGGATGATCCATCTCGCGCCGTGGTTTCTCAA





CTGATCAGTGCGGGCTTATGGCCGACAGAG






psnB
Codon
ATGACGAATTTAGACACGAGCATTGTGGTCGTAGGAAGTCCGGATG
513



optimized
ATCTTCACGTCCAGTCAGTGACGGAGGGTCTGCGTGCACGCGGTCA





CGAGCCTTACGTGTTTGACACCCAACGTTTTCCGGAAGAGATGACA





GTGTCACTTGGTGAACAGGGTGCCTCTATTTTTGTCGATGGCCAGC





AAATTGCACGTCCGGCGGCGGTGTACCTCCGTTCACTGTACCAGAG





CCCCGGCGCGTATGGGGTGGATGCCGACAAAGCGATGCAGGATAAC





TGGCGCCGCACATTGCTCGCTTTTCGCGAGCGTAGTACCCTGATGA





GCGCTGTGCTTCTGCGTTGGGAAGAAGCGGGGACTGCAGTGTATAA





TTCGCCACGCGCGTCGGCGAATATCACTAAACCGTTTCAGCTGGCG





CTGCTGCGCGACGCTGGTCTGCCGGTACCACGTAGCTTGTGGACAA





ACGACCCTGAAGCAGTGCGGCGGTTTCATGCGGAAGTGGGTGACTG





TATTTACAAACCGGTCGCCGGGGGAGCGCGTACACGCAAACTGGAA





GCGAAAGATCTCGAAGCGGACCGCATCGAACGCCTGAGTGCAGCGC





CGGTGTGTTTTCAAGAACTGCTCACAGGAGATGATGTGCGTGTTTA





CGTGATAGATGACCAGGTAATATGCGCCCTGCGCATCGTAACTGAT





GAGATCGATTTCCGCCAAGCAGAGGAACGTATCGAGGCCATCGAAA





TTTCAGATGAAGTAAAAGACCAATGTGTACGTGCCGCCAAACTTGT





TGGCCTGCGCTACACCGGTATGGATATCAAAGCCGGCGCCGATGGT





AACTATCGTGTTCTCGAACTGAACGCGAGTGCGATGTTTCGCGGTT





TCGAAGGCCGTGCGAATGTGGATATCTGTGGACCGCTGTGTGATGC





ATTGATCGCTCAGACCAAACGT






raxST
Codon
ATGGATTATCATTTCATCAGCGGACTGCCTCGTGCGGGGAGTTCAT
514



optimized. ST
TACTGGCTGCGTTACTGCGTCAAAATCCGCAGCTGCATGCCGATGT




stands for
TACATCTCCGGTGGCGCGCCTTTACGCGGCCATGCTGATGGGTATG




SulfoTransferase
AGTGAAGAACACCCGAGCAACGTGCAGATTGACGATGCCCAACGTG




and denotes
TCCGTCTGTTACGTGCAGTATTTGATGCGTATTATCAGAACCGTCA




a single gene,
GGAACTGGGGACAGTGTTCGATACTAACCGCGCATGGTGCTCTCGC




not two genes.
CTCACGGGCCTGGCGCGTCTGTTTCCGCGTAGTCGCATGATCTGCT





GTGTACGCGATGTGGGCTGGATTGTTGATTCTTTTGAACGCCTGGC





GCAGTCGCAGCCGTTACGCCTTTCGGCCCTGTTCGGTTACGACCCC





GAGGATTCGGTTAGCATGCACGCTGACTTACTCACTGCGCCTCGCG





GGGTAGTGGGCTACGCCCTGGATGGTTTACGTCAAGCGTTTTATGG





AGATCACGCGGATCGTCTGCTGTTGTTACGTTATGATACGCTGGCA





CAGCGTCCTGCACAAGCCATGGAACAGGTATATGCATTCCTGCAGC





TCCCTGCCTTTGCACATGATTATGCCGGTGTTCAGGCCGAAGCGGA





ACGCTTTGATGCCGCCCTGCAAATGCCTGGTTTGCACCGCGTGCGT





CGTGGTGTTCACTATGTTCCGCGACGTTCGGTTTTACCGCCTGCCC





TGTTTGACCAGCTGCAGGAACTTGCATTCTGGGAAAGTGCACCCAG





CCATGGAGCGCTGCTCGTG






sgbL
Codon
ATGACAAGCCATGCAACCGAGGTTGAATGGGAGGACCTTCTGCGCC
515



optimized
AAGCATTACACGCAACTGGTACAGGTGCTCGTTGGGCTGTAGAGGC





GGACGAGATGTGGTGCCGTGTCGCCCCGGTGCCTGGAACTCGCCGC





GAGCAAGGATGGAAGCTTCATGTAAGCGCGACGACCGCGAGTGCGC





CCGAAGTCTTAACTCGTGCATTAGGCGTACTTCTGCGTGAAAAGTC





CGGGTTCAAATTTGCCCGCTCACTTGAACAAGTCTCGGCCTTGAAT





AGTCGTGCTACGCCCCGTGGTAGTTCGGGTAAATTTATCACAGTAT





ACCCCCGCTCAGACGCCGAAGCCGTCGCACTGGCTCGCGACCTGCA





TGCGGCAACGGCCGGCTTGGCTGGGCCCCGTATTCTTTCCGATCAA





CCATACGCCGCGCACAGCCTGGTGCATTATCGTTATGGGGCTTTCG





TGGGACGTCGTCGCCTTTCAGATGACGGGCTTTTAGTTTGGTTTAT





TGAGGACCCAGATGGCAATCCCGTGGAGGATAAACGCACCGGACGT





TATGCGCCGCCTCCCTGGGCTGTATGTCCGTTTCCTGCGAGCGTCC





CCGTTGCGCCCCATGACGGCGAAGCTACGAGTCGTCCTGTTGTCTT





AGGTGGTCGCTTCGCGGTTCGTGAAGCCATCCGTCAAACGAATAAA





GGGGGCGTCTATCGCGGGTCGGACACACGCACTGGCACCGGCGTGG





TTATCAAAGAGGCGCGCCCACATGTTGAAGGAGACGCCAGTGGGGG





CGATGTTCGTGACTGGCTTCGCGCAGAGGCGCGTACGCTTGAAAAA





TTAAAAGGTACCGGCTTGGCACCAGAAGCGGTGGCGTTGTTTGAGC





ACGCTGGCCACTTGTTCTTAGCCCAAGACGAGGTCCCGGGGGTTAC





GTTACGCACCTGGGTAGCGGAACACTTCCGTGACGTTGGAGGAGAG





CGCTATCGTGCCGACGCCCTGGCTCAGGTGGCTCGTTTAGTTGATT





TAGTCGCGGCTGCTCATGCACGTGGCTTGGTCCTGCGCGATTTTAC





ACCAGGGAACGTGATGGTCCGTCCAGACGGCGAATTGCGCCTTATT





GATTTAGAGCTGGCGGTTCTTGAGGATGAGGCCGCATTGCCTACCC





ACGTCGGTACCCCGGGGTTTTCGGCACCCGAACGCCTTGCAGACGC





TCCAGTGCGTCCTACTGCTGACTACTATTCTCTGGGAGCCACAGCT





TGTTTTGTCTTGGCCGGTAAAGTCCCTAATTTACTTCCTGAAGAAC





CCGTGGGTCGCCCATCGGAGGAGCGTCTTGCTGCCTGGTTGACTGC





ATGTACACGTCCGCTGCGCCTGCCAGATGGAGTCGTTGACATGATC





TTGGGGTTAATGCGCGATGATCCTGCAGAGCGCTGGGACCCATCCC





GCGCGCGTGAAGCACTGCGCAAAGCTGACCCGACAGCACGCCCCGG





GGATGCTGATCGCACTGCAGTACGTCGTACGGGTTCGTCGGCAGTG





GCCGGGCCAGTTCCTGACTCACGTACAGCAGATGGTCGTACAGCGG





ACGGCCGTTCCGCGGATGAAGTTGTGGCAGGTCTTGTCGATCACTT





AGTCGATAGTATGACCCCGGCAGATGATCGTCTGTGGCCGGTAAGC





ACTCTTACGGGAGAATCGGATCCATGTACAGTCCAGCAAGGCGCTG





CTGGGGTGCTTGCGGTGTTGACCCGCTACTTCGAATTGACGGGCGA





TCCGCGCTTACCAGGCTTATTGTCGACAGCCGGACGTTGGATCGCA





GACCGCACGGATGTTCGTTCACCTCGTCCGGGATTACATTTCGGGG





GACGCGGAACAGCCTGGGCCTTATACGACGCGGGGCGTGCAGTCGA





CGATCGTCGCTTGGTGGAACATGCTCTGGACTTAGCATTAGCCCCG





CCCCAAGCGACTCCTCATCACGATGTCACGCATGGGACTGCGGGCT





CAGGCTTAGCCGCCTTGCACCTGTGGCAGCGTACTGGAGATACTCG





TTTCGCGGATTTAGCAGTAGAGGCAGCTGATCGCTTAACAGCTGCA





GCTCGTCGCGAGCCTTCGGGTGTTGGATGGGCAGTACCTGCAGAGG





CCGACTCCCCAGAAGGAGGCAAGCGTTACCTGGGCTTCGCTCATGG





CGCAGCTGGGATTGGGTGCTTCTTATTGGCTGCGGCGGAACTTAGT





CGTCAACCCGATCATCGTGCAACTGCTTTGGAAGTTGGCGAAGGCC





TGGTTGCTGATGCTGTTCGCATCGGAGAGGCGGCACAGTGGCCTGC





GCAATCCGGGGACTTGCCGACAGCGCCTTACTGGTGCCATGGGGCG





GCAGGTATCGGGACATTTCTTGTACGCTTATGGCAGGCGACCGGGG





ACGATCGCTTCGGTGATCTGGCCCGCGGGAGTGCTCACGCTGTGGC





CGAACGTGCTAGTCGCGCCCCATTGGCGCAATGTCACGGTTTGGCT





GGAAACGGAGATTTCTTGTTGGATTTGGCAGACGCGACAGGCGATC





CTGTGCATCGCGACACCGCGGAAGAGTTAGCAGGGTTGATCTTGGC





CGAAGGAACCCGTCGTCAGGGACATGTCGTTTTCCCTAATGAGTAT





GGGGAAGTATCATCTTCATGGTCCGACGGTAGTGCGGGGATTCTTG





CGTTCCTTCTGCGTACGCGTCATACGGGCCCTCGCCATTGGATGGT





AGAACAACGTGGG






stspM
Codon
ATGGCGGATCATATTGCGGCCGGTCATGACACCGTCCTGAGCCTGG
516



optimized
CCGAACGGACAGGTACCGATCCAGATCTGCTGGGCCGTGTGTTGCG





CTTCCTCGCTTGTCGTGGTGTTTTCGCCGAGCCTCGCCCAGGTACT





TATGCCTTGACCCCTCTGAGCTTAACTTTACTGGAAGGCCATCCGT





CCGGTTTAAGAGAATGGTTGGATGCGTCGGGTGCGGGAGCGCGCAT





GGACGCGGCAGTTGGAGATCTGCTTGGCGCCCTCCGCTCGGGTGAA





CCGAGCTATCCACGTCTGCATGGTCGTCCGTTTTATGAAGATCTGG





CGCTGCACAGCCGAGGCCCTGCTTTTGATGGACTGCGTCATACGCA





CGCCGAATCGTATGTTGCCGACCTGCTGGCAGCCTACCCGTGGGAA





CGCGTTCGTCGCGTGGTTGATGTAGGCGGTGGGACCGGCGTATTGG





TCGAGGCGCTTATGAGAACTCATGCGACCCTCCGTACAGTACTGGT





CGATCTTCCAGGCGCGGTGGCTACCGCTACCGCTCGAATTGCGGCT





GCGGGTTTTGGCAATAGATATACACCGGTCACGGGTTCCTTCTTTG





ATCCGCTGCCTGCGGGGGCGGATGTTTACACCCTGGTTAACGTGGT





TCACAACTGGAACGATGAGCGTGCCTCAGCTCTGCTGCGTCGGTGT





GCGGATGCGGGTCGCCGCGACAGTACGTTTGTTATCGTGGAACGCT





TAGCGGACGATGCAGACCCTCGTGCCATCACCGCCATGGACCTCCG





TATGTTCCTTTTTCTGGGCGGTAAAGAGCGCACGGCCGCACAGATT





CGCGAAGTAGCTAGTGCGGCTGGCATGGCCCACCAAAGCACCATTA





AAACACCGTCTGGCCTCCACTTACTTGTTTTCCGTAAGAAACGTTT





CGCTGCTCGCGGTCACGGTCGTCGCATGGTGACC






tgnB
Codon
ATGAAAACCATTCTGATTATTACCAATACCCTGGATCTGACCGTGG
517



optimized
ATTATATTATTAATCGCTATAATCATACCGCTAAATTTTTTCGTCT





GAATACCGATCGTTTTTTTGATTATGATATTAATATTACCAATAGC





GGTACCAGCATTCGTAATCGTAAATCTAATCTGATTATTAATATTC





AGGAAATTCATAGCCTGTATTATCGCAAAATTACCCTGCCGAATCT





GGATGGCTATGAAAGTAAATATTGGACCCTGATGCAGCGCGAAATG





ATGAGTATTGTTGAAGGCATTGCAGAAACCGCTGGCAATTTTGCAC





TGACCCGTCCGTCTGTGCTGCGCAAAGCTGATAATAAAATTGTGCA





GATGAAACTGGCAGAAGAAATTGGTTTTATTCTGCCGCAGAGTCTG





ATTACCAATTCAAATCAGGCGGCAGCCTCATTTTGCAATAAAAATA





ATACCAGCATTGTGAAACCGCTGAGTACCGGCCGCATTCTGGGTAA





AAATAAAATTGGCATTATTCAGACCAATCTGGTTGAAACCCATGAA





AATATTCAGGGCCTGGAACTGTCTCCGGCTTATTTTCAGGATTATA





TTCCGAAAGATACCGAAATTCGTCTGACCATTGTTGGTAATAAACT





GTTTGGCGCCAATATTAAATCAACCAATCAGGTTGATTGGCGCAAA





AATGATGCACTGCTGGAATATAAACCGGCCAATATTCCGGATAAAA





TTGCCAAAATGTGTCTGGAAATGATGGAAAAACTGGAAATTAATTT





TGCGGCGTTTGATTTTATTATTCGTAATGGTGATTATATTTTTCTG





GAACTGAATGCCAATGGTCAGTGGCTGTGGCTGGAAGATATTCTGA





AATTTGATATTTCAAATACCATTATTAATTATCTGCTGGGTGAACC





GATTTAA






thcoK
Codon
ATGACGAGAACCAACACCGGCTATCGTTATCGCGCGTTCGGCCTGC
518



optimized
GCATAGACTCAGATATTCCGCTGCCAGAATTAGGGGACGGTACGCG





CCCTGATGGTGACGCGGATCTGACGGTCGTCCGGTGTGGGGAAGCG





GAGCCGGAATGGGCTGAAGGTGGTGGCGGGGGTCGTCTGTATGCCG





CTGAAGGCATTGTATCTTTTCGCGTGCCGCAGACGGCAGCGTTCCG





TATTACTAATGGAAATCGCATCGAGGTGCATGCCTACTCGGGGGCT





GATGAGGATCGAATACGCCTGTACGTGTTAGGGACCTGTATGGGAG





CGCTGTTACTGCAACGTAGAATCTTACCGCTTCATGGTTCGGTCGT





CGCCCGTGATGGTCGTGCGTATGCCATAGTTGGCGAAAGCGGAGCG





GGCAAATCCACGATGAGTGCAGCACTTCTCGAACGTGGATTCCGCC





TCGTTACGGATGACGTGGCCGCCATCGTGTTCGATGAGCGTGGGAC





CCCACTGGTTATGCCGGCTTATCCACAGCAAAAACTGTGGCAGGAT





TCCCTGGACCGTCTGCAAATTGCGGGCTCGGGCCTTCGTCCGCTGT





TCGAACGCGAAACGAAATACGCTGTACCCGCGGATGGGGCATTCTG





GCCCGAACCGGTTCCATTGGTGCACATTTACGAACTGGTTCATAGC





GATGGTCAAACGCCTGAACTGCAGCCGATTGCCAAATTAGAGCGTT





GCTATACCTTGTATCGCCACACATTTCGTAGAAGCCTGATCGTCCC





CAGCGGCTTAAGCGCCTGGCATTTTGAAACGGCAGTGAAACTTGCG





GAGAAAACGGGGATGTACCGTCTTATGCGCCCGGCCAAAGTTTTCG





CGGCTCGCGAATCTGCTCGGCTGATTGAAACTCACGCCGATGGTGA





AGTGTCACGT






truD
Amplified
ATGCAACCAACCGCCCTCCAAATTAAGCCCCACTTCCACGTTGAGA
519



from Topo-El
TAATTGAGCCGAAGCAAGTGTATCTCCTGGGCGAACAGGGCAACCA





CGCTCTCACCGGGCAGCTCTACTGCCAAATTCTGCCTTTCTTAAAC





GGCGAATACACCCGAGAACAAATTGTGGAAAAGCTCGATGGGCAGG





TCCCGGAGGAATATATCGACTTCGTACTCAGTCGTCTGGTGGAGAA





GGGCTATCTAACTGAGGTGGCTCCAGAACTATCCCTGGAAGTGGCA





GCATTTTGGAGCGAATTGGGAATTGCCCCTTCTGTAGTGGCAGAAG





GGCTAAAGCAGCCAGTGACAGTGACAACGGCGGGCAAGGGCATTAG





GGAAGGGATAGTGGCTAACCTGGCAGCAGCGCTGGAGGAAGCTGGC





ATTCAGGTGTCAGACCCAAGGGACCCAAAGGCCCCAAAGGCAGGGG





ATTCTACTGCCCAGCTTCAGGTGGTGCTGACCGATGACTATTTACA





GCCGGAACTTGCAGCGATCAACAAGGAAGCCTTAGAGCGCCAACAA





CCCTGGTTGCTGGTTAAGCCTGTGGGCAGTATCCTCTGGTTGGGAC





CGTTGTTCGTTCCTGGGGAAACCGGATGTTGGCACTGTCTTGCTCA





ACGATTGCAAGGCAACCGGGAAGTTGAAGCATCGGTATTGCAACAA





AAGCGAGCGCTGCAGGAGCGCAACGGTCAAAATAAAAATGGTGCAG





TGAGTTGCTTGCCCACAGCACGGGCAACCCTACCTTCTACTCTACA





AACAGGTTTACAGTGGGCTGCCACTGAGATTGCTAAGTGGATGGTC





AAGCGGCACCTCAATGCCATAGCACCGGGAACGGCTCGTTTTCCCA





CTCTAGCTGGCAAGATATTTACATTCAACCAGACGACTCTGGAGTT





GAAAGCTCATCCTCTGAGCCGACGACCGCAATGTCCCACCTGTGGC





GATCGGGAAACTCTCCAACGGCGCGGGTTTGAACCACTGAAGCTAG





AGTCGCGCCCCAAACACTTCACCTCCGATGGCGGTCATCGCGCCAT





GACCCCAGAACAAACGGTGCAGAAGTACCAACACCTCATCGGGCCC





ATAACGGGGGTAGTGACGGAACTGGTGCGAATTTCTGACCCTGCCA





ATCCCTTGGTGCATACCTACCGGGCTGGGCATAGCTTTGGCAGTGC





TACGTCTCTGCGGGGGCTGCGCAATGTCCTACGCCACAAGAGTTCT





GGTAAAGGCAAGACCGATAGCCAATCTCGGGCCAGCGGACTTTGCG





AGGCGATCGAGCGCTATTCGGGCATTTTTCAGGGAGACGAACCCCG





CAAGCGGGCAACTTTGGCTGAGTTGGGAGATTTGGCGATTCATCCA





GAACAGTGTTTGCACTTTAGCGACAGGCAGTATGACAACCGGGAAA





GCTCGAACGAGCGAGCAACAGTGACTCACGACTGGATTCCCCAACG





GTTCGATGCAAGTAAGGCTCACGACTGGACTCCCGTGTGGTCCCTA





ACGGAGCAAACCCATAAGTATCTGCCTACAGCCCTGTGCTATTACC





GATACCCCTTCCCCCCAGAACACCGTTTCTGCCGTAGTGACTCCAA





CGGAAACGCGGCGGGAAATACCCTGGAAGAGGCGATTTTGCAAGGA





TTTATGGAACTGGTGGAACGGGATAGCGTGTGCCTGTGGTGGTACA





ATCGCGTTAGCCGTCCGGCTGTGGATTTGAGTAGCTTTGACGAGCC





TTATTTTTTGCAGTTGCAGCAGTTCTATCAAACTCAAAATCGCGAT





CTGTGGGTACTGGATTTAACAGCAGATTTGGGCATTCCGGCTTTTG





TAGGGGTATCGAATCGGAAAGCCGGCAGCTCGGAAAGAATAATTCT





CGGCTTTGGAGCGCACCTGGACCCGACAGTTGCCATCCTTCGCGCT





CTTACGGAGGTCAACCAAATAGGCTTGGAATTGGATAAAGTTTCTG





ATGAGAGCCTCAAGAACGATGCCACGGATTGGTTAGTGAATGCTAC





ATTGGCAGCTAGTCCCTATCTCGTTGCCGATGCTAGCCAACCCCTC





AAGACTGCGAAGGATTATCCCCGGCGTTGGAGTGACGATATTTACA





CCGATGTGATGACTTGTGTAGAAATAGCCAAGCAAGCAGGTCTAGA





GACTTTGGTACTGGATCAGACCAGACCCGACATAGGTTTAAATGTG





GTTAAAGTCATTGTGCCAGGAATGCGTTTTTGGTCGCGATTTGGCT





CCGGTCGGCTCTATGACGTGCCAGTGAAGTTGGGATGGCGAGAGCA





ACCACTTGCTGAGGCACAAATGAACCCTACACCGATGCCATTT










Precursor peptides













SEQ


Name
Details
Sequence
ID NO:





albsA
Codon
ATGGATTCACTGCTGTCAACAGAAACCGTCATTAGTGATGACGAAC
520



optimized
TGCTTCCGATTGAAGTTGGTGGTACCGCGGAATTGACAGAGGGGCA





GGGCGGCGGTCAGTCCGAGGATAAACGTCGCGCTTATAACTGC



amdnA
Codon
ATGCCGGAAAATCGGCAGGAAGATCTCAACGCTCAGGCTGTACCAT
521






optimized
TCTTCGCGCGTTTCTTGGAGGGTCAAAACTGCGAGGACCTTACTGA





TGAGGAATCGGAGGCGGTTAGCGGTGGAAAACGCGGCCAAACCCGT





AAATATCCAAGCGACTGCGAAGATGGGAATGGCGTGACCGGTAAAC





TGCGCGATGAAGATATTGCAGTGACCTTGAAGTACCCATCCGACAA





TGAAGATAATGGCGGCGGTGAAATTGTGACTCTGAAGTTTCCAAGT





GATGATGATGATCAACCAGTAGGC






atxA1
Codon
CCGATCATTAGCGAAACGGTCCAGCCTAAAACGGCTGGCCTGATTG
522



optimized
TTCTGGGCAAGGCAAGCGCGGAAACGCGCGGATTGAGCCAAGGCGT





GGAACCGGACATTGGTCAGACGTACTTCGAAGAAAGCCGTATTAAT





CAGGAT






bamA
Codon
CTGAAAATCCGCAAGGTGAAAATTGTCAGAGCGCAGAACGGCCACT
523



optimized
ACACGAAC






bmbC
Codon
ATGGGTCCGGTTGTTGTGTTCGATTGCATGACGGCCGACTTTCTGA
524



optimized
ACGACGATCCAAATAACGCGGAGTTGTCTGCCTTGGAAATGGAGGA





GCTCGAGTCCTGGGGCGCCTGGGACGGAGAGGCTACCAGC






bsjA2
Codon
ATGACCAATGAAGAGATCATTGTCGCGTGGAAAAACCCTAAAGTCC
525



optimized
GTGGCAAAAATATGCCAAGTCACCCGAGCGGCGTGGGATTCCAAGA





GCTTTCCATCAACGAGATGGCCCAAGTGACCGGCGGAGCAGTAGAA





CAGCGTGCAACACCAACCCTGGCAACCCCGCTGACCCCGCATACCC





CGTACGCAACCTATGTGGTTAGCGGAGGCGTGGTTAGCGCGATTTC





TGGTATCTTCAGCAACAATAAAACGTGTCTGGGC






bsjA3
Codon
ATGACCAATGAGGAAATTATCGTTGCGTGGAAAAACCCGAAGGTGC
526



optimized
GCGGCAAAAACATGCCTTCCCATCCGTCCGGTGTGGGCTTCCAGGA





ATTATCTATTAATGAAATGGCACAGGTGACTGGTGGCGCGGTTGAA





CAGCGCGCGACGCCGGCAACCCCAGCAACACCATGGCTGATTAAAG





CGTCTTATGTGGTGAGTGGGGCGGGAGTTTCTTTTGTCGCAAGCTA





TATCACTGTAAAC






capA
Codon
ATGGTGCGTTTCCTGGCTAAGCTGCTGCGTTCAACGATCCATGGCT
527



optimized
CTAATGGCGTGAGCCTCGACGCCGTCAGTTCCACGCATGGTACTCC





GGGGTTTCAGACACCTGATGCACGTGTTATTTCACGCTTTGGCTTT





AAT






cinA
Codon
ATGACGGCGAGTATTCTTCAGTCTGTCGTTGATGCGGACTTTCGTG
528



optimized
CGGCCCTGATTGAAAACCCAGCCGCATTCGGCGCGAGCACCGCAGT





TTTGCCGACCCCAGTCGAACAGCAGGATCAGGCATCACTGGATTTT





TGGACAAAAGATATTGCTGCCACTGAGGCGTTTGCTTGCAAACAGT





CTTGCTCATTTGGGCCGTTCACCTTTGTGTGCGACGGGAATACCAA





A






cln1A1
Codon
ACTCCCATTCAATCCAAATTCTGCCTCCTGCGCGTGGGCAGTGCCA
529



optimized
AACGGCTGACGCAGTCATTCGACGTGGGAACTATTAAGGAAGGTTT





AGTCAGCCAGTATTATTTTGCG






cln1A2
Codon
ACCCAGGTGAGCCCATCACCGCTGCGCCTGATTCGCGTCGGGAGAG
530



optimized
CCTTGGACCTGACCCGCTCTATCGGGGATAGTGGGCTGCGTGAGTC





CATGTCAAGCCAGACGTACTGGCCC






cln2A1
Codon
AACACTTTAAAAACGCGTCTTATTCGCTTTGGGTCGGCTAAACGTC
531



optimized
TGACGCGCGCAGGTACGGGCGTGCTGTTACCTGAAACCAACCAGAT





TAAGCGCTACGATCCAGCA






cln2A2
Codon
ACCACACCCAAATTTCGACTGATTCGGTTAGGTTCAGCTAAGCGAT
532



optimized
TGACCCGGTCGGGAATCGGGGATGTGTTTCCGGAGCCAAACATGGT





TCGCCGCTGGGAT






cln3A1
Codon
CAGCGTATAATAGATGAAACCACCGATGGTCTGATTGAACTGGGGG
533



optimized
CGGCCAGCGTACAGACACAGGGCGATGTTTTGTTTGCTCCGGAGCC





TGGCGTGGGCCGACCTCCAATGGGCCTTTCCGAAGAT






cln3A2
Codon
GAACGCATTGAAGATCATATTGATGATGAACTGATTGACCTGGGAG
534



optimized
CTGCTTCGGTTGAAACCCAGGGAGATGTGCTGAATGCACCGGAGCC





TGGTATCGGTCGTGAACCGACAGGCTTGAGCCGCGAT






cln3A3
Codon
GAATTTGAAGGTATCCCATCACCGGATGCGCGTATTGATTTGGGTC
535



optimized
TGGCGTCGGAAGAAACCTGTGGTCAGATTTATGATCACCCGGAAGT





AGGCATCGGTGCGTACGGGTGCGAGGGCCTGCAGCGT






comX
Codon
CAAGATCTGATTAATTACTTCCTGAATTATCCTGAGGCTCTGAAGA
536



optimized
AACTCAAGAATAAGGAAGCCTGCTTAATTGGGTTTGACGTCCAGGA





AACCGAAACGATTATCAAAGCCTATAACGATTACTACCGCGCTGAT





CCGATCACGCGTCAATGGGGTGAT






crnA1
Codon
ATGTCCGAACTGAGTATGGAGAAAGTGGTCGGCGAAACATTTGAGG
537



optimized
ATCTGAGCATCGCGGAAATGACGATGGTGCAGGGCAGCGGCGACAT





TAACGGCGAATTTACTACCTCGCCGGCATGTGTTTATTCCGTTATG





GTTGTATCGAAAGCAAGCAGCGCTAAATGTGCGGCCGGTGCATCGG





CAGTCTCGGGAGCCATTCTGAGTGCGATTCGTTGC






crnA2
Codon
ATGAGCGAATCCAACATGAAGAAGGTTGTTGGCGAAACCTTCGAAG
538



optimized
ATCTGAGCATCGCAGAAATGACGAAAGTTCAGGGCTCAGGGGACGT





GATGCCGGAATCTACCCCAATTTGTGCCGGCTTCGCAACCTTGATG





AGTTCTATCGGTCTTGTTAAAACCATCAAAGGCAATGTCAAAAGTT





TCTCCGTCTTAATT






csegA1
Codon
ACCAAGAAAAACGCAACACAGGCCCCACGTTTAGTACGTGTAGGCG
539



optimized
ATGCTCATCGTTTGACCCAAGGTGCTTTCGTTGGACAGCCGGAAGC





CGTAAATCCACTTGGACGTGAAATTCAAGGA






csegA2
Codon
ACCAAAACACACAGACTGATCAGATTGGGCGACGCGCAACGCTTGA
540



optimized
CCCAGGGCACATTGACTCCGGGCTTACCGGAGGACTTTCTGCCGGG





CCATTACATGCCGGGG






csegA3
Codon
ACTTCACGTTTCCAACTCCTGCGCCTGGGAAAAGCCGATCGTTTGA
541



optimized
CGCGTGGCGCGCTGGTCGGGCTCCTGATCGAAGATATTACTGTCGC





TCGCTACGACCCTATG






epiA
Codon
GAAGCAGTTAAAGAGAAGAACGATCTGTTCAACCTGGATGTTAAAG
542



optimized
TCAACGCAAAAGAAAGTAACGATAGTGGCGCAGAACCACGCATAGC





GTCGAAATTTATTTGCACACCAGGCTGCGCGAAAACGGGTTCGTTT





AACAGCTATTGTTGT






halA1
Codon
ACGAACTTGCTGAAAGAATGGAAAATGCCCCTGGAACGTACGCATA
543



optimized
ATAACTCCAACCCGGCGGGAGACATTTTTCAGGAACTGGAAGATCA





AGACATACTCGCCGGTGTGAATGGAGCAGAAAACTTATACTTTCAG





GGTTGTGCGTGGTATAACATTAGCTGCCGTCTGGGCAACAAAGGAG





CCTACTGCACCCTTACAGTTGAGTGCATGCCCTCCTGTAAC






halA2
Codon
GTGAATTCCAAAGACCTGAGAAATCCAGAATTTCGCAAAGCTCAGG
544



optimized
GTCTGCAGTTTGTAGATGAAGTTAATGAGAAGGAACTCTCGAGTTT





AGCCGGCAGCGAGAATCTTTACTTTCAAGGCACGACGTGGCCATGT





GCGACCGTCGGCGTTTCAGTTGCCTTGTGCCCGACGACCAAATGCA





CTTCACAGTGC






kgpE
Codon
AAGAACCCGACGCTGTTGCCCAAACTGACCGCGCCGGTCGAACGTC
545



optimized
CGGCCGTAACTTCGTCGGATTTAAAGCAAGCCTCAAGCGTCGATGC





TGCATGGTTAAATGGCGATAATAACTGGTCAACCCCATTCGCCGGT





GTGAACGCGGCATGGTTAAATGGGGACAACAACTGGTCCACGCCTT





TTGCGGGCGTGAATGCTGCATGGCTTAATGGCGACAATAACTGGAG





CACTCCATTTGCCGCCGATGGCGCTGAG






lasA
Codon
ATGGACAAACGTGTGCGTTACGAAAAACCGAGCCTGGTGAAAGAGG
546



optimized
GTACGTTTCGCAAAACTACCGCTGGCCTGCGGCGTCTGTTCGCTGA





CCAGCTGGTTGGCCGCCGTAACATT






lcnA
Codon
ACTAAAGGCCTGGACAAAATGCTTTTAACCAAAAAGAAGAAGGATA
547



optimized
GTATGGGTCTGCTGAACGAAATCGACGTTACCACCCTGGATGAACA





GTTAGGCGGTAAAATGAGCAAAGCATGGTGCCGATCCATGGTGGTG





TCCTGCGTGTATAACCTGGTTGATTTTTCGTCGTCGAGTGACGGGA





AAAAGACATGTGCTCTGTACCGCAAATATTGT






ltnA1
Codon
ATGAATAAAAACGAAATCGAAACCCAGCCAGTTACGTGGCTGGAGG
548



optimized
AAGTTTCTGATCAGAATTTTGATGAGGATGTCTTTGGTGCGTGTAG





CACAAACACCTTCTCGCTGAGCGATTACTGGGGTAACAACGGTGCT





TGGTGTACACTCACGCACGAATGTATGGCATGGTGCAAG






ltnA2
Codon
ATGAAGGAAAAGAATATGAAGAAAAACGACACCATCGAACTTCAGC
549



optimized
TTGGAAAATACCTGGAAGATGATATGATCGAACTGGCTGAAGGGGA





TGAGTCCCATGGGGGTACTACCCCGGCTACCCCTGCGATTTCTATC





CTCAGCGCGTATATCAGCACCAATACCTGCCCGACAACTAAGTGTA





CACGCGCGTGC






mcbA
Synthesized,
ATGGAATTAAAAGCGAGTGAATTTGGTGTAGTTTTGTCCGTTGATG
550



sequence from
CTCTTAAATTATCACGCCAGTCTCCATTAGGTGTTGGCATTGGTGG




genome
TGGTGGCGGCGGCGGCGGCGGCGGCGGTAGCTGCGGTGGTCAAGGT





GGCGGTTGTGGTGGTTGCAGCAACGGTTGTAGTGGTGGAAACGGTG





GCAGCGGCGGAAGTGGTTCACATATC






mdnA
Amplified
ATGGCATATCCCAACGATCAACAAGGTAAAGCACTTCCTTTCTTTG
551



from
CTCGTTTCTTGTCCGTAAGCAAAGAGGAATCTTCCATCAAGTCTCC




pARW071
TTCCCCTGAGCCTACCTACGGGGGCACCTTTAAATACCCTTCTGAC





TGGGAAGATTAT






mdnA*
Amplified
ATGGCACTTCCTTTCTTTGCTCGTTTCTTGTCCGTAAGCAAAGAGG
552



from mdnA
AATCTTCCATCAAGTCTCCTTCCCCTGAGCCTACCTACGGGGGCAC





CTTTAAATACCCTTCTGACTGGGAAGATTAT






mibA
Codon
ATGCCAGCCGATATTCTGGAGACTCGTACCAGCGAAACGGAGGACT
553



optimized
TACTGGATCTTGACCTGAGCATCGGTGTAGAAGAAATCACCGCAGG





CCCGGCAGTGACTTCTTGGTCACTGTGCACCCCTGGATGCACGAGT





CCGGGCGGTGGCTCCAATTGTTCGTTCTGTTGC






paaP
Codon
ATGATTAAATTTTCTACATTGTCTCAGCGCATCAGCGCCATCACGG
554



optimized
AAGAAAACGCCATGTACACTAAGGGTCAAGTGATCGTATTGAGC






padeA
Codon
AAAAAGCAATATAGCAAACCTAGCCTGGAGGTTCTGGACGTCCACC
555



optimized
AGACCATGGCTGGCCCGGGCACTAGTACGCCAGACGCGTTTCAGCC





AGATCCAGATGAAGATGTTCACTATGATTCG






palA
Codon
AAAGATCTTCTGAAGGAACTGATGTATGAAGTAGACCTCGAAGAGA
556



optimized
TGGAGAATCTTCAGGGTAGCGGGTACTCAGCCGCCCAGTGTGCCTG





GATGGCGCTGAGCTGCGTCAATTACATCCCGGGAGTGGGATTCGGT





TGTGGCGGCTACAGCGCATGTGAACTCTACAAGCGTTATTGT






papA
Codon
ATGTTGAAACAGATCAATGTGATTGCTGGCGTAAAAGAGCCTATTC
557



optimized
GCGCCTATGGTTGTTCGGCTAATGACGCATGCTATTTTTGCGACAC





GCGTGACAACTGCAAAGCCTGTGATGCCAGTGATTTTTGTATCAAA





AGTGATACG






papA_tev
Codon
TTGAAACAGATCAATGTGATTGCTGGCGTAAAAGAGCCTATTCGCG
558



optimized
CCTATGAGAACTTGTATTTCCAGGGTTGTTCGGCTAATGACGCATG





CTATTTTTGCGACACGCGTGACAACTGCAAAGCCTGTGATGCCAGT





GATTTTTGTATCAAAAGTGATACG






papoA
Codon
AGCAAGAAAGAATGGCAAGAGCCCACGATCGAAGTGCTCGATATTA
559



optimized
ATCAGACTATGGCGGGTAAGGGCTGGAAACAGATAGACTGGGTGAG





CGACCATGATGCTGACTTACACAATCCGTCT






pbtA
Codon
ATGAACCTGAACGATTTACCTATGGACGTCTTTGAAATGGCAGACA
560



optimized
GCGGTATGGAGGTGGAAAGCCTCACGGCTGGCCATGGCATGCCAGA





AGTTGGAGCTAGTTGCAACTGTGTGTGCGGGTTTTGCTGCAGCTGC





AGTCCGAGCGCG






pcpA
Codon
ATGTCGAGTAATATCCTCGAAAAAGTTAAGGAGTTTTTCGTCCGGC
561



optimized
TGGTGAAGGATGATGCGTTTCAAAGCCAGCTGCAGAACAACAGTAT





TGATGAAGTTCGAAATATCCTGCAGGAGGCCGGGTACATATTCAGC





AAAGAAGAATTCGAAACCGCAACCATTGAATTGCTGGATTTGAAGG





AACGCGATGAATTCCACGAGCTGACAGAAGAGGAGCTTGTCACCGC





TGTTGGCGGTGTTACGGGCGGGAGTGGTATATATGGCCCGATTCAA





GCTATGTACGGTGCCGTCGTAGGTGATCCAAAACCGGGTAAGGACT





GGGGGTGGCGCTTTCCGAGCCCGCTGCCAAAACCGAGTCCGATTCC





GAGTCCGTGGAAACCCCCGGTTGATGTCCAGCCTATGTATGGTGTG





GTAGTGTCAAACGATAGT






pgm2
Codon
ATGGAGCGCGAAATCGTGTGGACAGAAATTGAGGAGTCGGATTTAG
562



optimized
CCGCCGTCGTGTCGGCATCTAATGTCAAGGATGGTCCAACCGTTAG





CTCAAGTAATGTAAAGGACCGC






plpA1
Codon
ATGAGCATTGAGAATGCCAAGAGCTTTTATGAACGCGTCAGTACAG
563



optimized
ATAAGCAGTTCCGCACTCAACTGGAAAATACGGCCAGTGCTGAAGA





ACGGCAGAAAATCATTCAGGCAGCGGGCTTTGAGTTCACCAATCAG





GAGTGGGAAATTGCAAAAGAACAGATTCTTGCGACAAGTGAAAGTA





ATAACGGTGAACTGTCCGAGGCCGAACTGACCGCCGTCAGCGGTGG





GGTTGACTTAAGCATTTTCGAGCTGCTGGACGAAGAACCTTTATTC





CCGATTCGTCCTTTGTACGGCCTGCCTATT






plpA2
Codon
ATGTCTATTGAGAGTGCAAAGGCTTTCTACCAGCGTATGACGGATG
564



optimized
ACGCATCTTTTCGTACCCCTTTTGAAGCGGAACTGTCGAAAGAGGA





GCGCCAACAATTAATCAAAGATAGCGGATATGACTTTACTGCAGAA





GAATGGCAACAGGCTATGACCGAGATCCAGGCGGCACGCTCAAACG





AGGAACTGAATGAGGAAGAACTCGAGGCAATTGCCGGGGGCGCTGT





GGCCGCAATGTATGGTGTGGTTTTCCCATGGGACAACGAGTTCCCG





TGGCCCCGCTGGGGCGGT






pqqA
Amplified
ATGTGGAAGAAACCTGCTTTTATCGATTTACGTCTCGGTCTGGAAG
565



from genome
TGACGCTGTACATTTCTAACCGT






procA*
Codon
ATGTCAGAAGAACAACTCAAGGCATTCATTGCCAAGGTTCAAGCAG
566



optimized
ACACTTCACTGCAGGAACAGCTCAAAGTAGAAGGTGCTGATGTTGT





TGCTATTGCTAAAGCCTCAGGGTTCGCGATTACCACAGAGGACCTC





AATTCGCATCGCCAAAATCTGTCTGATGATGAGCTGGAGGGAGTCG





CGGGAGGCTTTTTCTGCGTACAGGGTACGGCCAACCGTTTCACTAT





CAACGTTTGC






procA1.7
Codon
ATGTCAGAAGAACAACTCAAGGCATTCATTGCCAAGGTTCAAGCAG
567



optimized
ACACTTCACTGCAGGAACAGCTCAAAGTAGAAGGTGCTGATGTTGT





TGCTATTGCTAAAGCCTCAGGGTTCGCGATTACCACAGAGGACTTA





AAAGCACATCAAGCCAACTCACAAAAGAACCTGTCTGATGCTGAGC





TGGAAGGTGTGGCTGGGCGAACCATTGGGGGAACCATTGTGTCGAT





AACCTGTGAGACTTGCGATCTGCTTGTGGGGAAAATGTGC






psnA2
Codon
ATGAGCAAAAATGAGAACAACAAGAAACAGCTGCGCGATCTTTTCA
568



optimized
TTGAAGATCTGGGCAAAGTTACTGGCGGTAAAGGTGGCCCGTATAC





CACCTTAGCCATTGGCGAAGAAGATCCGATTACCACTTTGGCTATC





GGAGAAGAGGACCCTGATCCAACGACACTTGCCTTAGGTGAAGAGG





ACCCAACTACGCTTGCAATCGGCGAAGAA






psnA2_tev
Codon
ATGAGCAAAAATGAGAACAACAAGAAACAGCTGCGCGATCTTTTCA
569



optimized
TTGAAGATCTGGGCAAAGTTACTGGCGAGAACTTGTATTTCCAGGG





TAAAGGTGGCCCGTATACCACCTTAGCCATTGGCGAAGAAGATCCG





ATTACCACTTTGGCTATCGGAGAAGAGGACCCTGATCCAACGACAC





TTGCCTTAGGTGAAGAGGACCCAACTACGCTTGCAATCGGCGAAGA





A






raxX
Codon
AACCACTCTAAGAAAAGTCCGGCAAAAGGGGCAGCGTCCCTGCAGC
570



optimized
GTCCTGCTGGGGCAAAAGGCCGCCCTGAACCTCTGGATCAACGCTT





GTGGAAACACGTCGGTGGTGGTGACTACCCACCCCCAGGAGCCAAC





CCAAAGCATGATCCACCACCCCGCAATCCGGGCCACCAT






sboA
Amplified
ATGAAAAAAGCTGTCATTGTAGAAAACAAAGGTTGTGCAACATGCT
571



from genome
CGATCGGAGCCGCTTGTCTAGTGGACGGTCCTATCCCTGATTTTGA





AATTGCCGGTGCAACAGGTCTATTCGGTCTATGGGGA






sgbA
Codon
TCTGGTCGCGGGCGCGATCCTGATGCTGCTGTACCTCCCTTGCCTC
572



optimized
GTGTACCTCGCACTACTAATCATGAGCCACGTACGGCGTCCCGAGA





ACCAAGAGCAGCTCCAAGAACTGGACCTACACGTCCGCCTTCGTCG





CGTCCATCTCCGTGTGGTCACTCTCCTCAAACCCCTGGTGCAGGAC





GCAGTGGATGTCGTGTGGAGCGTCAAAAATCGGCTGCGGCTTCGTC





TGAGAAGGAAAAGACAATGGAGAACCAAGATTTGGAGTTATTAGCA





CGCCTGCATGCACTTCCTGAGACTGAACCGGTGGGCGTCGACGGAT





TACCCTATGGCGAGACTTGTGAGTGCGTCGGGTTACTTACGTTGTT





GAACACCGTATGTATCGGCATTTCATGCGCT






strA
Codon
ATGAGTAAGGAATTAGAAAAAGTTCTTGAATCCAGTTCAATGGCAA
573



optimized
AGGGGGACGGCTGGAAGGTTATGGCTAAAGGTGACGGTTGGGAG






stspA
Codon
AAGAAATTCTATGAAGCGCCAGCTCTCATCGAACGTGGCGCCTTTG
574



optimized
CGGCTGCTACAGCGGGGTTTGGACGTCTGCTGGCGGATCAGCTGGT





GGGACGCCTGATTCCG






tbtA
Codon
ATGGACCTGAATGATCTGCCGATGGATGTTTTTGAACTGGCAGATA
575



optimized
GCGGTGTTGCAGTTGAAAGCCTGACCGCAGGTCATGGTATGACCGA





AGTTGGTGCAAGCTGTAATTGCTTTTGTTATATTTGTTGTAGCTGC





AGCAGCGCC






tfxA
Amplified
ATGGATAACAAGGTTGCGAAGAATGTCGAAGTGAAGAAGGGCTCCA
576



from genome
TCAAGGCGACCTTCAAGGCTGCTGTTCTGAAGTCGAAGACGAAGGT





CGACATCGGAGGTAGCCGTCAGGGCTGCGTCGCT






tgnA*
Codon
TATCGACCTTATATTGCCAAGTATGTCGAAGAACAAACTCTGCAGA
577



optimized
ATTCAACCAACCTGGTATATGACGACATCACGCAGATCTCTTTTAT





CAATAAAGAAAAGAACGTGAAAAAAATTAATCTGGGTCCCGATACT





ACGATCGTGACTGAAACCATCGAGAATGCGGACCCCGATGAGTATT





TCTTA






thcoA
Codon
CGCAAGAAAGAATGGCAGACACCAGAACTGGAAGTACTCGATGTAC
578



optimized
GCCTCACCGCAGCGGGCCCGGGTAAAGCTAAACCGGATGCTGTGCA





GCCAGACGAAGATGAAATAGTGCACTACTCA






truE*
Codon
ATGAACAAGAAGAACATTTTACCGCAGTTAGGACAACCAGTCATCC
579



optimized
GCCTTACTGCCGGTCAACTGTCAAGCCAACTGGCGGAGCTTTCTGA





GGAGGCTCTGGGAGGGGTCGATGCCTCGTACGCGGTGTTCTGGCCG





ATCTGTAGCTATGACGAC






truE
Codon
ATGAACAAGAAGAACATTTTACCGCAGTTAGGACAACCAGTCATCC
580



optimized
GCCTTACTGCCGGTCAACTGTCAAGCCAACTGGCGGAGCTTTCTGA





GGAGGCTCTGGGAGTCGATGCCTCGACCTTGCCGGTTCCGACGTTG





TGTAGCTATGACGGGGTGGACGCTAGCACAGTCCCTACACTTTGTA





GTTACGATGAC






truE_TEV
Codon
AACAAGAAGAACATTTTACCGCAGTTAGGACAACCAGTCATCCGCC
581



optimized
TTACTGCCGGTCAACTGTCAAGCCAACTGGCGGAGCTTTCTGAGGA





GGCTCTGGGAGAGAACTTGTATTTCCAGGGTGTCGATGCCTCGACC





TTGCCGGTTCCGACGTTGTGTAGCTATGACGGGGTGGACGCTAGCA





CAGTCCCTACACTTTGTAGTTACGATGAC










Plasmid origins













SEQ


Name
Details
Sequence
ID NO:





pSC101
var2 -
AGTAAGACGGGTAAGCCTGTTGATGATACCGCTGCCTTACTGGGTG
582



maintains at
CATTAGCCAGTCTGAATGACCTGTCACGGGATAATCCGAAGTGGTC




p15A-level
AGACTGGAAAATCAGAGGGCAGGAACTGCTGAACAGCAAAAAGTCA




copy number
GATAGCACCACATAGCAGACCCGCCATAAAACGCCCTGAGAAGCCC





GTGACGGGCTTTTCTTGTATTATGGGTAGTTTCCTTGCATGAATCC





ATAAAAGGCGCCTGTAGTGCCATTTACCCCCATTCACTGCCAGAGC





CGTGAGCGCAGCGAACTGAATGTCACGAAAAAGACAGCGACTCAGG





TGCCTGATGGTCGGAGACAAAAGGAATATTCAGCGATTTGCCCGAG





CTTGCGAGGGTGCTACTTAAGCCTTTAGGGTTTTAAGGTCTGTTTT





GTAGAGGAGCAAACAGCGTTTGCGACATCCTTTTGTAATACTGCGG





AACTGACTAAAGTAGTGAGTTATACACAGGGCTGGGATCTATTCTT





TTTATCTTTTTTTATTCTTTCTTTATTCTATAAATTATAACCACTT





GAATATAAACAAAAAAAACACACAAAGGTCTAGCGGAATTTACAGA





GGGTCTAGCAGAATTTACAAGTTTTCCAGCAAAGGTCTAGCAGAAT





TTACAGATACCCACAACTCAAAGGAAAAGGACTAGTAATTATCATT





GACTAGCCCATCTCAATTGGTATAGTGATTAAAATCACCTAGACCA





ATTGAGATGTATGTCTGAATTAGTTGTTTTCAAAGCAAATGAACTA





GCGATTAGTCGCTATGACTTAACGGAGCATGAAACCAAGCTAATTT





TATGCTGTGTGGCACTACTCAACCCCACGATTGAAAACCCTACAAG





GAAAGAACGGACGGTATCGTTCACTTATAACCAATACGCTCAGATG





ATGAACATCAGTAGGGAAAATGCTTATGGTGTATTAGCTAAAGCAA





CCAGAGAGCTGATGACGAGAACTGTGGAAATCAGGAATCCTTTGGT





TAAAGGCTTTTGGATTTTCCAGTGGACAAACTATGCCAAGTTCTCA





AGCGAAAAATTAGAATTAGTTTTTAGTGAAGAGATATTGCCTTATC





TTTTCCAGTTAAAAAAATTCATAAAATATAATCTGGAACATGTTAA





GTCTTTTGAAAACAAATACTCTATGAGGATTTATGAGTGGTTATTA





AAAGAACTAACACAAAAGAAAACTCACAAGGCAAATATAGAGATTA





GCCTTGATGAATTTAAGTTCATGTTAATGCTTGAAAATAACTACCA





TGAGTTTAAAAGGCTTAACCAATGGGTTTTGAAACCAATAAGTAAA





GATTTAAACACTTACAGCAATATGAAATTGGTGGTTGATAAGCGAG





GCCGCCCGACTGATACGTTGATTTTCCAAGTTGAACTAGATAGACA





AATGGATCTCGTAACCGAACTTGAGAACAACCAGATAAAAATGAAT





GGTGACAAAATACCAACAACCATTACATCAGATTCCTACCTACATA





ACGGACTAAGAAAAACACTACACGATGCTTTAACTGCAAAAATTCA





GCTCACCAGTTTTGAGGCAAAATTTTTGAGTGACATGCAAAGTAAG





TATGATCTCAATGGTTCGTTCTCATGGCTCACGCAAAAACAACGAA





CCACACTAGAGAACATACTGGCTAAATACGGAAGGATCTGAGGTTC





TTATGGCTCTTGTATCTATCAGTGAAGCATCAAGACTAACAAACAA





AAGTAGAACAACTGTTCACCGTTACATATCAAAGGGAAAACTGTCC





ATATGCACAGATGAAAACGGTGTAAAAAAGATAGATACATCAGAGC





TTTTACGAGTTTTTGGTGCATTCAAAGCTGTTCACCATGAACAGAT





CGACAATGTAACAGATGAACAGCATGTAACACCTAATAGAACAGGT





GAAACCAGTAAAACAAAGCAACTAGAACATGAAATTGAACACCTGA





GACAACTTGTTACAGCTCAACAGTCACACATAGACAGCCTGAAACA





GGCGATGCTGCTTATCGAATCAAAGCTGCCGACAACACGGGAGCCA





GTGACGCCTCCCGTGGGGAAAAAATCATGGCAATTCTGGAAGAAAT





AGCGCTTTCAGCCGGCAAACCGGCTGAAGCCGGATCTGCGATTCTG





ATAACAAACTAGCAACACCAGAACAGCCCGTTTGCGGGCAGCAAAA





CCCGTAC






p15A

TTAATAAGATGATCTTCTTGAGATCGTTTTGGTCTGCGCGTAATCT
583




CTTGCTCTGAAAACGAAAAAACCGCCTTGCAGGGCGGTTTTTCGAA





GGTTCTCTGAGCTACCAACTCTTTGAACCGAGGTAACTGGCTTGGA





GGAGCGCAGTCACCAAAACTTGTCCTTTCAGTTTAGCCTTAACCGG





CGCATGACTTCAAGACTAACTCCTCTAAATCAATTACCAGTGGCTG





CTGCCAGTGGTGCTTTTGCATGTCTTTCCGGGTTGGACTCAAGACG





ATAGTTACCGGATAAGGCGCAGCGGTCGGACTGAACGGGGGGTTCG





TGCATACAGTCCAGCTTGGAGCGAACTGCCTACCCGGAACTGAGTG





TCAGGCGTGGAATGAGACAAACGCGGCCATAACAGCGGAATGACAC





CGGTAAACCGAAAGGCAGGAACAGGAGAGCGCACGAGGGAGCCGCC





AGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACC





ACTGATTTGAGCGTCAGATTTCGTGATGCTTGTCAGGGGGGCGGAG





CCTATGGAAAAACGGCTTTGCCGCGGCCCTCTCACTTCCCTGTTAA





GTATCTTCCTGGCATCTTCCAGGAAATCTCCGCCCCGTTCGTAAGC





CATTTCCGCTCGCCGCAGTCGAACGACCGAGCGTAGCGAGTCAGTG





AGCGAGGAAGCGGAATATATCCTGTATCACATATTCTGCTGACGCA





CCGGTGCAGCCTTTTTTCTCCTGCCACATGAAGCACTTCACTGACA





CCCTCATCAGTGCCAACATAGTAAGCCAGTATACACTCCGCTA
















TABLE 19







Plasmid Sequences













SEQ





ID


Namea
Description
Sequenceb
NO





pEG3017
HIS6-MBP-
CATTTCCCCGAAAAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGACAT
584



TruE*
TAACCTATAAAAATAGGCGTATCACGAGGCAGAATTTCAGATAAAAAAAATCCT






TAGCTTTCGCTAAGGATGATTTCTGGAATTCGCGGCCGCTTCTAGAGGGCatcc






cgaaaatttatcaaaaagagtattgacttaaagtctaacctataggatacttac







embedded image








TCATATTACCACCATCACCATCATCACGACTATGATATTCCCACAAGCATGAAA







ATCGAAGAAGGTAAACTGGTAATCTGGATTAACGGCGATAAAGGCTATAACGGA







TTGGCTGAAGTCGGTAAGAAATTCGAGAAAGATACCGGAATTAAAGTCACCGTT







GAGCATCCGGATAAACTGGAAGAGAAATTCCCACAGGTTGCGGCAACTGGCGAT







GGCCCTGACATTATCTTCTGGGCACACGACCGCTTTGGTGGCTACGCTCAATCT







GGCCTGTTGGCTGAAATCACCCCGGACAAAGCGTTCCAGGACAAGCTGTATCCG







TTTACCTGGGATGCCGTACGTTACAACGGCAAGCTGATTGCTTACCCGATCGCT







GTTGAAGCGTTATCGCTGATTTATAACAAAGATCTGCTGCCGAACCCGCCAAAA







ACCTGGGAAGAGATCCCGGCGCTGGATAAAGAACTGAAAGCGAAAGGTAAGAGC







GCGCTGATGTTCAACCTGCAAGAACCGTACTTCACCTGGCCGCTGATTGCTGCT







GACGGGGGTTATGCGTTCAAGTATGAAAACGGCAAGTACGACATTAAAGACGTG







GGCGTGGATAACGCTGGCGCGAAAGCGGGTCTGACCTTCCTGGTTGACCTGATT







AAAAACAAACACATGAATGCAGACACCGATTACTCCATCGCAGAAGCTGCCTTT







AATAAAGGCGAAACAGCGATGACCATCAACGGCCCGTGGGCATGGTCCAACATC







GACACCAGCAAAGTGAATTATGGTGTAACGGTACTGCCGACCTTCAAGGGTCAA







CCATCCAAACCGTTCGTTGGCGTGCTGAGCGCAGGTATTAACGCCGCCAGTCCG







AACAAAGAGCTGGCGAAAGAGTTCCTCGAAAACTATCTGCTGACTGATGAAGGT







CTGGAAGCGGTTAATAAAGACAAACCGCTGGGTGCCGTAGCGCTGAAGTCTTAC







GAGGAAGAGTTGGCGAAAGATCCACGTATTGCCGCCACCATGGAAAACGCCCAG







AAAGGTGAAATCATGCCGAACATCCCGCAGATGTCCGCTTTCTGGTATGCCGTG







CGTACTGCGGTGATCAACGCCGCCAGCGGTCGTCAGACTGTCGATGAAGCCCTG







AAAGACGCGCAGACTCGTATCACCAAGTCGTACTACCATCACCATCACCATCAC







GGCGGTAGTGGCGAAAACCTGTATTTTCAGGGTATGAACAAGAAGAACATTTTA







CCGCAGTTAGGACAACCAGTCATCCGCCTTACTGCCGGTCAACTGTCAAGCCAA







CTGGCGGAGCTTTCTGAGGAGGCTCTGGGAGGGGTCGATGCCTCGTACGCGGTG







TTCTGGCCGATCTGTAGCTATGACGACTAATAA
TTCAGCCAAAAAACTTAAGAC







CGCCGGTCTTGTCCACTACCTTGCAGTAATGCGGTGGACAGGATCGGCGGTTTT







CTTTTCTCTTCTCAACTGTACTAGTAGCGGCCGCTGCAGTCCGGCAAAAAAGGG







CAAGGTGTCACCACCCTGCCCTTTTTCTTTAAAACCGAAAAGATTACTTCGCGT






TATGCAGGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCG





AGCGGTATCAGCTCACTCAAAGGCGGTAATGACAGTAAGACGGGTAAGCCTGTT





GATGATACCGCTGCCTTACTGGGTGCATTAGCCAGTCTGAATGACCTGTCACGG





GATAATCCGAAGTGGTCAGACTGGAAAATCAGAGGGCAGGAACTGCTGAACAGC





AAAAAGTCAGATAGCACCACATAGCAGACCCGCCATAAAACGCCCTGAGAAGCC





CGTGACGGGCTTTTCTTGTATTATGGGTAGTTTCCTTGCATGAATCCATAAAAG





GCGCCTGTAGTGCCATTTACCCCCATTCACTGCCAGAGCCGTGAGCGCAGCGAA





CTGAATGTCACGAAAAAGACAGCGACTCAGGTGCCTGATGGTCGGAGACAAAAG





GAATATTCAGCGATTTGCCCGAGCTTGCGAGGGTGCTACTTAAGCCTTTAGGGT





TTTAAGGTCTGTTTTGTAGAGGAGCAAACAGCGTTTGCGACATCCTTTTGTAAT





ACTGCGGAACTGACTAAAGTAGTGAGTTATACACAGGGCTGGGATCTATTCTTT





TTATCTTTTTTTATTCTTTCTTTATTCTATAAATTATAACCACTTGAATATAAA





CAAAAAAAACACACAAAGGTCTAGCGGAATTTACAGAGGGTCTAGCAGAATTTA





CAAGTTTTCCAGCAAAGGTCTAGCAGAATTTACAGATACCCACAACTCAAAGGA





AAAGGACTAGTAATTATCATTGACTAGCCCATCTCAATTGGTATAGTGATTAAA





ATCACCTAGACCAATTGAGATGTATGTCTGAATTAGTTGTTTTCAAAGCAAATG





AACTAGCGATTAGTCGCTATGACTTAACGGAGCATGAAACCAAGCTAATTTTAT





GCTGTGTGGCACTACTCAACCCCACGATTGAAAACCCTACAAGGAAAGAACGGA





CGGTATCGTTCACTTATAACCAATACGCTCAGATGATGAACATCAGTAGGGAAA





ATGCTTATGGTGTATTAGCTAAAGCAACCAGAGAGCTGATGACGAGAACTGTGG





AAATCAGGAATCCTTTGGTTAAAGGCTTTTGGATTTTCCAGTGGACAAACTATG





CCAAGTTCTCAAGCGAAAAATTAGAATTAGTTTTTAGTGAAGAGATATTGCCTT





ATCTTTTCCAGTTAAAAAAATTCATAAAATATAATCTGGAACATGTTAAGTCTT





TTGAAAACAAATACTCTATGAGGATTTATGAGTGGTTATTAAAAGAACTAACAC





AAAAGAAAACTCACAAGGCAAATATAGAGATTAGCCTTGATGAATTTAAGTTCA





TGTTAATGCTTGAAAATAACTACCATGAGTTTAAAAGGCTTAACCAATGGGTTT





TGAAACCAATAAGTAAAGATTTAAACACTTACAGCAATATGAAATTGGTGGTTG





ATAAGCGAGGCCGCCCGACTGATACGTTGATTTTCCAAGTTGAACTAGATAGAC





AAATGGATCTCGTAACCGAACTTGAGAACAACCAGATAAAAATGAATGGTGACA





AAATACCAACAACCATTACATCAGATTCCTACCTACATAACGGACTAAGAAAAA





CACTACACGATGCTTTAACTGCAAAAATTCAGCTCACCAGTTTTGAGGCAAAAT





TTTTGAGTGACATGCAAAGTAAGTATGATCTCAATGGTTCGTTCTCATGGCTCA





CGCAAAAACAACGAACCACACTAGAGAACATACTGGCTAAATACGGAAGGATCT





GAGGTTCTTATGGCTCTTGTATCTATCAGTGAAGCATCAAGACTAACAAACAAA





AGTAGAACAACTGTTCACCGTTACATATCAAAGGGAAAACTGTCCATATGCACA





GATGAAAACGGTGTAAAAAAGATAGATACATCAGAGCTTTTACGAGTTTTTGGT





GCATTCAAAGCTGTTCACCATGAACAGATCGACAATGTAACAGATGAACAGCAT





GTAACACCTAATAGAACAGGTGAAACCAGTAAAACAAAGCAACTAGAACATGAA





ATTGAACACCTGAGACAACTTGTTACAGCTCAACAGTCACACATAGACAGCCTG





AAACAGGCGATGCTGCTTATCGAATCAAAGCTGCCGACAACACGGGAGCCAGTG





ACGCCTCCCGTGGGGAAAAAATCATGGCAATTCTGGAAGAAATAGCGCTTTCAG





CCGGCAAACCGGCTGAAGCCGGATCTGCGATTCTGATAACAAACTAGCAACACC





AGAACAGCCCGTTTGCGGGCAGCAAAACCCGTACCGATTATCAAAAAGGATCTT





CACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATA





TGAGTAAACTTGGTCTGATTACGCCCCGCCCTGCCACTCATCACAGTACTGTTG





TAATTCATTAAGCATGCGGCCGACATGGAAGCCATCACAAACGGCATGATGAAC





CTGGATCGCCAGCGGCATCAGCACCTTGTCGCCTTGCGTATAATATTTGCCCAT





CGTGAAAACGGGGGCGAAGAAGTTGTCCATATTGGCCACGTTTAAATCAAAACT





GGTGAAACTCACCCAGGGATTGGCTGAGACAAAAAACATATTCTCAATAAACCC





TTTAGGGAAATAGGCCAGGTTTTCACCGTAACACGCCACATCTTGCGAATATAT





GTGGAGAAACTGCCGGAAATCGTCGTGGTATTCACTCCAGAGGGACGAAAACGT





TTCAGTTTGCTCATGGAAAACGGTGTAACAAGGGTGAACACTATCCCAGATCAC





CAGCTCACCGTCTTTCATGGCCATACGAAACTCCGGGTGAGCGTTCATCAGGCG





GGCAAGAATGTGAATAAAGGCCGGATAAAACTTGTGCTTATTTTTCTTTACGGT





CTTTAAAAAGGCCGTAATATCCAGCTGAACGGTCTGGTTATAGGTACATTGAGC





AACTGACTGAAATGCCTCAAAATGTTCTTTACGATGCCATTGGGATATATCAAC





GGTGGTATATCCCGTGATTTTTTTCTCCATACTCTTCCTTTTTCAATATTATTG





AAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTA





GAAAAATAAACAAATAGGGGTTCCGCG






bEG_S2
N-term
CACATTTCCCCGAAAAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGAC
585



HIS6-Tag
ATTAACCTATAAAAATAGGCGTATCACGAGGCAGAATTTCAGATAAAAAAAATC




with ATag-

CTTAGCTTTCGCTAAGGATGATTTCTGGAATTCGCGGCCGCTTCTAGAGGGAGA





1
ACGATCGTTGGCTGaatcataaaaaatttatttgctttgtgagcggataacaat







embedded image









embedded image








ATATTCCCACAAGCGAGAACTTGTACTTTCAAGGG

ATGAGCAAAGGAGAAGAAC









TTTTCACTGGAGTTGTCCCAATTCTTGTTGAATTAGATGGTGATGTTAATGGGC









ACAAATTTTCTGTCCGTGGAGAGGGTGAAGGTGATGCTACAAACGGAAAACTCA









CCCTTAAATTTATTTGCACTACTGGAAAACTACCTGTTCCGTGGCCAACACTTG









TCACTACTCTGACCTATGGTGTTCAATGCTTTTCCCGTTATCCGGATCACATGA









AACGGCATGACTTTTTCAAGAGTGCCATGCCCGAAGGTTATGTACAGGAACGCA









CTATATCTTTCAAAGATGACGGGACCTACAAGACGCGTGCTGAAGTCAAGTTTG









AAGGTGATACCCTTGTTAATCGTATCGAGTTAAAGGGTATTGATTTTAAAGAAG









ATGGAAACATTCTTGGACACAAACTCGAGTACAACTTTAACTCACACAATGTAT









ACATCACGGCAGACAAACAAAAGAATGGAATCAAAGCTAACTTCAAAATTCGCC









ACAACGTTGAAGATGGTTCCGTTCAACTAGCAGACCATTATCAACAAAATACTC









CAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTCGACACAAT









CTGTCCTTTCGAAAGATCCCAACGAAAAGCGTGACCACATGGTCCTTCTTGAGT









TTGTAACTGCTGCTGGGATTACACATGGCATGGATGAGCTCTACAAATAA

TTCA







GCCAAAAAACTTAAGACCGCCGGTCTTGTCCACTACCTTGCAGTAATGCGGTGG







ACAGGATCGGCGGTTTTCTTTTCTCTTCTCAACCAATGgcggcgcgccatcgaa








embedded image









embedded image








GTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCG







AAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAAC







CGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTTATTGGCGTTGCCACC







TCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGC







GCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTC







GAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTG







ATCATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCCTGC







ACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGACACCCATCAACAGT







ATTATTTTCTCCCATGAGGACGGTACGCGACTGGGCGTGGAGCATCTGGTCGCA







TTGGGTCACCAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCG







CGTCTGCGTCTGGCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCG







ATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATG







CAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTTGCCAACGATCAG







ATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGCTGCGCGTTGGTGCG







GATATCTCGGTAGTGGGATACGACGATACCGAAGATAGCTCATGTTATATCCCG







CCGTTAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGAC







CGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCA







GTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCT







CCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTG







GAAAGCGGGCAGTGATAA
TTGGTAACGAATCAGACAATTGACGGCTCGAGGGAG







TAGCATAGGGTTTGCAGAATCCCTGCTTCGTCCATTTGACAGGCACATTATGCA







TCGATGATAAGCTGTCAAACATGAGCACGCTTACTAGTAGCGGCCGCTGCAGTC







CGGCAAAAAAGGGCAAGGTGTCACCACCCTGCCCTTTTTCTTTAAAACCGAAAA







GATTACTTCGCGTTATGCAGGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCG






TTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATGACAGTAAGAC





GGGTAAGCCTGTTGATGATACCGCTGCCTTACTGGGTGCATTAGCCAGTCTGAA





TGACCTGTCACGGGATAATCCGAAGTGGTCAGACTGGAAAATCAGAGGGCAGGA





ACTGCTGAACAGCAAAAAGTCAGATAGCACCACATAGCAGACCCGCCATAAAAC





GCCCTGAGAAGCCCGTGACGGGCTTTTCTTGTATTATGGGTAGTTTCCTTGCAT





GAATCCATAAAAGGCGCCTGTAGTGCCATTTACCCCCATTCACTGCCAGAGCCG





TGAGCGCAGCGAACTGAATGTCACGAAAAAGACAGCGACTCAGGTGCCTGATGG





TCGGAGACAAAAGGAATATTCAGCGATTTGCCCGAGCTTGCGAGGGTGCTACTT





AAGCCTTTAGGGTTTTAAGGTCTGTTTTGTAGAGGAGCAAACAGCGTTTGCGAC





ATCCTTTTGTAATACTGCGGAACTGACTAAAGTAGTGAGTTATACACAGGGCTG





GGATCTATTCTTTTTATCTTTTTTTATTCTTTCTTTATTCTATAAATTATAACC





ACTTGAATATAAACAAAAAAAACACACAAAGGTCTAGCGGAATTTACAGAGGGT





CTAGCAGAATTTACAAGTTTTCCAGCAAAGGTCTAGCAGAATTTACAGATACCC





ACAACTCAAAGGAAAAGGACTAGTAATTATCATTGACTAGCCCATCTCAATTGG





TATAGTGATTAAAATCACCTAGACCAATTGAGATGTATGTCTGAATTAGTTGTT





TTCAAAGCAAATGAACTAGCGATTAGTCGCTATGACTTAACGGAGCATGAAACC





AAGCTAATTTTATGCTGTGTGGCACTACTCAACCCCACGATTGAAAACCCTACA





AGGAAAGAACGGACGGTATCGTTCACTTATAACCAATACGCTCAGATGATGAAC





ATCAGTAGGGAAAATGCTTATGGTGTATTAGCTAAAGCAACCAGAGAGCTGATG





ACGAGAACTGTGGAAATCAGGAATCCTTTGGTTAAAGGCTTTTGGATTTTCCAG





TGGACAAACTATGCCAAGTTCTCAAGCGAAAAATTAGAATTAGTTTTTAGTGAA





GAGATATTGCCTTATCTTTTCCAGTTAAAAAAATTCATAAAATATAATCTGGAA





CATGTTAAGTCTTTTGAAAACAAATACTCTATGAGGATTTATGAGTGGTTATTA





AAAGAACTAACACAAAAGAAAACTCACAAGGCAAATATAGAGATTAGCCTTGAT





GAATTTAAGTTCATGTTAATGCTTGAAAATAACTACCATGAGTTTAAAAGGCTT





AACCAATGGGTTTTGAAACCAATAAGTAAAGATTTAAACACTTACAGCAATATG





AAATTGGTGGTTGATAAGCGAGGCCGCCCGACTGATACGTTGATTTTCCAAGTT





GAACTAGATAGACAAATGGATCTCGTAACCGAACTTGAGAACAACCAGATAAAA





ATGAATGGTGACAAAATACCAACAACCATTACATCAGATTCCTACCTACATAAC





GGACTAAGAAAAACACTACACGATGCTTTAACTGCAAAAATTCAGCTCACCAGT





TTTGAGGCAAAATTTTTGAGTGACATGCAAAGTAAGTATGATCTCAATGGTTCG





TTCTCATGGCTCACGCAAAAACAACGAACCACACTAGAGAACATACTGGCTAAA





TACGGAAGGATCTGAGGTTCTTATGGCTCTTGTATCTATCAGTGAAGCATCAAG





ACTAACAAACAAAAGTAGAACAACTGTTCACCGTTACATATCAAAGGGAAAACT





GTCCATATGCACAGATGAAAACGGTGTAAAAAAGATAGATACATCAGAGCTTTT





ACGAGTTTTTGGTGCATTCAAAGCTGTTCACCATGAACAGATCGACAATGTAAC





AGATGAACAGCATGTAACACCTAATAGAACAGGTGAAACCAGTAAAACAAAGCA





ACTAGAACATGAAATTGAACACCTGAGACAACTTGTTACAGCTCAACAGTCACA





CATAGACAGCCTGAAACAGGCGATGCTGCTTATCGAATCAAAGCTGCCGACAAC





ACGGGAGCCAGTGACGCCTCCCGTGGGGAAAAAATCATGGCAATTCTGGAAGAA





ATAGCGCTTTCAGCCGGCAAACCGGCTGAAGCCGGATCTGCGATTCTGATAACA





AACTAGCAACACCAGAACAGCCCGTTTGCGGGCAGCAAAACCCGTACCGATTAT





CAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAA





TCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTG





AGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCC





CCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTG





CAATGATACCGCGAGAACCACGCTCACCGGCTCCAGATTTATCAGCAATAAACC





AGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCA





TCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATA





GTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGT





TTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGAT





CCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCA





GAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATT





CTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAA





CCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGT





CAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTG





GAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCA





GTTCGATATAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCA





CCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAA





TAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATT





GAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTT





AGAAAAATAAACAAATAGGGGTTCCGCG






pEG3045
HIS6-MdnA

ATGGCATATCCCAACGATCAACAAGGTAAAGCACTTCCTTTCTTTGCTCGTTTC

586





TTGTCCGTAAGCAAAGAGGAATCTTCCATCAAGTCTCCTTCCCCTGAGCCTACC







TACGGGGGCACCTTTAAATACCCTTCTGACTGGGAAGATTATTAATAA







pEG3046
HIS6-BmbC

ATGGGTCCGGTTGTTGTGTTCGATTGCATGACGGCCGACTTTCTGAACGACGAT

587





CCAAATAACGCGGAGTTGTCTGCCTTGGAAATGGAGGAGCTCGAGTCCTGGGGC







GCCTGGGACGGAGAGGCTACCAGCTAGTAA







pEG3047
HIS6-StrA

ATGAGTAAGGAATTAGAAAAAGTTCTTGAATCCAGTTCAATGGCAAAGGGGGAC

588





GGCTGGAAGGTTATGGCTAAAGGTGACGGTTGGGAGTAATAA







pEG3048
HIS6-PqqA

ATGTGGAAGAAACCTGCTTTTATCGATTTACGTCTCGGTCTGGAAGTGACGCTG

589





TACATTTCTAACCGTTAATAA







pEG3049
HIS6-SboA

ATGAAAAAAGCTGTCATTGTAGAAAACAAAGGTTGTGCAACATGCTCGATCGGA

590





GCCGCTTGTCTAGTGGACGGTCCTATCCCTGATTTTGAAATTGCCGGTGCAACA







GGTCTATTCGGTCTATGGGGATAA







pEG3051
HIS6-TfxA

ATGGATAACAAGGTTGCGAAGAATGTCGAAGTGAAGAAGGGCTCCATCAAGGCG

591





ACCTTCAAGGCTGCTGTTCTGAAGTCGAAGACGAAGGTCGACATCGGAGGTAGC







CGTCAGGGCTGCGTCGCTTAATAA







pEG3052
HIS6-

ATGTCAGAAGAACAACTCAAGGCATTCATTGCCAAGGTTCAAGCAGACACTTCA

592



ProcA1.7

CTGCAGGAACAGCTCAAAGTAGAAGGTGCTGATGTTGTTGCTATTGCTAAAGCC







TCAGGGTTCGCGATTACCACAGAGGACTTAAAAGCACATCAAGCCAACTCACAA







AAGAACCTGTCTGATGCTGAGCTGGAAGGTGTGGCTGGGCGAACCATTGGGGGA







ACCATTGTGTCGATAACCTGTGAGACTTGCGATCTGCTTGTGGGGAAAATGTGC







TGATAA







PEG3053
HIS6-TbtA

ATGGACCTGAATGATCTGCCGATGGATGTTTTTGAACTGGCAGATAGCGGTGTT

593





GCAGTTGAAAGCCTGACCGCAGGTCATGGTATGACCGAAGTTGGTGCAAGCTGT







AATTGCTTTTGTTATATTTGTTGTAGCTGCAGCAGCGCCTAATAA







pEG3055
HIS6-Pgm2

ATGGAGCGCGAAATCGTGTGGACAGAAATTGAGGAGTCGGATTTAGCCGCCGTC

594





GTGTCGGCATCTAATGTCAAGGATGGTCCAACCGTTAGCTCAAGTAATGTAAAG







GACCGCTAATAA







bEG_S3
RSTN*
CACATTTCCCCGAAAAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGAC
595



expression
ATTAACCTATAAAAATAGGCGTATCACGAGGCAGAATTTCAGATAAAAAAAATC




vector

CTTAGCTTTCGCTAAGGATGATTTCTGGAATTCGCGGCCGCTTCTAGAGGGAGA






ACGATCGTTGGCTGaatcataaaaaatttatttgctttgtgagcggataacaat







embedded image









embedded image









TGCAGGACTCAGAAGTCAATCAAGAAGCTAAGCCAGAGGTCAAGCCAGAAGTCA









AGCCTGAGACTCACATCAATTTAAAGGTGTCCGATGGATCTTCAGAGATCTTCT









TCAAGATCAAAAAGACCACTCCTTTAAGAAGGCTGATGGAAGCGTTCGCTAAAA









GACAGGGTAAGGAAATGGACTCCTTAAGATTCTTGTACGACGGTATTAGAATTC









AAGCTGATCAGGCCCCTGAAGATTTGGACATGGAGGATAACGATATTATTGAGG









CTCACCGCGAACAGATTGGAGGTCATCACCATCACCACCATGGATATGATATTA









GCACAGGTATGAGCAAAGGAGAAGAACTTTTCACTGGAGTTGTCCCAATTCTTG









TTGAATTAGATGGTGATGTTAATGGGCACAAATTTTCTGTCCGTGGAGAGGGTG









AAGGTGATGCTACAAACGGAAAACTCACCCTTAAATTTATTTGCACTACTGGAA









AACTACCTGTTCCGTGGCCAACACTTGTCACTACTCTGACCTATGGTGTTCAAT









GCTTTTCCCGTTATCCGGATCACATGAAACGGCATGACTTTTTCAAGAGTGCCA









TGCCCGAAGGTTATGTACAGGAACGCACTATATCTTTCAAAGATGACGGGACCT









ACAAGACGCGTGCTGAAGTCAAGTTTGAAGGTGATACCCTTGTTAATCGTATCG









AGTTAAAGGGTATTGATTTTAAAGAAGATGGAAACATTCTTGGACACAAACTCG









AGTACAACTTTAACTCACACAATGTATACATCACGGCAGACAAACAAAAGAATG









GAATCAAAGCTAACTTCAAAATTCGCCACAACGTTGAAGATGGTTCCGTTCAAC









TAGCAGACCATTATCAACAAAATACTCCAATTGGCGATGGCCCTGTCCTTTTAC









CAGACAACCATTACCTGTCGACACAATCTGTCCTTTCGAAAGATCCCAACGAAA









AGCGTGACCACATGGTCCTTCTTGAGTTTGTAACTGCTGCTGGGATTACACATG









GCATGGATGAGCTCTACAAATAA

TTCAGCCAAAAAACTTAAGACCGCCGGTCTT







GTCCACTACCTTGCAGTAATGCGGTGGACAGGATCGGCGGTTTTCTTTTCTCTT







CTCAACCAATGgcggcgcgccatcgaatggcgcaaaacctttcgcggtatggca








embedded image








TTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTG







GTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCG







ATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAA







CAGTCGTTGCTTATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTCG







CAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTG







GTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAAT







CTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAG







GATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGAT







GTCTCTGACCAGACACCCATCAACAGTATTATTTTCTCCCATGAGGACGGTACG







CGACTGGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTA







GCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAA







TATCTCACTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGT







GCCATGTCCGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCC







ACTGCGATGCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATT







ACCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGAT







ACCGAAGATAGCTCATGTTATATCCCGCCGTTAACCACCATCAAACAGGATTTT







CGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAG







GCGGTGAAGGGCAATCAGCTGTTGCCAGTCTCACTGGTGAAAAGAAAAACCACC







CTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATG







CAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGATAATTGGTAACG







AATCAGACAATTGACGGCTCGAGGGAGTAGCATAGGGTTTGCAGAATCCCTGCT







TCGTCCATTTGACAGGCACATTATGCATCGATGATAAGCTGTCAAACATGAGCA






CGCTTACTAGTAGCGGCCGCTGCAGTCCGGCAAAAAAGGGCAAGGTGTCACCAC






CCTGCCCTTTTTCTTTAAAACCGAAAAGATTACTTCGCGTTATGCAGGCTTCCT






CGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTC





ACTCAAAGGCGGTAATGACAGTAAGACGGGTAAGCCTGTTGATGATACCGCTGC





CTTACTGGGTGCATTAGCCAGTCTGAATGACCTGTCACGGGATAATCCGAAGTG





GTCAGACTGGAAAATCAGAGGGCAGGAACTGCTGAACAGCAAAAAGTCAGATAG





CACCACATAGCAGACCCGCCATAAAACGCCCTGAGAAGCCCGTGACGGGCTTTT





CTTGTATTATGGGTAGTTTCCTTGCATGAATCCATAAAAGGCGCCTGTAGTGCC





ATTTACCCCCATTCACTGCCAGAGCCGTGAGCGCAGCGAACTGAATGTCACGAA





AAAGACAGCGACTCAGGTGCCTGATGGTCGGAGACAAAAGGAATATTCAGCGAT





TTGCCCGAGCTTGCGAGGGTGCTACTTAAGCCTTTAGGGTTTTAAGGTCTGTTT





TGTAGAGGAGCAAACAGCGTTTGCGACATCCTTTTGTAATACTGCGGAACTGAC





TAAAGTAGTGAGTTATACACAGGGCTGGGATCTATTCTTTTTATCTTTTTTTAT





TCTTTCTTTATTCTATAAATTATAACCACTTGAATATAAACAAAAAAAACACAC





AAAGGTCTAGCGGAATTTACAGAGGGTCTAGCAGAATTTACAAGTTTTCCAGCA





AAGGTCTAGCAGAATTTACAGATACCCACAACTCAAAGGAAAAGGACTAGTAAT





TATCATTGACTAGCCCATCTCAATTGGTATAGTGATTAAAATCACCTAGACCAA





TTGAGATGTATGTCTGAATTAGTTGTTTTCAAAGCAAATGAACTAGCGATTAGT





CGCTATGACTTAACGGAGCATGAAACCAAGCTAATTTTATGCTGTGTGGCACTA





CTCAACCCCACGATTGAAAACCCTACAAGGAAAGAACGGACGGTATCGTTCACT





TATAACCAATACGCTCAGATGATGAACATCAGTAGGGAAAATGCTTATGGTGTA





TTAGCTAAAGCAACCAGAGAGCTGATGACGAGAACTGTGGAAATCAGGAATCCT





TTGGTTAAAGGCTTTTGGATTTTCCAGTGGACAAACTATGCCAAGTTCTCAAGC





GAAAAATTAGAATTAGTTTTTAGTGAAGAGATATTGCCTTATCTTTTCCAGTTA





AAAAAATTCATAAAATATAATCTGGAACATGTTAAGTCTTTTGAAAACAAATAC





TCTATGAGGATTTATGAGTGGTTATTAAAAGAACTAACACAAAAGAAAACTCAC





AAGGCAAATATAGAGATTAGCCTTGATGAATTTAAGTTCATGTTAATGCTTGAA





AATAACTACCATGAGTTTAAAAGGCTTAACCAATGGGTTTTGAAACCAATAAGT





AAAGATTTAAACACTTACAGCAATATGAAATTGGTGGTTGATAAGCGAGGCCGC





CCGACTGATACGTTGATTTTCCAAGTTGAACTAGATAGACAAATGGATCTCGTA





ACCGAACTTGAGAACAACCAGATAAAAATGAATGGTGACAAAATACCAACAACC





ATTACATCAGATTCCTACCTACATAACGGACTAAGAAAAACACTACACGATGCT





TTAACTGCAAAAATTCAGCTCACCAGTTTTGAGGCAAAATTTTTGAGTGACATG





CAAAGTAAGTATGATCTCAATGGTTCGTTCTCATGGCTCACGCAAAAACAACGA





ACCACACTAGAGAACATACTGGCTAAATACGGAAGGATCTGAGGTTCTTATGGC





TCTTGTATCTATCAGTGAAGCATCAAGACTAACAAACAAAAGTAGAACAACTGT





TCACCGTTACATATCAAAGGGAAAACTGTCCATATGCACAGATGAAAACGGTGT





AAAAAAGATAGATACATCAGAGCTTTTACGAGTTTTTGGTGCATTCAAAGCTGT





TCACCATGAACAGATCGACAATGTAACAGATGAACAGCATGTAACACCTAATAG





AACAGGTGAAACCAGTAAAACAAAGCAACTAGAACATGAAATTGAACACCTGAG





ACAACTTGTTACAGCTCAACAGTCACACATAGACAGCCTGAAACAGGCGATGCT





GCTTATCGAATCAAAGCTGCCGACAACACGGGAGCCAGTGACGCCTCCCGTGGG





GAAAAAATCATGGCAATTCTGGAAGAAATAGCGCTTTCAGCCGGCAAACCGGCT





GAAGCCGGATCTGCGATTCTGATAACAAACTAGCAACACCAGAACAGCCCGTTT





GCGGGCAGCAAAACCCGTACCGATTATCAAAAAGGATCTTCACCTAGATCCTTT





TAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGT





CTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTAT





TTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGG





AGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGAACCACGCTCAC





CGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAA





GTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAG





CTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTA





CAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTT





CCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTA





GCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCAC





TCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGAT





GCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGC





GGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATA





GCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCT





CAAGGATCTTACCGCTGTTGAGATCCAGTTCGATATAACCCACTCGTGCACCCA





ACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAG





GAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATAC





TCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCA





TGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGC





G






pEG3057
RSTx*

ATGAACAAGAAGAACATTTTACCGCAGTTAGGACAACCAGTCATCCGCCTTACT

596



TruE*

GCCGGTCAACTGTCAAGCCAACTGGCGGAGCTTTCTGAGGAGGCTCTGGGAGGG







GTCGATGCCTCGTACGCGGTGTTCTGGCCGATCTGTAGCTATGACGACTAATAA







pEG3058
RSTx*-

ATGGCATATCCCAACGATCAACAAGGTAAAGCACTTCCTTTCTTTGCTCGTTTC

597



MdnA

TTGTCCGTAAGCAAAGAGGAATCTTCCATCAAGTCTCCTTCCCCTGAGCCTACC







TACGGGGGCACCTTTAAATACCCTTCTGACTGGGAAGATTATTAATAA







pEG3059
RSTx*-

ATGAAAAAAGCTGTCATTGTAGAAAACAAAGGTTGTGCAACATGCTCGATCGGA

598



SboA

GCCGCTTGTCTAGTGGACGGTCCTATCCCTGATTTTGAAATTGCCGGTGCAACA







GGTCTATTCGGTCTATGGGGATAA







pEG3060
RSTx*

ATGTGGAAGAAACCTGCTTTTATCGATTTACGTCTCGGTCTGGAAGTGACGCTG

599



PqqA

TACATTTCTAACCGTTAATAA







pEG3061
RSTN*-StrA

ATGAGTAAGGAATTAGAAAAAGTTCTTGAATCCAGTTCAATGGCAAAGGGGGAC

600





GGCTGGAAGGTTATGGCTAAAGGTGACGGTTGGGAGTAATAA







pEG3062
RSTN*-

ATGGGTCCGGTTGTTGTGTTCGATTGCATGACGGCCGACTTTCTGAACGACGAT

601



BmbC

CCAAATAACGCGGAGTTGTCTGCCTTGGAAATGGAGGAGCTCGAGTCCTGGGGC







GCCTGGGACGGAGAGGCTACCAGCTAGTAA







pEG3063
RSTN*-

ATGGATAACAAGGTTGCGAAGAATGTCGAAGTGAAGAAGGGCTCCATCAAGGCG

602



TfxA

ACCTTCAAGGCTGCTGTTCTGAAGTCGAAGACGAAGGTCGACATCGGAGGTAGC







CGTCAGGGCTGCGTCGCTTAATAA







pEG3064
RSTN*-

ATGTCAGAAGAACAACTCAAGGCATTCATTGCCAAGGTTCAAGCAGACACTTCA

603



ProcA1.7

CTGCAGGAACAGCTCAAAGTAGAAGGTGCTGATGTTGTTGCTATTGCTAAAGCC







TCAGGGTTCGCGATTACCACAGAGGACTTAAAAGCACATCAAGCCAACTCACAA







AAGAACCTGTCTGATGCTGAGCTGGAAGGTGTGGCTGGGCGAACCATTGGGGGA







ACCATTGTGTCGATAACCTGTGAGACTTGCGATCTGCTTGTGGGGAAAATGTGC







TGATAA







pEG3065
RSTN*-

ATGGACCTGAATGATCTGCCGATGGATGTTTTTGAACTGGCAGATAGCGGTGTT

604



TbtA

GCAGTTGAAAGCCTGACCGCAGGTCATGGTATGACCGAAGTTGGTGCAAGCTGT







AATTGCTTTTGTTATATTTGTTGTAGCTGCAGCAGCGCCTAATAA







pEG3067
RSTN*-

ATGGAGCGCGAAATCGTGTGGACAGAAATTGAGGAGTCGGATTTAGCCGCCGTC

605



Pgm2

GTGTCGGCATCTAATGTCAAGGATGGTCCAACCGTTAGCTCAAGTAATGTAAAG







GACCGCTAATAA







bEG_S4
RSTN
CACATTTCCCCGAAAAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGAC
606



expression
ATTAACCTATAAAAATAGGCGTATCACGAGGCAGAATTTCAGATAAAAAAAATC




vector

CTTAGCTTTCGCTAAGGATGATTTCTGGAATTCGCGGCCGCTTCTAGAGGGAGA






ACGATCGTTGGCTGaatcataaaaaatttatttgctttgtgagcggataacaat







embedded image









embedded image








TGCAGGACTCAGAAGTCAATCAAGAAGCTAAGCCAGAGGTCAAGCCAGAAGTCA







AGCCTGAGACTCACATCAATTTAAAGGTGTCCGATGGATCTTCAGAGATCTTCT







TCAAGATCAAAAAGACCACTCCTTTAAGAAGGCTGATGGAAGCGTTCGCTAAAA







GACAGGGTAAGGAAATGGACTCCTTAAGATTCTTGTACGACGGTATTAGAATTC







AAGCTGATCAGGCCCCTGAAGATTTGGACATGGAGGATAACGATATTATTGAGG







CTCACCGCGAACAGATTGGAGGTTGCATGTCATATTACGACTCCATTCCCACAA







GCGAGAACTTGTACTTTCAAGGGTGC

ATGAGCAAAGGAGAAGAACTTTTCACTG









GAGTTGTCCCAATTCTTGTTGAATTAGATGGTGATGTTAATGGGCACAAATTTT









CTGTCCGTGGAGAGGGTGAAGGTGATGCTACAAACGGAAAACTCACCCTTAAAT









TTATTTGCACTACTGGAAAACTACCTGTTCCGTGGCCAACACTTGTCACTACTC









TGACCTATGGTGTTCAATGCTTTTCCCGTTATCCGGATCACATGAAACGGCATG









ACTTTTTCAAGAGTGCCATGCCCGAAGGTTATGTACAGGAACGCACTATATCTT









TCAAAGATGACGGGACCTACAAGACGCGTGCTGAAGTCAAGTTTGAAGGTGATA









CCCTTGTTAATCGTATCGAGTTAAAGGGTATTGATTTTAAAGAAGATGGAAACA









TTCTTGGACACAAACTCGAGTACAACTTTAACTCACACAATGTATACATCACGG









CAGACAAACAAAAGAATGGAATCAAAGCTAACTTCAAAATTCGCCACAACGTTG









AAGATGGTTCCGTTCAACTAGCAGACCATTATCAACAAAATACTCCAATTGGCG









ATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTCGACACAATCTGTCCTTT









CGAAAGATCCCAACGAAAAGCGTGACCACATGGTCCTTCTTGAGTTTGTAACTG









CTGCTGGGATTACACATGGCATGGATGAGCTCTACAAATAA

TTCAGCCAAAAAA







CTTAAGACCGCCGGTCTTGTCCACTACCTTGCAGTAATGCGGTGGACAGGATCG







GCGGTTTTCTTTTCTCTTCTCAACCAATGgcggcgcgccatcgaatggcgcaaa






acctttcgcggtatggcatgatagcgcccGGAAGAGAGTCAATTCAGGGTGGTG





AATATGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTAT






CAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGG







GAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCA







CAACAACTGGCGGGCAAACAGTCGTTGCTTATTGGCGTTGCCACCTCCAGTCTG







GCCCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAA







CTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGT







AAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAAC







TATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTT







CCGGCGTTATTTCTTGATGTCTCTGACCAGACACCCATCAACAGTATTATTTTC







TCCCATGAGGACGGTACGCGACTGGGCGTGGAGCATCTGGTCGCATTGGGTCAC







CAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGT







CTGGCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGAA







CGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATGCAAATGCTG







AATGAGGGCATCGTTCCCACTGCGATGCTGGTTGCCAACGATCAGATGGCGCTG







GGCGCAATGCGCGCCATTACCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCG







GTAGTGGGATACGACGATACCGAAGATAGCTCATGTTATATCCCGCCGTTAACC







ACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTG







CAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCAGTCTCACTG







GTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCG







TTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGG







CAGTGATAA
TTGGTAACGAATCAGACAATTGACGGCTCGAGGGAGTAGCATAGG







GTTTGCAGAATCCCTGCTTCGTCCATTTGACAGGCACATTATGCATCGATGATA







AGCTGTCAAACATGAGCACGCTTACTAGTAGCGGCCGCTGCAGTCCGGCAAAAA







AGGGCAAGGTGTCACCACCCTGCCCTTTTTCTTTAAAACCGAAAAGATTACTTC






GCGTTATGCAGGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGC





GGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATGACAGTAAGACGGGTAAGCC





TGTTGATGATACCGCTGCCTTACTGGGTGCATTAGCCAGTCTGAATGACCTGTC





ACGGGATAATCCGAAGTGGTCAGACTGGAAAATCAGAGGGCAGGAACTGCTGAA





CAGCAAAAAGTCAGATAGCACCACATAGCAGACCCGCCATAAAACGCCCTGAGA





AGCCCGTGACGGGCTTTTCTTGTATTATGGGTAGTTTCCTTGCATGAATCCATA





AAAGGCGCCTGTAGTGCCATTTACCCCCATTCACTGCCAGAGCCGTGAGCGCAG





CGAACTGAATGTCACGAAAAAGACAGCGACTCAGGTGCCTGATGGTCGGAGACA





AAAGGAATATTCAGCGATTTGCCCGAGCTTGCGAGGGTGCTACTTAAGCCTTTA





GGGTTTTAAGGTCTGTTTTGTAGAGGAGCAAACAGCGTTTGCGACATCCTTTTG





TAATACTGCGGAACTGACTAAAGTAGTGAGTTATACACAGGGCTGGGATCTATT





CTTTTTATCTTTTTTTATTCTTTCTTTATTCTATAAATTATAACCACTTGAATA





TAAACAAAAAAAACACACAAAGGTCTAGCGGAATTTACAGAGGGTCTAGCAGAA





TTTACAAGTTTTCCAGCAAAGGTCTAGCAGAATTTACAGATACCCACAACTCAA





AGGAAAAGGACTAGTAATTATCATTGACTAGCCCATCTCAATTGGTATAGTGAT





TAAAATCACCTAGACCAATTGAGATGTATGTCTGAATTAGTTGTTTTCAAAGCA





AATGAACTAGCGATTAGTCGCTATGACTTAACGGAGCATGAAACCAAGCTAATT





TTATGCTGTGTGGCACTACTCAACCCCACGATTGAAAACCCTACAAGGAAAGAA





CGGACGGTATCGTTCACTTATAACCAATACGCTCAGATGATGAACATCAGTAGG





GAAAATGCTTATGGTGTATTAGCTAAAGCAACCAGAGAGCTGATGACGAGAACT





GTGGAAATCAGGAATCCTTTGGTTAAAGGCTTTTGGATTTTCCAGTGGACAAAC





TATGCCAAGTTCTCAAGCGAAAAATTAGAATTAGTTTTTAGTGAAGAGATATTG





CCTTATCTTTTCCAGTTAAAAAAATTCATAAAATATAATCTGGAACATGTTAAG





TCTTTTGAAAACAAATACTCTATGAGGATTTATGAGTGGTTATTAAAAGAACTA





ACACAAAAGAAAACTCACAAGGCAAATATAGAGATTAGCCTTGATGAATTTAAG





TTCATGTTAATGCTTGAAAATAACTACCATGAGTTTAAAAGGCTTAACCAATGG





GTTTTGAAACCAATAAGTAAAGATTTAAACACTTACAGCAATATGAAATTGGTG





GTTGATAAGCGAGGCCGCCCGACTGATACGTTGATTTTCCAAGTTGAACTAGAT





AGACAAATGGATCTCGTAACCGAACTTGAGAACAACCAGATAAAAATGAATGGT





GACAAAATACCAACAACCATTACATCAGATTCCTACCTACATAACGGACTAAGA





AAAACACTACACGATGCTTTAACTGCAAAAATTCAGCTCACCAGTTTTGAGGCA





AAATTTTTGAGTGACATGCAAAGTAAGTATGATCTCAATGGTTCGTTCTCATGG





CTCACGCAAAAACAACGAACCACACTAGAGAACATACTGGCTAAATACGGAAGG





ATCTGAGGTTCTTATGGCTCTTGTATCTATCAGTGAAGCATCAAGACTAACAAA





CAAAAGTAGAACAACTGTTCACCGTTACATATCAAAGGGAAAACTGTCCATATG





CACAGATGAAAACGGTGTAAAAAAGATAGATACATCAGAGCTTTTACGAGTTTT





TGGTGCATTCAAAGCTGTTCACCATGAACAGATCGACAATGTAACAGATGAACA





GCATGTAACACCTAATAGAACAGGTGAAACCAGTAAAACAAAGCAACTAGAACA





TGAAATTGAACACCTGAGACAACTTGTTACAGCTCAACAGTCACACATAGACAG





CCTGAAACAGGCGATGCTGCTTATCGAATCAAAGCTGCCGACAACACGGGAGCC





AGTGACGCCTCCCGTGGGGAAAAAATCATGGCAATTCTGGAAGAAATAGCGCTT





TCAGCCGGCAAACCGGCTGAAGCCGGATCTGCGATTCTGATAACAAACTAGCAA





CACCAGAACAGCCCGTTTGCGGGCAGCAAAACCCGTACCGATTATCAAAAAGGA





TCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTA





TATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTA





TCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGT





AGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATAC





CGCGAGAACCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCG





GAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTA





TTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCA





ACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGG





CTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGT





TGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGT





TGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTG





TCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCAT





TCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGG





ATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTT





CTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATAT





AACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTT





CTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGA





CACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTT





ATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATA





AACAAATAGGGGTTCCGCG






pEG3121
MdnA*

ATGGCACTTCCTTTCTTTGCTCGTTTCTTGTCCGTAAGCAAAGAGGAATCTTCC

607





ATCAAGTCTCCTTCCCCTGAGCCTACCTACGGGGGCACCTTTAAATACCCTTCT







GACTGGGAAGATTATTAATAA







pEG3128
ProcA*

ATGTCAGAAGAACAACTCAAGGCATTCATTGCCAAGGTTCAAGCAGACACTTCA

608





CTGCAGGAACAGCTCAAAGTAGAAGGTGCTGATGTTGTTGCTATTGCTAAAGCC







TCAGGGTTCGCGATTACCACAGAGGACCTCAATTCGCATCGCCAAAATCTGTCT







GATGATGAGCTGGAGGGAGTCGCGGGAGGCTTTTTCTGCGTACAGGGTACGGCC







AACCGTTTCACTATCAACGTTTGCTGATAA







pEG3132
PaaP

ATGATTAAATTTTCTACATTGTCTCAGCGCATCAGCGCCATCACGGAAGAAAAC

609





GCCATGTACACTAAGGGTCAAGTGATCGTATTGAGCTGATAA







pEG3248
SboA

ATGAAAAAAGCTGTCATTGTAGAAAACAAAGGTTGTGCAACATGCTCGATCGGA

610





GCCGCTTGTCTAGTGGACGGTCCTATCCCTGATTTTGAAATTGCCGGTGCAACA







GGTCTATTCGGTCTATGGGGATAA







bEG_S5
RSTn
CACATTTCCCCGAAAAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGAC
611



expression
ATTAACCTATAAAAATAGGCGTATCACGAGGCAGAATTTCAGATAAAAAAAATC




vector (w/

CTTAGCTTTCGCTAAGGATGATTTCTGGAATTCGCGGCCGCTTCTAGAGGGAGG





flanking
GTCTCAGTGCAACGATCGTTGGCTGaatcataaaaaatttatttgctttgtgag




restriction


embedded image






sites)


embedded image








TCACGGGTCCCTGCAGGACTCAGAAGTCAATCAAGAAGCTAAGCCAGAGGTCAA







GCCAGAAGTCAAGCCTGAGACTCACATCAATTTAAAGGTGTCCGATGGATCTTC







AGAGATCTTCTTCAAGATCAAAAAGACCACTCCTTTAAGAAGGCTGATGGAAGC







GTTCGCTAAAAGACAGGGTAAGGAAATGGACTCCTTAAGATTCTTGTACGACGG







TATTAGAATTCAAGCTGATCAGGCCCCTGAAGATTTGGACATGGAGGATAACGA







TATTATTGAGGCTCACCGCGAACAGATTGGAGGTTGCATGTCATATTACGACTC







CATTCCCACAAGCGAGAACTTGTACTTTCAAGGGTGC

ATGAGCAAAGGAGAAGA









ACTTTTCACTGGAGTTGTCCCAATTCTTGTTGAATTAGATGGTGATGTTAATGG









GCACAAATTTTCTGTCCGTGGAGAGGGTGAAGGTGATGCTACAAACGGAAAACT









CACCCTTAAATTTATTTGCACTACTGGAAAACTACCTGTTCCGTGGCCAACACT









TGTCACTACTCTGACCTATGGTGTTCAATGCTTTTCCCGTTATCCGGATCACAT









GAAACGGCATGACTTTTTCAAGAGTGCCATGCCCGAAGGTTATGTACAGGAACG









CACTATATCTTTCAAAGATGACGGGACCTACAAGACGCGTGCTGAAGTCAAGTT









TGAAGGTGATACCCTTGTTAATCGTATCGAGTTAAAGGGTATTGATTTTAAAGA









AGATGGAAACATTCTTGGACACAAACTCGAGTACAACTTTAACTCACACAATGT









ATACATCACGGCAGACAAACAAAAGAATGGAATCAAAGCTAACTTCAAAATTCG









CCACAACGTTGAAGATGGTTCCGTTCAACTAGCAGACCATTATCAACAAAATAC









TCCAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTCGACACA









ATCTGTCCTTTCGAAAGATCCCAACGAAAAGCGTGACCACATGGTCCTTCTTGA









GTTTGTAACTGCTGCTGGGATTACACATGGCATGGATGAGCTCTACAAATAA

TT







CAGCCAAAAAACTTAAGACCGCCGGTCTTGTCCACTACCTTGCAGTAATGCGGT







GGACAGGATCGGCGGTTTTCTTTTCTCTTCTCAACAAGTGAGACCATGGgcggc








embedded image









embedded image








AGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCC







ACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATT







ACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTTATTG







GCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGTCGCGGCGA







TTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAAC







GAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCG







TCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGG







AAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGACAC







CCATCAACAGTATTATTTTCTCCCATGAGGACGGTACGCGACTGGGCGTGGAGC







ATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTT







CTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCTCACTCGCAATC







AAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTC







AACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTTG







CCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGCTGC







GCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGATAGCTCAT







GTTATATCCCGCCGTTAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAA







CCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATC







AGCTGTTGCCAGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGC







AAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGG







TTTCCCGACTGGAAAGCGGGCAGTGATAA
TTGGTAACGAATCAGACAATTGACG







GCTCGAGGGAGTAGCATAGGGTTTGCAGAATCCCTGCTTCGTCCATTTGACAGG







CACATTATGCATCGATGATAAGCTGTCAAACATGAGCACGCTTACTAGTAGCGG






CCGCTGCAGTCCGGCAAAAAAGGGCAAGGTGTCACCACCCTGCCCTTTTTCTTT






AAAACCGAAAAGATTACTTCGCGTTATGCAGGCTTCCTCGCTCACTGACTCGCT






GCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAAT





GACAGTAAGACGGGTAAGCCTGTTGATGATACCGCTGCCTTACTGGGTGCATTA





GCCAGTCTGAATGACCTGTCACGGGATAATCCGAAGTGGTCAGACTGGAAAATC





AGAGGGCAGGAACTGCTGAACAGCAAAAAGTCAGATAGCACCACATAGCAGACC





CGCCATAAAACGCCCTGAGAAGCCCGTGACGGGCTTTTCTTGTATTATGGGTAG





TTTCCTTGCATGAATCCATAAAAGGCGCCTGTAGTGCCATTTACCCCCATTCAC





TGCCAGAGCCGTGAGCGCAGCGAACTGAATGTCACGAAAAAGACAGCGACTCAG





GTGCCTGATGGTCGGAGACAAAAGGAATATTCAGCGATTTGCCCGAGCTTGCGA





GGGTGCTACTTAAGCCTTTAGGGTTTTAAGGTCTGTTTTGTAGAGGAGCAAACA





GCGTTTGCGACATCCTTTTGTAATACTGCGGAACTGACTAAAGTAGTGAGTTAT





ACACAGGGCTGGGATCTATTCTTTTTATCTTTTTTTATTCTTTCTTTATTCTAT





AAATTATAACCACTTGAATATAAACAAAAAAAACACACAAAGGTCTAGCGGAAT





TTACAGAGGGTCTAGCAGAATTTACAAGTTTTCCAGCAAAGGTCTAGCAGAATT





TACAGATACCCACAACTCAAAGGAAAAGGACTAGTAATTATCATTGACTAGCCC





ATCTCAATTGGTATAGTGATTAAAATCACCTAGACCAATTGAGATGTATGTCTG





AATTAGTTGTTTTCAAAGCAAATGAACTAGCGATTAGTCGCTATGACTTAACGG





AGCATGAAACCAAGCTAATTTTATGCTGTGTGGCACTACTCAACCCCACGATTG





AAAACCCTACAAGGAAAGAACGGACGGTATCGTTCACTTATAACCAATACGCTC





AGATGATGAACATCAGTAGGGAAAATGCTTATGGTGTATTAGCTAAAGCAACCA





GAGAGCTGATGACGAGAACTGTGGAAATCAGGAATCCTTTGGTTAAAGGCTTTT





GGATTTTCCAGTGGACAAACTATGCCAAGTTCTCAAGCGAAAAATTAGAATTAG





TTTTTAGTGAAGAGATATTGCCTTATCTTTTCCAGTTAAAAAAATTCATAAAAT





ATAATCTGGAACATGTTAAGTCTTTTGAAAACAAATACTCTATGAGGATTTATG





AGTGGTTATTAAAAGAACTAACACAAAAGAAAACTCACAAGGCAAATATAGAGA





TTAGCCTTGATGAATTTAAGTTCATGTTAATGCTTGAAAATAACTACCATGAGT





TTAAAAGGCTTAACCAATGGGTTTTGAAACCAATAAGTAAAGATTTAAACACTT





ACAGCAATATGAAATTGGTGGTTGATAAGCGAGGCCGCCCGACTGATACGTTGA





TTTTCCAAGTTGAACTAGATAGACAAATGGATCTCGTAACCGAACTTGAGAACA





ACCAGATAAAAATGAATGGTGACAAAATACCAACAACCATTACATCAGATTCCT





ACCTACATAACGGACTAAGAAAAACACTACACGATGCTTTAACTGCAAAAATTC





AGCTCACCAGTTTTGAGGCAAAATTTTTGAGTGACATGCAAAGTAAGTATGATC





TCAATGGTTCGTTCTCATGGCTCACGCAAAAACAACGAACCACACTAGAGAACA





TACTGGCTAAATACGGAAGGATCTGAGGTTCTTATGGCTCTTGTATCTATCAGT





GAAGCATCAAGACTAACAAACAAAAGTAGAACAACTGTTCACCGTTACATATCA





AAGGGAAAACTGTCCATATGCACAGATGAAAACGGTGTAAAAAAGATAGATACA





TCAGAGCTTTTACGAGTTTTTGGTGCATTCAAAGCTGTTCACCATGAACAGATC





GACAATGTAACAGATGAACAGCATGTAACACCTAATAGAACAGGTGAAACCAGT





AAAACAAAGCAACTAGAACATGAAATTGAACACCTGAGACAACTTGTTACAGCT





CAACAGTCACACATAGACAGCCTGAAACAGGCGATGCTGCTTATCGAATCAAAG





CTGCCGACAACACGGGAGCCAGTGACGCCTCCCGTGGGGAAAAAATCATGGCAA





TTCTGGAAGAAATAGCGCTTTCAGCCGGCAAACCGGCTGAAGCCGGATCTGCGA





TTCTGATAACAAACTAGCAACACCAGAACAGCCCGTTTGCGGGCAGCAAAACCC





GTACCGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAG





TTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATG





CTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGT





TGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGG





CCCCAGTGCTGCAATGATACCGCGAGAACCACGCTCACCGGCTCCAGATTTATC





AGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTT





ATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTC





GCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTC





ACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCG





AGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCC





GATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGC





ACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGG





TGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTC





TTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGT





GCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCT





GTTGAGATCCAGTTCGATATAACCCACTCGTGCACCCAACTGATCTTCAGCATC





TTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGC





AAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTT





TCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATT





TGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCG






pEG2192
PapoA

AGCAAGAAAGAATGGCAAGAGCCCACGATCGAAGTGCTCGATATTAATCAGACT

612





ATGGCGGGTAAGGGCTGGAAACAGATAGACTGGGTGAGCGACCATGATGCTGAC







TTACACAATCCGTCTTAATAA







pEG2194
BamA

CTGAAAATCCGCAAGGTGAAAATTGTCAGAGCGCAGAACGGCCACTACACGAAC

613





TAATAA







pEG2195
EpiA

GAAGCAGTTAAAGAGAAGAACGATCTGTTCAACCTGGATGTTAAAGTCAACGCA

614





AAAGAAAGTAACGATAGTGGCGCAGAACCACGCATAGCGTCGAAATTTATTTGC







ACACCAGGCTGCGCGAAAACGGGTTCGTTTAACAGCTATTGTTGTTAATAA







pEG2199
HalA1

ACGAACTTGCTGAAAGAATGGAAAATGCCCCTGGAACGTACGCATAATAACTCC

615





AACCCGGCGGGAGACATTTTTCAGGAACTGGAAGATCAAGACATACTCGCCGGT







GTGAATGGAGCAGAAAACTTATACTTTCAGGGTTGTGCGTGGTATAACATTAGC







TGCCGTCTGGGCAACAAAGGAGCCTACTGCACCCTTACAGTTGAGTGCATGCCC







TCCTGTAACTGATAA







pEG2200
HalA2

GTGAATTCCAAAGACCTGAGAAATCCAGAATTTCGCAAAGCTCAGGGTCTGCAG

616





TTTGTAGATGAAGTTAATGAGAAGGAACTCTCGAGTTTAGCCGGCAGCGAGAAT







CTTTACTTTCAAGGCACGACGTGGCCATGTGCGACCGTCGGCGTTTCAGTTGCC







TTGTGCCCGACGACCAAATGCACTTCACAGTGCTGATAA







pEG2312
PapA_tev

TTGAAACAGATCAATGTGATTGCTGGCGTAAAAGAGCCTATTCGCGCCTATGAG

617





AACTTGTATTTCCAGGGTTGTTCGGCTAATGACGCATGCTATTTTTGCGACACG







CGTGACAACTGCAAAGCCTGTGATGCCAGTGATTTTTGTATCAAAAGTGATACG







pEG2571
TruE_tev

AACAAGAAGAACATTTTACCGCAGTTAGGACAACCAGTCATCCGCCTTACTGCC

618





GGTCAACTGTCAAGCCAACTGGCGGAGCTTTCTGAGGAGGCTCTGGGAGAGAAC







TTGTATTTCCAGGGTGTCGATGCCTCGACCTTGCCGGTTCCGACGTTGTGTAGC







TATGACGGGGTGGACGCTAGCACAGTCCCTACACTTTGTAGTTACGATGAC







pEG2575
PsnA2_tev

ATGAGCAAAAATGAGAACAACAAGAAACAGCTGCGCGATCTTTTCATTGAAGAT

619





CTGGGCAAAGTTACTGGCGAGAACTTGTATTTCCAGGGTAAAGGTGGCCCGTAT







ACCACCTTAGCCATTGGCGAAGAAGATCCGATTACCACTTTGGCTATCGGAGAA







GAGGACCCTGATCCAACGACACTTGCCTTAGGTGAAGAGGACCCAACTACGCTT







GCAATCGGCGAAGAA







pEG3157
MibA

ATGCCAGCCGATATTCTGGAGACTCGTACCAGCGAAACGGAGGACTTACTGGAT

620





CTTGACCTGAGCATCGGTGTAGAAGAAATCACCGCAGGCCCGGCAGTGACTTCT







TGGTCACTGTGCACCCCTGGATGCACGAGTCCGGGCGGTGGCTCCAATTGTTCG







TTCTGTTGCTAATAA







pEG3161
PlpA1

ATGAGCATTGAGAATGCCAAGAGCTTTTATGAACGCGTCAGTACAGATAAGCAG

621





TTCCGCACTCAACTGGAAAATACGGCCAGTGCTGAAGAACGGCAGAAAATCATT







CAGGCAGCGGGCTTTGAGTTCACCAATCAGGAGTGGGAAATTGCAAAAGAACAG







ATTCTTGCGACAAGTGAAAGTAATAACGGTGAACTGTCCGAGGCCGAACTGACC







GCCGTCAGCGGTGGGGTTGACTTAAGCATTTTCGAGCTGCTGGACGAAGAACCT







TTATTCCCGATTCGTCCTTTGTACGGCCTGCCTATTTAATAA







pEG3162
PlpA2

ATGTCTATTGAGAGTGCAAAGGCTTTCTACCAGCGTATGACGGATGACGCATCT

622





TTTCGTACCCCTTTTGAAGCGGAACTGTCGAAAGAGGAGCGCCAACAATTAATC







AAAGATAGCGGATATGACTTTACTGCAGAAGAATGGCAACAGGCTATGACCGAG







ATCCAGGCGGCACGCTCAAACGAGGAACTGAATGAGGAAGAACTCGAGGCAATT







GCCGGGGGCGCTGTGGCCGCAATGTATGGTGTGGTTTTCCCATGGGACAACGAG







TTCCCGTGGCCCCGCTGGGGCGGTTAATAA







pEG3165
PbtA

ATGAACCTGAACGATTTACCTATGGACGTCTTTGAAATGGCAGACAGCGGTATG

623





GAGGTGGAAAGCCTCACGGCTGGCCATGGCATGCCAGAAGTTGGAGCTAGTTGC







AACTGTGTGTGCGGGTTTTGCTGCAGCTGCAGTCCGAGCGCGTAATAA







pEG3172
LtnA1

ATGAATAAAAACGAAATCGAAACCCAGCCAGTTACGTGGCTGGAGGAAGTTTCT

624





GATCAGAATTTTGATGAGGATGTCTTTGGTGCGTGTAGCACAAACACCTTCTCG







CTGAGCGATTACTGGGGTAACAACGGTGCTTGGTGTACACTCACGCACGAATGT







ATGGCATGGTGCAAGTAATAA







pEG3173
LtnA2

ATGAAGGAAAAGAATATGAAGAAAAACGACACCATCGAACTTCAGCTTGGAAAA

625





TACCTGGAAGATGATATGATCGAACTGGCTGAAGGGGATGAGTCCCATGGGGGT







ACTACCCCGGCTACCCCTGCGATTTCTATCCTCAGCGCGTATATCAGCACCAAT







ACCTGCCCGACAACTAAGTGTACACGCGCGTGCTAATAA







pEG3174
CrnA1

ATGTCCGAACTGAGTATGGAGAAAGTGGTCGGCGAAACATTTGAGGATCTGAGC

626





ATCGCGGAAATGACGATGGTGCAGGGCAGCGGCGACATTAACGGCGAATTTACT







ACCTCGCCGGCATGTGTTTATTCCGTTATGGTTGTATCGAAAGCAAGCAGCGCT







AAATGTGCGGCCGGTGCATCGGCAGTCTCGGGAGCCATTCTGAGTGCGATTCGT







TGCTAATAA







pEG3175
CrnA2

ATGAGCGAATCCAACATGAAGAAGGTTGTTGGCGAAACCTTCGAAGATCTGAGC

627





ATCGCAGAAATGACGAAAGTTCAGGGCTCAGGGGACGTGATGCCGGAATCTACC







CCAATTTGTGCCGGCTTCGCAACCTTGATGAGTTCTATCGGTCTTGTTAAAACC







ATCAAAGGCAATGTCAAAAGTTTCTCCGTCTTAATTTAATAA







pEG3176
BsjA2

ATGACCAATGAAGAGATCATTGTCGCGTGGAAAAACCCTAAAGTCCGTGGCAAA

628





AATATGCCAAGTCACCCGAGCGGCGTGGGATTCCAAGAGCTTTCCATCAACGAG







ATGGCCCAAGTGACCGGCGGAGCAGTAGAACAGCGTGCAACACCAACCCTGGCA







ACCCCGCTGACCCCGCATACCCCGTACGCAACCTATGTGGTTAGCGGAGGCGTG







GTTAGCGCGATTTCTGGTATCTTCAGCAACAATAAAACGTGTCTGGGCTAATAA







pEG3177
BsjA3

ATGACCAATGAGGAAATTATCGTTGCGTGGAAAAACCCGAAGGTGCGCGGCAAA

629





AACATGCCTTCCCATCCGTCCGGTGTGGGCTTCCAGGAATTATCTATTAATGAA







ATGGCACAGGTGACTGGTGGCGCGGTTGAACAGCGCGCGACGCCGGCAACCCCA







GCAACACCATGGCTGATTAAAGCGTCTTATGTGGTGAGTGGGGCGGGAGTTTCT







TTTGTCGCAAGCTATATCACTGTAAACTAATAA







pEG3178
CinA

ATGACGGCGAGTATTCTTCAGTCTGTCGTTGATGCGGACTTTCGTGCGGCCCTG

630





ATTGAAAACCCAGCCGCATTCGGCGCGAGCACCGCAGTTTTGCCGACCCCAGTC







GAACAGCAGGATCAGGCATCACTGGATTTTTGGACAAAAGATATTGCTGCCACT







GAGGCGTTTGCTTGCAAACAGTCTTGCTCATTTGGGCCGTTCACCTTTGTGTGC







GACGGGAATACCAAATAATAA







pEG3180
LasA

ATGGACAAACGTGTGCGTTACGAAAAACCGAGCCTGGTGAAAGAGGGTACGTTT

631





CGCAAAACTACCGCTGGCCTGCGGCGTCTGTTCGCTGACCAGCTGGTTGGCCGC







CGTAACATTTAATAA







pEG3181
AlbsA

ATGGATTCACTGCTGTCAACAGAAACCGTCATTAGTGATGACGAACTGCTTCCG

632





ATTGAAGTTGGTGGTACCGCGGAATTGACAGAGGGGCAGGGCGGCGGTCAGTCC







GAGGATAAACGTCGCGCTTATAACTGCTAATAA







pEG3182
McbA

ATGGAATTAAAAGCGAGTGAATTTGGTGTAGTTTTGTCCGTTGATGCTCTTAAA

633





TTATCACGCCAGTCTCCATTAGGTGTTGGCATTGGTGGTGGTGGCGGCGGCGGC







GGCGGCGGCGGTAGCTGCGGTGGTCAAGGTGGCGGTTGTGGTGGTTGCAGCAAC







GGTTGTAGTGGTGGAAACGGTGGCAGCGGCGGAAGTGGTTCACATATCTAATAA







pEG3194
PsnA2

ATGAGCAAAAATGAGAACAACAAGAAACAGCTGCGCGATCTTTTCATTGAAGAT

634





CTGGGCAAAGTTACTGGCGGTAAAGGTGGCCCGTATACCACCTTAGCCATTGGC







GAAGAAGATCCGATTACCACTTTGGCTATCGGAGAAGAGGACCCTGATCCAACG







ACACTTGCCTTAGGTGAAGAGGACCCAACTACGCTTGCAATCGGCGAAGAATAA







TAA







pEG3197
AMdnA

ATGCCGGAAAATCGGCAGGAAGATCTCAACGCTCAGGCTGTACCATTCTTCGCG

635





CGTTTCTTGGAGGGTCAAAACTGCGAGGACCTTACTGATGAGGAATCGGAGGCG







GTTAGCGGTGGAAAACGCGGCCAAACCCGTAAATATCCAAGCGACTGCGAAGAT







GGGAATGGCGTGACCGGTAAACTGCGCGATGAAGATATTGCAGTGACCTTGAAG







TACCCATCCGACAATGAAGATAATGGCGGCGGTGAAATTGTGACTCTGAAGTTT







CCAAGTGATGATGATGATCAACCAGTAGGCTAATAA







pEG3283
PapA

ATGTTGAAACAGATCAATGTGATTGCTGGCGTAAAAGAGCCTATTCGCGCCTAT

636





GGTTGTTCGGCTAATGACGCATGCTATTTTTGCGACACGCGTGACAACTGCAAA







GCCTGTGATGCCAGTGATTTTTGTATCAAAAGTGATACGTAATAA







pEG3286
PcpA

ATGTCGAGTAATATCCTCGAAAAAGTTAAGGAGTTTTTCGTCCGGCTGGTGAAG

637





GATGATGCGTTTCAAAGCCAGCTGCAGAACAACAGTATTGATGAAGTTCGAAAT







ATCCTGCAGGAGGCCGGGTACATATTCAGCAAAGAAGAATTCGAAACCGCAACC







ATTGAATTGCTGGATTTGAAGGAACGCGATGAATTCCACGAGCTGACAGAAGAG







GAGCTTGTCACCGCTGTTGGCGGTGTTACGGGCGGGAGTGGTATATATGGCCCG







ATTCAAGCTATGTACGGTGCCGTCGTAGGTGATCCAAAACCGGGTAAGGACTGG







GGGTGGCGCTTTCCGAGCCCGCTGCCAAAACCGAGTCCGATTCCGAGTCCGTGG







AAACCCCCGGTTGATGTCCAGCCTATGTATGGTGTGGTAGTGTCAAACGATAGT







TAATAA







pEG3563
PadeA

AAAAAGCAATATAGCAAACCTAGCCTGGAGGTTCTGGACGTCCACCAGACCATG

638





GCTGGCCCGGGCACTAGTACGCCAGACGCGTTTCAGCCAGATCCAGATGAAGAT







GTTCACTATGATTCGTAATAA







pEG3564
ThcoA

CGCAAGAAAGAATGGCAGACACCAGAACTGGAAGTACTCGATGTACGCCTCACC

639





GCAGCGGGCCCGGGTAAAGCTAAACCGGATGCTGTGCAGCCAGACGAAGATGAA







ATAGTGCACTACTCATAATAA







pEG3565
StspA

AAGAAATTCTATGAAGCGCCAGCTCTCATCGAACGTGGCGCCTTTGCGGCTGCT

640





ACAGCGGGGTTTGGACGTCTGCTGGCGGATCAGCTGGTGGGACGCCTGATTCCG







TAATAA







pEG3567
LcnA

ACTAAAGGCCTGGACAAAATGCTTTTAACCAAAAAGAAGAAGGATAGTATGGGT

641





CTGCTGAACGAAATCGACGTTACCACCCTGGATGAACAGTTAGGCGGTAAAATG







AGCAAAGCATGGTGCCGATCCATGGTGGTGTCCTGCGTGTATAACCTGGTTGAT







TTTTCGTCGTCGAGTGACGGGAAAAAGACATGTGCTCTGTACCGCAAATATTGT







TAATAA







pEG3568
PalA

AAAGATCTTCTGAAGGAACTGATGTATGAAGTAGACCTCGAAGAGATGGAGAAT

642





CTTCAGGGTAGCGGGTACTCAGCCGCCCAGTGTGCCTGGATGGCGCTGAGCTGC







GTCAATTACATCCCGGGAGTGGGATTCGGTTGTGGCGGCTACAGCGCATGTGAA







CTCTACAAGCGTTATTGTTAATAA







pEG3570
RaxX

AACCACTCTAAGAAAAGTCCGGCAAAAGGGGCAGCGTCCCTGCAGCGTCCTGCT

643





GGGGCAAAAGGCCGCCCTGAACCTCTGGATCAACGCTTGTGGAAACACGTCGGT







GGTGGTGACTACCCACCCCCAGGAGCCAACCCAAAGCATGATCCACCACCCCGC







AATCCGGGCCACCATTAATAA







pEG3571
ComX

CAAGATCTGATTAATTACTTCCTGAATTATCCTGAGGCTCTGAAGAAACTCAAG

644





AATAAGGAAGCCTGCTTAATTGGGTTTGACGTCCAGGAAACCGAAACGATTATC







AAAGCCTATAACGATTACTACCGCGCTGATCCGATCACGCGTCAATGGGGTGAT







TAATAA







pEG3572
KgpE

AAGAACCCGACGCTGTTGCCCAAACTGACCGCGCCGGTCGAACGTCCGGCCGTA

645





ACTTCGTCGGATTTAAAGCAAGCCTCAAGCGTCGATGCTGCATGGTTAAATGGC







GATAATAACTGGTCAACCCCATTCGCCGGTGTGAACGCGGCATGGTTAAATGGG







GACAACAACTGGTCCACGCCTTTTGCGGGCGTGAATGCTGCATGGCTTAATGGC







GACAATAACTGGAGCACTCCATTTGCCGCCGATGGCGCTGAGTAATAA







pEG3574
TgnA*

TATCGACCTTATATTGCCAAGTATGTCGAAGAACAAACTCTGCAGAATTCAACC

646





AACCTGGTATATGACGACATCACGCAGATCTCTTTTATCAATAAAGAAAAGAAC







GTGAAAAAAATTAATCTGGGTCCCGATACTACGATCGTGACTGAAACCATCGAG







AATGCGGACCCCGATGAGTATTTCTTATAATAA







pEG3871
SgbA

TCTGGTCGCGGGCGCGATCCTGATGCTGCTGTACCTCCCTTGCCTCGTGTACCT

647





CGCACTACTAATCATGAGCCACGTACGGCGTCCCGAGAACCAAGAGCAGCTCCA







AGAACTGGACCTACACGTCCGCCTTCGTCGCGTCCATCTCCGTGTGGTCACTCT







CCTCAAACCCCTGGTGCAGGACGCAGTGGATGTCGTGTGGAGCGTCAAAAATCG







GCTGCGGCTTCGTCTGAGAAGGAAAAGACAATGGAGAACCAAGATTTGGAGTTA







TTAGCACGCCTGCATGCACTTCCTGAGACTGAACCGGTGGGCGTCGACGGATTA







CCCTATGGCGAGACTTGTGAGTGCGTCGGGTTACTTACGTTGTTGAACACCGTA







TGTATCGGCATTTCATGCGCTTAATAA







pEG3905
TruE

ATGAACAAGAAGAACATTTTACCGCAGTTAGGACAACCAGTCATCCGCCTTACT

648





GCCGGTCAACTGTCAAGCCAACTGGCGGAGCTTTCTGAGGAGGCTCTGGGAGTC







GATGCCTCGACCTTGCCGGTTCCGACGTTGTGTAGCTATGACGGGGTGGACGCT







AGCACAGTCCCTACACTTTGTAGTTACGATGAC







bEG_S6
RSTc
CACATTTCCCCGAAAAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGAC
649



expression
ATTAACCTATAAAAATAGGCGTATCACGAGGCAGAATTTCAGATAAAAAAAATC




vector

CTTAGCTTTCGCTAAGGATGATTTCTGGAATTCGCGGCCGCTTCTAGAGGGAGA






ACGATCGTTGGCTGaatcataaaaaatttatttgctttgtgagcggataacaat







embedded image









embedded image









AAGGAGAAGAACTTTTCACTGGAGTTGTCCCAATTCTTGTTGAATTAGATGGTG









ATGTTAATGGGCACAAATTTTCTGTCCGTGGAGAGGGTGAAGGTGATGCTACAA









ACGGAAAACTCACCCTTAAATTTATTTGCACTACTGGAAAACTACCTGTTCCGT









GGCCAACACTTGTCACTACTCTGACCTATGGTGTTCAATGCTTTTCCCGTTATC









CGGATCACATGAAACGGCATGACTTTTTCAAGAGTGCCATGCCCGAAGGTTATG









TACAGGAACGCACTATATCTTTCAAAGATGACGGGACCTACAAGACGCGTGCTG









AAGTCAAGTTTGAAGGTGATACCCTTGTTAATCGTATCGAGTTAAAGGGTATTG









ATTTTAAAGAAGATGGAAACATTCTTGGACACAAACTCGAGTACAACTTTAACT









CACACAATGTATACATCACGGCAGACAAACAAAAGAATGGAATCAAAGCTAACT









TCAAAATTCGCCACAACGTTGAAGATGGTTCCGTTCAACTAGCAGACCATTATC









AACAAAATACTCCAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACC









TGTCGACACAATCTGTCCTTTCGAAAGATCCCAACGAAAAGCGTGACCACATGG









TCCTTCTTGAGTTTGTAACTGCTGCTGGGATTACACATGGCATGGATGAGCTCT









ACAAA

CGACTGGTTCCGCGTGGTAGCTATTACGACTCCATTCCCACAAGCGAGA







ACGACTCAGAAGTCAATCAAGAAGCTAAGCCAGAGGTCAAGCCAGAAGTCAAGC







CTGAGACTCACATCAATTTAAAGGTGTCCGATGGATCTTCAGAGATCTTCTTCA







AGATCAAAAAGACCACTCCTTTAAGAAGGCTGATGGAAGCGTTCGCTAAAAGAC







AGGGTAAGGAAATGGACTCCTTAAGATTCTTGTACGACGGTATTAGAATTCAAG







CTGATCAGGCCCCTGAAGATTTGGACATGGAGGATAACGATATTATTGAGGCTC







ACCGCGAACAGATTGGAGGCTCCATTACAAGCCACCATCACCATCATCACGGTT







AATACTTTCAGCCAAAAAACTTAAGACCGCCGGTCTTGTCCACTACCTTGCAGT







AATGCGGTGGACAGGATCGGCGGTTTTCTTTTCTCTTCTCAACAAGTGAGACCA






TGGgcggcgcgccatcgaatggcgcaaaacctttcgcggtatggcatgatagcg







embedded image








TGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCA







GGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGA







GCTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTT







GCTTATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGT







CGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGAT







GGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGC







GCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCAT







TGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGA







CCAGACACCCATCAACAGTATTATTTTCTCCCATGAGGACGGTACGCGACTGGG







CGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTAGCGGGCCC







ATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCTCAC







TCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTC







CGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGAT







GCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTC







CGGGCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGA







TAGCTCATGTTATATCCCGCCGTTAACCACCATCAAACAGGATTTTCGCCTGCT







GGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAA







GGGCAATCAGCTGTTGCCAGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCC







CAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGC







ACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGATAA
TTGGTAACGAATCAGAC







AATTGACGGCTCGAGGGAGTAGCATAGGGTTTGCAGAATCCCTGCTTCGTCCAT







TTGACAGGCACATTATGCATCGATGATAAGCTGTCAAACATGAGCACGCTTACT






AGTAGCGGCCGCTGCAGTCCGGCAAAAAAGGGCAAGGTGTCACCACCCTGCCCT






TTTTCTTTAAAACCGAAAAGATTACTTCGCGTTATGCAGGCTTCCTCGCTCACT






GACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAG





GCGGTAATGACAGTAAGACGGGTAAGCCTGTTGATGATACCGCTGCCTTACTGG





GTGCATTAGCCAGTCTGAATGACCTGTCACGGGATAATCCGAAGTGGTCAGACT





GGAAAATCAGAGGGCAGGAACTGCTGAACAGCAAAAAGTCAGATAGCACCACAT





AGCAGACCCGCCATAAAACGCCCTGAGAAGCCCGTGACGGGCTTTTCTTGTATT





ATGGGTAGTTTCCTTGCATGAATCCATAAAAGGCGCCTGTAGTGCCATTTACCC





CCATTCACTGCCAGAGCCGTGAGCGCAGCGAACTGAATGTCACGAAAAAGACAG





CGACTCAGGTGCCTGATGGTCGGAGACAAAAGGAATATTCAGCGATTTGCCCGA





GCTTGCGAGGGTGCTACTTAAGCCTTTAGGGTTTTAAGGTCTGTTTTGTAGAGG





AGCAAACAGCGTTTGCGACATCCTTTTGTAATACTGCGGAACTGACTAAAGTAG





TGAGTTATACACAGGGCTGGGATCTATTCTTTTTATCTTTTTTTATTCTTTCTT





TATTCTATAAATTATAACCACTTGAATATAAACAAAAAAAACACACAAAGGTCT





AGCGGAATTTACAGAGGGTCTAGCAGAATTTACAAGTTTTCCAGCAAAGGTCTA





GCAGAATTTACAGATACCCACAACTCAAAGGAAAAGGACTAGTAATTATCATTG





ACTAGCCCATCTCAATTGGTATAGTGATTAAAATCACCTAGACCAATTGAGATG





TATGTCTGAATTAGTTGTTTTCAAAGCAAATGAACTAGCGATTAGTCGCTATGA





CTTAACGGAGCATGAAACCAAGCTAATTTTATGCTGTGTGGCACTACTCAACCC





CACGATTGAAAACCCTACAAGGAAAGAACGGACGGTATCGTTCACTTATAACCA





ATACGCTCAGATGATGAACATCAGTAGGGAAAATGCTTATGGTGTATTAGCTAA





AGCAACCAGAGAGCTGATGACGAGAACTGTGGAAATCAGGAATCCTTTGGTTAA





AGGCTTTTGGATTTTCCAGTGGACAAACTATGCCAAGTTCTCAAGCGAAAAATT





AGAATTAGTTTTTAGTGAAGAGATATTGCCTTATCTTTTCCAGTTAAAAAAATT





CATAAAATATAATCTGGAACATGTTAAGTCTTTTGAAAACAAATACTCTATGAG





GATTTATGAGTGGTTATTAAAAGAACTAACACAAAAGAAAACTCACAAGGCAAA





TATAGAGATTAGCCTTGATGAATTTAAGTTCATGTTAATGCTTGAAAATAACTA





CCATGAGTTTAAAAGGCTTAACCAATGGGTTTTGAAACCAATAAGTAAAGATTT





AAACACTTACAGCAATATGAAATTGGTGGTTGATAAGCGAGGCCGCCCGACTGA





TACGTTGATTTTCCAAGTTGAACTAGATAGACAAATGGATCTCGTAACCGAACT





TGAGAACAACCAGATAAAAATGAATGGTGACAAAATACCAACAACCATTACATC





AGATTCCTACCTACATAACGGACTAAGAAAAACACTACACGATGCTTTAACTGC





AAAAATTCAGCTCACCAGTTTTGAGGCAAAATTTTTGAGTGACATGCAAAGTAA





GTATGATCTCAATGGTTCGTTCTCATGGCTCACGCAAAAACAACGAACCACACT





AGAGAACATACTGGCTAAATACGGAAGGATCTGAGGTTCTTATGGCTCTTGTAT





CTATCAGTGAAGCATCAAGACTAACAAACAAAAGTAGAACAACTGTTCACCGTT





ACATATCAAAGGGAAAACTGTCCATATGCACAGATGAAAACGGTGTAAAAAAGA





TAGATACATCAGAGCTTTTACGAGTTTTTGGTGCATTCAAAGCTGTTCACCATG





AACAGATCGACAATGTAACAGATGAACAGCATGTAACACCTAATAGAACAGGTG





AAACCAGTAAAACAAAGCAACTAGAACATGAAATTGAACACCTGAGACAACTTG





TTACAGCTCAACAGTCACACATAGACAGCCTGAAACAGGCGATGCTGCTTATCG





AATCAAAGCTGCCGACAACACGGGAGCCAGTGACGCCTCCCGTGGGGAAAAAAT





CATGGCAATTCTGGAAGAAATAGCGCTTTCAGCCGGCAAACCGGCTGAAGCCGG





ATCTGCGATTCTGATAACAAACTAGCAACACCAGAACAGCCCGTTTGCGGGCAG





CAAAACCCGTACCGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAA





AAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGT





TACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCA





TCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTA





CCATCTGGCCCCAGTGCTGCAATGATACCGCGAGAACCACGCTCACCGGCTCCA





GATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCT





GCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTA





AGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATC





GTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGA





TCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTC





GGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTT





ATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCT





GTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCG





AGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACT





TTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATC





TTACCGCTGTTGAGATCCAGTTCGATATAACCCACTCGTGCACCCAACTGATCT





TCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAA





AATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTC





TTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGA





TACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCG






pEG3212
CapA

ATGGTGCGTTTCCTGGCTAAGCTGCTGCGTTCAACGATCCATGGCTCTAATGGC

650





GTGAGCCTCGACGCCGTCAGTTCCACGCATGGTACTCCGGGGTTTCAGACACCT







GATGCACGTGTTATTTCACGCTTTGGCTTTAAT







pEG3213
LasA

ATGGACAAACGTGTGCGTTACGAAAAACCGAGCCTGGTGAAAGAGGGTACGTTT

651





CGCAAAACTACCGCTGGCCTGCGGCGTCTGTTCGCTGACCAGCTGGTTGGCCGC







CGTAACATT







pEG3214
AlbsA

ATGGATTCACTGCTGTCAACAGAAACCGTCATTAGTGATGACGAACTGCTTCCG

652





ATTGAAGTTGGTGGTACCGCGGAATTGACAGAGGGGCAGGGCGGCGGTCAGTCC







GAGGATAAACGTCGCGCTTATAACTGC







pEG3215
AtxAl

CCGATCATTAGCGAAACGGTCCAGCCTAAAACGGCTGGCCTGATTGTTCTGGGC

653





AAGGCAAGCGCGGAAACGCGCGGATTGAGCCAAGGCGTGGAACCGGACATTGGT







CAGACGTACTTCGAAGAAAGCCGTATTAATCAGGAT







pEG3553
ClnlAl

ACTCCCATTCAATCCAAATTCTGCCTCCTGCGCGTGGGCAGTGCCAAACGGCTG

654





ACGCAGTCATTCGACGTGGGAACTATTAAGGAAGGTTTAGTCAGCCAGTATTAT







TTTGCG







pEG3554
ClnlA2

ACCCAGGTGAGCCCATCACCGCTGCGCCTGATTCGCGTCGGGAGAGCCTTGGAC

655





CTGACCCGCTCTATCGGGGATAGTGGGCTGCGTGAGTCCATGTCAAGCCAGACG







TACTGGCCC







pEG3555
Cln2Al

AACACTTTAAAAACGCGTCTTATTCGCTTTGGGTCGGCTAAACGTCTGACGCGC

656





GCAGGTACGGGCGTGCTGTTACCTGAAACCAACCAGATTAAGCGCTACGATCCA







GCA







pEG3556
Cln2A2

ACCACACCCAAATTTCGACTGATTCGGTTAGGTTCAGCTAAGCGATTGACCCGG

657





TCGGGAATCGGGGATGTGTTTCCGGAGCCAAACATGGTTCGCCGCTGGGAT







pEG3557
Cln3Al

CAGCGTATAATAGATGAAACCACCGATGGTCTGATTGAACTGGGGGCGGCCAGC

658





GTACAGACACAGGGCGATGTTTTGTTTGCTCCGGAGCCTGGCGTGGGCCGACCT







CCAATGGGCCTTTCCGAAGAT







pEG3558
Cln3A2

GAACGCATTGAAGATCATATTGATGATGAACTGATTGACCTGGGAGCTGCTTCG

659





GTTGAAACCCAGGGAGATGTGCTGAATGCACCGGAGCCTGGTATCGGTCGTGAA







CCGACAGGCTTGAGCCGCGAT







pEG3559
Cln3A3

GAATTTGAAGGTATCCCATCACCGGATGCGCGTATTGATTTGGGTCTGGCGTCG

660





GAAGAAACCTGTGGTCAGATTTATGATCACCCGGAAGTAGGCATCGGTGCGTAC







GGGTGCGAGGGCCTGCAGCGT







pEG3560
CsegAl

ACCAAGAAAAACGCAACACAGGCCCCACGTTTAGTACGTGTAGGCGATGCTCAT

661





CGTTTGACCCAAGGTGCTTTCGTTGGACAGCCGGAAGCCGTAAATCCACTTGGA







CGTGAAATTCAAGGA







pEG3561
CsegA2

ACCAAAACACACAGACTGATCAGATTGGGCGACGCGCAACGCTTGACCCAGGGC

662





ACATTGACTCCGGGCTTACCGGAGGACTTTCTGCCGGGCCATTACATGCCGGGG







pEG3562
CsegA3

ACTTCACGTTTCCAACTCCTGCGCCTGGGAAAAGCCGATCGTTTGACGCGTGGC

663





GCGCTGGTCGGGCTCCTGATCGAAGATATTACTGTCGCTCGCTACGACCCTATG







bEG_S7
Lux Mod
pEG1128 below contains the full sequence of this




Backbone
backbone.






pEG1128
TruD
AACACCCCTTGTATTACTGTTTATGTAAGCAGACAGTTTTATTGTTCATGATGA
664




TATATTTTTATCTTGTGCAATGTACATCAGAGATTTTGAGACACAACCAATTAT






TGAAGGCCTCCCTAACGGGGGGCCTTTTTTTGTTTCTGGTCTCCACGACGCTTA






ACGATCGTTGGCTGacctgtaggatcgtacaggtttacgcaagaaaatggtttg





ttacagtcgaataaaCAGCCCCATAGGGTGGTGTGTACCACCCCTGATGAGTCC







embedded image









embedded image








TCCACGTTGAGATAATTGAGCCGAAGCAAGTGTATCTCCTGGGCGAACAGGGCA







ACCACGCTCTCACCGGGCAGCTCTACTGCCAAATTCTGCCTTTCTTAAACGGCG







AATACACCCGAGAACAAATTGTGGAAAAGCTCGATGGGCAGGTCCCGGAGGAAT







ATATCGACTTCGTACTCAGTCGTCTGGTGGAGAAGGGCTATCTAACTGAGGTGG







CTCCAGAACTATCCCTGGAAGTGGCAGCATTTTGGAGCGAATTGGGAATTGCCC







CTTCTGTAGTGGCAGAAGGGCTAAAGCAGCCAGTGACAGTGACAACGGCGGGCA







AGGGCATTAGGGAAGGGATAGTGGCTAACCTGGCAGCAGCGCTGGAGGAAGCTG







GCATTCAGGTGTCAGACCCAAGGGACCCAAAGGCCCCAAAGGCAGGGGATTCTA







CTGCCCAGCTTCAGGTGGTGCTGACCGATGACTATTTACAGCCGGAACTTGCAG







CGATCAACAAGGAAGCCTTAGAGCGCCAACAACCCTGGTTGCTGGTTAAGCCTG







TGGGCAGTATCCTCTGGTTGGGACCGTTGTTCGTTCCTGGGGAAACCGGATGTT







GGCACTGTCTTGCTCAACGATTGCAAGGCAACCGGGAAGTTGAAGCATCGGTAT







TGCAACAAAAGCGAGCGCTGCAGGAGCGCAACGGTCAAAATAAAAATGGTGCAG







TGAGTTGCTTGCCCACAGCACGGGCAACCCTACCTTCTACTCTACAAACAGGTT







TACAGTGGGCTGCCACTGAGATTGCTAAGTGGATGGTCAAGCGGCACCTCAATG







CCATAGCACCGGGAACGGCTCGTTTTCCCACTCTAGCTGGCAAGATATTTACAT







TCAACCAGACGACTCTGGAGTTGAAAGCTCATCCTCTGAGCCGACGACCGCAAT







GTCCCACCTGTGGCGATCGGGAAACTCTCCAACGGCGCGGGTTTGAACCACTGA







AGCTAGAGTCGCGCCCCAAACACTTCACCTCCGATGGCGGTCATCGCGCCATGA







CCCCAGAACAAACGGTGCAGAAGTACCAACACCTCATCGGGCCCATAACGGGGG







TAGTGACGGAACTGGTGCGAATTTCTGACCCTGCCAATCCCTTGGTGCATACCT







ACCGGGCTGGGCATAGCTTTGGCAGTGCTACGTCTCTGCGGGGGCTGCGCAATG







TCCTACGCCACAAGAGTTCTGGTAAAGGCAAGACCGATAGCCAATCTCGGGCCA







GCGGACTTTGCGAGGCGATCGAGCGCTATTCGGGCATTTTTCAGGGAGACGAAC







CCCGCAAGCGGGCAACTTTGGCTGAGTTGGGAGATTTGGCGATTCATCCAGAAC







AGTGTTTGCACTTTAGCGACAGGCAGTATGACAACCGGGAAAGCTCGAACGAGC







GAGCAACAGTGACTCACGACTGGATTCCCCAACGGTTCGATGCAAGTAAGGCTC







ACGACTGGACTCCCGTGTGGTCCCTAACGGAGCAAACCCATAAGTATCTGCCTA







CAGCCCTGTGCTATTACCGATACCCCTTCCCCCCAGAACACCGTTTCTGCCGTA







GTGACTCCAACGGAAACGCGGCGGGAAATACCCTGGAAGAGGCGATTTTGCAAG







GATTTATGGAACTGGTGGAACGGGATAGCGTGTGCCTGTGGTGGTACAATCGCG







TTAGCCGTCCGGCTGTGGATTTGAGTAGCTTTGACGAGCCTTATTTTTTGCAGT







TGCAGCAGTTCTATCAAACTCAAAATCGCGATCTGTGGGTACTGGATTTAACAG







CAGATTTGGGCATTCCGGCTTTTGTAGGGGTATCGAATCGGAAAGCCGGCAGCT







CGGAAAGAATAATTCTCGGCTTTGGAGCGCACCTGGACCCGACAGTTGCCATCC







TTCGCGCTCTTACGGAGGTCAACCAAATAGGCTTGGAATTGGATAAAGTTTCTG







ATGAGAGCCTCAAGAACGATGCCACGGATTGGTTAGTGAATGCTACATTGGCAG







CTAGTCCCTATCTCGTTGCCGATGCTAGCCAACCCCTCAAGACTGCGAAGGATT







ATCCCCGGCGTTGGAGTGACGATATTTACACCGATGTGATGACTTGTGTAGAAA







TAGCCAAGCAAGCAGGTCTAGAGACTTTGGTACTGGATCAGACCAGACCCGACA







TAGGTTTAAATGTGGTTAAAGTCATTGTGCCAGGAATGCGTTTTTGGTCGCGAT







TTGGCTCCGGTCGGCTCTATGACGTGCCAGTGAAGTTGGGATGGCGAGAGCAAC







CACTTGCTGAGGCACAAATGAACCCTACACCGATGCCATTTTAATAAGATACGA






ATTTATGTATAGACTCGGTACCAAAAAAAAAAAAAAAGACGCTGAAAAGCGTCT






TTTTTTTTTTTGGTCCTACTATCCTTAAACGCATATCGTGGTACAGGAGACCGT






CCAATGgcggcgcgccatcgaatggcgcaaaacctttcgcggtatggcatgata





gcgcccggaagagagtcaattcagggtggtgaatATGAAAAACATAAATGCCGA






CGACACATACAGAATAATTAATAAAATTAAAGCTTGTAGAAGCAATAATGATAT







TAATCAATGCTTATCTGATATGACTAAAATGGTACATTGTGAATATTATTTACT







CGCGATCATTTATCCTCATTCTATGGTTAAATCTGATATTTCAATCCTAGATAA







TTACCCTAAAAAATGGAGGCAATATTATGATGACGCTAATTTAATAAAATATGA







TCCTATAGTAGATTATTCTAACTCCAATCATTCACCAATTAATTGGAATATATT







TGAAAACAATGCTGTAAATAAAAAATCTCCAAATGTAATTAAAGAAGCGAAAAC







ATCAGGTCTTATCACTGGGTTTAGTTTCCCTATTCATACGGCTAACAATGGCTT







CGGAATGCTTAGTTTTGCACATTCAGAAAAAGACAACTATATAGATAGTTTATT







TTTACATGCGTGTATGAACATACCATTAATTGTTCCTTCTCTAGTTGATAATTA







TCGAAAAATAAATATAGCAAATAATAAATCAAACAACGATTTAACCAAAAGAGA







AAAAGAATGTTTAGCGTGGGCATGCGAAGGAAAAAGCTCTTGGGATATTTCAAA







AATATTAGGTTGCAGTGAGCGTACTGTCACTTTCCATTTAACCAATGCGCAAAT







GAAACTCAATACAACAAACCGCTGCCAAAGTATTTCTAAAGCAATTTTAACAGG







AGCAATTGATTGCCCATACTTTAAAAATTGATAAGGATCCTAATTGGTAACGAA







TCAGACAATTGACGGCTCGAGGGAGTAGCATAGGGTTTGCAGAATCCCTGCTTC







GTCCATTTGACAGGCACATTATGCATCGATGATAAGCTGTCAAACATGAGCAGA







TCCTCTACGCCGGACGCATCGTGGCCGGCATCACCGGCGCCACAGGTGCGGTTG







CTGGCGCCTATATCGCCGACATCACCGATGGGGAAGATCGGGCTCGCCACTTCG







GGCTCATGAGCAAATATTTTATCTGAGGTGCTTCCTCGCTCACTGACTCGCTGC






ACGAGGCAGACCTCAGCGCTAGCGGAGTGTATACTGGCTTACTATGTTGGCACT





GATGAGGGTGTCAGTGAAGTGCTTCATGTGGCAGGAGAAAAAAGGCTGCACCGG





TGCGTCAGCAGAATATGTGATACAGGATATATTCCGCTTCCTCGCTCACTGACT





CGCTACGCTCGGTCGTTCGACTGCGGCGAGCGGAAATGGCTTACGAACGGGGCG





GAGATTTCCTGGAAGATGCCAGGAAGATACTTAACAGGGAAGTGAGAGGGCCGC





GGCAAAGCCGTTTTTCCATAGGCTCCGCCCCCCTGACAAGCATCACGAAATCTG





ACGCTCAAATCAGTGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTT





TCCCCTGGCGGCTCCCTCGTGCGCTCTCCTGTTCCTGCCTTTCGGTTTACCGGT





GTCATTCCGCTGTTATGGCCGCGTTTGTCTCATTCCACGCCTGACACTCAGTTC





CGGGTAGGCAGTTCGCTCCAAGCTGGACTGTATGCACGAACCCCCCGTTCAGTC





CGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGAAAGACA





TGCAAAAGCACCACTGGCAGCAGCCACTGGTAATTGATTTAGAGGAGTTAGTCT





TGAAGTCATGCGCCGGTTAAGGCTAAACTGAAAGGACAAGTTTTGGTGACTGCG





CTCCTCCAAGCCAGTTACCTCGGTTCAAAGAGTTGGTAGCTCAGAGAACCTTCG





AAAAACCGCCCTGCAAGGCGGTTTTTTCGTTTTCAGAGCAAGAGATTACGCGCA





GACCAAAACGATCTCAAGAAGATCATCTTATTAAGGGGTCTGACGCTCAGTGGA





ACGAAAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCTTA





GAAAAACTCATCGAGCATCAAATGAAACTGCAATTTATTCATATCAGGATTATC





AATACCATATTTTTGAAAAAGCCGTTTCTGTAATGAAGGAGAAAACTCACCGAG





GCAGTTCCATAGGATGGCAAGATCCTGGTATCGGTCTGCGATTCCGACTCGTCC





AACATCAATACAACCTATTAATTTCCCCTCGTCAAAAATAAGGTTATCAAGTGA





GAAATCACCATGAGTGACGACTGAATCCGGTGAGAATGGCAAAAGCTTATGCAT





TTCTTTCCAGACTTGTTCAACAGGCCAGCCATTACGCTCGTCATCAAAATCACT





CGCATCAACCAAACCGTTATTCATTCGTGATTGCGCCTGAGCGAGACGAAATAC





GCGATCGCTGTTAAAAGGACAATTACAAACAGGAATCGAATGCAACCGGCGCAG





GAACACTGCCAGCGCATCAACAATATTTTCACCTGAATCAGGATATTCTTCTAA





TACCTGGAATGCTGTTTTCCCGGGGATCGCAGTGGTGAGTAACCATGCATCATC





AGGAGTACGGATAAAATGCTTGATGGTCGGAAGAGGCATAAATTCCGTCAGCCA





GTTTAGTCTGACCATCTCATCTGTAACATCATTGGCAACGCTACCTTTGCCATG





TTTCAGAAACAACTCTGGCGCATCGGGCTTCCCATACAATCGATAGATTGTCGC





ACCTGATTGCCCGACATTATCGCGAGCCCATTTATACCCATATAAATCAGCATC





CATGTTGGAATTTAATCGCGGCCTCGAGCAAGACGTTTCCCGTTGAATATGGCT





CAT






bEG_S8
Cym Mod
AACACCCCTTGTATTACTGTTTATGTAAGCAGACAGTTTTATTGTTCATGATGA
665



Backbone
TATATTTTTATCTTGTGCAATGTACATCAGAGATTTTGAGACACAACCAATTAT




without

TGAAGGCCTCCCTAACGGGGGGCCTTTTTTTGTTTCTGGTCTCCCAAGCGCTTA





SapI sites
ACGATCGTTGGCTGaacaaacagacaatctggtctgtttgtattatggaaaatt




around
tttctgtataatagattcaacaaacagacaatctggtctgtttgtattatCAGC




CDS

GGTCAACGCATGTGCTTTGCGTTCTGATGAGACAGTGATGTCGAAACCGCCTCT








embedded image









CTTTTCACTGGAGTTGTCCCAATTCTTGTTGAATTAGATGGTGATGTTAATGGG









CACAAATTTTCTGTCCGTGGAGAGGGTGAAGGTGATGCTACAAACGGAAAACTC









ACCCTTAAATTTATTTGCACTACTGGAAAACTACCTGTTCCGTGGCCAACACTT









GTCACTACTCTGACCTATGGTGTTCAATGCTTTTCCCGTTATCCGGATCACATG









AAACGGCATGACTTTTTCAAGAGTGCCATGCCCGAAGGTTATGTACAGGAACGC









ACTATATCTTTCAAAGATGACGGGACCTACAAGACGCGTGCTGAAGTCAAGTTT









GAAGGTGATACCCTTGTTAATCGTATCGAGTTAAAGGGTATTGATTTTAAAGAA









GATGGAAACATTCTTGGACACAAACTCGAGTACAACTTTAACTCACACAATGTA









TACATCACGGCAGACAAACAAAAGAATGGAATCAAAGCTAACTTCAAAATTCGC









CACAACGTTGAAGATGGTTCCGTTCAACTAGCAGACCATTATCAACAAAATACT









CCAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTCGACACAA









TCTGTCCTTTCGAAAGATCCCAACGAAAAGCGTGACCACATGGTCCTTCTTGAG









TTTGTAACTGCTGCTGGGATTACACATGGCATGGATGAGCTCTACAAATAA
GGA






TGAGCTCTACAAATAAGCAGAGGTGGTTGTGTTGCGAAAAAAAAAAAAAAACAC






CCTAACGGGTGTTTTTTTTTTTTTGGTGTCCCCACGTGTGGCGCTGGAGACCGT






CCAATGgcggcgcgccatcgaatggtgcaaaacctttcgcggtatggcatgata







embedded image








CCAGGCAGAACGTGCAATGGAAACCCAGGGTAAACTGATTGCAGCAGCACTGGG







TGTTCTGCGTGAAAAAGGTTATGCAGGTTTTCGTATTGCAGATGTTCCGGGTGC







AGCCGGTGTTAGCCGTGGTGCACAGAGCCATCATTTTCCGACCAAACTGGAACT







GCTGCTGGCAACCTTTGAATGGCTGTATGAGCAGATTACCGAACGTAGCCGTGC







ACGTCTGGCAAAACTGAAACCGGAAGATGATGTTATTCAGCAGATGCTGGATGA







TGCAGCAGATTTTTTTCTGGATGATGATTTTAGCATCGGCCTGGATCTGATTGT







TGCAGCAGATCGTGATCCGGCACTGCGTGAAGGTATTCTGCGTACCGTTGAACG







TAATCGTTTTGTTGTTGAAGATATGTGGCTGGGTGTGCTGGTGAGCCGTGGTCT







GAGCCGTGATGATGCCGAAGATATTCTGTGGCTGATTTTTAACAGCGTTCGTGG







TCTGACAGTTCGTAGCCTGTGGCAGAAAGATAAAGAACGTTTTGAACGTGTGCG







TAATAGCACCCTGGAAATTGCACGTGAACGTTATGCAAAATTCAAACGTTGATA







AGGATCCTAATTGGTAACGAATCAGACAATTGACGGCTCGAGGGAGTAGCATAG







GGTTTGCAGAATCCCTGCTTCGTCCATTTGACAGGCACATTATGCATCGATGAT







AAGCTGTCAAACATGAGCAGATCCTCTACGCCGGACGCATCGTGGCCGGCATCA







CCGGCGCCACAGGTGCGGTTGCTGGCGCCTATATCGCCGACATCACCGATGGGG







AAGATCGGGCTCGCCACTTCGGGCTCATGAGCAAATATTTTATCTGAGGTGCTT






CCTCGCTCACTGACTCGCTGCACGAGGCAGACCTCAGCGCTAGCGGAGTGTATA





CTGGCTTACTATGTTGGCACTGATGAGGGTGTCAGTGAAGTGCTTCATGTGGCA





GGAGAAAAAAGGCTGCACCGGTGCGTCAGCAGAATATGTGATACAGGATATATT





CCGCTTCCTCGCTCACTGACTCGCTACGCTCGGTCGTTCGACTGCGGCGAGCGG





AAATGGCTTACGAACGGGGCGGAGATTTCCTGGAAGATGCCAGGAAGATACTTA





ACAGGGAAGTGAGAGGGCCGCGGCAAAGCCGTTTTTCCATAGGCTCCGCCCCCC





TGACAAGCATCACGAAATCTGACGCTCAAATCAGTGGTGGCGAAACCCGACAGG





ACTATAAAGATACCAGGCGTTTCCCCTGGCGGCTCCCTCGTGCGCTCTCCTGTT





CCTGCCTTTCGGTTTACCGGTGTCATTCCGCTGTTATGGCCGCGTTTGTCTCAT





TCCACGCCTGACACTCAGTTCCGGGTAGGCAGTTCGCTCCAAGCTGGACTGTAT





GCACGAACCCCCCGTTCAGTCCGACCGCTGCGCCTTATCCGGTAACTATCGTCT





TGAGTCCAACCCGGAAAGACATGCAAAAGCACCACTGGCAGCAGCCACTGGTAA





TTGATTTAGAGGAGTTAGTCTTGAAGTCATGCGCCGGTTAAGGCTAAACTGAAA





GGACAAGTTTTGGTGACTGCGCTCCTCCAAGCCAGTTACCTCGGTTCAAAGAGT





TGGTAGCTCAGAGAACCTTCGAAAAACCGCCCTGCAAGGCGGTTTTTTCGTTTT





CAGAGCAAGAGATTACGCGCAGACCAAAACGATCTCAAGAAGATCATCTTATTA





AGGGGTCTGACGCTCAGTGGAACGAAAAATCAATCTAAAGTATATATGAGTAAA





CTTGGTCTGACAGTTACCTTAGAAAAACTCATCGAGCATCAAATGAAACTGCAA





TTTATTCATATCAGGATTATCAATACCATATTTTTGAAAAAGCCGTTTCTGTAA





TGAAGGAGAAAACTCACCGAGGCAGTTCCATAGGATGGCAAGATCCTGGTATCG





GTCTGCGATTCCGACTCGTCCAACATCAATACAACCTATTAATTTCCCCTCGTC





AAAAATAAGGTTATCAAGTGAGAAATCACCATGAGTGACGACTGAATCCGGTGA





GAATGGCAAAAGCTTATGCATTTCTTTCCAGACTTGTTCAACAGGCCAGCCATT





ACGCTCGTCATCAAAATCACTCGCATCAACCAAACCGTTATTCATTCGTGATTG





CGCCTGAGCGAGACGAAATACGCGATCGCTGTTAAAAGGACAATTACAAACAGG





AATCGAATGCAACCGGCGCAGGAACACTGCCAGCGCATCAACAATATTTTCACC





TGAATCAGGATATTCTTCTAATACCTGGAATGCTGTTTTCCCGGGGATCGCAGT





GGTGAGTAACCATGCATCATCAGGAGTACGGATAAAATGCTTGATGGTCGGAAG





AGGCATAAATTCCGTCAGCCAGTTTAGTCTGACCATCTCATCTGTAACATCATT





GGCAACGCTACCTTTGCCATGTTTCAGAAACAACTCTGGCGCATCGGGCTTCCC





ATACAATCGATAGATTGTCGCACCTGATTGCCCGACATTATCGCGAGCCCATTT





ATACCCATATAAATCAGCATCCATGTTGGAATTTAATCGCGGCCTCGAGCAAGA





CGTTTCCCGTTGAATATGGCTCAT






pEG7172
HalM1


embedded image


666





AGCGAAGTGGTTTTTGGACCGAATCTTGAGAAGATTGTAGGAGAAAAGCGCCTC







AATTTTTGGCTCAAACTTATAGGTGAGGACCCGGAAAACCTGAAGGAGTTTCTC







TCGAGAAAGGGCAATTCTTTCGAAGAACAAACCTTACCGGAAAAGGAAGCTATC







GTTCCGAACCGCTTAGGTGAAGAGGCGCTGGAAAAAGTCCGCGAAGAACTTGAG







TTCCTCAATACTTACAGCACTAAACATGTGCGTCGCGTTAAAGAGTTGGGAGTG







CAGATCCCTTTCGAAGGGATTCTGCTGCCATTCATTAGCATGTATATCGAAAAA







TTTCAGCAGCAGCAACTTCGCAAAAAGATAGGGCCGATTCACGAAGAGATCTGG







ACGCAGATTGTTCAAGATATCACCTCCAAATTAAATGCGATTCTGCACCGTACC







CTGATCCTGGAACTGAATGTAGCTCGTGTTACCTCCCAACTTAAAGGTGATACT







CCGGAAGAAAGATTCGCCTACTACTCGAAAACCTATTTAGGCAAACGTGAAGTA







ACTCACCGTCTGTATAGCGAATATCCGGTGGTTCTGCGGTTGCTGTTCACCACC







ATTTCACACCACATTTCGTTCATTACGGAAATCCTTGAACGCGTTGCAAATGAC







CGTGAAGCCATTGAAACCGAATTTTCACCGTGTTCCCCGATTGGTACCCTCGCC







TCTCTCCACTTAAACTCGGGAGATGCTCACCATAAACAGCGTACTGTGACGATT







TTGGAATTCTCCTCCTCGCTGAAACTTGTCTACAAACCTCGCTCCCTCAAAGTT







GATGGGGTGTTCAACGGTTTACTCGCTTTCCTGAACGATAGAACGGGGGAAGTC







ATTAAGGACCAGTATTGCCCTAAGGTGTTACAGCGCGATGGCTACGGCTATGTG







GAATTTGTCACTCACCAGTCTTGTCAATCCCTTGAGGAAGTGTCAGACTTCTAC







GAGAGACTCGGCTCTCTGATGAGTCTGTCCTACGTACTGAATAGTTCTGACTTT







CATTTCGAGAACATTATAGCTCATGGTCCCTATCCTGTCCTGATCGATCTTGAA







ACCATCATTCATAATACAGCGGATAGCAGCGAGGAAACGTCTACCGCTATGGAT







CGCGCGTTCCGTATGTTGAACGATTCGGTGCTGTCCACTGGTATGCTTCCCTCC







TCTATTTATTATCGCGATCAGCCGAATATGAAGGGTCTGAACGTCGGAGGTGTG







AGCAAATCAGAAGGTCAGAAAACACCGTTCAAAGTTAATCAAATCGCCAATCGC







AACACCGATGAGATGCGTATCGAAAAAGATCACGTTACCCTGAGCAGCCAGAAA







AATCTGCCCATTTTTCAGTCTGCCGCAATGGAGAGCGTACATTTCTTAGATCAG







ATCCAGAAAGGCTTTACCTCCATGTATCAGTGGATCGAGAAGAACAAACAAGAA







TTTAAAGAACAGGTGCGTAAGTTTGAAGGTGTGCCGGTTCGTGCTGTTCTTCGG







AGCACGACTCGCTATACCGAACTGCTGAAATCTTCCTACCACCCTGACCTGCTC







CGCAGCGCGTTGGACCGTGAAGTACTGCTGAACCGTTTGACTGTTGACTCGGTA







ATGACCCCGTATCTCAAAGAGATTATTCCACTCGAGGTGGAAGATCTGCTGAAC







GGTGACGTGCCATACTTCTACACCCTGCCGGAAGAACGCGCCCTGTATCAGGAA







GCGTCTGCGATCAATAGTACGTTCTTTACCACTTCGATTTTCCATAAGATTGAC







CAGAAAATCGATAAGCTGGGTATCGAGGACCATACCCAGCAAATGAAGATCTTA







CACATGAGTATGCTTGCCTCTAACGCTAACCATTACGCCGATGTTGCCGACTTG







GATATTCAGAAAGGACACACCATTAAAAACGAACAGTACGTTGAGATGGCCAAA







GACATCGGTGATTACCTGATGGAGTTATCGGTCGAGGGTGAAAATCAAGGGGAA







CCAGATCTGTGTTGGATTTCGACCGTCCTGGAAGGGAGCTCTGAAATCATTTGG







GACATCAGCCCAGTGGGCGAAGATTTATACAACGGCAGCGCTGGCGTCGCTCTC







TTTTATGCGTACCTGTTCAAAATTACAGGTGAAAAGCGTTACCAAGAGATCGCA







TACAAAGCCCTGGTTCCGGTTCGCCGCAGTGTGGCCCAATTCCAGCACCATCCG







AATTGGAGCATTGGTGCGTTTAACGGAGCGTCAGGCTATCTGTACGCGATGGGT







ACGATAGCGGCCCTGTTTAATGATGAACGTTTGAAGCATGAAGTAACCCGCAGC







ATTCCGCACATTGAACCGATGATCCACGAGGATAAGATCTATGATTTCATTGGC







GGTTCCGCAGGGGCGCTGAAGGTGTTCCTGAGCCTGTCGGGGCTGTTTGACGAG







CCGAAGTTTTTGGAACTTGCCATTGCATGCAGCGAACATCTGATGAAAAACGCC







ATTAAAACGGATCAAGGTATCGGCTGGAAACCACCGTGGGAGGTCACCCCACTG







ACCGGTTTCAGCCATGGGGTTAGCGGCGTCATGGCATCCTTCATCGAACTGTAC







CAGCAAACCGGTGATGAGCGCTTGCTCAGTTACATTGATCAGAGTTTAGCCTAT







GAACGTTCCTTCTTCAGCGAACAAGAGGAGAACTGGCTGACTCCGAACAAAGAA







ACACCCGTGGTAGCTTGGTGCCACGGCGCGCCGGGAATTTTGGTATCACGACTG







CTTCTGAAGAAATGCGGCTATTTGGATGAAAAAGTCGAAAAAGAAATTGAGGTG







GCATTATCCACAACTATCCGTAAAGGCCTTGGTAACAATCGCAGTCTTTGCCAT







GGTGATTTCGGCCAGCTGGAAATTCTTCGCTTTGCGGCGGAAGTGTTAGGCGAT







AGCTATCTCCAGGAAGTTGTCAACAATCTGTCCGGCGAGTTGTATAATCTTTTC







AAAACGGAGGGATATCAGAGCGGAACCAGCCGCGGTACTGAATCCGTGGGCCTG







ATGGTAGGTCTGTCCGGGTTTGGGTATGGTTTACTTTCAGCGGCATATCCATCT







GCTGTCCCCTCAATCTTAACATTGGATGGTGAGATCCAGAAGTACCGGGAGCCT







CATGAAGCCTGA







pEG7173
HalM2


embedded image


667





TCAGTGCCGACGACGCTGCCGCATACTAACGACACCGATTGGCTCGAGCAATTA







CATGACATTTTGTCCATTCCTGTTACGGAAGAAATCCAGAAATATTTCCACGCC







GAAAATGATCTGTTCTCGTTTTTCTATACACCGTTCCTGCAGTTTACGTACCAG







AGCATGTCGGACTACTTTATGACCTTCAAGACCGATATGGCCCTGATCGAAAGA







CAGAGCCTCCTGCAAAGCACGCTGACCGCGGTACATCACCGACTCTTCCACTTA







ACGCATCGCACCCTTATTAGTGAAATGCATATTGATAAACTTACCGTTGGCCTG







AATGGCTCTACGCCGCACGAGCGCTACATGGATTTCAACCACAAATTCAACAAA







ACCTCGAAGTCGAAGAACCTGTTTAACATCTACCCAATTTTGGGAAAATTGGTC







GTTAACGAAACTCTGCGCACTATTAACTTCGTCAAGAAAATCATTCAGCACTAC







ATGAAGGACTACCTGCTCCTGTCGGACTTCTTCAAAGAGAAGGACTTGCGTCTT







ACCAACCTGCAATTAGGCGTGGGGGATACACACGTTAATGGGCAATGCGTCACC







ATTCTGACGTTTGCATCAGGCCAAAAAGTGGTATACAAACCTAGATCATTGTCG







ATAGATAAACAGTTCGGAGAATTCATCGAGTGGGTAAACTCGAAAGGTTTTCAG







CCTTCCTTGCGTATCCCTATTGCGATTGATCGTCAAACCTATGGTTGGTATGAA







TTCATCCCTCATCAAGAGGCCACCAGCGAAGATGAAATAGAACGCTACTATTCT







CGCATCGGTGGTTATCTGGCGATCGCCTACTTGTTCGGGGCAACCGACCTGCAC







CTGGATAACCTGATCGCCTGCGGCGAACATCCGATGCTTATTGATTTGGAAACA







CTCTTTACCAACGATCTCGACTGCTATGACAGTGCGTTTCCGTTCCCGGCGCTG







GCCCGCGAATTAACCCAATCCGTTTTTGGCACCCTTATGCTTCCCATCACCATC







GCGTCGGGGAAACTGCTGGATATAGACCTGTCAGCAGTAGGAGGCGGTAAAGGT







GTGCAGTCCGAAAAGATCAAAACCTGGGTCATCGTGAATCAGAAAACTGATGAG







ATGAAGCTGGTCGAGCAGCCGTATGTTACCGAGAGTTCCCAGAATAAACCAACA







GTTAATGGGAAAGAGGCGAACATTGGCAATTATATTCCTCATGTCACAGATGGC







TTTCGTAAAATGTACCGCCTGTTTCTGAATGAAATTGATGAGTTAATGGATCAT







AACGGGCCAATCTTTGCGTTTGAGAGTTGTCAGATTCGTCATGTTTTTCGAGCT







ACCCACGTGTATGCGAAATTTTTGGAGGCAAGTACCCACCCAGATTACTTGCAA







GAACCTACCAGACGTAATAAACTGTTCGAGTCCTTTTGGAACATCACGTCGCTG







ATGGCACCGTTCAAGAAAATTGTACCGCACGAAATCGCGGAGTTGGAGAACCAT







GATATTCCGTACTTCGTCCTGACTTGTGGCGGCACCATTGTTAAAGATGGATAC







GGCCGGGATATCGCAGACCTGTTTCAAAGTAGCTGCATCGAACGTGTAACTCAT







CGTCTGCAGCAGCTGGGAAGCGAGGATGAGGCGCGTCAAATTCGCTACATTAAA







AGCAGCCTGGCGACGTTGACCAACGGTGATTGGACCCCATCCCATGAGAAAACC







CCGATGTCTCCGGCCTCGGCCGACCGTGAAGATGGTTACTTCCTGCGCGAGGCT







CAGGCCATCGGCGACGACATTTTGGCGCAGCTGATTTGGGAGGATGACCGTCAC







GCCGCTTACCTTATTGGCGTAAGCGTGGGCATGAACGAAGCCGTCACTGTGTCA







CCCCTGACGCCTGGCATCTACGACGGCACACTTGGCATAGTGCTGTTCTTCGAT







CAGCTGGCCCAGCAGACCGGCGAAACCCATTATCGCCACGCCGCCGACGCTTTA







CTGGAAGGAATGTTCAAACAGCTGAAACCTGAACTGATGCCGTCTAGCGCTTAC







TTCGGACTGGGTAGCCTGTTCTATGGCCTGATGGTGTTGGGCCTCCAGCGTTCC







GACTCGCATATCATTCAGAAAGCGTATGAGTATCTGAAACATTTGGAAGAGTGT







GTGCAGCATGAGGAAACGCCAGATTTTGTCTCGGGTTTGTCTGGTGTACTGTAT







ATGCTCACGAAAATTTATCAGCTCACGAATGAACCGAGAGTTTTCGAAGTGGCC







AAAACCACAGCTTCGCGTCTGTCTGTGCTGCTTGACAGCAAGCAGCCCGACACT







GTGCTCACCGGGTTATCCCATGGCGCCGCAGGATTCGCCCTTGCATTACTGACC







TACGGAACCGCTGCAAATGATGAACAGTTGCTGAAACAGGGCCACTCCTATCTG







GTGTACGAACGTAATCGGTTTAACAAACAGGAAAACAACTGGGTTGATTTACGT







AAAGGCAACGCGTATCAAACATTTTGGTGCCATGGCGCCCCGGGTATTGGCATC







TCACGCCTCCTGTTAGCGCAATTTTACGATGACGAACTGCTGCATGAAGAGTTA







AACGCAGCACTGAACAAGACTATTTCGGACGGCTTCGGCCACAATCACTCACTG







TGTCATGGCGATTTCGGCAACCTCGATCTGTTATTGCTTTATGCCCAATATACG







AATAACCCAGAACCAAAGGAACTCGCTCGCAAACTGGCCATAAGCAGTATCGAT







CAAGCGCACACGTATGGCTGGAAACTCGGGCTCAATCATAGCGATCAACTGCAG







GGTATGATGTTAGGGGTGACTGGTATCGGCTATCAGCTCCTTCGTCATATAAAT







CCGACAGTCCCCAGCATTTTGGCACTGGAACTGCCCAGCTCCACGTTAACTGAA







AAAGAGCTGAGAATCCATGATCGTTGATAA







bEG_S9
Cym Mod
AACACCCCTTGTATTACTGTTTATGTAAGCAGACAGTTTTATTGTTCATGATGA
668



Backbone
TATATTTTTATCTTGTGCAATGTACATCAGAGATTTTGAGACACAACCAATTAT






TGAAGGCCTCCCTAACGGGGGGCCTTTTTTTGTTTCTGGTCTCCCAAGCGCTTA






ACGATCGTTGGCTGaacaaacagacaatctggtctgtttgtattatggaaaatt





tttctgtataatagattcaacaaacagacaatctggtctgtttgtattatCAGC






GGTCAACGCATGTGCTTTGCGTTCTGATGAGACAGTGATGTCGAAACCGCCTCT








embedded image









GGAGAAGAACTTTTCACTGGAGTTGTCCCAATTCTTGTTGAATTAGATGGTGAT









GTTAATGGGCACAAATTTTCTGTCCGTGGAGAGGGTGAAGGTGATGCTACAAAC









GGAAAACTCACCCTTAAATTTATTTGCACTACTGGAAAACTACCTGTTCCGTGG









CCAACACTTGTCACTACTCTGACCTATGGTGTTCAATGCTTTTCCCGTTATCCG









GATCACATGAAACGGCATGACTTTTTCAAGAGTGCCATGCCCGAAGGTTATGTA









CAGGAACGCACTATATCTTTCAAAGATGACGGGACCTACAAGACGCGTGCTGAA









GTCAAGTTTGAAGGTGATACCCTTGTTAATCGTATCGAGTTAAAGGGTATTGAT









TTTAAAGAAGATGGAAACATTCTTGGACACAAACTCGAGTACAACTTTAACTCA









CACAATGTATACATCACGGCAGACAAACAAAAGAATGGAATCAAAGCTAACTTC









AAAATTCGCCACAACGTTGAAGATGGTTCCGTTCAACTAGCAGACCATTATCAA









CAAAATACTCCAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTG









TCGACACAATCTGTCCTTTCGAAAGATCCCAACGAAAAGCGTGACCACATGGTC









CTTCTTGAGTTTGTAACTGCTGCTGGGATTACACATGGCATGGATGAGCTCTAC









AAATAA
TGAAGAGCGCAGAGGTGGTTGTGTTGCGAAAAAAAAAAAAAACACCCT







AACGGGTGTTTTTTTTTTTTTGGTGTCCCCACGTGTGGCGCTGGAGACCGTCCA






ATGgcggcgcgccatcgaatggtgcaaaacctttcgcggtatggcatgatagcg







embedded image








GGCAGAACGTGCAATGGAAACCCAGGGTAAACTGATTGCAGCAGCACTGGGTGT







TCTGCGTGAAAAAGGTTATGCAGGTTTTCGTATTGCAGATGTTCCGGGTGCAGC







CGGTGTTAGCCGTGGTGCACAGAGCCATCATTTTCCGACCAAACTGGAACTGCT







GCTGGCAACCTTTGAATGGCTGTATGAGCAGATTACCGAACGTAGCCGTGCACG







TCTGGCAAAACTGAAACCGGAAGATGATGTTATTCAGCAGATGCTGGATGATGC







AGCAGATTTTTTTCTGGATGATGATTTTAGCATCGGCCTGGATCTGATTGTTGC







AGCAGATCGTGATCCGGCACTGCGTGAAGGTATTCTGCGTACCGTTGAACGTAA







TCGTTTTGTTGTTGAAGATATGTGGCTGGGTGTGCTGGTGAGCCGTGGTCTGAG







CCGTGATGATGCCGAAGATATTCTGTGGCTGATTTTTAACAGCGTTCGTGGTCT







GACAGTTCGTAGCCTGTGGCAGAAAGATAAAGAACGTTTTGAACGTGTGCGTAA







TAGCACCCTGGAAATTGCACGTGAACGTTATGCAAAATTCAAACGTTGATAAGG






ATCCTAATTGGTAACGAATCAGACAATTGACGGCTCGAGGGAGTAGCATAGGGT






TTGCAGAATCCCTGCTTCGTCCATTTGACAGGCACATTATGCATCGATGATAAG







CTGTCAAACATGAGCAGATCCTCTACGCCGGACGCATCGTGGCCGGCATCACCG







GCGCCACAGGTGCGGTTGCTGGCGCCTATATCGCCGACATCACCGATGGGGAAG







ATCGGGCTCGCCACTTCGGGCTCATGAGCAAATATTTTATCTGAGGTGCTTCCT






CGCTCACTGACTCGCTGCACGAGGCAGACCTCAGCGCTAGCGGAGTGTATACTG





GCTTACTATGTTGGCACTGATGAGGGTGTCAGTGAAGTGCTTCATGTGGCAGGA





GAAAAAAGGCTGCACCGGTGCGTCAGCAGAATATGTGATACAGGATATATTCCG





CTTCCTCGCTCACTGACTCGCTACGCTCGGTCGTTCGACTGCGGCGAGCGGAAA





TGGCTTACGAACGGGGCGGAGATTTCCTGGAAGATGCCAGGAAGATACTTAACA





GGGAAGTGAGAGGGCCGCGGCAAAGCCGTTTTTCCATAGGCTCCGCCCCCCTGA





CAAGCATCACGAAATCTGACGCTCAAATCAGTGGTGGCGAAACCCGACAGGACT





ATAAAGATACCAGGCGTTTCCCCTGGCGGCTCCCTCGTGCGCTCTCCTGTTCCT





GCCTTTCGGTTTACCGGTGTCATTCCGCTGTTATGGCCGCGTTTGTCTCATTCC





ACGCCTGACACTCAGTTCCGGGTAGGCAGTTCGCTCCAAGCTGGACTGTATGCA





CGAACCCCCCGTTCAGTCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGA





GTCCAACCCGGAAAGACATGCAAAAGCACCACTGGCAGCAGCCACTGGTAATTG





ATTTAGAGGAGTTAGTCTTGAAGTCATGCGCCGGTTAAGGCTAAACTGAAAGGA





CAAGTTTTGGTGACTGCGCTCCTCCAAGCCAGTTACCTCGGTTCAAAGAGTTGG





TAGCTCAGAGAACCTTCGAAAAACCGCCCTGCAAGGCGGTTTTTTCGTTTTCAG





AGCAAGAGATTACGCGCAGACCAAAACGATCTCAAGAAGATCATCTTATTAAGG





GGTCTGACGCTCAGTGGAACGAAAAATCAATCTAAAGTATATATGAGTAAACTT





GGTCTGACAGTTACCTTAGAAAAACTCATCGAGCATCAAATGAAACTGCAATTT





ATTCATATCAGGATTATCAATACCATATTTTTGAAAAAGCCGTTTCTGTAATGA





AGGAGAAAACTCACCGAGGCAGTTCCATAGGATGGCAAGATCCTGGTATCGGTC





TGCGATTCCGACTCGTCCAACATCAATACAACCTATTAATTTCCCCTCGTCAAA





AATAAGGTTATCAAGTGAGAAATCACCATGAGTGACGACTGAATCCGGTGAGAA





TGGCAAAAGCTTATGCATTTCTTTCCAGACTTGTTCAACAGGCCAGCCATTACG





CTCGTCATCAAAATCACTCGCATCAACCAAACCGTTATTCATTCGTGATTGCGC





CTGAGCGAGACGAAATACGCGATCGCTGTTAAAAGGACAATTACAAACAGGAAT





CGAATGCAACCGGCGCAGGAACACTGCCAGCGCATCAACAATATTTTCACCTGA





ATCAGGATATTCTTCTAATACCTGGAATGCTGTTTTCCCGGGGATCGCAGTGGT





GAGTAACCATGCATCATCAGGAGTACGGATAAAATGCTTGATGGTCGGAAGAGG





CATAAATTCCGTCAGCCAGTTTAGTCTGACCATCTCATCTGTAACATCATTGGC





AACGCTACCTTTGCCATGTTTCAGAAACAACTCTGGCGCATCGGGCTTCCCATA





CAATCGATAGATTGTCGCACCTGATTGCCCGACATTATCGCGAGCCCATTTATA





CCCATATAAATCAGCATCCATGTTGGAATTTAATCGCGGCCTCGAGCAAGACGT





TTCCCGTTGAATATGGCTCAT






pEG7034
TruD


embedded image


669





AATTAAGCCCCACTTCCACGTTGAGATAATTGAGCCGAAGCAAGTGTATCTCCT







GGGCGAACAGGGCAACCACGCTCTCACCGGGCAGCTCTACTGCCAAATTCTGCC







TTTCTTAAACGGCGAATACACCCGAGAACAAATTGTGGAAAAGCTCGATGGGCA







GGTCCCGGAGGAATATATCGACTTCGTACTCAGTCGTCTGGTGGAGAAGGGCTA







TCTAACTGAGGTGGCTCCAGAACTATCCCTGGAAGTGGCAGCATTTTGGAGCGA







ATTGGGAATTGCCCCTTCTGTAGTGGCAGAAGGGCTAAAGCAGCCAGTGACAGT







GACAACGGCGGGCAAGGGCATTAGGGAAGGGATAGTGGCTAACCTGGCAGCAGC







GCTGGAGGAAGCTGGCATTCAGGTGTCAGACCCAAGGGACCCAAAGGCCCCAAA







GGCAGGGGATTCTACTGCCCAGCTTCAGGTGGTGCTGACCGATGACTATTTACA







GCCGGAACTTGCAGCGATCAACAAGGAAGCCTTAGAGCGCCAACAACCCTGGTT







GCTGGTTAAGCCTGTGGGCAGTATCCTCTGGTTGGGACCGTTGTTCGTTCCTGG







GGAAACCGGATGTTGGCACTGTCTTGCTCAACGATTGCAAGGCAACCGGGAAGT







TGAAGCATCGGTATTGCAACAAAAGCGAGCGCTGCAGGAGCGCAACGGTCAAAA







TAAAAATGGTGCAGTGAGTTGCTTGCCCACAGCACGGGCAACCCTACCTTCTAC







TCTACAAACAGGTTTACAGTGGGCTGCCACTGAGATTGCTAAGTGGATGGTCAA







GCGGCACCTCAATGCCATAGCACCGGGAACGGCTCGTTTTCCCACTCTAGCTGG







CAAGATATTTACATTCAACCAGACGACTCTGGAGTTGAAAGCTCATCCTCTGAG







CCGACGACCGCAATGTCCCACCTGTGGCGATCGGGAAACTCTCCAACGGCGCGG







GTTTGAACCACTGAAGCTAGAGTCGCGCCCCAAACACTTCACCTCCGATGGCGG







TCATCGCGCCATGACCCCAGAACAAACGGTGCAGAAGTACCAACACCTCATCGG







GCCCATAACGGGGGTAGTGACGGAACTGGTGCGAATTTCTGACCCTGCCAATCC







CTTGGTGCATACCTACCGGGCTGGGCATAGCTTTGGCAGTGCTACGTCTCTGCG







GGGGCTGCGCAATGTCCTACGCCACAAGAGTTCTGGTAAAGGCAAGACCGATAG







CCAATCTCGGGCCAGCGGACTTTGCGAGGCGATCGAGCGCTATTCGGGCATTTT







TCAGGGAGACGAACCCCGCAAGCGGGCAACTTTGGCTGAGTTGGGAGATTTGGC







GATTCATCCAGAACAGTGTTTGCACTTTAGCGACAGGCAGTATGACAACCGGGA







AAGCTCGAACGAGCGAGCAACAGTGACTCACGACTGGATTCCCCAACGGTTCGA







TGCAAGTAAGGCTCACGACTGGACTCCCGTGTGGTCCCTAACGGAGCAAACCCA







TAAGTATCTGCCTACAGCCCTGTGCTATTACCGATACCCCTTCCCCCCAGAACA







CCGTTTCTGCCGTAGTGACTCCAACGGAAACGCGGCGGGAAATACCCTGGAAGA







GGCGATTTTGCAAGGATTTATGGAACTGGTGGAACGGGATAGCGTGTGCCTGTG







GTGGTACAATCGCGTTAGCCGTCCGGCTGTGGATTTGAGTAGCTTTGACGAGCC







TTATTTTTTGCAGTTGCAGCAGTTCTATCAAACTCAAAATCGCGATCTGTGGGT







ACTGGATTTAACAGCAGATTTGGGCATTCCGGCTTTTGTAGGGGTATCGAATCG







GAAAGCCGGCAGCTCGGAAAGAATAATTCTCGGCTTTGGAGCGCACCTGGACCC







GACAGTTGCCATCCTTCGCGCTCTTACGGAGGTCAACCAAATAGGCTTGGAATT







GGATAAAGTTTCTGATGAGAGCCTCAAGAACGATGCCACGGATTGGTTAGTGAA







TGCTACATTGGCAGCTAGTCCCTATCTCGTTGCCGATGCTAGCCAACCCCTCAA







GACTGCGAAGGATTATCCCCGGCGTTGGAGTGACGATATTTACACCGATGTGAT







GACTTGTGTAGAAATAGCCAAGCAAGCAGGTCTAGAGACTTTGGTACTGGATCA







GACCAGACCCGACATAGGTTTAAATGTGGTTAAAGTCATTGTGCCAGGAATGCG







TTTTTGGTCGCGATTTGGCTCCGGTCGGCTCTATGACGTGCCAGTGAAGTTGGG







ATGGCGAGAGCAACCACTTGCTGAGGCACAAATGAACCCTACACCGATGCCATT







TTAATAA







pEG7035
AlbA


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670





ATTTATTAATGAAAGTGTAAGAGTTCACCAGCTTCCTGAGGGCGGCGTGTTAGA







AATCGACTACTTGCGCGATAATGTCTCCATTTCTGACTTTGAGTATTTGGATCT







CAACAAAACGGCTTACGAGCTCTGCATGCGCATGGATGGCCAAAAAACAGCTGA







GCAGATTTTAGCTGAGCAATGTGCAGTGTATGATGAATCACCGGAAGATCATAA







AGATTGGTATTACGACATGCTCAACATGCTCCAGAACAAGCAGGTTATTCAGCT







TGGAAACCGGGCCAGCCGCCATACAATCACCACGAGCGGAAGCAATGAATTTCC







GATGCCCCTGCACGCCACCTTTGAACTGACGCACCGCTGTAATTTGAAATGCGC







CCACTGTTATTTGGAAAGCTCACCTGAAGCGCTCGGCACCGTGTCGATTGAGCA







ATTCAAAAAAACGGCTGATATGCTGTTTGATAACGGTGTATTGACATGCGAAAT







CACAGGTGGAGAAATTTTTGTCCATCCAAACGCCAATGAGATTCTTGACTATGT







GTGTAAAAAGTTCAAAAAAGTCGCTGTCTTAACAAACGGAACACTCATGCGAAA







AGAGAGCCTGGAGCTTTTGAAAACTTACAAGCAAAAAATCATCGTCGGCATTTC







TCTAGATAGTGTCAATTCCGAGGTCCATGACTCCTTTAGAGGGAGAAAAGGCTC







TTTTGCCCAAACTTGTAAAACGATAAAATTGTTGAGTGACCACGGTATATTTGT







CAGAGTCGCTATGTCTGTATTCGAAAAAAACATGTGGGAAATCCACGATATGGC







CCAAAAGGTTCGGGATCTCGGGGCGAAGGCGTTTTCTTACAATTGGGTTGACGA







TTTCGGAAGAGGCAGGGATATTGTCCATCCAACGAAAGACGCCGAGCAGCACCG







CAAGTTTATGGAATACGAGCAACATGTGATTGATGAGTTTAAAGATCTGATTCC







GATTATTCCCTATGAGAGAAAACGCGCGGCAAATTGCGGCGCTGGCTGGAAGTC







CATTGTGATCAGTCCGTTCGGCGAAGTACGTCCTTGCGCCCTCTTTCCAAAGGA







ATTTTCATTGGGAAATATTTTTCATGATTCCTATGAAAGCATCTTTAACTCCCC







TCTCGTCCATAAACTGTGGCAAGCGCAAGCGCCGCGGTTCAGCGAACATTGCAT







GAAAGACAAATGCCCGTTCAGCGGCTATTGCGGAGGCTGTTACTTAAAAGGGCT







GAACTCTAACAAATATCACCGGAAAAACATTTGCTCTTGGGCGAAAAATGAACA







ATTAGAAGATGTGGTCCAGCTTATTTAGTAA







pEG7037
MdnC


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671





CTTTTAGCCACGATAATGAAAGTATTCCTCTGGTAATCAAAGCCATAGAAGCCA







TGGGTAAAAAAGCCTTCCGTTTTGATACTGATCGCTTCCCTACAGAGGTGAAAG







TTGATCTTTACTCAGGCGGTCAAAAAGGCGGAATTATTACCGATGGAGAACAAA







AATTAGAGCTAAAAGAAGTTTCTTCTGTCTGGTATCGACGCATGAGATACGGAC







TAAAATTACCCGATGGGATGGATAGTCAATTTCGCGAAGCTTCTCTTAAGGAAT







GTCGGTTAAGTATTCGAGGAATGATTGCTAGTTTATCTGGCTTTCATCTTGATC







CAATTGCTAAGGTAGATCATGCTAATCATAAACAATTGCAGTTACAAGTGGCGC







AACAATTAGGTTTATTAATTCCGGGGACTTTAACTTCTAATAATCCTGAAGCTG







TCAAGCAATTTGCTCGGGAGTTTGAAGCGACGGGAATTGTGACTAAAATGCTTT







CTCAATTTGCTATTTATGGAGACAAGCAAGAGGAAATGGTTGTTTTTACCAGTC







CTGTTACAAAGGAAGATCTAGATAATTTGGAAGGTTTGCAATTTTGTCCAATGA







CTTTTCAGGAAAACATTCCTAAAGCTTTGGAATTACGCATCACTATCGTCGGTG







AACAAATATTTACGGCGGCGATTAATTCCCAACAATTAGACGGTGCTATCTACG







ATTGGCGAAAAGAGGGACGCGCGCTCCATCAACAATGGCAACCCTACGATTTAC







CGAAAACTATTGAAAAACAACTACTAGAATTAGTGAAATATTTCGGTCTTAATT







ATGGTGCAATTGATATGATTGTCACACCAGATGAACGTTATATCTTTTTAGAAA







TTAATCCCGTTGGCGAGTTTTTCTGGCTAGAACTTTATCCTCCTTATTTTCCTA







TCTCCCAGGCGATCGCTGAAATCCTAGTTAACTCATAATAA







pEG7043
ProcM


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672





GAAAACATCGTGGCTGGCCGCCATCGCTCCGGATGAACCCCACAAATTCGACCG







CCGCTTAGAATGGGACGAGCTTTCAGAGGAGAACTTCTTCGCAGCACTGAACTC







AGAACCTGCATCGTTGGAAGAGGATGATCCATGTTTTGAAGAAGCACTGCAAGA







CGCCCTGGAGGCCTTGAAGGCAGCATGGGATTTACCCCTTCTTCCCGTCGATAA







TAATCTTAATCGTCCCTTCGTAGATGTCTGGTGGCCCATTCGCTGTCACTCTGC







GGAGAGCTTGCGTCAAAGCTTCGTCAGTGATAGTGCTGGACTTGCGGACGAGAT







TTTTGATCAGCTGGCCGATTCGTTACTGGACCGTCTGTGCGCCCTGGGAGATCA







GGTGTTGTGGGAGGCGTTTAACAAGGAGCGTACACCAGGAACGATGTTGTTAGC







CCACTTAGGAGCCGCAGGCGACGGCTCCGGACCCCCTGTACGTGAGCATTACGA







ACGTTTTATTCAGTCTCACCGCCGTAATGGATTAGCGCCTTTGCTTAAGGAATT







CCCTGTACTGGGCCGCCTTATTGGAACAGTTTTGTCCCTTTGGTTCCAAGGGAG







CGTGGAAATGCTGCAACGTATCTGCGCTGACCGCACCGTTCTGCAACAGTGTTT







CGCTATCCCTTGCGGGCATCACCTGAAAACTGTAAAGCAGGGACTTTCTGATCC







ACACCGCGGCGGTCGCGCTGTGGCAGTTTTGGAATTTGCGGACCCAAATTCCAC







CGCTAATTCAAGTATGCACGTAGTGTATAAACCGAAGGATATGGCTGTGGATGC







AGCTTACCAGGCCACCTTAGCAGATCTTAATACTCATAGCGACCTTTCCCCGTT







GCGCACGCTTGCCATTCATAACGGCAACGGATATGGTTACATGGAACATGTGGT







TCACCATCTTTGCGCTAACGACAAAGAGCTGACAAATTTCTATTTCAACGCTGG







GCGTTTAACCGCGCTTCTGCATCTTCTTGGATGTACTGACTGTCACCATGAAAA







TTTGATTGCATGTGGTGATCAATTACTGTTGATCGATACAGAAACATTATTGGA







GGCGGATTTACCCGATCACATTTCGGATGCTTCGAGCACCACGGCGCAACCAAA







GCCTAGTAGCCTTCAAAAGCAATTTCAGCGTTCTGTTTTGCGTAGCGGGTTACT







TCCTCAATGGATGTTCCTGGGGGAGTCGAAGTTGGCCATCGACATCTCGGCTCT







GGGAATGTCCCCACCCAATAAGCCTGAGCGTATTGCACTTGGCTGGTTAGGATT







CAATTCTGACGGGATGATGCCTGGGCGTGTATCCCAACCAGTTGAGATTCCTAC







ATCCTTGCCCGTTGGGATTGGTGAGGTTAATCCCTTTGATCGTTTTTTAGAGGA







TTTTTGTGATGGCTTTTCCATGCAATCAGAGGCCCTTATTAAGCTTCGCAACCG







TTGGCTGGACGTTAATGGGGTTCTTGCTCATTTCGCGGGTCTGCCCCGCCGTAT







CGTTCTTCGCGCGACTCGCGTATACTTCACTATCCAGCGTCAGCAGTTAGAGCC







TACGGCACTGCGCTCTCCACTTGCACAGGCCTTGAAACTTGAGCAGCTTACTCG







TTCTTTCTTGTTGGCAGAGTCAAAGCCTCTTCACTGGCCCATTTTCGCAGCTGA







AGTAAAGCAGATGCAGCACCTTGACATTCCTTTCTTCACACACTTAATCGACGC







TGACGCTCTGCAGCTGGGCGGCCTGGAACAAGAATTACCAGGCTTCATCCAGAC







TAGTGGCTTGGCAGCTGCTTACGAGCGTTTGCGTAATTTAGATACGGACGAGAT







TGCTTTCCAACTTCGTCTGATCCGCGGTGCAGTAGAGGCTCGCGAGTTGCATAC







TACGCCGGAGTCGAGCCCGACGTTGCCGCCGCCTGCCACCCCCGAGGCTCTTAT







GTCCTCTTCAGCCGAGACTAGTTTAGAAGCTGCTAAGCGCATCGCTCACCGCTT







ACTGGAGTTGGCAATTCGTGATTCTCAAGGGCAAGTAGAATGGCTGGGCATGGA







TCTGGGGGCAGATGGAGAGAGCTTCTCCTTTGGCCCAGTTGGCTTGAGCCTTTA







TGGGGGCTCAATCGGTATCGCTCACCTTCTGCAACGTTTGCAGGCGCAGCAAGT







TTCCTTGATGGACGCAGACGCTATCCAAACGGCAATTTTACAGCCCCTTGTGGG







ACTGGTTGATCAACCTAGCGACGACGGACGTCGCCGTTGGTGGCGTGATCAGCC







GCTGGGCTTAAGTGGATGTGGCGGTACCTTGCTTGCACTTACACTTCAAGGTGA







ACAAGCGATGGCTAATTCCCTGCTGGCCGCTGCTTTGCCCCGTTTTATCGAGGC







TGATCAGCAACTTGACCTGATTGGTGGCTGCGCTGGACTGATCGGTTCGTTGGT







ACAATTAGGTACTGAAAGTGCCTTACAATTAGCTTTGCGTGCGGGCGACCATCT







TATTGCGCAACAGAATGAAGAGGGGGCGTGGTCTAGCTCGTCATCACAGCCCGG







TTTGTTGGGCTTTAGTCATGGTACTGCAGGTTACGCAGCAGCCTTAGCACACTT







ACATGCATTTTCCGCTGATGAGCGTTACCGCACCGCAGCCGCTGCCGCTTTAGC







ATACGAACGCGCACGTTTTAATAAAGATGCCGGCAACTGGCCAGACTACCGCTC







GATCGGACGTGACTCTGATTCAGATGAACCGTCCTTTATGGCTTCCTGGTGTCA







CGGCGCACCCGGCATTGCCCTGGGCCGCGCCTGTTTGTGGGGTACGGCGCTTTG







GGACGAAGAATGCACCAAGGAGATCGGAATTGGGTTACAGACCACAGCTGCTGT







TTCGTCTGTTAGTACTGACCACCTGTGTTGTGGTTCACTTGGCCTTATGGTATT







ATTAGAGATGCTGTCAGCAGGACCCTGGCCCATCGACAATCAATTACGTTCCCA







TTGCCAGGACGTAGCATTCCAGTACCGCCTGCAGGCTTTGCAGCGCTGTTCAGC







CGAGCCGATTAAGCTTCGTTGCTTCGGTACAAAAGAGGGCCTTTTAGTCCTGCC







TGGATTTTTCACTGGCTTATCAGGAATGGGTTTAGCACTGCTTGAGGATGATCC







ATCTCGCGCCGTGGTTTCTCAACTGATCAGTGCGGGCTTATGGCCGACAGAGTG







ATAA







pEG7047
MibHS


embedded image


673





CTCTGGCACGTCTGTTTGACGTGTTGGGTGACGATGCCGCTGCCGCACGTGAAT







GGGTAACGGAACCCCATCGTCTGATCGCTAGCAATGAGCGCCTGGGCACAGCTC







CGGAAGCCCCGGCGGATGACGATCCGGAGGCCATTCGGACGGTTGGAGTGATCG







GAGGGGGCACAGCCGGGTATTTAACGGCGTTGGCTCTGAAGGCTAAACGCCCTT







GGTTGGATGTGGCGCTCGTCGAAAGTGCGGATATCCCGATCATTGGGGTAGGAG







AGGCGACGGTGTCTTATATGGTGATGTTTCTGCACCATTATCTGGGCATTGATC







CGGCGGAGTTTTACCAACATGTGCGCCCTACTTGGAAACTGGGCATCCGTTTTG







AATGGGGGTCACGTCCGGAGGGCTTTGTTGCGCCATTCGATTGGGGGACCGGAT







CTGTTGGCCTGGTTGGGAGCCTGCGTGAAACGGGCAATGTCAACGAAGCTACGT







TACAGGCGATGCTCATGACGGAGGATCGCGTTCCGGTATATCGTGGCGAAGGTG







GGCATGTTAGTCTGATGAAATATCTGCCATTCGCATATCATATGGATAACGCTC







GCCTGGTTCGCTACCTGACGGAACTCGCCACTCGTCGTGGCGTGCATCATGTCG







ATGCGACTGTAGCTGAAGTTCGCCTGGATGGTCCTGACCACGTTGGGGACCTGA







TTACTACGGACGGTCGTCGCCTGCACTATGACTTTTACGTCGATTGTACTGGAT







TTCGTTCCCTGCTGCTGGAAAAAGCCCTGGGTATCCCGTTCGAATCTTATGCGT







CAAGCCTGTTTACCGACGCGGCAATTACCGGTACCCTTGCACATGGGGGTCATC







TTAAACCTTACACTACGGCAACTACCATGAATGCGGGCTGGTGTTGGACGATCC







CTACTCCTGAGTCCGATCACCTGGGGTACGTTTTCAGTAGTGCCGCGATCGATC







CAGACGATGCAGCAGCAGAAATGGCCCGCCGTTTCCCGGGCGTTACCCGCGAAG







CATTAGTTCGCTTTCGCTCCGGCCGTCACCGTGAAGCTTGGCGCGGCAATGTCA







TCGCGGTAGGAAACAGCTATGCTTTCGTGGAACCTCTGGAGAGTTCGGGACTCC







TGATGATTGCTACCGCAGTCCAGATCCTGGTGAGTTTGCTGCCGAGTAGTCGTC







GTGACCCGCTGCCTAGCAATGTGGCGAATCAGGCGTTAGCTCACCGGTGGGACG







CGATTCGTTGGTTTCTGAGTATTCATTACCGTTTCAACGGCCGCCTCGATACTC







CGTTCTGGAAGGAAGCCCGTGCCGAAACAGATATTAGCGGTATTGAACCGTTGC







TTCGTCTGTTCAGTGCCGGTGCCCCTCTGACCGGTCGCGATAGCTTTGCGCGCT







ATTTGGCCGACGGAGCAGCCCCGTTGTTCTATGGCCTGGAGGGTGTTGATACCT







TACTGCTGGGACAGGAAGTGCCTGCGCGTCTGTTACCACCGCGTGAATCTCCTG







AGCAGTGGCGTGCCCGTGCTGCAGCAGCCCGCTCATTAGCCTCGCGTGGCTTAC







GTCAGAGCGAAGCTCTGGATGCTTACGCTGCGGACCCCTGTCTCAATGCGGAAC







TGCTGTCTGATAGCGACTCATGGGCGGGTGAACGCGTCGCGGTACGTGCAGGTC








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GACGACTGGCACCACGGTAGCGCATGCTGTAGAACCAGACGGTTTCCGCGCCGT







GATGGCCACACTGCCGGCCGCTGTGGCGATCGTTACGGCAGCTGCGGCAGATGG







GCGCCCGTGGGGTATGACCTGCAGTTCGGTTTGCTCAGTGACCTTGACCCCGCC







GACCCTTCTGGTCTGCCTTCGGACGGCGTCCCCGACTCTGGCCGCAGTCGTGTC







AGGTCGTGCATTTAGCGTGAACCTTCTGTGTGCGCGGGCCTATCCTGTGGCGGA







ATTGTTTGCATCTGCGGCAGCAGACCGGTTTGATCGCGTTCGTTGGCGTCGCCC







GCCGGGTACAGGCGGTCCACATCTTGCCGATGATGCACGTGCAGTGTTAGACTG







TCGCCTGAGCGAAAGCGCAGAAGTAGGCGACCATGTGGTCGTATTTGGCCAAGT







CCGGGCGATTCGTCGCCTGAGTGATGAACCACCACTGATGTATGGTTATCGTCG







TTACGCACCTTGGCCGGCAGATCGTGGTCCGGGTGCGGCAGGCGGCTAATAA







pEG7048
MibD


embedded image


674





AGCGACGCAGGAGGTGACCCACGCCCGCCTGAACGCTTACTGTTGGGGGTGTCA







GGAAGTGTCGCTGCACTGAACTTACCGGCGTACATTTATGCCTTTCGGGCAGCC







GGTGTGGCACGTCTTGCGGTCGTGCTGACACCAGCGGCTGAAGGGTTCCTTCCA







GCGGGTGCGTTACGCCCGATTGTGGATGCCGTTCATACGGAACATGACCAAGGC







AAAGGTCACGTAGCGCTGTCACGCTGGGCGCAACACTTACTCGTGCTGCCGGCA







ACAGCGAATTTGCTTGGCTGTGCAGCGTCAGGACTTGCGCCGAACTTTTTAGCG







ACCGTTCTGCTCGCGGCAGATTGCCCAATCACATTCGTCCCGGCGATGAATCCG







GTCATGTGGCGTAAACCAGCCGTACGCCGGAACGTTGCAACCTTACGCGCAGAT







GGTCATCACGTGGTGGATCCTCTGCCGGGCGCTGTGTACGAAGCTGCCTCACGT







TCTATCGTGGAAGGTCTTGCTATGCCGCGCCCTGAAGCGTTAGTCCGTTTACTG







GGTGGCGGTGATGACGGTTCTCCAGCAGGACCGGCAGGTCCGGTTGGACGCGCA







GAGCATGTTGGGGCTGTTGAGGCTGTTGAAGCCGTGGAAGCAGTTGAGGCCGTT







GAGGCTGCGGAAGCACTTGCGTAATAA







pEG7056
PlpXY


embedded image


675





TCCTACGCAGTGTGGGAAATCACCCTGAAATGCAATCTGGCATGCTCTCATTGT







GGCAGCCGCGCCGGCCAAGCCCGTACGAAAGAGCTGAGTACCGAAGAAGCGTTC







AACCTGGTCCGCCAGCTGGCCGACGTGGGCATTAAGGAAGTCACCCTGATCGGT







GGTGAAGCCTTTATGCGTTCGGATTGGCTGGAAATCGCGAAAGCCGTCACTGAA







GCCGGCATGATCTGTGGCATGACCACAGGGGGCTTCGGGGTCAGTCTGGAAACG







GCGCGTAAAATGAAAGAAGCGGGCATTAAAACGGTGAGCGTTAGCATTGACGGT







GGTATTCCTGAAACCCACGACCGCCAGCGCGGTAAAAAGGGTGCGTGGCATAGT







GCATTCCGGACTATGAGCCATCTGAAAGAAGTCGGGATCTACTTCGGTTGCAAC







ACTCAAATCAATCGTTTATCGGCGTCAGAATTCCCGATTATCTATGAACGTATT







CGCGATGCTGGGGCACGTGCGTGGCAAATTCAGCTGACGGTTCCGATGGGCAAC







GCCGCGGATAACGCAGATATGCTGCTGCAACCGTATGAATTGCTCGACATCTAT







CCGATGTTAGCCCGCGTTGCCAAACGTGCGAAACAGGAAGGCGTGCGTATTCAG







GCAGGTAACAACATCGGGTACTATGGACCGTATGAGCGTCTGCTGCGTGGCAGC







GACGAATGGACGTTTTGGCAAGGATGTGGTGCGGGCCTTAACACCCTCGGCATC







GAAGCCGACGGCAAAATCAAAGGCTGTCCATCCCTGCCGACCGCCGCGTACACC







GGCGGTAACATTCGCGATCGCCCGCTGCGGGAAATCGTCGAACAGACCGAAGAA







CTGAAATTTAACTTAAAAGCTGGTACAGAACAAGGTACGGACCATATGTGGGGC







TTTTGTAAAACCTGCGAATTCGCGGAACTCTGTCGCGGCGGATGCAGCTGGACT







GCGCATGTGTTCTTTGACCGGCGCGGCAATAATCCGTACTGCCACCATCGGGCT







CTGAAACAAGCCCAAAAAGACATTCGCGAACGCTTTTATTTAAAAGTGAAAGCA







AAGGGCAACCCGTTCGACAATGGTGAATTTGTTATCATTGAAGAACCTTTTAAC







GCTCCGTTACCCGAGAATGACCTGCTGCACTTTAACAGTGATCACATTCAATGG








embedded image









embedded image








CGCGGCACAGAAATCTGACGACAGCAGCAGCGTATTACCGCGCCAGGGGTGGCA







AGACAAACAAGCCTTTATTAAGGCACTCATTAAAGCCAAACAGTCTCTCGAAAT







TGCCGAAATTAGCAACTTTTTAACC







pEG7058
PbtO


embedded image


676





ATCCCCTGTCGCGTCCAGAACCGCTGGGCGTGCACCCAGATTATCGTCGCCTGC







GTGAGACTTGCCCGGTTGCACGTGTGGGTAGCCCGTATGGCCCAGCGTGGCTTG







TCACCCGTTACGCCGATGTGGCCGCAGTTCTGACCGATGCCCGTTTTAGTCGTG







CAGCCGCTCCGGAAGATGATGGTGGCATCCTGCTGAACACCGATCCGCCGGAAC







ATGATCGTCTGCGTAAACTGATTGTAGCACACACAGGCACCGCTCGCGTGGAAC







GGCTGCGTCCGCGTGCTGAAGAGATCGCTGTTGCGTTAGCGCGCCGTATCCCGG







GCGAAGGCGAATTCATTAGTGCATTTGCCGAGCCCTTCAGCCATCGCGTTTTGT







CTTTATTTGTTGGCCATCTTGTTGGGTTACCAGCGCAGGACCTGGGCCCCTTAG







CGACCGTAGTGACTCTGGCACCCGTTCCCGACCGCGAACGTGGCGCGGCATTTG







CAGAGCTGTGTCGTCGGCTGGGTCGTCAGGTGGATCGCGAAACGCTTGCAGTAG







TTTTAAACGTGGTCTTTGGCGGACATGCGGCTGTAGTGGCCGCGCTGGGTTATT







GCCTGTTAGCTGCATTAGATGCGCCACTGCCACGTCTGGCCGGTGACCCAGAGG







GCATTGCCGAACTGGTGGAAGAAACCCTTCGTTTGGCTCCACCGGGAGATCGTA







CACTGTTGCGTCGTACTACAGAACCTGTGGAACTTGGCGGTCGCACATTACCAG







CGGGTGCGCTTGTAATCCCGTCCATTGCAGCCGCAAACCGTGATCCGGATCGCC







CTGTGGGCCGTCGTATGCCACGTCATCTTGCATTTGGACGTGGAGCGCATGCCT







GTTTAGGCATGGCGCTGGCGCGCATGGAACTCCAGGCAGCACTGAAAGCGTTAG







CGGAACACGCGCCAGACGTACGGTTGCCGGCTGGTACAGGCGCGCTGGTCCGCA







CACACGAAGAACTCTCGGTGAGCCCGCTCGCAGGAATCCCAATTCAACGCTAAT







AA







pEG7059
PbtM1


embedded image


677





TCGATGAAGCTGCGGTGGCGGCGGACTTACGCGAATTGGCCGCAGCTCTGGATC







GCAGTGGTTATGGTGAAATCCTCACCTGTTTTCTGCCTCAGAAGGCACAGGCGC







ATATCTGGGCTCAGACCGCTGCAAAAATTGATGGGCCGTTGCGTACCCTGATGG







AATTATTCCTTCTGGGTCGGGCGGTTCCCCAGGATGATCTCCCGCCTCGCATCG







CGGCCGTGATTCCCGGTTTAGTTAGCGCAGGTCTGGTTAAGACTGGACAGGGCG







CGGTTTGGCTGCCGAACTTGATTCTGCTGCGTCCTATGGGCCAGTGGTTATGGT







GTCAGCGGCCTCACCCCTCACCGACCATGTACTTTGGTGACGATAGCCTGGCGC







TGGTTCACCGGATGGTAACATATCGTGGCGGCCGTGCCCTGGATTTATGTGCAG







GTCCGGGTGTTCAGGCCCTTACCGCAGCCCTCCGCTCAGAGCACGTTACCGCGG







TTGAGATCAATCCGGTCGCGGCAGCCCTTTGCCGCACCAACATTGCCATGAACG







GTCTGTCCGACCGCATGGAGGTTCGCCTGGGCTCACTGTACGACGTCGTGCGCG







GTGAGGTTTTTGATGATATTGTATCAAACCCGCCGCTGCTGCCTGTTCCGGAGG







ATGTGCAATTCGCCTTTGTGGGAGATGGCGGACGCGATGGTTTCGATATTTCTT







GGACGATTCTGGATGGCCTGCCTGAACATCTGTCCGACCGTGGTGCGTGTCGCA







TCGTTGGTTGTGTTCTGTCCGATGGCTATGTGCCTGTTGTGATGGAAGGCTTGG







GAGAATGGGCCGCTAAACACGATTTCGACGTGCTTCTTACAGTGACCGCACATG







TCGAGGCGCATAAAGATAGTAGTTTTCTGCGTTCAATGAGCCTGATGAGTTCGG







CGATCTCAGGCCGCCCAGCGGAGGAGCTGCAAGAACGGTACGCAGCTGATTATG







CCGAACTGGGCGGTTCCCACGTTGCGTTCTATGAACTGTGTGCCCGCCGTGGTG







GGGGTTCTGCACGTCTGGCCGACGTGAGCGCTACAAAACGCAGTGCGGAAGTGT







GGTTTGTTTAATAA







pEG7060
PaaA


embedded image


678





TTAAAGAATCCCACCACATCATTTTAGCTGACGATGGTGACATTTGCATTGGGG







AAATTCCGGGGGTGTCTCAGGTAATCAATGACCCGCCGTCGTGGGTTCGTCCTG







CCCTGGCAAAGATGGATGGCAAGCGTACTGTCCCCCGTATTTTCAAAGAACTGG







TCAGTGAAGGCGTACAGATCGAATCCGAACATCTGGAAGGCCTGGTAGCCGGGC







TTGCCGAACGCAAACTTCTCCAGGATAACAGTTTCTTTTCCAAGGTGTTAAGCG







GTGAAGAAGTGGAGCGCTATAACCGCCAGATTCTGCAGTTCAGCCTTATCGATG







CGGATAACCAGCACCCTTTCGTTTACCAAGAGCGGCTGAAACAGTCTAAAGTCG







CTATCTTCGGTATGGGTGGCTGGGGCACGTGGTGTGCATTGCAGCTGGCCATGT







CAGGCATTGGTACACTGCGGCTGATCGACGGCGATGATGTGGAACTGTCGAACA







TTAACCGCCAAGTTCTGTATCGCACGGATGATGTAGGTAAAAACAAAGTTGATG







CCGCCAAAGACACTATCCTGGCATACAACGAAAACGTGCATGTTGAAACCTTCT







TTGAATTCGCCAGCCCGGACCGTGCCCGGCTTGAAGAACTTGTGGGTGATTCTA







CCTTTATTATCCTGGCTTGGGCCGCGTTGGGTTACTACCGTAAAGATACGGCAG







AGGAAATTATCCATTCGATTGCGAAAGATAAAGCGATCCCTGTAATTGAACTCG







GCGGTGATCCTTTGGAAATCTCTGTCGGTCCTATTTACCTGAATGATGGCGTAC







ACAGCGGCTTCGACGAGGTGAAAAATTCCGTTAAAGATAAATACTACGACAGCA







ACAGCGATATCCGCAAATTTCAAGAGGCGCGGTTGAAACACAGCTTCATCGATG







GCGATCGTAAAGTGAACGCGTGGCAATCAGCGCCCAGCCTGAGTATTATGGCTG







GTATCGTAACGGATCAGGTTGTGAAAACCATTACCGGGTACGACAAGCCACATC







TCGTTGGCAAGAAATTTATCTTGAGTCTGCAAGATTTCCGCAGCCGCGAGGAGG







AGATCTTTAAATAATAA







pEG7066
CinX


embedded image


679





TTCTGCGCGATGCGTTAGATCCGGATCGCTTCGGCCGCGAGATGAAGGCAGTAA







CAGAAATTCCCGAGATCGTTAAACTCGGCCATCGTCATGGTTATGGATTTACTG







CCGAAGAATTTCTGACCAAAGCTATGAGTTTTGGTGCTCCGCCGGCAGGAGCAG







CAGCACCTGGCGAATCAGCCAGCGTTCCTGGCCAGAACGGTTCCTCCCCCGGAC







ACGCTGCGCGTGCAGCTATGGCTGGTCCAGAAGCAGGGGCCACCAGCTTTGCCC







ACTATGAATACCGTCTGGATGAGCTGCCGGAATTCGCCCCCGTTGTGGCCGAGC







TTCCGAAACTGAAAGTCATGCCGCCTTCCGTGGGACCTGATCGGTTTGCAGCAC







GCTACCGTGATGAAGATATGCGCACAATTTCAATGAGTCCGGCGGATCCGGCTT







ACCAGGCTTGGCACCAGGAACTGGCGGGTCGTGGTTGGCGCGATGCAGAAGATA







CGGCTGCTGCTCCAGATGCCCCACGGCGCGATTTTCATCTGCTGAACCTCGATG







AGCATGTAGATTACCCAGGTTATGAAGAATATTTTGCGGCCAAGACCCGTGTCG







TCGCGGCACTCGAAAACCTGTTTGGTGGTGACGTGCGTTGCTCAGGCTCTATGT







GGTATCCGCCGTCGAGCTATCGCTTATGGCATACAAATGCCGATCAACCGGGGT







GGCGTATGTACCTGGTAGATGTAGATCGCCCATTCGCGGACCCCGACCGTACCT







CCTTCTTTCGCTACCTGCATCCACGTACCCGTGAAATCGTCACGCTGCGCGAAA







GCCCTCGTATTGTCCGTTTCTTTAAAGTCGAACAGGATCCCGAGAAGCTGTTCT







GGCACTGTATCGCGAACCCCACCGATCGCCATCGCTGGTCGTTTGGTTACGTTG







TTCCGGAAAACTGGATGGACGCCCTCCGTCACCATGGCTAATAA







pEG7067
CapBC


embedded image


680





CCTGGAGGTTGTTGATGTTCGTCGCGGCGAGTCGTTCAAGGCATGGTCGCATGG







GTACCCATATCGCACTGTTCGCTGGCACTTCCATCCTGAGTTTGAAGTACATCT







GATCGTGGAAACCACCGGCCAGATGTTTGTGGGTGATTATGTCGGAGGCTTTGG







TCCGGGTAATCTGGTCCTGATGGGTCCCAATCTGCCTCATAATTGGGTGTCTGA







CGTTCCTGAGGGTAAAACCGTTGCAGAGCGTAACCTTGTTGTTCAATTTGGGCA







AGCGTTCGTTTCCCGTTGCGAGGATTCCTTAACGGAGTGGCGTCACGTGGAAAC







GTTACTGGCGGATGCGCGGCGTGGCGTGCAATTTGGGCCGCGCACCTCTGAGGC







CATTAAACCTCTGTTCGCGGAACTGATTCACGCGCGCGGCCTGCGTCGCATTGT







GCTGTTTCTGTCTATGCTGCAAATCCTCGTCGATGCAACGGATCGCGAACTGCT







GGCATCTCCAGCTTATCAGGCGGATCCTTCGACATTTGCAAGCACGCGCATTAA







TCATGCGCTGGCCTACATTGGAAAGAATCTGGCGAACGAGCTTCGTGAAACAGA







TTTAGCACGGCTGGCCGGACAGTCTGTTTCCGCCTTCTCTCATTATTTTCGTCG







TCATACCGGCCTGCCTTTCGTGCAGTACGTTAATCGCATGCGTATCAACCTGGC







CTGTCAGCTTCTGATGGACGGGGACGCATCGGTGACAGATATTTGTTTCCGTAG







CGGTTTTAACAACCTGTCCAATTTTAACCGTCAGTTTCTGGCAGTGAAAGGTAT







GTCACCCAGTCGGTTCCGTCGCTACCAGGCTCTCAACGACGCGTCACGTGATGC







GAGTGAAGCGGCTGCAAAACGCGGCGCAGGTATTGCAGGTGCACCGGCAATCGT







TCCAGCGGCTCAAGCACGTGGCGAGGCACGCCCAATTCCTGAAGTGCTGCTTAG








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TGACGGCGAGCTCCACACCGGCATCCGGTAATCCAGCTGCCCGTGCATTGCGCG







CCGCTGCCTTTGCACTGGCCTTAGGCGGAGCATGCGTTGCGCATGCCGCACCTC







TGCGGATTGGCATGACATTCCAAGAATTGAATAACCCGTATTTTGTGACCATGC







AGAAAGCACTGAACGAAGCCGCGGCGAGCATTGGCGCGCAAGTGATTGTAACAG







ACGCACATCACGACGTGTCAAAACAGGTATCAGACGTTGAGGATATGCTGCAGA







AGAAAATTGATATTTTACTGGTGAATCCAACCGACTCCACGGGCATCCAGAGTG







CGATTGTTTCCGCAAAGAAGGCTGGCGCCGTGGTCGTGGCGGTCGATGCCAATG







CCAATGGCCCGGTGGATTCCTTCGTAGGGTCCAAGAATTTTGATGCCGGCGCTA







TGTCATGCGAGTACCTTGCGAAAGCGATCAACGGCGGCGGCGAAGTGGCCATTC







TGGATGGCATCCCGGTCGTCCCAATCCTGGAACGTGTCCGCGGCTGCCGCGCGG







CACTGGCCAAATTCCCGAATGTGAAAATTGTCGACGTTCAGAATGGAAAACAGG







AACGTGCGACAGCGTTAACGGTAACCGAGAATATGATCCAGGCGCACCCGAAAC







TGAAAGGTGTGTTTAGTGTAAACGACGGCGGGTCAATGGGCGCTTTGAGCGCCA







TTGAAGCGAGCGGCAAAGATATCCGCCTCACGTCCGTAGATGGTGCCCCAGAGG







CGGTGGCGGCGATTCAAAAGCCGAACTCCAAATTTATTGAAACAAGCGCTCAAT







TTCCGCGCGACCAGATCCGTTTAGCGATTGGTATTGGCCTGGCCAAGAAATGGG







GCGCGAACGTGCCAAAAGCGATTCCAGTCGACGTGAAACTGATTGACAAAGGGA







ACGCGAAAACCTTTAGTTGGTAATAA







pEG7068
LasBCD


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681





ACAGACCGGTTTTGTTGTACTGCCAGACAACGATGCCACCGGCGACGTGACGGG







CCGCCTGTTACCTTGGGGTGATGTAGTTACAGTGTATCCGTCTGGCCGTCCATG







GATCATCGGCAACTGCTGGGATCGCCCAGTCCTCGTCCATGATGGCGTGATCGT







CTTGGGTCATACCAGCGTCACGCGTGATCAAATTGCCCGTCATGGGAACGATCC







GCATCGCTTACTGGACGAGGCCGACGGCGCATTTCATGCGGCGGTCCTGATCGG







ACACGAAGTTCATGTTCGCGGCTCCGCCTACGGTGTCTGTCGTCTGTATACATG







CGTTGTTGACGGTGTGACCTTAGTGAGTGATCGTACAGACGTCCTGCAGCGTCT







GGCAGGTACTGATGTGGACGTCGACGTGCTGGCTGGCCACTTGTTAGAGCCGAT







CCCGCACTGGTTAGGCGAACAACCGTTATTGACGTCCGTGGAGCCCGTGCCACC







GACACATCACGTTATTTTAACTCCGGACGCACGTAGTCGTTTACGGCCATCACG







TCGTCGTCGGCCTGAACCGTCGCTGGGTTTGCGGGACGGTGCGGAACTTGTCCG







GGAGCGTCTGGCCGCAGCTGTGGCTACCCGTGTGGACAGTCCAGCGTTAATTAC







CAGTGAACTGAGTGGCGGCTATGATTCCACTAGTGTGTCATACTTGGCAGCGCG







CGGTAAAGCCGAGGTGGTGCTGGTCACGGCCGCGGGACGTGACAGCACAAGCGA







GGATCTGTGGTGGGCTGAACGCGCAGCCGCAGGGCTCCCGGAACTCGATCACGT







AGTGTTACCTGCGGATGAATTACCGTTTACGTACGCCGGCCTGACGGAGCCTGG







TGCACTTTTGGATGAACCGTGTACGGCTGTTGCCGGCCGTGAGCGTGTACTGGC







GCTGGTACGTAAAGCCGCGGCCCGCGGCTCTACACTTCATCTGACTGGCCATGG







TGGCGATCACCTGTTTACTTCACTGCCGACACCGTTTCATGACCTGTTTCGTAC







GCGTCCAGTCGCCGCGCTCCGCCAGTTGCGTGCATTTGGCGCGTTGGCTGCGTG







GCCGACCCGTAAGCTGATGCGCGAACTCGCGGACCGCCGCGATCATAGCACCTG







GTGGCGCGCGCACGCACGTCCTCAGAATGGCCAGCCGGATCCGCACAGCCCCAT







GTTAGGCTGGGCAATTCCCCCGACTGTCCCGGCGTGGGTTACTGCTGACGGCGT







GCGCGCGATCGAACTTGGGATTTTAGAAATGGCAGAACGCGCGGAGCCCCTTGG







TCATGCGCGCGGAGAACACGCTGAGCTGGATTCAATCTTTGAAGGGGCGCGTAT







GGCCCGTGGCCTCAATCGTATGGCTACGCATGCCGGAGTCCCGCTTGCAGCCCC







GTTCCATGACGATCGGGTCGTGGAAGCGTGTCTGTCGATCCGGCCGGAGGAACG







catttctgcatggcagtacaaacccttactgaacgccgcaatgcagggtgtggt







GCCGAGCACCGTTCTTGATCGTAGCGCTAAAGATGACGGGAGTATTGATGTGGC







CTATGGGCTGCAGGAACACCGTGATGAACTGGTAGCGCTGTGGGAATCATCACG







TCTGGCGGAAACCGGTCTGATTGATGCGGGTATGCTGCGGCGTTTATGCGCGCA







GCCGTCCTCCCACGAGCTCGAGCATGGATCCTTGTACGCTACTATCGCTTGTGA








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GTCTTTTACGGCTACGGAATACGGCGGCGTGCTGCTGGATGAAACCAAAGGCGC







ATACTGGCGTCTGAACACCACAGGCGCCGAAGTTGTTCGCGCCATGGGGGAAGC







CGAGCGGGATGAGATTGTACGGCATGTGGTGGCGACCTTCGATGTTGATGCGCA







AACCGCAGCCCAGGATGTCGATGTCCTGCTGGCAGAACTTCGTGATGCCGGCCT








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AATATGGCTCTCCGTGGCCATGGTATGTCCGGTCGCCGTCGTCGCTTAGATGCC







ACGCGTGCTCGCCTGGCCGTTGTGGTTGCCCGTGTCCTGAATCTCTTACCGCCG







CGCTTAATCCGTCGTTGTTTGCGTGTACTGAGTCGCGGAGCCCGCCCTGCCTCG







ATTGAGGCAGCAGAAGCTGCTCGTCGTACTGTGGTTGCGGTGAGTCCAGCTGCC







GCCGGTGCGTACGGCTGTTTAATCCGCAGCATTGCCACCACCCTGGTTCTTCGT







TCACGCGGGCAATGGCCAACCTGGTGTGTTGGTGTACGTGCGGAGCCTCCTTTT







GGTGCCCATGCCTGGATTGAAGCAGAGGAGCGGCTGGTGGATGAACCTGGTACT







ATGCATACTTACCGTCGTCTTATCACCGTTGGTCCACTGTCTCGCAAAGTTCGT







TAATAA







pEG7069
LasF


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682





TGGCCGATCTGGTCGATCCACTTCCAGGTCACGCACTGCGCGCTGCGGCGACAT







TACGTCTGGCAGATCTGATTGCGGCTGGTGCAGATACTGCACCGGCATTAGCAG







CGGCGGCACGCATTGATGCTGACGCGATCGCGCGTCTTATGCGGTATCTGTGCA







GTCGCGGGATTTTTCAAGCACATGAAGGCCGGTACGCGTTGACTGAATTTAGCG







AATTGCTGCTGGATGAAGATCCATCTGGCCTGCGTAAAACCTTAGATCAGGATA







GCTATGGGGATCGTTTCGACCGCGCGGTTGCGGAACTGGTGGACGTTGTACGGT







CCGGTGAACCTTCTTATCCTCGCCTTTACGGCTCGACGGTTTATGATGACCTGG







CAGCCGATCCTGCCCTCGGCGAGGTGTTCGCGGATGTTCGTGGCTTGCACTCCG







CAGGGTATGGGGAAGATGTCGCGGCAGTGGCGGGTTGGTCCTCATGCCTGCGCG







TTGTCGATCTGGGTGGAGGGACTGGCTCCGTCCTGCTTGCTGTGTTAGAGCGTC







ACCCGTCCCTGTCAGGCGCAGTACTGGATCTGCCATACGTCGCCCCGCAGGCAA







AGAAAGCTCTGCAGGCCTCAGCGTTTGCCCAACGTTGTGAATTTATCAAAGGGA







GCTTCTTCGATCCGTTACCTCCGGCAGACCGTTACCTGTTGTGTAACGTGCTGT







TCAACTGGGATGACGCGCAAGCAGGCGCTATTTTGGCACGCTGTGCGCAGGCGG







GCCCTGTGGCCGGAGTAGTGGTAGCCGAACGTTTGATCGATCCGGATGCGGAAG







TGGAACTCGTAGCAGCTCAAGATCTGCGTCTGTTGGCTGTTTGCGGCGGTCGGC







AGCGTGGCACCGCTGAATTCGAAGCGCTTGGGGCAGCCCATGGCCTGGCGTTAA







CCAGCGTTACCCTCACGGCATCTGGTATGAGCCTGCTCCGTTTCGATGTGTGTC







GTGCCGGGAGTGCTGGCGGGGAAGTTGTGGAAAAATCTTAATAA







pEG7070
AlbsBC


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683





GCGACGGCCCCTCGTCACGTGCGTGCCCTGGATTTCGGTCATGTTCTGGTCCTG







ATCGATTACCGTTCCAATCACGTCCAGTGCCTGCTTCCGGCAGCCGCAGCCCAT







TGGACAGCCACAGCGCGTACCGGCCGCTTGGACACCATGCCGGCAGCGCTGGCC







ACCCAGTTACTGACATCGGCGTTATTAGTACCGCGGCCGACCGCAACACCGTGG







ACGGCACCTGTAGCGGCACCACCTGCTCCACCGTCATGGGGTGGATCCGAGCAT







CCTGCCGGGACATCACGCCCTCGGGCACGTCATCGGCACTCAACCACGGCTGCG







GCGGCGCTGGCATGTGTGCTGGCGATTAAGGCAGCAGGCCCAACCCGCTATGCT







ATGCAGCGCTTGACCACGGTCGTGAAGGCAGCCGCTTCTACGTGCCGTCGCCCG







GCAACGCCAGCACAAGCGACGGCTGCTGCGCTTGCGGTCCGTCAGGCATGCTGG







TACTCGCCAGCGCGTACAGCCTGTCTGGAAGAATCCGCCGCGACTGTCATTTTA







CTCGCTACCCGGCGTTTGAGTTCGACATGGTGCCATGGAGTAGCTCCCGATCCG







ATTCGCCTCCATGCCTGGGTGGAAACTGAGGATGGGACACCTGTAGCAGAGCCA







GCCTCGACCCTTGCGTACACCCCGGCCTTAACCATTGGAGGCCACCATCAACAC








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GGATTTTCGACGACCCGTGAAGTTCGTCAACGCCCTGGTAATGCCGAGTTTATT







GCTACGGACTCGCCTATTTGGCGCCTCGGTCGTAGTCCAGCTCGTTGCGTGGCT







GCGGACCATGGACAGCGTCGCCTGGTAGTGTTGGGAGAATGCGGGGCAACGGAT







GGCGAATTATCTCGCCTGGCGACCGCGGGGCTGCCCACGGATATTACCTGGCGC







TGGCCAGGCGTGTACGTGGTGGTCGAAGAACAACCGGAACGTACGGTGCTGCAC







ACTGATCCAGCAGCTGCACTCCCGGTATACGCAACCCCTTGGCAAGGCGGCTGG







GCATGGTCAACCAGCGCGCGCATCCTGGCACGTTTAACAGAAGCTCCAATTGAT







GGTCAACGCCTGGCATGTTCAGTGCTGGCCCCGTCTGTTCCGGCTCTGAGCGGT







ACCCGCACATTCTTTGCGGGTATCGAACAATTGGCCCTGGGTTCGCGTATTGAA







CTGCCGGTGGATGGGTCCCGTCTGCGTGTTACGGTACGTTGGCGCCCGGATCCA







GTCCCGGGAGAACCATATCATCGCTTGCGCACAGCGTTGACCGAGGCGGTCGCC







CTGCGTGTCAACCGCGCACCAGACCTGTCATGCGACCTCTCGGGCGGCCTCGAT







TCCACGTCACTGGCAGTCCTGGCGGCTGTGTGCTTACCGGAGTCCCACCATCTG







AATGCTATCACGATTCATCCGGAGGGCGATGAAAGTGGCGCGGACTTACGGTAT







GCGCGCTTGGCAGCTGCGCACCACGGGCGTATTCGCCACCACCTTCTCCCCCTT







GCGGCAGAACACCTGCCGTATACTGAAATTACGGCGGTGCCCCCTACCACCGAA







CCGGCACCTTCAACATTAACGCGTGCACGCCTCGCGTGGCAGTTAGATTGGATG







CGCCAGCACTTAGGCAGCCGCACCCATATGACTGGCGATGGAGGCGACAGCGTA







CTGTTCCAACCGCCGGCACATCTGGCGGATCTCCTGCGGCATCGGCAGTGGCGT







CGGACTTTGTCGGAAAGTTTGGGATGGGCACGCCTTCGCCATACGTCTGTTTTA







CCCTTACTGCGTGGAGCAGCAACTCTTGCACGTACATCACGTCGGTCGGGCCTC







CAGGATCTCGCACGCGCATTGGCGGGTGCAGGTCAGCAGGGCGATGGTCGTGGC







AATGTGAGCTGGTTCGCACCATTACCGCTGCCTGGCTGGGCGACCCCAACCGCT







CGTCGCTTACTGCTTGATGCAGCCGATGAAGCTATCTCGACCGCGGATCCGTTA







CCGGGACTGGATACGTCGCTGCGCGTACTGATCGATGAAATTCGCGAAGTCGCC







CGCACGGCAGCGGCAGATGCCGAACTGGCGGATGCTCACGGAACGACTCTGCAT







AACCCATTTCTCGATCCGCGCACTATTGATGCAGTCCTGCGCACGCCAATCGCA







CATCGCCCGGCGGTCCACTCGTATAAGCCAGCGCTGGGGCATGCAATGCAGGAT







TTGCTCCCGGGTGCAGTCGCTCGGCGCTCAACTAAAGGCTCTTTTAACGCCGAT







CATTATGCGGGGATGCGTGCAAATCTGCCAGCATTGACAGCGCTGGCAGATGGC







CACCTGGCCGACCTGGGTTTGTTGGAGCCGACGCGCTTCCGCAGTCATCTTCGC







CAAGCCGCCGCGGGCATTCCGATGCCGCTTGCGGCGATCGAACAGGCGCTGTCT







GCCGAAGCATGGTGTCATGCACATCACGCCACCCCAAGCCCTGCCTGGACAACG







CAGCCACCGGAACACCCGCATGCCTAATAA







pEG7071
AlbsT


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684





CCCTCTGGATCTCAACTGATACCTGTGGTCTGGGGCCGTATCGCGCTGACTTGG







TGGATACCTATTGGCAGTGGGAACAAGACCCAACATTGCTTGTAGGCTACGGTC







GTCAGTCACCGCAGTCACTGGAGGCCCGCACGGAAGGTATGGCCCACCAATTGC







GTGGCGATAACATCCGTTTCACTATCTATGATCTGTGCAGCAGTACACCTACCC







CGGCGGGCGTGGCAACGCTGCTGCCCGATCATAGCGTCCGTACTGCCGAGTATG







TTATTATGCTTGCGCCTGAAGCACGTGGGCGTGGCTTAGGAACCACCGCCACGC







AGCTGACGTTAGATTATGCGTTTCACATCACCAATCTGCGGATGGTCTGGTTGA







AAGTACTGGCGCCGAACACCGCGGGCATCCGTGCGTATGAGAAAGCTGGCTTTC







GTACAGTTGGAGCGCTTCGCGAAGCCGGCTATTGGCTGGGGAAGGTCTGCGATG







AGGTACTGATGGATGCCTTAGCGAAAGACTTCACGGGTCCAAGTGCAGTCCACG







CAGCATTAACTGGCGCCAGCGGTCGCCAGCTGCGCCGTGCACCTTAATAA







pEG7073
McbCD


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685





TGGAAGTAACGCATTACACAGATCCTGAAGTTCTGGCCATTGTTAAAGATTTTC







ATGTCAGAGGTAACTTTGCTTCCCTCCCCGAATTTGCTGAACGAACTTTCGTGT







CCGCGGTACCTCTTGCCCATCTGGAGAAATTTGAAAATAAAGAAGTTCTCTTCA







GGCCAGGTTTCAGCTCCGTAATAAACATATCCTCATCACATAATTTTAGTCGTG







AAAGGCTCCCATCAGGAATAAACTTTTGCGACAAAAATAAACTTTCCATTCGTA







CTATTGAAAAGTTATTAGTCAATGCATTCAGCTCACCTGATCCTGGCTCTGTAA







GGCGGCCTTATCCTTCTGGGGGGGCATTGTACCCGATTGAAGTTTTTTTATGCA







GATTATCTGAAAATACAGAAAACTGGCAGGCAGGAACTAATGTTTATCACTACC







TGCCGCTAAGTCAGGCACTAGAACCTGTTGCTACATGTAATACTCAGTCACTCT







ACCGAAGCCTGTCCGGTGGGGATTCGGAACGTCTTGGTAAACCCCATTTTGCTC







TCGTCTATTGCATTATTTTTGAAAAAGCTTTGTTCAAATATCGCTACAGAGGAT







ACCGGATGGCCTTAATGGAAACAGGTTCGATGTATCAGAACGCAGTATTGGTTG







CAGATCAAATAGGACTGAAAAACCGGGTATGGGCGGGATATACCGATTCATACG







TAGCAAAAACAATGAATCTGGATCAGAGGACTGTAGCGCCACTGATCGTTCAGT







TTTTTGGAGATGTAAACGATGATAAATGTCTACAGTAACCTTATGTCCGCATGG







CCGGCCACAATGGCCATGAGTCCAAAACTGAACAGAAATATGCCAACGTTTTCT







CAGATATGGGACTATGAGCGTATTACACCAGCCAGCGCGGCCGGTGAAACTCTG







AAGTCAATTCAGGGGGCAATAGGTGAATATTTTGAACGCCGTCATTTTTTTAAT







GAGATAGTCACCGGTGGTCAGAAAACATTATATGAGATGATGCCTCCATCTGCT







GCAAAGGCTTTTACCGAAGCATTTTTTCAGATCTCATCACTGACCCGCGATGAA







ATCATAACCCATAAATTTAAAACGGTCAGAGCCTTTAATCTGTTTAGCCTTGAA







CAACAAGAAATACCTGCAGTCATAATTGCACTCGACAATATAACCGCTGCAGAT







GATCTGAAATTTTATCCTGACAGAGATACATGCGGATGTAGCTTTCATGGTAGT







TTGAACGATGCCATAGAAGGTTCCTTGTGTGAATTTATGGAGAGACAGTCCCTC







CTTCTTTACTGGTTACAGGGAAAAGCCAATACTGAAATATCCAGTGAAATAGTA







ACAGGCATAAATCATATAGATGAGATTTTACTGGCTCTCAGGTCAGAAGGAGAT







ATCAGGATTTTCGATATCACCCTGCCCGGAGCTCCTGGACACGCAGTACTAACC







CTGTATGGCACAAAAAACAAAATCAGTCGAATAAAATACAGTACCGGATTATCC







TATGCTAATAGTCTGAAAAAAGCACTTTGTAAATCCGTAGTGGAATTGTGGCAA







TCGTATATATGCCTGCACAACTTTCTTATTGGCGGTTATACTGATGATGACATT







ATTGATAGTTACCAGCGTCACTTTATGTCATGCAACAAGTACGAGTCGTTTACG







GATTTGTGTGAAAATACGGTACTACTGTCTGATGATGTCAAGTTAACGTTTGAG







GAAAATATTACGTCAGACACAAATTTATTAAACTATCTTCAACAAATTTCTGAT







AATATTTTTGTTTACTATGCCAGGGAAAGAGTAAGTAACAGCCTTGTCTGGTAC







ACAAAAATAGTAAGCCCTGATTTTTTCCTTCATATGAATAACTCAGGTGCAATA







AACATTAATAATAAAATTTACCATACCGGGGACGGTATTAAAGTCAGAGAATCA







AAGATGGTACCATTCCCATAATAA







pEG7074
MibO


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686





ATCCGTATCCAGTGTATCGTCGTCTGCGTGATGAGGCTCCGTGCCACCATGAAC







CAGCGTTAGGTCTGTATGCGTTGAGCCGCTACGAGGACGTTCTGGCTGCCCTTC







GTCAGCCCACCGTGTTCAGCTCAGCAGCGCGTGCGGTAGCCTCCAGTGCAGCGG







GAGCAGGTCCATACCGCGGTGCCGACACCGTTAGTCCGGAGCGGGAAACTGCGG







CTGAAGGGCCCGCCCGTAGCCTGTTGTTCCTGGATCCGCCAGAGCACCAGGTGC







TGCGTCAGGCGGTGTCCCGTGGCTTTACGCCGCAGGCAGTATTGCGCCTTGAGC







CGGCCGTCCGCGACATTGCGGCGGGTCTTGCTGATCGTATCCCCGATCGCGGTG







GTGGCGAGTTCGTTACCGAATTTGCGGCTCCGCTGGCAATCGCAGTGATTCTGC







GGTTACTTGGTGTACCGGAAGCAGATCGTGCCCGCGTAAGCGAACTTTTATCGG







CATCAGCCCTGTCGGGGGCGGAAGCAGAACTGCGCTCCTATTGGCTGGGCCTTT







CGGCACTCCTCCGCGATCGTGAAGATGCAGGCGAAGGTGACGGAGAGGATCGTG







GTGTGGTGGCGGCTCTGGTCCGTCCTGATGCTGGACTGCGCGACGCGGATGTTG







CCGCAGGACCTGCCGTGCGTGCACCGCTGACGGATGAGCAGGTTGCAGCATTCT







GCGCCTTAGTGGGGCAAGCCGGCACTGAAAGTGTGGCAATGGCGCTCTCCAACG







CATTGGTCCTGTTCGGGCGTCACCATGACCAGTGGCGCACACTGTGTGCGCGTC







CGGATGCGATTCCAGCAGCATTCGAAGAGGTCCTCCGCTATTGGGCACCTACGC







AGCATCAAGGTCGGACGTTAACCGCGGCGGTACGTTTACATGGCCGTCTGCTGC







CGGCCGGTGCGCATGTACTGCTGCTGACCGGTTCAGCCGGCCGGGATGAACGTG







CGTACCCAGACCCCGATGTATTTGACATCGGTCGCTTCCACCCGGATCGTCGTC







CGTCGACCGCGCTGGGTTTTGGTCTGGGCGCACACTTTTGTTTAGGCGCTGCTC







TCGCTCGTCTGCAGGCACGCGTAGCGCTGCGCGAACTGACACGCCGGTTCCCGC







GTTATCGTACGGACGAGGAACGCACTGTGCGTTCGGAAGTGATGAACGGGTTCG







GCCACAGCCGTGTACCATTTTCCACGTAATAA







pEG7076
LtM1


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687





TTCCCAGAGATCAATGAAACGGATTTCGATAACAATATCAAGCCCCTGCTGGAT







GAACTGGAATCTCGTATTACCATTCCGCAGGAGGAACTGAGCTTTTCAAGCATT







AACGATGATTTATTTCGCGAGTTAACCCGCAACGAGGAGTACCCTTACCAGAGC







ATTTGTACGATCGTTGCAAACATCGTGATGGATGACGGCAGTGAGATTTGGCGC







AAAGATATTTTTGTTGATTCCAATAGTGTGCGCGAAGCCGTATGCGACATTCTG







AGCCAAACGTTATTCCTCTATTTCATCCGCTGCTTCTCCGAACAAATTAAAGAC







ATTCGCAAAACTGATGAGGATAAAGAGTCCACCTACAACCGCTACATTAACCTC







CTGTTCAGCTCCAACTTCAAAATCTTCTCCGACGAATACCCTGTCCTGTGGTAT







CGGACCATTCGCATCATCAAAAATCGCTGGTATTCTATCAAGAAATCGTTACTG







CTGACTCAAAAACACCGTGTGGAGATCGATAAGCAGTTGGACATCCCGCACAAG







ATGAAGATTAAAGGCCTGAAAATCGGGGGAGACACGCATAACGGCGGTGCCACA







GTGACCACGATCTTCTTTGAGAAAGGGTATAAACTGATTTATAAGCCGCGGAGC







ACATCCGGCGAATTCTCGTACAAGAAATTTATCGAAAAGATTAACCCGTACCTG







AAGAAAGACATGGGAGCGATTAAAGCGATCGATTTCGGTGAATACGGCTTTTCT







GAGTATATTGAGTGTAACACGGATGAAGAGGACATGAAACAGGTCGGTCAGCTT







GCATTTTTCATGTACCTGTTGAATGCATCAGATATGCATTATAGCAATGTCATT







TGGACCAAACAGGGCCCTGTGCCGATTGATTTAGAAACCTTGTTCCAGCCGGAT







CGTATTCGCAAAGGCCTGAAGCAGTCGGAAACTAACGCGTACCACAAAATGGAG







AAAAGTGTATACGGAACGGGAATTATTCCAATTTCCCTGAGCGTTAAAGGCAAA







AAGGGTGAGGTCGACGTCGGCTTTAGTGGAATCCGTGATGAGCGCTCTAGTTCG







CCGTTTCGCGTTCTGGAAATTTTGGATGGGTTTTCGAGCGACATCAAAATCGTG







TGGAAAAAGCAGCAGAAGTCTAGCTCCAGCAAAAACAATCTGATTGTCGATCAC







AAAAAGGAGCGCGAAATCCTTCAGCGTGCCCAGTCCGTCGTAGAAGGTTTCCAG







GAAACCTCTAAAATCTTCATGAAACATCGTGAGGAATTCATCTCCATTATCTTA







GACTCATTCGAGAACATCAAAATTCGCTACATCCATAACATGACGTTTCGCTAC







GAACAGTTGCTGCGCACTCTGACGGATGCCGAGCCGGCCCAGAAGATTGAGTTA







GACCGTCTGCTGCTGAGTCGTACCGGAATTCTGTCCATCTCGTCTAGTCCCTAC







ATCTCGCTCTCCGAATGTCAACAGATGTGGCAGGGTGACGTGCCGTACTTCTAC







TCGAAGTTTTCGAGCAAAAGTATCTTTGATACCAATGGCTTCGTTGATGAAATC







GAGCTGACGCCCCGCCAGGCATTTATCATCAAAGCCGAAAGTATCACCAACGAT







GAAGTCGATTTTCAGTCCAAGATCATTAAACTGGCGTTCATGGCACGCTTAAGT







GACCCGCACACAACCAACGACAACAAACTGAATAAAAAGGTGATTATCGAAAGC







AACCAGCAGAGCAACAGCAGTGAATCAGGTAACAAAGCCATTTTGTTCCTGAGC







GATCTGCTGAAAAATAACGTACTGGAAGATCGTTATAGTCATCTGCCGAAAACT







TGGATTGGCCCTGTAGCACGTGATGGCGGTTTGGGTTGGGCGCCGGGCGTGCTG







GGATACGATCTGTACTCGGGCCGTACAGGACCTGCGTTAGCATTGGCTGCGGCC







GGGCGCGTTTTGAAAGATAAAGACAGTATCGAACTTAGCGCCGACATTTTTAAT







AAATCGTCCCAGATTCTGCAGGAAAAGACTTACGACTTTCGTAACCTGTTCGCA







TCAGGTATCGGCGGTTTTAGCGGGATTACCGGTCTGTTTTGGGCGCTGAACGCG







GCAGGGAATATTCTGAACAATGATGACTGGATTAAAACCTCGAATCAGAGTATG







CTGCTGCTGAATGAGAACATGCTGAAAGTGGACAAAAATTTCTTTGACCTGATT







AGCGGCAACTCGGGAGCGATCGGTATGATGTACCTGACCAATCCAAATTTCTAT







TTGTCTCGCTCGAAAATTAACGACATTCTGCTGACCACGGACTGCTTGATTACT







GAAATGGAAAAAGACGAAACGAGCGGACTGGCCCATGGCGTGTCTCAGATCCTG







TGGTTCCTTAGCATTATGATGCAACGTCAGCCCTCAAGTGAAATCAAAATCCGC







GCGACGATTGTCGACAACATCATCAAGAAGAAGTATACGAATTCCTATGGCGAA







ATCGAATGCTACTATCCGACTGATGGGCACTCCAAATCCACCTCGTGGTGCAAC







GGGACAAGTGGGATTCTGGTCGCCTATATTGAGGGGTATAAAGCTAATATCGTG







GACAAATCCTCGGTGTATCATATTATTAATCAGATCAACGTCGAACAACTTCAG







CATGATAACATTCCGATCATGTGCCATGGTAGCCTTGGTGTGTATGAATCGCTT







AAATATGCGTCAAAGTACTTTGAAATCGAAACCAAGTACCTTCTGGATGTGATG







CGCAATGGCGGCTGCTCCTCCCAAGAAGTATTAAAGTACTATGGCAAGGGTAAC







GGCCGTTACCCGCTGTCACCAGGTTTAATGGCGGGTCAGTCGGGCGCGTTGCTG







CACTGTTGCAAACTGGAGGATAACGATATCAGCGTGAGCCCCATTTCACTGATG







ACGTAATAA







pEG7077
LtnM2


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688





CGTGGATTCTATCATCGAATTCTACAAAAAGGACATCTACCTGGCATACAAAGA







GCTGGAACGCGAAATCAAAAACATCGATAAGACCATCTACAACACTTCAAATGA







CGAGATCTTGCGGATTTTTAAAGAGAGCCTGATCAGCATCATCACCGATGATAT







TTACCGCCTCTCGATTAAAACCTTCATCTATGAGTTTCACAAGTTTCGTATCGA







TAACGGGTTTCCGGCTGTCAAAGATAGCGAAAGCGCCTTCAATTATTACATCAG







TACCTTTGACGTGAAAACGATCGCTCGCTGGTTTGAGAAATTCCCAATGCTGGA







ATCCATCATCTCCAGTAGCATCAAAAACGATTGCACATTTATGGTGGATGTATG







TGTCAATTTCATCTTAGACCTGTCGGAATGCGAGAAGATTAATCTGATCTCAGA







GGATAGCCGGCTCATCACGATCTCATCCAGCAACTCTGACCCGCACAACGGTGG







CACGCGTGTCTTGTTCTTTCGTTTCCACAACGGTGATACCATTCTTTACAAACC







CCGCAGCCTGACCGTGGACAAGCTGATCTCTAATATTTTCGAAGAGGTATTCGA







ATTCGATGCGACGAACTCGAAAAATCCTATTCCCAAGGTGCTGGATCGGGGTAC







CTATGGCTGGCAGGAATTCATTGAGAAGAAATCGATCTCTTCCTCAGAGATTAA







GCAGGCCTACTATAACCTGGGTATCTTTAGCAGTATCTTTACAGTGTTAGGGTC







TACTGATATCCACGATGAAAACTTGATTTTTAAAGGTACGACCCCGTATTTCAT







CGATCTGGAAACAGCCCTCTCTCCGCGTATCCGGTATGAAGGTAATGAGGAAAA







CCTGTTCTATCGGATGAGCTCATCGTTGTTCACTTCTATCGTGGGGACGACTAT







TATTCCTGCAAAACTTGCTGTCCATTCCCAGGAAATTATGATCGGCGCAATTAA







CACCCCTGCGAAACAGAAAACCAAGAAGGATGGCTTTAACATCATCAACTTCGG







CACGGATGCCGTCGATATCGCAAAACAGAATATTGAGGTGGAGCGTATTGCTAA







CCCTATGCGCATTAAAAATAACATCGTGAACGATCCGCTGCCGTACCAGAACAT







CTTTACGCGCGGCTTCAAAGAGGGGATCAAATCCATCATCCTGAAGAAAGGCTC







GATCATTTCCATTCTGAACAACTTCAACAGCCCGATTCGTTACATCATGCGGCC







GACGGCAAAATATTATTTGATTCTGGATGCCGCGGTATTTCCCGAAAACCTGTA







TTCGGAACAGACACTGAACAAAACCCTGAATTACTTAAAGCCGCCAAAAATCGT







GGAAAATTCCCTGATTTCTAAACAGCTCTTTCTTGCCGAAAAACGCATTCTGTC







CGAAGGCGATATTCCGAGCTTCTATGTGCTGGGCAAAGAGAAAAATATCCGTGC







GCAGAACTTCATTAGCGAACAGATCTTCGAGGAAACCGCGGTCGATAACGCGAT







TCAAATTCTGGAATCCATTTCGCAAGACTGGGTGAATTTTAATGAGCGCCTGAT







TGCGGAGGGCTTCTCCTATATTCGTGAACAGAGTCGTGGCTATCTGTCCAGTGA







TTTTGAGAACTCTGATATTTTCAAAAGCTCACTGACCGAAACAAAGAAGTCCGG







TTATACCGCAATGCTGAAAACAATTATCTCCATGTCGGTCAAGACCTCGGAAAA







CAAAAAGATCGGTTGGCTGCCAGGCATTTATGATGATTATCCGATCAGCTATAT







GAGTGCCGCGTTTTGTTCGTTCCATGATTCCGGCGGTATCATCACTTTGCTTGA







ACACCACTTTGGGCACTGCTCCCCCGAATATAACGAGATGAAGCGCGGGCTGCT







GGAACTGGGCAAAATGTTGAAAATTAACAATAGTAACCTGAGCATCATCTCCGG







CTCAGAGTCTCTGGAATTTCTGTATACGCACCGCGAAGTCGAATGCCTGGAACT







GGAATACATTTTAAACAATTCAGCGGAAATCATGGGCGACGTGTTCCTGGGGAA







ATTAGGCCTTTATCTTATCCTGGCGAGCTACCTGAAAACAGACCTGAAAATTTT







CCAAGATTTCAGTATCATCTGCCAGAAAAACCTCGAGTTTAAAAAGTTCGGGAT







CGCGCACGGTGAATTAGGGTATCTGTGGACCATCTTCCGTATTCAAAACAAACT







GAAGAACAAAAATGCGTGTCTGAGCATCTATCATGAAGTGTTGAACATTTATAA







AGGTAAGCGCATTGAATCCGTGGGATGGTGCAACGGTTTATCGGGTATTCTGAT







GATTTTGTCAGAAATGAGCACCGTATTAGAGAAAAATCAAGACTATCTGTTCAA







GCTGGCAAATCTGAGCACTAAACTGAATGAGGAATCCGTTGACCTGAGTGTGTG







CCACGGCGCCAGCGGGGTGCTTCAAACACTGCTTTTCGTCTATAGCAACACGAA







CGATAAACGTTATCTCAGCCTGGCCAATAAGTATTGGAAGAAAGTGCTGGATAA







CAGCATTAAGTACGGTTTCTACAATGGAGAACGCGATAAGGATTATCTGTTGGG







ATATTTCCAGGGTTGGTCAGGCTTCACGGACAGCGCACTCCTGCTGGATAAATA







CAATAACAATGAGCAAGTGTGGATTCCGATCAACCTGAGCTCCGATATCTATCA







GCATAATCTGAACAACTGCAAAGAGAAGAATTATGAGGGCGATGGCTGCCATAA







ATCTTAATAA







pEG7078
CrnM


embedded image


689





AAAACTAAAACCATTAACGAAAAGATTAAAATTTTCACCAAAGAAGAGGTGATT







GATATCAGTTACTTTGAAGAATGGCGCAGCGTTCGTACTCTGCTTAACGAAAAC







TACTTTAAAATTATGCTCGAGGAAATGAATATTTCCAAAAACCAATTTTCGTAT







GCGCTGCAACCGTTAAACGACGAGTTCAAACTGCATACTAACGTTAAAAATGAA







GAATGGATCAAATGCTTTAATCGCGTCATTAACAATTTTAACTATAAAAATATT







AACTATAAAGTTGGTTTGTACCTGCCTATTCAGCCTTTCTCCGTTTATTTACAG







GAGAAACTGAAAGAGATCCTGAAGAAGCTGAACAACATTAAGATTAATGATAAA







ATTATCGACGCCTTTATCGAAGCTCACCTGATCGAAATGTTCGACCTCGTCGGT







AAAGTAATCGCCCTTAAATTTGAAGATTATAAACAGATCAACTTCCTGAAAAAC







ACAAATAATGGCACCCGCTTGGAGGAATTCTTGCGTAGCACCTTTTATTCTCGG







AAGTCATTTCTGAAACTGTTTAACGAGTTTCCGGTACTCGCGCGGGTTTGCACC







GTACGTACGATCTATTTGATCAATAACTTTAGTGCTATCATCCAGAACATCAAT







AGCGACTACCTGGAAATCCAGGAATTTCTGAACGTCGATTTCCTGAACTTGACA







AACATCACTCTTTCGACGGGTGATTCCCACGAACAGGGTAAAAGTGTGTCCATC







CTCTATTTTGATGAAAAAAAGCTGATTTATAAACCGAAAAATCTGAAGATTTCA







GAAATTTTCGAGAGCTTCATCGACTGGTACACCAACGTCTCTAACCATAAGCTG







CTCGACCTGAAAATCCCGAAAGGAATTTTTAAAGACGATTACACTTATAACGAA







TTTATTGAGCCAAACTACTGCGAGAATAAGCGCGAAATTGAAAATTACTATAAC







CGTTATGGGTACCTGATCGCAATCTGTTATCTGTTCAACCTGAATGACCTGCAT







GTAGAAAATGTGATCGCCCATGGCGAGTACCCGGTTATTGTTGATATTGAAACG







AGCTTTCAAGTCCCTGTGCAAATGGAGGACGATACTTTATATGTGAAGCTGTTG







CGCGAGCTGGAATTGGAAAGCGTTTCATCGTCGTTTCTGTTACCTACCAATCTG







TCGTTTGGTATGGACGATAAAGTGGACCTGTCCGCGCTGAGCGGAACCATGGTC







GAGCTGAATCAGCAAATTCTGGCGCCTGTCAACATTAATATGGACAACTTTCAT







TACGAGAAATCACCGAGCTATTTTCCAGGCGGAAACAATATCCCTAAAAACAAC







AAATCAGTGACTGTTGATTATAAAAAATACTTGCTCAATATTGTGACTGGTTTC







GACGAATTTATGAAGTATACCCAAGAAAATCAGCTGGAATTTATTGAGTTCCTG







AAAAAATTCTCAGATAAAAAAATCCGGGTGCTGGTGAAGGGTACGGAAAAATAT







GCGTCCATGATTCGCTACAGCAACCATCCGAACTACAACAAAGAAATGAAATAT







CGCGAGCGTCTCATGATGAACTTGTGGGCGTACCCTTACAAAGACAAGCGTATT







GTTAATAGCGAAGTACAGGACCTGTTATTTAACGATATCCCGATCTTTTACTCC







TTTCCAAATAGCCGTGACCTCATTGATAGTCGCGGCTTGGTGTATAAAGATTAC







CTTCCTGTGACAGGACTGCAGAAAGCAATTGATCGCGTGAAAGATACCTCGGTA







AAAAGCTTGTTCGACCAGAAGCTGATTCTTCAGAGTAGCTTAGGTCTGTGGGAT







GAGATTCTCAACAAGCCGGTCCAGAAAAAGGAACTGCTCTTTGAAAAGCAGAAC







TTTAACTATGTGAAAGAGGCGATCAATATTGCGGAATTGCTGATTGGCTATTTA







ATCGAAACGGACGACCAGAGCACCATGCTGAGCATTGATTGTTCTGAAGATAAA







CACTGGAAGATTGTTCCTTTAGACGAATCCCTGTATGGTGGGCTGTCCGGCATT







GCATTATTTTTTCTCGATATTTATAAAATTACCAAAGATGAAAAATATTTTAAT







TACTATGATAAAATCATTTCCACGGCCATTAAACAATGTAAAGCGACCATCTTC







TCGTCAAGCTTCACGGGTTGGCTGAGTCCCATTTATCCGTTGATTCTGGAAAAG







AAATACTTTGGTACCATGAAAGATAAGAAATTCTTTGACTACACGATGGAAAAG







CTGTCGAATATGACTGAAGAACAAATTAACAACATGGATGGTATGGACTATATC







AGTGGCAAGGCGGGTATTGTCAAACTGCTGATTAGCGCGTACCGGGAATCGAAG







AACAATGAAAACATCGGACTGGCCCTGAGTAAATTCAGCAACGATCTGATTCAA







AATATTGGCACCGGCAAAGTCAGTGAATTACAAAACGTGGGCCTGGCGCACGGC







ATTTCTGGTATTATGGTCGTAGTAGCCTCACTGGACACGTTTAAAAGTGAATAT







ATTCGCGAGCAGCTGGCAATTGAATATGAGATGTTCTGTTTGCGTGAAGATTCA







TACAAATGGTGTTGGGGCATCTCTGGAATGATTCAAGCCCGTCTCGAAATTCTG







AAACTGAGCCCGGAGTGTGTGGATAAAAAAGAGCTGAACTTGCTTATTAAGCGT







TTTAAAAACATCTTGAATCAGATGATTAACGAAGATTCCCTTTGTCACGGCAAC







GGTTCGATCATTACTACGATGAAGATGATCTATATGTACACCCAAGACACCGAG







TGGAACTCTCTGATTAATCTGTGGTTATCAAATGTAAGTATCTATTCGACCTTA







CAAGGCTATAGCATTCCAAAGCTGGGCGATGTAACAATTAAGGGGTTGTTTGAT







GGCATTTGTGGTATTGGCTGGTTATACCTGTATTCGAACTTTAGCATTGAAAAC







GTGCTGCTCCTCGAGGTCTAATAA







pEG7079
BsjM


embedded image


690





GAGGCCATTAAAGGTTTGACCGTATCAGAACGTTATGACACTCTGAAAAATTCG







GGAGTCAACCTGAATCTGAACATTTCGGCTTTGGAAGAGTGGCGCAACCGTAAG







AATCTTTTAGCCGATGAGGACTTTACGGAGATGCTGACGGTGCTGGAATATGAC







CCGGTGTATTTTAGCCACGCGATTAACGAGAACATCGAAGAACATATCGATATC







TACAAGAGCAAAATTCTGGGGGAAAACTGGTTTATCGTGCTGAACGATATTCTG







GACGAGCTCGATAATCCCATCGAATACAAGAAAGAGATGAATCACAGCTACCTC







CTGCGTCCGTTCTTGCTCTACGCCGAAAAGGAGATGAACAAATACATTGTCAAT







CGTAAGGAGTTACTTCCGGTGGAACCCCAGGTCATCCAACAGATCATGGAAAAT







TTGGCCTCCAAACTGTTCGCCGTTTCTGTGAAAAGCTTTGTCCTGGAGCTGAAT







ATTTCGAAATTGAAGGACGAACTGGCCGGCGAAACACCGGACGAACGCTTTCAC







TCATTTATTCGTTTGATGGGTGAGAAAACGCGCCTGGTGGACTTTTACAACGAA







TATATCGTTCTGAGTCGTATTCTGGTGAACATCACGATCTTATTCGTCAACAAC







ATTATTGAGCTGTTTGAGCGCCTGCAGGAATCCAAGCTGGATATTGTTAAGAAA







CTTGGCGTGCAGGAGGAGTTCAAAATCAGTAATATTAGCATTGGCGAAGGTGAT







ACACATCAGCAAGGACGCTCGGTTATCGTTCTTACGTTCGTGAGTGGAAAGAAA







GTGGTGTATAAACCAAAAAATCTGAAAGTTGTTTCTGCTTATAATTCTTTAATT







GACTGGATCAACAATAAAAATAATATTCTGAAAATGCCTTCGTATAACACATTG







ATTTATGATGATTTCGTGATCGAGGAGTTTGTCGAGAAACGTGACTGCAAAAGT







ATCGAGGAGGTCAAAAAATATTATATTCGTTATGGGCAAATTTTGGGGATTATG







TATATCTTAAATGGGAACGATTTTCATATGGAAAACCTGATTGCCTCGGGTGAA







TATCCGATCATTGTTGACTTGGAAACGCTGCTTCAGAACATTATCAATTTTAAA







AACAAACCATCAGCGGACTTGATCACCACCAAAAAGATGCTTAACCTGGTAAAC







AGTACTCTGCTGCTCCCTGAAAAACTTCTGAAGGGCGACATCACGGACGAAGGA







ATCGACATGTCAGCCTTGGCAGGGAAAGAACAACACTTGGAACGCCGCGAATAC







CAGTTGAAAAACCTGTTCACCGACAACATGGTTTTTGATCTCGAAAAAGTGAAA







ATCGAAGGTGCGAACAACATCCCGAAATTAAACGGTGAAAACGTTGACTACAGC







ACCTATATTGATGAGATTGTGGTTGGGTTCGAAAATATCTGTAACCTGTTCATT







CAATATCGCGACGAGTTACTGCATTCCGGCATCCTGGAGGAGTTTAAAGATGTG







AAGGTTCGTCATGTGCTTCGCAATACGGTTGTTTATGCTAAGATGCTGGCGAAT







ACATATCATCCAGATTACCTGCGTGATTCGTTGAATCGCGAACAGGTTCTTGAA







AACATTTGGGTGCATCCGTTTGAGCGCAAAGAATTCATTAAGAGCGAGATGGAA







GATATCCTCAACAACGACATCCCGATCTTTTTCTCATACGCGTCGTCTAAGGAT







ATTATCGATTCGAATGGCAAACTGCACAAAAACGTTATGGAAATTTCGGGTTAC







GAACGTTTTACCACCAAACTGAAGGAACTGAATCCCTTTCTGATTGAACAGCAG







GTGAGCGTTATTAATATTAAAACCGGCCGCTATGGGGATAAGAAATTCGAAAAA







AATTATAGCGTGCGCGACGTTGCAACGGAGAAAAAAGATAATCCGATTGATTTC







CTGCAGGAGGCAATGAATATCGGCGATAAAATTTTGGAACATGCTATCATCTGT







GATGAGACCAAAACGATTTCGTGGCTTACCATTAACAACCATCATGATAAAAAT







TGGGAAATTGGGCCTATTTCCGGTGAATTTTATGATGGTCTGGCGGGAATTTCA







CTCTTCTACCACTACCTCTATAAAAAATCCCACAATGTCGAGTATAAAAAAATT







CGTGATTACGCGTTCAACATGGCGAAAGTCAAAGCCCTGTCACTGAAATACGAT







AGTGGCTTGACCGGTTACGCTTCCTTGCTGTATACGGCACACAAGATTGTTCAG







GATGAACCGCGGAAGCAATACAAAGACGTGATCAACGAAGTGTTCAAGTACATT







GATGAGAGCAAAGTCGTGACCGCTAAGTATAACTGGTTGCATGGCACTGCCTCT







ATTATTCATGTGTTATTGAACCTCTACGAGGACTCTCGTGATATGGCGTACCTG







ACTAAATGTATTCAGTACGGCAAATATTTGGTCAAGCAAATCAAAGAACACAAG







GATATGCTTGCGCCTGGCTTTAGCCAGGGCATCTCTTCGGTCATTATGGTTCTG







GTGCGCTTAAGTAAAAAGTGTGAAGTCGAAGAATTTCTCGAATTAGCTCTGGAA







TTAATGGAAATGGAACGCAACAAACTGGGAAACCTTTCTGAATCAAACTGGCTG







AACGGCTTGGTGGGCATTGGCTTATCACGTATCAAACTGAAAGGACTGGATTCC







AACTTACAGGTCGACAACGACATCGAACTCGTCCTGGATGGCGTCATGAACAGC







TTGTACTCAAAAGATGATACTTTGAGCTGTGGTAACTCTGGCACAGTGGAATTG







TTCCTGAGTCTGTTTGAACAGACGAAAAAGAAAGAGTATCTGGATATGGCGAAA







GCAATCTGCGGGAAAATGATCGAAGAGAGTCGCATCTCCTTTGAGTATCAGACA







AAGAGTCTGCCGGGTTTAGAACTGGTGGGCCTCTACTCTGGCTTAGCCGGAATT







GGTTATCAATTCTTACGTATCTCGGACGTTGAGGATATTGCGAGCATTGCTACC







TTAGATTAATAA







pEG7127
PsnB


embedded image


691





TAGGAAGTCCGGATGATCTTCACGTCCAGTCAGTGACGGAGGGTCTGCGTGCAC







GCGGTCACGAGCCTTACGTGTTTGACACCCAACGTTTTCCGGAAGAGATGACAG







TGTCACTTGGTGAACAGGGTGCCTCTATTTTTGTCGATGGCCAGCAAATTGCAC







GTCCGGCGGCGGTGTACCTCCGTTCACTGTACCAGAGCCCCGGCGCGTATGGGG







TGGATGCCGACAAAGCGATGCAGGATAACTGGCGCCGCACATTGCTCGCTTTTC







GCGAGCGTAGTACCCTGATGAGCGCTGTGCTTCTGCGTTGGGAAGAAGCGGGGA







CTGCAGTGTATAATTCGCCACGCGCGTCGGCGAATATCACTAAACCGTTTCAGC







TGGCGCTGCTGCGCGACGCTGGTCTGCCGGTACCACGTAGCTTGTGGACAAACG







ACCCTGAAGCAGTGCGGCGGTTTCATGCGGAAGTGGGTGACTGTATTTACAAAC







CGGTCGCCGGGGGAGCGCGTACACGCAAACTGGAAGCGAAAGATCTCGAAGCGG







ACCGCATCGAACGCCTGAGTGCAGCGCCGGTGTGTTTTCAAGAACTGCTCACAG







GAGATGATGTGCGTGTTTACGTGATAGATGACCAGGTAATATGCGCCCTGCGCA







TCGTAACTGATGAGATCGATTTCCGCCAAGCAGAGGAACGTATCGAGGCCATCG







AAATTTCAGATGAAGTAAAAGACCAATGTGTACGTGCCGCCAAACTTGTTGGCC







TGCGCTACACCGGTATGGATATCAAAGCCGGCGCCGATGGTAACTATCGTGTTC







TCGAACTGAACGCGAGTGCGATGTTTCGCGGTTTCGAAGGCCGTGCGAATGTGG







ATATCTGTGGACCGCTGTGTGATGCATTGATCGCTCAGACCAAACGTTAATAA







pEG7130
AMdnC


embedded image


692





CCACGATAACGAGAGCATTTCATTGGTAACCCAAGCCATTGAATCCCAGGGTGG







TAAAGCATTTCGCTTCGATACCGATCGTTTTCCGACGGAAGTCCAGCTGGACAT







CTATTACTCAAATACAGAGAAATGCGTGCTGGTGGCTGACGATCAAAAACTGGA







TTTAAATGAAGTAACCGCGGTCTGGTATCGCCGCATTGCGATCGGTGGCAAAAT







CCCGCCCACGATGGATAAGCAACTTCGTCAGGCCTCGATTCAGGAGAGTCGTGC







TACAATTCAAGGCATGATAGCGAGCATTCGCGGCTTTCACCTTGACCCAGTGCC







GAACATTCGTCGCGCTGAAAATAAGCAACTGCAGCTGCAGGTTGCCCGCAAAAT







CGGACTGGATACCCCACGCACTCTCACCACTAATAATCCGCAGGCCGTGAAGGA







ATTTGCGGCAGAATGCCAGCAGGACGTAATCACCAAAATGCTGAGTAGTTTTGC







GATTTATGATGAGAAAGGCGGAGAACAGGTGGTTTTCACCAATCCCGTGAAATC







TGAGGATCTGGAAAATTTAGAAGGTCTGCGCTTTTGCCCTATGACGTTTCAAGA







GAAAATCGCAAAGGTTCTGGAGCTCCGGATCACCATCGTGGGTAAGTCAATTTT







AACGGCTGCGGTGAATTCACAGGCCCTGGACAAATCCCGTTATGATTGGCGCAA







GCAGGGCGTAGCATTACTGGATGCATGGCAGACCCATACGTTACCCCAGGACGT







GGCTGATAAATTGCTTCAACTGATGGCCCATTTCGGGTTAAACTATGGAGCCAT







TGACGTGATTCTGACCCCGGATAATCGCTATGTGTTCTTGGAGGTCAATCCGGT







GGGCGAATTCTTTTGGCTTGAGCGTTGCCCAGGTCTGCCGATTAGTCAAGCTAT







TGCTAAAGTGCTGCTTTCTCATATATAATAA







pEG7132
AtxBC


embedded image


693





AGGTTTGGCCCTCGTGGATCAGCATCCGATTTTTCTGGACCTGAAAACAGACCG







TTACCTGTCGTTGAGTCCAGATGGGGCAGCAGTCCTGCTGGGAGCAGCGCCAGC







CACCAAAGAGAGTCCACTGTTTCTCGGATTAGAATCCATTGGCTTGGTCAAAAA







CGGTCCGTCAGGCCTTAAGCCTTGCCAAATTGCCGTAGCCACTGGGTCTGCACC







GCCCCGTAAGGTGCAATTCGAGTCGTTGTCACTCCTGCTTTTGCGCTTAATTCG







TGCACGTCTGGATCAACGTGCTCTTTTGAAGCGTGTGACCGACTTAAAGAAGGC







CGGCACCATTGCCCAGACGAAGAACCGTGACTGCGCCTTGTCATTATTAGGTAG







CGTGGAGACTGAGGCAAAGGCTTGTCGTACCCTTTTAAGTAGTACAGACAAATG







CCTGCCCGACGCATTCGCAATTGCAACGCACCTGCGCCGTCGCGGAGTAGACGC







CAAGTTAGTTTTCGGTGTGCGCCTGCCATTCGCGGCACATGCCTGGGTCCAGGT







AGATGATATTGTAGTGGGTGATCGTCCCGACCGTATCCTTGCGTTCACCCCCAT








embedded image








TATGTCGCGTCTTTCTTTGTTCGCGGACATGTCAGCACACCAGCACTGCGTCAC







CCAGAGCCAAAGGGTTTCGCTTATGCAAAAGTCAGTGGCGGACTGAGCGTATGG







AGCGATGCGCCGATTCGTCACCGTGCGCCCCTTATTACAGTGGGCGCGGTGTTC







GATCGCGCGTCTTTTAAAGGGCTGGATTGCGACTTATCAGGTCTGCGTCAGGAT







GGTCTTAATACATTGAAAGCGGAAACGTTCGGACCCTACCTGGCGTTAGAGGTT







GCCGATAACGGCACCCTTCGCGTTTATCGCGATCCGTCAGGCGGCGCGCCTTGC







TATTACCTGCAGACCGAGGACGGCTTCTGGCTTGCAAGCGATGCTGATTTGTTA







TTCACTCATTCGGGCGTACATCCATCAGTAAGCTTACCGGGACTGATTGAACAC







TTGCGTCGTCCAGAGTTCCAAAATGAGGGCACATGCTTAAACGTCAAGCAAGTA







CGCCCTGGGGAGCAGGTTGATTTATCGCTCTCGGGCGAGGTCCGTGCCTGTTTG







TTCCCGCCTGCATCATCCCTGCGCCCGCCTGAGTTGCACCGCGCATACGATGAC







ATTAAGGCTGAGCTGCGCGCTCTGATTTTACGCAGCATTAAGGCCTATGCCAGT







GATTTCCCTCACGTTGTTGTTAGCTTCAGCGGTGGTCTGGATAGCAGTGTTGTT







GCGGCCGGCTTAGCGCAAACTTCCACTAAGGTCCTGCTTCACACCTTTAAGGGC







CCAGATGCCAAAGGGGACGAGACTGCCTTCGCCGCAGAATGCGCGGCATATCTG







GGTTTAAGCTTAGAGATTGATACTCTCAGTATCGATGACGTTGATCTGTCGGCA







ACTATTTCCCCGCACCTGCCGCGCCCCAGCACATCATTCTTCTTGCCATCACTG







CTGCGCGGTTTCTCTACCTCGAGCCAAACGCGCACAGGCGGGGCAATCTTTTCG







GGAAACGGCGGTGACTCGGTCTTTTGTTTCATGCATAGCGCGACCCCGCTGGCC







GATTTGATGTGTCGTCCGTCAGGTCTTACGCCGTTCATGCAAACATGGGCCGAC







GTGCAAAAGCTTACCCGTGCCTCAGCGACCGAAGTGCTGCGTCGCGCGTTAAAG







ACAGCCATGGCGCGTGGCTACATCTGGCCTGAATCCAATCTCCTCTTGTCCCGC







GACACAAGCTCGAGCCGTTTAACACCTGACTCCGTTCTGTCGAGCCTTGAGGGG







ATTCTGCCCGGTCGCTTGCGTCACCTCGCCCTGATTCGTCGTGCTCACAACACC







TTCGAGCCATTCGCCCCTTGGCGTACGCCGCCAGTCGTTCACCCTCTCATGGCC







AAGCCGATTCAAGCCTTCTGCCTTTCTCTTCCTTCATGGATGTGGGTCAGCGGT







GGTAAAGACCGCTCGCTCGTGCGTGACGCGTTCGAAGGATTACTTCCAGATTCA







GTGCGCCTTCGTAAATCAAAGGGAAGTCCTGCAGGCTTTCTGCATGCGCTGTAC







CGCGCCAAGGGTCGTCAAATGATTGAGCGTATCCGTCACGGTTACCTGCGTCGT







GAGGGGATCATCGATATCTCTACTGGCCCGGACGCATTGTTCTCGGAAGGGTTC







CGCAATCCGCGTGTAATGCACCGTTTCTTTGAGCTCGCCGCAACTGAGGTGTGG







ATCGATCACTGGCGCAACTGGCGCCGCCCCCGCACATAATAA







pEG7133
Cln1BC


embedded image


694





CCACGCGGTCGCTCTGGACGAAGATATCGTGGTGCTGGATGCGGTGAGCGACGC







ATACCTGTGTTTAGTTGGTGCCAGCGCTCTGATCAGCTTGGGCAGCGAGCGTTC







CGTCAGTGCAGATCCGGTGGCCGCTGAGACACTTCGTGAGGCTGGTCTGGTGGG







TCCACATCCTAGCGGCGCCACCCGACCAATACCTCCGAAGCCGACGATTGACTT







ACCTGATGCAGCCCGTCAGGCGCAAGGTCGTGAATTACGTGCCGCCGCGTGGGC







TGGCGCGGCAACCGCAATCGATTTCCGCCGGCGTTCATTTAGACAACTCCTCGC







GAGAGCAGGGCAACGCCCGCCGGGTCAAGCAGCTGCTCCGGCTGATGAGGTATT







GGCAGCAGCCGCAGTGTTCATGCGGTTACGTCCATGGTCACCCGTTGGAGGCGC







GTGCCTTATGCGTTCGTATTACTTATTACGGCATTTGCGCATCCTCGGTTTCGA







TGCCGATTGGATCATTGGTGTGCGTACGTGGCCATTTATGGCCCATTGCTGGCT







GCAGGTCGGTGCCGTCGCACTCGACGATGACGTCGAGAGATTAACAGCATACAC








embedded image








ACCTGGCTCTGTACTGGCCGCGCGGCATGCCCGGTGTAGCTGCAGACGCAATGC







GGGCCGCCATCGAAGCTGAGGGCGCCTGGACCCTGGCGTTCGAGGCCTACCAGC







TGGTAGTGTATGTCAAAGGGCCCCGAGCACCTAAAGTGCGTGCCCTGCCGGATC







AGGGCGGGGTGGTCATTGGGGAACTGTTTGATACTGCAGCAACCCGCGAAGGAC







GCGTGCAGGACTTTCCTATAGCGCTGATCAAAGACGTCGCAGCTCAGGATGCCG







CACGTATTCTTGCTACCCATGCGTGGGGTCGTTATGTGGCTGTATTAAAAGCCG







GTGATCGTCCGCCATGGATCTTTCGCGATCCAAGCGGGGCGGTGGAATGTCTGG







CGTGGGTCCGCGATGAAGTGACCATCATTAGCAGCGATGTTGCAGCGCAACGAG







CTTGGTCCCCTGATCGGCTGGCGATTGACTGGTCGGGACTGGGACGTGTACTGG







CACGCGGAAACTTATGGGGAGAAATTTGCCCGCTGGCTGGCGTCACGGCGATTG







CGCCAGGTACCGCACGGTGTGATCTCGGTGATGCAGCTCTGAGCCTGTGGCGCC







CAGGAGATCATGCACGTCGTAGTCGTCATGATGTTTCCCCACGTGATTTGGCAA







GAGTGGTGGATGCTAGCGTTGCAGCCCTGGCTAGAGATCGCAGCGCTATTCTGG







TCGAAATCAGCGGGGGACTGGATTCCGCTATCGTTGCCACGTCGCTGGCTCGTT







GTGGAGCCCCAGTTGTTGCTGGAATTAACCATTACTGGCCCGAACCGGAGGGTG







ATGAACGTCGCTGGGCCCAGGACATCGCAGATCGGTGCGGTTTTCGCCTGATCG







CGGGCCAACGTCAGCGGCTGTTGCTGGACGAGGCAAAGCTGCTGAGACATGCAC







AGGGCCCGCGACCTGGTCTGAATGCGCAGGACCCGGACCTCGATCACGATCTGG







CGGAACAGGCTAAAGCGTTGGGTGCCGATGCACTGTTCTCAGGGCAAGGTGGCG







ATGGTGTGTTCTATCAAATGGCAAATGCTGCACTGGCAGCCGATATCCTCATGG







GGAAACCTGCTCCTATGGGTAGAGCCGCGTCTTTAGCCGCTGTGGCTCGTCGGG







CACGAGCCACGGTCTGGAGTTTGTGCGGCCAGGCTATGTTTCCGTCGCGCGCAT







TTGCCGCTGGTATGCCGCCGCCAAGTTTCTTGAGCGCCGGTTTGGCGCCGCCAC







CCGTGCACCCGTGGATTGCAGACCAGCGCGGTGTTTCACCGGCGAAACGTATTC







AAATTCGGGGGCTGACCAATATTCAATGTGCTTTCGGCGATAGCTTACGGGGCC







GAGCAGCAGATCTTTTATATCCGCTTATGGCCCAACCGGTCATGGAACTGTGTC







TGTCTATCCCTGCACCGCTGTTGGCAGTAGGCGCATTGGATCGCCCTTTCGCAC







GTGCGGCGTTCGCAGATCGATTACCTCCTCGTTCACTCGTTCGACGCTCAAAAG







GTGATGTTACCGTGTTTTTCAGCAAAAGCCTTGCAGCAAGCCTGCCGGCCCTTC







GTCCTTTCCTGCTGGACGGGCGCCTTGCAGAACAGGGTCTGATCGATCGAGCAA







AACTGGAACCTCTGCTGCACCCCGAACCGATGATTTGGCGCGACTCAGTCGGCG







AGGTAATGCTGGCAGCGTATCTTGAAGCCTGGGTGCGCGCATGGGAAGCCAAGT







TGCGTGTTAGCTAATAA







pEG7134
Cln2BC


embedded image


695





CGGTAATGGTCGAAGATGATCTGGTTCTGCTGGATGAAGCAGCGGACGCTTATG







TCTGTTTGTTGGATGGCGCCAAAGTGGTTAGCGTCCGGGCTGACGGTGCTCTGA







GCTTCAATCCCCCACATGCAGCAGAAGATATGATCGCGGGTGGCCTCGTCGAAC







CTTCATCAAGTGCCGCGGCGTCAGCAAACCCGCCGGCAAAACTCCCATGTACTC







CGCTGGCGCGCTTATCGCGCCCGCGGCATGTAAAAGTGCGTCCGGCTGAAGCGG







CCTTGTTCCTGATCCAAGCCTGGGGTGTTGCGCGTGCGGTACGTCGTTGGCCAA







TGGCTAGATTATTAGAAGCATTACGTGGAGATCGTGCCGCAGAACCGGCGAAAG







GCCGCCGATCGATGGCGGAGGCGTGCGCTGTTTTTGATGCGCTTCTGGCCTGGA







GCCCTTTTGACGGTGAATGTTTGTTTCGCTCAGTATTACGACGTAGATTTTTAA







TGGCACTGGGCCATTCGCCGGACTTGGTGATAGGCGTGCGTACCTGGCCGTTCC







GCGCACATTGCTGGCTGCAGAGCGGAGTGGATGCCCTGGATGATTGGCCGGAAC







GGCTCTGCGCATATCGCCCGATTCTGGCAGCTTCTGCAAGCCAGGGTAGATAAT








embedded image








TGGCCGCCGGGGCAGCCGAGCGTAGAAGCTGATGCACTTCACGCAGCCTTTAAC







GGGCAGGGTGGATGGAGCCTGGTTTTGGAACGATTCTGCCTGCGCGTATACGTG







CGTGGCGCGGCAGCCCCTGCAGTTACCCTTACCCCGAAAGGAGGCGTGCTCATT







GGTGAGATGTTTGATCGGGCTGCCACAGAAACGGGCGCCGTTGCCGCTTATGAT







CTGAGCCGCCTGGGAGATGACGACGGTATGGCCGTAGCCCGGCGTGTGGTGGAC







GAAGCGTGGGGGAGATATGTGTTGGTGCTGCCAGTTAAAGAACGCCGTCCAGTG







GTTTTGCGAGAACCACTGGGCGCGCTGGATGCGCTGATCTGGCGCAAAGGCGAT







GTCTGGTGCGTGGGGGCAGACGTACCCCCGGGTCTTGAACCAAAAGATCTGGGT







GTGGAAGAGACTAGACTGACGCACCTGATCGCGGAACCGGATCTGGCATCTGCG







AGCCTGCCCTTAACCGGCGTCGCGGCAGTGATGCCAGGTACTGCGGTCGATGAA







ACCGGCCAGGTGCACCGTCTGTGGACCCCCGCGCGTTTTGCTCGCTCCCCTCGC







ACTGACGCGTGGACTGCAGCCGAACGTATTCCGCTGGTTACCCGTGCGTGCATC







GCGGCGCTGTCTGCGAATCGAAGTGGTATTCTGTGCGAGATTTCGGGCGGCCTG







GATAGCGCTATTGTTGCGACCTCTCTGAAAGCGGAAGGTGCGAAGATTAGTAGC







GGGATCAACTTCCATTGGCCCCAGGCTGAAGCAGATGAGCGCCCGTACGCACGC







GCTGTTGCGAAAAGCGTGCGAACCCGGTTACAGGTGGTAGCGAGTCGTGTAGCG







CCCGTTGACCCGGAAACGTTTGATGAGATCGTGGTCGCGCGACCAAGTTTTAAT







GCCATTGATCCAGTCTATGATACCGTACTGGCCCAACGTCTGATTCAGGGCGGT







GAAGGAGCCCTGTTTACCGGACAAGGTGGTGACGCAGTTTTCTATCAGATGCCA







GCACCACAACTTTCGTTGGATTTGTTGGCTCGTGGCCCCCGCCGCCGCGGTCTT







ATGGGATTATCACGCCGCACCAACCGCAGTGTCTGGTCGTTGCTGCGCATGGGC







TTACGTGCACCCGTACGAGCAACCTTTCCCTACGGTGCGAGAGGTGCCGATCGT







CCTCCGATGCACCCGTGGCTGGAGGACGCGCGTGGTGTTGGGGCCGCGAAACGG







ATTCAGATCGAAGCGCTGGTTGCTAACCAGGCCGTGTTTGAAGCATCTCGTCGC







GGTGCGGCGGCTCATTTGGTGCACCCACTGCTGTCGCAACCGCTTGTGGAGCTG







TGCCTTTCAACCCCAGCGGCCGTGCTGGCGGGTGCCGAACAAGATAGAGCATTC







GTGCGTAGCGCTTTTCGTGCGCAACTGCCACGCCTGGTCTTAGATCGTCAAAGC







AAAGGAGATCTGAGCGTTTTCTTTGCTAAAGGTGTGGCGCGGAGCTTGCCGGGC







TTGCGTCCGCGTCTGCTCGAAGGACGCTTAGCGGCACGTGGCCTGATCGACGTG







GAAGCGTTATCACAAGCGATGCAGCCAGAAGCGATGATTTGGCGTGACGGTTCG







GCCGAAATCCTGTGCCTTGCTGTTCTGGAATCATGGCTCCGCTCTTGGGAGGCT







CGTGGTGCATAATAA







pEG7135
Cln3BC


embedded image


696





ATTGCGTAAAACAAGGTGGAGTTACGTTTCTGGACGTCCGCGGGGATCGTTACT







TCGGCCTGCCGCCGGTGCTGGAACACGCGTTCGTTGCCATTGCCGAGGCGGATT







TTCTGCTGAAAGAACCAAATTCACTTCTGGAGCCACTCGAAGCACTGGGTGTCT







TAGTGCGAGGCCAAGCCCGCCGTGCCGATCTGACAATTCCGTCTGCAAATCTGT







CATGGGTGGATGAGGTCAGCCCGACCCCACCACGTCTTGACCCTGCGTCACTCG







TCGCAACCGTCACGTCTGTTATTCGAACGCGTCTGAGCCAAAAGAGTAAGTCCT







TGCAGGCTCTCTTGGAAGAGGTCCGTACCCGCCGTCCGGGATCGCCGGCCCATA







ATTGGCAGCTGATGCGTCGTCTGACGGCTGGATTCCGTGCATCGCGTGCTTGGG







CGCCGATAGAACCCATCTGCCTCCTGGACAGCTTGGCGTTACTGGATTTTCTGC







ATCGCCGTGGCCTGTATCCGCATATTGTTTTCGGTGTGATCCGCCAACCGTTTG







CCGCTCATTGTTGGGTGCAAGCTGATGATGTAGTCCTGAATGACCGGCTGGATC








embedded image









embedded image








CACGCGACTTGATTCGTCGCCTGCCGAAACTCAAAACCGTCATTGAAACTAGCG







GATTGGTGGTACTGCGCCCCGAAAATGGTGCGGGTCTGCGGGTAGGCGGGAACG







GTGTGGTCCTGGGTAGCGTCTTTCGCACCGGCGGTGATCGCGAAACTGTTGCGG







AATTTTCGGAATCGGAAGCATCCGCGATCGCCACGAGTCGTGGTCAGCAGTTAG







TGACAGAGTTCTGGGGTGGCTACCTGGCTGTTCTTGGAGATGCTTCGCGTTCCG







AAGTGATGGTCCTGCGAGATCCTTCAGGTGCAATGCCGGCTTATTGTTTAGTTC







ATGGCGAAGTCCAGATCATCTGCTCTCGCTTGGAGGTCCTGGAGGACGCAGGAC







TGGGGCAGCAGGCGCTGAACTGGGACGTGGTGGCGCAATTACTGGCCTTCCCAA







ACCTTCGAGGTCGCTCAACGGGTCTTAAAGGCGTGGAAGAATTACTTCCCGGTT







GCCGTCTGACATTTACGGGAGGACTGAAAACCGAAACGCTGACCTGGAACCCGT







GGCTTTTTGCCCGCCCATCTGCGCAAGCGCCTGAACGTGGAGTTGCGGCGACCG







CCGTGCGTCAGGCGGTGGAAGTAAGCGTTCGAAAATGGGCTGATCAGAGTTCAC







CGGTACTTTTGGAATTGTCAGGCGGGCTGGATAGTAGTATCATCGCCTGCTGTC







TGGACGAACCGCGCACCGCGGCCACCTTCGTGAACTTTGTCACACCGACGGCCG







AAGGCGATGAACGAGGATATGCACGTCTGGTTGCCAAGGCAGCAGATAAACAAC







TGATCGAGCAGGACATCCGGGCTGACGAAGTAGATGTTACCCGTCCAAGACCTG







GCCGCCATCCTCGTCCGGCCAGTCAGGCGCTGTTACAGCCGCTGGAACAGGCTT







GCGCTGAACTGGCACCTCAGTTGGGTGCGAGAAGTTTCTTCTCCGGTCTGGGAG







GAGACAACGTGTTTTGTAGCATTGCAACCGCAAGCCCGGCTGCGGATGCACTTT







TGACTAGCGGTCTGGGCCGACAGTTCTGGGCCGCAATCGGGGACCTGTGTGCAC







GTCATAACTGCACCGTATGGGCAGCCTTAAGCGCCACGCTGAAGAAACTGCTCC







GCTCAGATCGTCGTCTGGTGATCAAACCAAACCTGGATTTTCTGTCCTTTCGGG







AGGACGCCATAGACCGTCCGGATCACCCATGGCTTGAAGTGGCCGCCGATCGTC







TGCCGGGGAAACGCGAACATGTCGCAAGCATTCTGTTGGCGCAAGGCTTCCTGG







ATCGTTATGAGCACGCTCAGGTTGCTGCCGTCCGCTTTCCCTTGTTAACGCAAC







CGGTTATGGAGGCTTGTCTGCGCGTGCCGACCTGGATGGCAAACCACCAGGGTC







GCAATCGGGCGGTCGCACGCGATGCCTTCTTTGATCGCTTGCCCCCGAGAGTAC







GTGATCGGCAGACAAAAGGAGGTTTGAACGCGTTTATGGGTGTTGCGTTCGAAC







GCAACCGTCAGGCCTTAGCTCGTCATCTGTTAGACGGGCGCCTGGTACAGCGTG







GCCTGATAGATGCAGTGGCAATAAAATCGGCGCTGGCCTCACCAGTCCTGGAAG







GAGGAGCCATGAACCGCTTACTGTACCTGGCCGATGTCGAATCCTGGGTACGCT







CATGGGAAGATGTGTAATAA







pEG7136
CsegBC


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697





TCTATGCTGTCATGATCGATGATGATGTAGTTTTCCTGGACGTCGCCACCAATG







CATACTTCTGCCTCCCAGCCGTTGGGAGCGTGTTGGCACTCGAAGGTCGTTCGC







TGCGTGTGGCGGCTCGCGAACTGGCAGAAGATCTTATTCAGGCAGGCTTAGCAT







CCGCGGCTGCGGCAATCGAACCCCCACCGAGCACACCAGCCCCAGTTCGCACTG







CGCGTGCGGTATTGGAAGCTCTGCCGGCGCGTGAAAGACCACGTCCACGTCTTG







CCCACTGGCGTCAGGCGATTATGGCTGGCTTGGCGTCCCGTGCCGCTGAACGTC







GACCATTCGCGCAGAGACTGCCGCCGCCTTCAACGGGGGTTTCACCTCCGGCAT







CAGAAGGCCTGCTTGCCGATCTGGATGCGTTCCGTCGACTTCAGCCATGGTTGC







CGTTCGACGGTGCTTGTCTGTTCCGTAGCCAAATGCTGCGCGATTATCTCCTTG







CGCTGGGTCACCGCGTTGACTGGATTTTCGGTGTACGTACGTGGCCGTTTGGTG







CCCACTGTTGGTTGCAGGCCGGCGACCTGGTGCTGGATGATGAGGCCGAACGTC








embedded image









embedded image








AGCAGCGTTTGATGAGATGGTAGAAGCACTGATCGATGCTGGATGGACCTTGGC







GTTGCGTGCGTTCAGACTCGCCGTTCTCACCGATGGTCAGGCTCCAGCCGTGTC







GCCGCTGATGGGCAGAGGCGGCGTAGCAGGCGTTCTCATCGGCGAAGCGTTTGA







TCGTCGCGCCACATTAGGTGGCGCGGTCGCACGTGCCGCGCTGGATGGTTTGGC







TGACATCGATCCGCTGGAAGCAGGTCGCCATCTGATTGAAACCGCGTGGGGCGG







CTACGTGGGTATGTGGATTGGTCGGGCCGAAGCTGGTCCGACACTGCTGCGCGA







TCCTAGTGGCGCGCTCGAAGCCTTAGCGTGGCGCCGTGACGGTGTAACCGTTAT







GTCAGCGCGCCCGTTGACGGGGCGCGCAGGCCCAGCTGATTTAGCAATCGATTG







GCCACGTATCGTGCAGATTCTGGCCGATCCCATTTCCGCGGCTCTCGGCCCGCC







CCCTCTGACTGGCTTAGCGACCATAGACCCGGGCGCGGCGGTTCATGGCGCGGA







TGGCCAAGAACGCTCAGTGCTGTGGACCCCAGCTGCAGTTGTCCGTGGTGCTCG







TCACCGTCCTTGGCCAAGCCGTCAGGATCTGCGTCGCACCATCGATGCGACTGT







CGCGGCACTGGCCTCGGATGCGGGCCCGATTGTCTGCGAAATTTCAGGAGGTCT







GGACTCGGCCATAGTTGCGACTAGCCTTGCGGCGTCCGGTCTGGGTCCGCAGCT







GACAGTGAATTTTTACGGTGACCAGCCTGAAGCTGATGAACGCGGATACGCTCA







AGCCGTCGCCGAACGTATCGGTGCGCCTCTGCGGACCCTTCGTCGAGAGCCGTT







CGCGTTCGATGAAACCGTGCTGGCAGCCGCTGGACAGGCCGCACGTCCGAATTT







TAACGCCCTCGATCCTGGATACGATGCCGGGCTCGTGGGTGCCCTGGAAGCTAT







CGATGCTCGTGCATTATTTACGGGCCATGGCGGTGATACCGTGTTTTATCAAGT







GGCGGCCAGTGCCTTGGCCGCAGACTTACTGGGCGGCGCACCATGTGAAGGTAG







CCGCCGTGCACGTTTAGAGGAAGTAGCTCGGCGGACCCGACGCTCGATTTGGAG







TCTTGCATGGGAAGCGTTTTCTGGTCGACCCAGCACTGTAAGCATTGAAGGTCA







GTTGCTTCGACAGGAAGCAGAGAGAATTCGGCGCGTCGGCCTGACCCATCCGTG







GGTTGGAGGCCTGTCGTCTGTGACCCCTGCGAAACGCCAGCAAATCCGCGCGCT







GGTCAGTAACCTGAACGCGCATGGCGCCACTGGTCGCGCCGAACGCGCTAGAAT







CGTGCACCCGCTTTTAGCTCAGCCGGTGGTTGAAGCCTGCCTGGCGATTCCTGC







CCCTATCCTCAGTGCGGGCGAAGGAGAACGCTCATTTGCGAGAGAAGCCTTTGC







AGACCGTTTGCCACCGAGCATTGTGGGCCGCCGAAGCAAAGGGGAAATTAGTGT







GTTTCTTAACAGATCTTTAGCAGCCAGCGCCCCCTTTCTGCGTGGCTTTTTACT







TGAAGGACGGCTGGCGGCTCGCGGGCTGATTGATCGTGACGAACTTGCAGCCGC







GCTGGAACCGGAAGCAATCGTCTGGAAGGATGCGTCACGCGACCTGCTTACTGC







GGCGGCCCTGGAGGCGTGGGTCAGACATTGGGAAGCACGTATTGGCGAGGGGGA







AGCAGCGGAAGGTGAGCGTGCTGCCGGTCGTGGTACCGCAGCGACGGGACCGCG







TACAAGCGCGCGGAAGGCGAACACCCGTTAATAA







pEG7137
PadeK


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698





ACCATTATAAAGCCTTTGGGTTTAGAATTGAAAGCGATTTCGTGCTCCCGGAAC







TTCCGCCCGCAGGCGAACGCGAACCGCTCGATAATATTACGGTTCGTCGTACCG







ACCTGCAGCCGCTCTGGAATTCTAGTATCCATTTTTACGGAAACTTTGCCATTC







TGGATCACGGACGCACGGTTATGTTTCGAGTTCCGGGTGCTGCTATCTATGCGG







TACAGGATGCTAGCAGCATATTAGTGTCCCCATTCGATCAGGCAGAAGAAAACT







GGGTACGTCTTTTTATTCTGGGTACCTGTATTGGGATCATCCTGCTGCAGCGTA







AGATTATGCCGCTGCACGGTAGCGCCGTTGCCATTGATGGCAAAGCCTACGCGA







TTATCGGCGAATCTGGTGCCGGCAAAAGCACTCTTGCACTGCATCTTGTCAGTA







AGGGTTATCCATTGCTTTCGGATGATGTGATTCCGGTCGTTATGACCCAGGGCT







CCCCCTGGGTGGTGCCGTCGTACCCGCAACAAAAACTTTGGGTGGACACTCTGA







AGCACATGGGAATGGATAATGCAAACTATACGCCGCTGTACGAACGTAAAACGA







AGTTCGCGGTGCCCGTGGGCAGTAATTTCCACGAAGAACCGCTGCCGTTAGCTA







GCATTTTCGAGCTTGTCCCGTGGGATGCGGCAACGCACATTGCCCCGATCCAAG







GGATGGAACGCTTTCGTGTCCTGTTCCACCACACTTATCGGAACTTTCTGGTTC







AGCCGCTGGGTCTTATGGAATGGCATTTTAAAACTCTGAGCTCGTTCGTTCACC







AAATTGGAATGTATCGTCTGCATAGACCTATGGTCGGATTCAGTACCTTAGATT







TAACGTCGCACATTCTGAATATAACGCGTCAGGGAGAGAACGATCAATAATAA







pEG7138
ThcoK


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699





TCGCGCGTTCGGCCTGCGCATAGACTCAGATATTCCGCTGCCAGAATTAGGGGA







CGGTACGCGCCCTGATGGTGACGCGGATCTGACGGTCGTCCGGTGTGGGGAAGC







GGAGCCGGAATGGGCTGAAGGTGGTGGCGGGGGTCGTCTGTATGCCGCTGAAGG







CATTGTATCTTTTCGCGTGCCGCAGACGGCAGCGTTCCGTATTACTAATGGAAA







TCGCATCGAGGTGCATGCCTACTCGGGGGCTGATGAGGATCGAATACGCCTGTA







CGTGTTAGGGACCTGTATGGGAGCGCTGTTACTGCAACGTAGAATCTTACCGCT







TCATGGTTCGGTCGTCGCCCGTGATGGTCGTGCGTATGCCATAGTTGGCGAAAG







CGGAGCGGGCAAATCCACGATGAGTGCAGCACTTCTCGAACGTGGATTCCGCCT







CGTTACGGATGACGTGGCCGCCATCGTGTTCGATGAGCGTGGGACCCCACTGGT







TATGCCGGCTTATCCACAGCAAAAACTGTGGCAGGATTCCCTGGACCGTCTGCA







AATTGCGGGCTCGGGCCTTCGTCCGCTGTTCGAACGCGAAACGAAATACGCTGT







ACCCGCGGATGGGGCATTCTGGCCCGAACCGGTTCCATTGGTGCACATTTACGA







ACTGGTTCATAGCGATGGTCAAACGCCTGAACTGCAGCCGATTGCCAAATTAGA







GCGTTGCTATACCTTGTATCGCCACACATTTCGTAGAAGCCTGATCGTCCCCAG







CGGCTTAAGCGCCTGGCATTTTGAAACGGCAGTGAAACTTGCGGAGAAAACGGG







GATGTACCGTCTTATGCGCCCGGCCAAAGTTTTCGCGGCTCGCGAATCTGCTCG







GCTGATTGAAACTCACGCCGATGGTGAAGTGTCACGTTAATAA







pEG7139
StspM


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700





CACCGTCCTGAGCCTGGCCGAACGGACAGGTACCGATCCAGATCTGCTGGGCCG







TGTGTTGCGCTTCCTCGCTTGTCGTGGTGTTTTCGCCGAGCCTCGCCCAGGTAC







TTATGCCTTGACCCCTCTGAGCTTAACTTTACTGGAAGGCCATCCGTCCGGTTT







AAGAGAATGGTTGGATGCGTCGGGTGCGGGAGCGCGCATGGACGCGGCAGTTGG







AGATCTGCTTGGCGCCCTCCGCTCGGGTGAACCGAGCTATCCACGTCTGCATGG







TCGTCCGTTTTATGAAGATCTGGCGCTGCACAGCCGAGGCCCTGCTTTTGATGG







ACTGCGTCATACGCACGCCGAATCGTATGTTGCCGACCTGCTGGCAGCCTACCC







GTGGGAACGCGTTCGTCGCGTGGTTGATGTAGGCGGTGGGACCGGCGTATTGGT







CGAGGCGCTTATGAGAACTCATGCGACCCTCCGTACAGTACTGGTCGATCTTCC







AGGCGCGGTGGCTACCGCTACCGCTCGAATTGCGGCTGCGGGTTTTGGCAATAG







ATATACACCGGTCACGGGTTCCTTCTTTGATCCGCTGCCTGCGGGGGCGGATGT







TTACACCCTGGTTAACGTGGTTCACAACTGGAACGATGAGCGTGCCTCAGCTCT







GCTGCGTCGGTGTGCGGATGCGGGTCGCCGCGACAGTACGTTTGTTATCGTGGA







ACGCTTAGCGGACGATGCAGACCCTCGTGCCATCACCGCCATGGACCTCCGTAT







GTTCCTTTTTCTGGGCGGTAAAGAGCGCACGGCCGCACAGATTCGCGAAGTAGC







TAGTGCGGCTGGCATGGCCCACCAAAGCACCATTAAAACACCGTCTGGCCTCCA







CTTACTTGTTTTCCGTAAGAAACGTTTCGCTGCTCGCGGTCACGGTCGTCGCAT







GGTGACCTAATAA







pEG7141
LenG


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701





ACAAGTGGTTTGATATTAACTTCCTGGAAATGTATACACGCAGCTGCCTGAAAA







CTTTTGGCTACTTCGACGAAATTCTGATCGTGAAGAAACGCATCGAGGTCCTGA







AGAACGTGCTTGAAAAACAGTACTTGTCTACCAATGATTATGCTGAGGAGTTTT







TCGAGCTGAATACCACCTTGGAGAGCATAAAAGAATACATCAAACTGAATCTGG







TCATCGAGAAAGAACCGATCTCAATTTGCATTATGGTCAAAAACGAAGAACGTT







GCATCAAGCGCTGCATTGATAGCGTTGAAATCCTCGCCGAGGAGATAATCATTA







TCGATACCGGCTCTACGGATAATACCATTAACATTATTGAGGAATGCGCAAACG







ACAAAATTAAAGTGTTCTCAAAAGAATGGCGTAACGATTTTTCCGAAATTCGGA







ACTATGCCATCGAGAAAGCGAGTAGCGAATGGCTGGTGTTTATAGATGCCGATG







AATATCTGGACGAAGCCTCGGTGCTCAACCTGCTCAGTACGCTCAACATCTTTA







ACAATCATAAGCTCAAAGACTCTATTGTCCTGTGCCCCATGATCAACGAAGCCA







ATAACACCATCCATTTCCGTACCGGGAAATTTTTCAGAAAAGACTCCGGGATTA







AATTCTTTGGTACCTGCCATGAGGAGCCCCGCATTAAAGGCATGCCGAATTCTA







CCCTGCTGATTCCGATCAAGGTTGATTATCTGCATGACGGCTACCTGGCAAAAG







TACAATCAAATAAAGACAAGAAAACCCGTAACATCGAACTGTTAGAAGGTATGG







TGGAACTGGAACCGGATAATCCTCGTTGGGCGTATATGTTTGTGCGCGACGGAT







TTGCAATCCTCGATAACGAATACATTGAGAAAACTTGTTTGCGGTTTTTACTGC







TGGACAAAAACGTACGCATCTGCGTCAACAACCTGCAAGACCATAAATTCACTT







TGTCACTCCTGACGATCCTGGGCCGCCTCTATCTGCGCGAGTGCGAATTCGAGA







AAAGCAATCTGATAATTCGCATTCTTGACGAACTCATCCCTAATAGTCTGGATG







GTAAATTTCTGGCATTCATGGAGCGATTCAGCAAACTGAAAATTGAGATTAATA







CGCTGTTAACGGAGGTCATCGAATATCGTCGTAACCACGAAGTAGATGAAACCA







GTTTAATCAACACACAAGGCTACCATATCGACTATGTTCTGTCGATTTTGCTGT







TCGAAACGGGTAATTACGCGCAAAGTAAGAAATACTTCGATTTCCTGCAGGAGA







ACCATTTTCTGGAAGAACTGTTTCAAGACAGCTCTTATTCTATCATACTGAAAA







TGCTCGAGTCAGTAGAAGATTAATAA







pEG7142
PalS


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702





GATGAAAGATAACTATGCGGACTCTAATCTGTTCAAGGATTTGAATCTGATCCA







CAATATCTCCAACGACATCCAAATTGGAATTAATTGCGATTTCTCTGAAATGCT







GGGAGAACTGGTAGGTAATTACGATTCCCTGAACTATCCGTCAATCACCTGTGG







TATTCTGACGTATAATGAAGAACGCTGCATTAAACGTTGTCTGGAAAGTGTGGT







GAACGAATTCGATGAGATTATTGTCTTGGATAGTGTATCCGAGGACAATACCGT







GAAAATTATCAAGGAGAATTTCAACGATGTCAAAGTCTACGTCGAGCCATGGAA







GAACGATTTTTCATTTCACCGCAACAAGATCATTAATCTCGCAACGTGCGACTG







GATCTACTTTATCGACGCGGATAATTATTATGATTCGAAGAACAAGGGTAAAGC







CATGCGCATCGCTAAGGTTATGGATTTCTTGAAAATCGAAGGCGTTGTGAGCCC







AACGGTCATTGAGCATGACAATAGCATGAGCCGTGATACCCGTAAGATGTTTCG







TCTGAAAGATAACATTCTGTTTAGCGGTAAAGTTCATGAAGAACCGGTGTATGC







CAATGGTGAGATCCCCCGGAACATCATAGTAGACATCAACGTGTTTCACGACGG







CTATAACCCAAAGATTATCAACATGATGGAAAAGAACGAGCGCAATATCACCCT







GACTAAAGAGATGATGAAGATCGAACCGAACAATCCGAAATGGCTGTACTTCTA







TAGCCGCGAACTCTATCAGACGCAACGTGACATTGCCCTTGTGCAAAGTGTACT







GTTCAAGGCACTGGAACTGTATGAAAACAGTTCATATACGCGTTATTATGTTGA







CACCATTGCCTTACTGTGCCGAGTGCTGTTCGAATCTAAAAACTACCAGAAACT







TACGGAATGTCTGAACATCCTGGAGAACAATACGCTTAACTGTTCCGATATCGA







TTACTATAATTCAGCGCTGCTGTTCTACAACCTGTTACTGCGCATCAAGAAAAT







TAGCTCCACCCTGAAGGAGAACATTGATATGTACGAACGTGACTATCATAGCTT







TATCAACCCCTCGCATGATCACATTAAGATTCTGATATTAAATATGCTCCTGCT







GCTCGGCGATTACCAGGATGCCTTTAAGGTTTACAAGGAGATCAAGTCCATTGA







GATTAAAGATGAGTTTCTGGTGAACGTGAACAAATTCAAAGACAATCTTCTGAG







CTTCATTGACTCCATTAACAAAATTTAATAA







pEG7143
SgbL


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703





GACCTTCTGCGCCAAGCATTACACGCAACTGGTACAGGTGCTCGTTGGGCTGTA







GAGGCGGACGAGATGTGGTGCCGTGTCGCCCCGGTGCCTGGAACTCGCCGCGAG







CAAGGATGGAAGCTTCATGTAAGCGCGACGACCGCGAGTGCGCCCGAAGTCTTA







ACTCGTGCATTAGGCGTACTTCTGCGTGAAAAGTCCGGGTTCAAATTTGCCCGC







TCACTTGAACAAGTCTCGGCCTTGAATAGTCGTGCTACGCCCCGTGGTAGTTCG







GGTAAATTTATCACAGTATACCCCCGCTCAGACGCCGAAGCCGTCGCACTGGCT







CGCGACCTGCATGCGGCAACGGCCGGCTTGGCTGGGCCCCGTATTCTTTCCGAT







CAACCATACGCCGCGCACAGCCTGGTGCATTATCGTTATGGGGCTTTCGTGGGA







CGTCGTCGCCTTTCAGATGACGGGCTTTTAGTTTGGTTTATTGAGGACCCAGAT







GGCAATCCCGTGGAGGATAAACGCACCGGACGTTATGCGCCGCCTCCCTGGGCT







GTATGTCCGTTTCCTGCGAGCGTCCCCGTTGCGCCCCATGACGGCGAAGCTACG







AGTCGTCCTGTTGTCTTAGGTGGTCGCTTCGCGGTTCGTGAAGCCATCCGTCAA







ACGAATAAAGGGGGCGTCTATCGCGGGTCGGACACACGCACTGGCACCGGCGTG







GTTATCAAAGAGGCGCGCCCACATGTTGAAGGAGACGCCAGTGGGGGCGATGTT







CGTGACTGGCTTCGCGCAGAGGCGCGTACGCTTGAAAAATTAAAAGGTACCGGC







TTGGCACCAGAAGCGGTGGCGTTGTTTGAGCACGCTGGCCACTTGTTCTTAGCC







CAAGACGAGGTCCCGGGGGTTACGTTACGCACCTGGGTAGCGGAACACTTCCGT







GACGTTGGAGGAGAGCGCTATCGTGCCGACGCCCTGGCTCAGGTGGCTCGTTTA







GTTGATTTAGTCGCGGCTGCTCATGCACGTGGCTTGGTCCTGCGCGATTTTACA







CCAGGGAACGTGATGGTCCGTCCAGACGGCGAATTGCGCCTTATTGATTTAGAG







CTGGCGGTTCTTGAGGATGAGGCCGCATTGCCTACCCACGTCGGTACCCCGGGG







TTTTCGGCACCCGAACGCCTTGCAGACGCTCCAGTGCGTCCTACTGCTGACTAC







TATTCTCTGGGAGCCACAGCTTGTTTTGTCTTGGCCGGTAAAGTCCCTAATTTA







CTTCCTGAAGAACCCGTGGGTCGCCCATCGGAGGAGCGTCTTGCTGCCTGGTTG







ACTGCATGTACACGTCCGCTGCGCCTGCCAGATGGAGTCGTTGACATGATCTTG







GGGTTAATGCGCGATGATCCTGCAGAGCGCTGGGACCCATCCCGCGCGCGTGAA







GCACTGCGCAAAGCTGACCCGACAGCACGCCCCGGGGATGCTGATCGCACTGCA







GTACGTCGTACGGGTTCGTCGGCAGTGGCCGGGCCAGTTCCTGACTCACGTACA







GCAGATGGTCGTACAGCGGACGGCCGTTCCGCGGATGAAGTTGTGGCAGGTCTT







GTCGATCACTTAGTCGATAGTATGACCCCGGCAGATGATCGTCTGTGGCCGGTA







AGCACTCTTACGGGAGAATCGGATCCATGTACAGTCCAGCAAGGCGCTGCTGGG







GTGCTTGCGGTGTTGACCCGCTACTTCGAATTGACGGGCGATCCGCGCTTACCA







GGCTTATTGTCGACAGCCGGACGTTGGATCGCAGACCGCACGGATGTTCGTTCA







CCTCGTCCGGGATTACATTTCGGGGGACGCGGAACAGCCTGGGCCTTATACGAC







GCGGGGCGTGCAGTCGACGATCGTCGCTTGGTGGAACATGCTCTGGACTTAGCA







TTAGCCCCGCCCCAAGCGACTCCTCATCACGATGTCACGCATGGGACTGCGGGC







TCAGGCTTAGCCGCCTTGCACCTGTGGCAGCGTACTGGAGATACTCGTTTCGCG







GATTTAGCAGTAGAGGCAGCTGATCGCTTAACAGCTGCAGCTCGTCGCGAGCCT







TCGGGTGTTGGATGGGCAGTACCTGCAGAGGCCGACTCCCCAGAAGGAGGCAAG







CGTTACCTGGGCTTCGCTCATGGCGCAGCTGGGATTGGGTGCTTCTTATTGGCT







GCGGCGGAACTTAGTCGTCAACCCGATCATCGTGCAACTGCTTTGGAAGTTGGC







GAAGGCCTGGTTGCTGATGCTGTTCGCATCGGAGAGGCGGCACAGTGGCCTGCG







CAATCCGGGGACTTGCCGACAGCGCCTTACTGGTGCCATGGGGCGGCAGGTATC







GGGACATTTCTTGTACGCTTATGGCAGGCGACCGGGGACGATCGCTTCGGTGAT







CTGGCCCGCGGGAGTGCTCACGCTGTGGCCGAACGTGCTAGTCGCGCCCCATTG







GCGCAATGTCACGGTTTGGCTGGAAACGGAGATTTCTTGTTGGATTTGGCAGAC







GCGACAGGCGATCCTGTGCATCGCGACACCGCGGAAGAGTTAGCAGGGTTGATC







TTGGCCGAAGGAACCCGTCGTCAGGGACATGTCGTTTTCCCTAATGAGTATGGG







GAAGTATCATCTTCATGGTCCGACGGTAGTGCGGGGATTCTTGCGTTCCTTCTG







CGTACGCGTCATACGGGCCCTCGCCATTGGATGGTAGAACAACGTGGGTAATAA







pEG7144
RaxST


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704





CTGCCTCGTGCGGGGAGTTCATTACTGGCTGCGTTACTGCGTCAAAATCCGCAG







CTGCATGCCGATGTTACATCTCCGGTGGCGCGCCTTTACGCGGCCATGCTGATG







GGTATGAGTGAAGAACACCCGAGCAACGTGCAGATTGACGATGCCCAACGTGTC







CGTCTGTTACGTGCAGTATTTGATGCGTATTATCAGAACCGTCAGGAACTGGGG







ACAGTGTTCGATACTAACCGCGCATGGTGCTCTCGCCTCACGGGCCTGGCGCGT







CTGTTTCCGCGTAGTCGCATGATCTGCTGTGTACGCGATGTGGGCTGGATTGTT







GATTCTTTTGAACGCCTGGCGCAGTCGCAGCCGTTACGCCTTTCGGCCCTGTTC







GGTTACGACCCCGAGGATTCGGTTAGCATGCACGCTGACTTACTCACTGCGCCT







CGCGGGGTAGTGGGCTACGCCCTGGATGGTTTACGTCAAGCGTTTTATGGAGAT







CACGCGGATCGTCTGCTGTTGTTACGTTATGATACGCTGGCACAGCGTCCTGCA







CAAGCCATGGAACAGGTATATGCATTCCTGCAGCTCCCTGCCTTTGCACATGAT







TATGCCGGTGTTCAGGCCGAAGCGGAACGCTTTGATGCCGCCCTGCAAATGCCT







GGTTTGCACCGCGTGCGTCGTGGTGTTCACTATGTTCCGCGACGTTCGGTTTTA







CCGCCTGCCCTGTTTGACCAGCTGCAGGAACTTGCATTCTGGGAAAGTGCACCC







AGCCATGGAGCGCTGCTCGTGTAATAA







pEG7145
ComQ


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705





TCAGTAACAAAGACCTGTCGCAACTCCTGTGTTCCTTCATTGATTCAAAGGAAA







CTTTCAGTTTTGCCGAGAGCGCTATACTGCATTATGTAGTATTCGGCGGTGAGA







ACCTGGACGTAGCTACCTGGCTGGGCGCCGGAATTGAAATTCTGATCCTGAGCA







GCGATATCATGGACGACCTGGAGGACGAGGATAACCATCATGCGTTGTGGATGA







AAATTAACCGCAGCGAGAGCTTGAATGCGGCCCTGTCCTTATACACCGTCGGCT







TAACGAGCATCTATTCCCTGAACACAAATCCGTTGATATTTAAGTATGTGCTGC







GCTACGTCAATGAGGCCATGCAGGGTCAGCATGATGATATAACCAATAAAAGCA







AAACCGAAGATGAATCGCTTGAAGTGATTCGCCTTAAATGCGGCAGCCTGATCG







CCCTGGCAAATGTCGCGGGCGTGCTGTTAGCCACGGGCGAGTACAATGAAACAG







TTGAACGTTACTCTTATTACAAAGGCATCGTGGCGCAAATTTCCGGCGACTATC







ACGTGCTGCTGTCAGGAAACCGGAGCGATATCGAGAAAAACAAACAGACACTGA







TTTACCTGTATCTGAAACGCCTGTTTAACAACGCGAGCGAGGAATTGCTGTATC







TGTTCTCCCATAAAGATTTGTACTATAAAGCCCTGCTCGACCGTGAAAAGTTTG







AAGAAAAACTGATCCAGGCCGGGGTGACGCAGTACATCAGCGTTCTGCTCGAAA







TATATAAGCAGAAGTGCTTCTCCACCATAGAACAGCTGAACTTAGATAAAGAAA







AGAAAGAGCTGATCAAGGAGAGCCTGCTGTCATATAAGAAAGGCGACACCCGTT







GCAAGACCTAATAA







pEG7146
KgpF


embedded image


706





CTCCATAAGAGTAAAAACTTGATGTATATGAAAGCCCACGAAAACATCTTCGAA







ATCGAGGCGCTGTACCCGCTGGAATTGTTCGAGCGTTTTATGCAGTCCCAAACC







GATTGCTCCATCGATTGTGCCTGTAAAATTGATGGTGACGAATTGTATCCCGCC







CGTTTTAGTCTGGCCCTGTATAACAACCAGTATGCCGAAAAGCAAATTCGCGAA







ACCATCGACTTCTTCCATCAGGTAGAGGGTCGGACCGAGGTGAAACTGAACTAT







CAGCAACTGCAGCACTTCCTGGGTGCTGACTTCGATTTTAGCAAAGTGATTCGA







AACCTGGTGGGTGTGGATGCACGCCGCGAACTGGCTGATTCCCGGGTTAAACTG







TATATTTGGATGAACGATTACCCAGAGAAAATGGCGACCGCCATGGCATGGTGC







GATGATAAGAAGGAATTGTCGACGTTGATAGTAAATCAGGAGTTTCTGGTCGGG







TTCGATTTTTATTTCGATGGTCGCACGGCAATAGAATTATACATTAGTCTGTCA







TCCGAAGAATTTCAGCAGACACAAGTTTGGGAACGCCTCGCAAAGGTAGTGTGC







GCCCCAGCGCTGCGCCTTGTTAATGATTGCCAGGCGATCCAGATTGGCGTGAGC







CGTGCCAATGATAGTAAGATCATGTATTACCATACCCTTAATCCGAACTCGTTT







ATCGACAATCTGGGCAATGAAATGGCAAGCAGAGTTCACGCGTATTACCGACAT







CAACCGGTTCGCTCTCTGGTAGTATGCATACCAGAACAGGAGTTGACCGCCCGG







TCCATACAGCGCTTAAACATGTATTACTGTATGAACTAATAA







pEG7147
TgnB


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707





CCTGGATCTGACCGTGGATTATATTATTAATCGCTATAATCATACCGCTAAATT







TTTTCGTCTGAATACCGATCGTTTTTTTGATTATGATATTAATATTACCAATAG







CGGTACCAGCATTCGTAATCGTAAATCTAATCTGATTATTAATATTCAGGAAAT







TCATAGCCTGTATTATCGCAAAATTACCCTGCCGAATCTGGATGGCTATGAAAG







TAAATATTGGACCCTGATGCAGCGCGAAATGATGAGTATTGTTGAAGGCATTGC







AGAAACCGCTGGCAATTTTGCACTGACCCGTCCGTCTGTGCTGCGCAAAGCTGA







TAATAAAATTGTGCAGATGAAACTGGCAGAAGAAATTGGTTTTATTCTGCCGCA







GAGTCTGATTACCAATTCAAATCAGGCGGCAGCCTCATTTTGCAATAAAAATAA







TACCAGCATTGTGAAACCGCTGAGTACCGGCCGCATTCTGGGTAAAAATAAAAT







TGGCATTATTCAGACCAATCTGGTTGAAACCCATGAAAATATTCAGGGCCTGGA







ACTGTCTCCGGCTTATTTTCAGGATTATATTCCGAAAGATACCGAAATTCGTCT







GACCATTGTTGGTAATAAACTGTTTGGCGCCAATATTAAATCAACCAATCAGGT







TGATTGGCGCAAAAATGATGCACTGCTGGAATATAAACCGGCCAATATTCCGGA







TAAAATTGCCAAAATGTGTCTGGAAATGATGGAAAAACTGGAAATTAATTTTGC







GGCGTTTGATTTTATTATTCGTAATGGTGATTATATTTTTCTGGAACTGAATGC







CAATGGTCAGTGGCTGTGGCTGGAAGATATTCTGAAATTTGATATTTCAAATAC







CATTATTAATTATCTGCTGGGTGAACCGATTTAATAATAA







pEG7149
PapB


embedded image


708





TGATTCATTTCCATCCGTACAAACTGTTCGAGGTGGATTCAAAAACCTTCTTCT







ATAACGTAGTCACCAACGCGATTTTTGAAATTGATAGCCTGATAATCGACATTC







TTCACTCAAAAGGTAAAAATGAGGAGCACGTTGTGAAAGATTTGGCTGAACGCT







ATGAGCTGTCTCAGGTTCGCGAAGCGATCCAGAACATGAAAGAGGCATACATTA







TAGCAACCGATGCTAACATCTCCGACGTAGAGAAGATGGGTATCTTAGATAACT







CGCAGCGCGTTTTTAAACTGTCTAGCCTGACGCTCTTTATGGTGCAGGAATGCA







ACCTGCGGTGTACGTATTGTTACGGCGAAGAAGGAGAATACAACCAGAAAGGTA







AAATGACGTCCGAAATCGCCCGGAGCGCAGTGGATTTTCTGATTCAACAGAGTG







GTGAAATCGAACAGTTGAACATCACATTCTTTGGAGGCGAACCGCTGCTCAACT







TTCCATTAATACAAGAAACCGTGCAGTATGTGCACGAACAGAGCGAGATCCATA







ACAAGAAATTTAGCTTTTCCATCACCACCAATGGCACGCTCATTACCCCCAAAA







TCAAAAACTTCTTCTATAAACACCACTTTGCAGTCCAGACTTCTATCGATGGTG







ATGAAAAGACGCACAATTTCAATCGCTTCTTCAAAGGAGGCCAGGGCTCTTATG







ATCTGCTGTTAAAGCGGACGGAAGAAATGCGCAATGACCGTAAAATTGGTGCAC







GTGGAACCGTGACCCCTGCCGAGCTGGACCTCTCAAAATCATTTGACCACTTAG







TTAAACTCGGCTTTCGCAAAATCTACTTATCACCCGCTTTATATAGTCTCTCTG







ACGATCACTACGACACCCTGAGCAAAGAGATGGTCAAACTTGTTGAACAATTCC







GTGAGCTGCTGGAGCGTGAAGATTACGTCACCGCGAAGAAAATGTCTAATGTTC







TGGGTATGTTATCGAAGATTCACTCCGGTGGCCCGCGCATTCATTTTTGCGGTG







CCGGCACTAATGCTGCCGCTGTCGATGTCCGCGGCAACCTTTTCCCGTGTCATC







GTTTCGTGGGTGAAGATGAATGTTCAATCGGTAACCTGTTCGACGAGGACCCGC







TGTCAAAACAGTACAACTTTATAGAGAATTCTACAGTACGCAACCGTACTACGT







GTTCGAAATGCTGGGCGAAGAATCTGTGCGGCGGTGGTTGTCACCAAGAAAATT







TCGCCGAGAATGGTAATGTGAACCAGCCAGTGGGCAAATTATGCAAAGTGACCA







AAAACTTCATCAACGCGACCATCAATCTGTACTTGCAACTTACTCAAGAACAAC







GCAGCATTCTGTTCGGCTAATAA







pEG7152
PcpXY


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709





AGATCACGCTGAAATGCAATCTGGCATGTTCGCACTGTGGAAGTCGTGCCGGGC







ACACGCGAGCAAAAGAACTGTCCACACAGGAAGCGCTGGATCTGGTCCGTCAGA







TGGCTGATGTCGGCATTATCGAAGTTACTCTGATTGGGGGTGAAGCGTTCCTGC







GTCCAGACTGGCTGCAGATTGCCGAGGCGATAACGAAAGCCGGGATGCTGTGCA







GCATGACTACGGGCGGTTATGGCATATCGCTGGAAACCGCCCGCAAAATGAAAG







CGGCAGGAATCGCGAGCGTGAGCGTTAGCATCGATGGCTTGGAGGAAACCCATG







ATCGCTTACGCGGTCGCAAAGGCTCTTGGCAGGCTGCGTTTAAAACAATGAGCC







ATTTGAGAGAAGTGGGCATCTTCTTTGGCTGTAACACCCAGATTAACCGTCTGT







CGGCCCCTGAATTTCCGCTGATATATGAACGCATCCGTGACGCCGGGGCACGTG







CCTGGCAGATCCAGCTTACGGTGCCGATGGGCCGCGCTGCCGATAACGCAAATA







TCCTTCTGCAACCGTACGAACTGCTTGATCTGTATCCGATGATTGCTCGAGTGG







CCCGCCGGGCCCGTCAAGAGGGCGTGCAAATCCAGCCAGGTAATAATATTGGGT







ATTACGGCCCTTACGAACGTCTTTTACGTGGCCGGGGGAGCGATAGTGAGTGGG







cattttggcagggctgtgccgcgggcttaagtaccctgggtattgaagcggatg







GTGCTATAAAAGGTTGTCCCTCACTGCCAACGAGCGCGTATACCGGCGGTAACA







TTCGCGAACATAGTCTGCGAGAAATAGTGGAAGAATCGGAACAGCTGCGTTTTA







ACCTCGGTGCAGGGACGAGCCAAGGGACCGCCCACTTGTGGGGCTTTTGCCAGA







CGTGTGAATTTAGTGAATTGTGCAGAGGTGGTTGTACGTGGACAGCTCACGTGT







TCTTTAACCGCCGTGGGAATAACCCGTATTGTCATCATCGGGCGCTTTTCCAAG







CGGAGCAGGGTATCAGAGAACGTGTCGTGCCAAAGGTCGAAGCTCAGGGCCTGC







CGTTTGACAACGGTGAATTTGAACTTATCGAAGAACCTATTGACGCGCCTCTGC







CCGAAAATGATCCACTGCACTTTACCAGCGACTTAGTGCAGTGGTCAGCGAGTT








embedded image









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TGAACCGGAAAGCCTGCTTCTGCCGCGCCAGGCTTGGCAGTCGCAGATCGCCTA







TCTTAAAGCGATTCTGAAAGCCAAACAGGCGCTTGACCGGATCGAAAAACGTTA







TCTGCGGTAATAA







pEG7160
LynD


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710





ACATTTCCATGTAGAGGTCATTGAACCAAAGCAAGTCTACTTGTTGGGTGAACA







AGCTAATCATGCATTGACAGGCCAATTATACTGCCAAATTTTGCCATTGTTAAA







CGGACAATACACATTGGAACAAATCGTTGAAAAACTAGACGGAGAAGTACCACC







TGAATACATTGATTATGTGCTGGAGAGACTAGCTGAGAAGGGCTATCTGACTGA







AGCAGCACCTGAATTATCTAGTGAAGTGGCCGCTTTCTGGTCTGAGCTGGGGAT







TGCACCTCCTGTCGCGGCCGAAGCATTACGTCAACCTGTGACTTTAACACCTGT







TGGAAACATCAGCGAAGTAACAGTAGCAGCCTTAACCACAGCCCTACGTGATAT







CGGTATTTCCGTTCAAACACCTACAGAAGCTGGATCGCCAACTGCATTGAACGT







TGTACTTACCGATGATTATCTCCAACCAGAACTCGCTAAGATCAATAAGCAAGC







CTTAGAAAGTCAACAAACTTGGCTACTTGTCAAACCAGTTGGCTCCGTGTTATG







GTTGGGTCCGGTATTCGTGCCAGGAAAAACAGGTTGCTGGGATTGTTTGGCTCA







CAGATTAAGGGGGAATAGAGAGGTAGAGGCCTCTGTATTGAGACAAAAACAAGC







TCAACAACAACGTAATGGACAAAGCGGGTCTGTAATAGGATGCCTTCCCACGGC







TAGAGCGACACTGCCCTCAACACTCCAAACTGGGCTGCAGTTCGCTGCTACCGA







AATTGCTAAATGGATAGTTAAGTATCATGTTAATGCCACAGCGCCTGGCACCGT







ATTCTTCCCTACATTGGATGGTAAGATAATTACGCTAAATCACTCCATACTGGA







TTTGAAGTCACATATTCTGATCAAGCGTTCTCAATGTCCCACCTGTGGTGACCC







AAAAATCTTACAGCACCGTGGTTTCGAACCTTTAAAACTTGAGTCAAGGCCTAA







ACAGTTCACCTCAGACGGCGGACATCGTGGTACTACCCCTGAACAAACTGTCCA







GAAATATCAACATTTAATCTCGCCTGTTACCGGTGTAGTTACTGAATTGGTCAG







GATAACTGATCCGGCCAATCCACTAGTTCACACATATAGAGCTGGTCATAGCTT







CGGGAGCGCTACATCGCTGAGAGGGCTGCGTAATACCTTAAAGCATAAGAGTTC







AGGTAAGGGTAAGACTGATTCTCAAAGTAAAGCCTCGGGCCTGTGTGAGGCGGT







AGAACGTTACTCAGGAATCTTTCAAGGTGACGAACCGAGAAAACGCGCCACATT







GGCTGAATTGGGAGATTTGGCAATTCACCCTGAGCAATGCTTGTGTTTTTCCGA







CGGTCAGTACGCTAATAGAGAAACTTTAAACGAACAGGCAACGGTGGCACATGA







TTGGATACCTCAACGTTTTGATGCATCACAAGCTATTGAATGGACTCCAGTCTG







GTCCCTAACTGAACAGACCCATAAATATTTGCCCACCGCATTGTGTTACTACCA







TTATCCTCTACCCCCAGAACACAGATTCGCACGTGGAGATTCGAATGGTAATGC







TGCCGGAAATACGTTGGAAGAGGCTATACTCCAAGGCTTCATGGAATTAGTCGA







GAGAGATGGTGTGGCTTTATGGTGGTATAACAGGCTACGCAGACCCGCTGTAGA







CTTAGGCTCATTTAACGAGCCATACTTCGTTCAGTTGCAACAATTCTACAGAGA







AAACGATAGAGATTTGTGGGTTTTGGACTTGACAGCTGATTTAGGTATCCCGGC







TTTCGCGGGCGTTTCTAATAGAAAAACTGGTAGTTCGGAGAGGTTGATATTAGG







ATTCGGTGCACACCTCGATCCTACTATTGCAATTCTGAGAGCAGTTACAGAAGT







TAACCAGATTGGCCTTGAATTAGATAAAGTTCCAGACGAGAACCTTAAGAGCGA







CGCAACAGATTGGCTAATTACTGAAAAATTAGCTGACCACCCTTATTTGTTACC







AGATACAACTCAACCTCTAAAAACTGCTCAAGATTATCCTAAAAGGTGGTCTGA







CGATATATACACGGACGTAATGACTTGCGTTAATATTGCTCAACAAGCAGGACT







TGAAACTCTAGTTATTGATCAAACACGTCCGGACATTGGTTTGAATGTTGTTAA







GGTGACAGTCCCGGGGATGAGGCACTTTTGGTCAAGATTTGGAGAGGGGAGGCT







TTATGACGTGCCCGTCAAATTAGGTTGGCTTGACGAACCTTTGACCGAAGCGCA







AATGAACCCCACGCCGATGCCTTTTTAATAA







pEG7166
PapoK


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711





ACCAAATACATCGCGTTTGGTCTGCGCATTGCCAGCGAACTCAACTTACCGGAA







CTGATATTGGCGGCTCCCGAAGCCGTTGAGGATGTTGTCATACGCCAGGCAGAT







CTCACGGCCTGGTCTGGCCAACTTGAACAGGCAAATTTTGTCATGTTGGACGAA







CGTTTCATGTTTCAGATCCCGGGGACCGCCATTTATGCGGTACGCGAAGGCAAA







GAGATTGAAGTGAGCATCTTCTCTGGGGCCGACCCGGACACCGTGCGCCTTTTC







GTGCTGGGGACGTGCATGGGCGTGCTCTTGATGCAGCGCCGCATTCTGCCTATC







CACGGCTCCGCCGTCGTTATCGGTGGCCGCGCGTATGCCTTTGTTGGTGAATCA







GGCACAGGTAAATCGACCTTAGCTGCAGCATTTCGGCAGGCCGGTTACCAAATG







GTTAGCGATGATGTCATTGCCGTCAAAGCGACCGCATCTAGCGCTATTGTTTAC







CCTGCGTATCCACAGCAAAAACTGGGTTTAGATTCGCTGTTGCAGCTTGAAGCG







CTCCGTGAGAATAAGCACGCCCGCAAGCGTAACAACATCCGTTCTCTGACGGAT







GGCAATAGTGTGATGCCGCAGTACAGCGATCTGCGCATGCTGGCGGGGGAACTG







AATAAATATGCAGTTCCAGCCGTCGATGAATTCTTTAATGACCCGCTGCCGTTG







GGCGGTGTTTTCGAACTGGTAGCAGACAGTCCGATTCGAGCATTAATGCGCGAA







GGCGAACTCGTCGCTGTGACCGAGCAACCGCTGAACGTTCTGGAATGTTTACAT







ACTCTTCTGCAACACACGTACCGTCGGGTAATCATCCCTCGAATGGGACTGAGC







GAGTGGAGCTTCGATACTGCGGCCCGAATGGCACGCAAGGTCGAGGGCTGGCGA







CTCCTCCGTGATAGCTCCGTGTTCACGGCTAGTGAAGTCGTCCAGCGCGTCCTC







GACATCATCCGTAAGGAGGAAAAGAGCTACGGATCACACTAATAA







pEG7169
EpiD


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712





GCTTCGATCAACGTCATCAATATCAACCATTATATTGTGGAGCTGAAACAGCAC







TTCGATGAGGTGAATATCCTGTTTTCACCTTCCTCGAAGAACTTTATCAACACC







GATGTCCTGAAGCTGTTTTGCGATAATCTGTATGACGAGATCAAAGATCCGCTG







CTGAACCACATCAACATAGTGGAGAACCACGAGTATATCTTGGTGCTGCCTGCC







AGTGCCAATACGATCAACAAAATCGCGAACGGTATATGCGATAACCTCTTGACG







ACCGTATGCTTAACCGGGTACCAGAAACTGTTTATCTTTCCGAATATGAACATC







CGCATGTGGGGAAATCCGTTCTTACAGAAAAATATTGACCTGCTTAAAAGCAAC







GACGTGAAGGTGTATTCCCCCGACATGAACAAATCTTTTGAGATAAGCTCAGGC







CGCTACAAAAATAACATCACGATGCCGAATATCGAAAACGTGCTGAATTTTGTC







CTGAACAATGAGAAACGCCCGCTGGATTAATAA







pEG7171
BamB


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713





AAGTGCATAGTCGTATACACAAACTGCAAAATAATATCGCAATAGGTAGCATGC







CGCCTCACGCGCTGATCATCGAGGATGCCCCCGAATATTTGTCAAACGTTCTGC







GCTTCTTTAGTAGCAAAAAGACTATAAAAGAAGCTGAAGTGTACCTGTCGGATA







ATACGAATCTGAGCTCCAATGAGATCAACCTGTTGTTAGGTGATCTGATTGAGA







ACGAGATTATCGTAAAGCAAAACTACGACTCGAATAATCGGTACAGTCGACACA







GTCTGTATTACGAGATGATTGATGCCAACGCTGAAAACGCGCAGAAAATTCTGG







CAGAGAAAACAGTGGGCCTCGTTGGGATGGGCGGGATTGGTTCCAATGTAGCCA







TGAATCTCGCAGCCGCCGGTGTTGGCAAACTGATCTTTAGTGATGGCGATACCA







TAGAACTGTCTAATTTAACGCGACAGTATCTTTACAAAGAGGATCAGGTGGGCT







TGAGCAAAGTAGAGAGCGCCAAAGAACAACTGCAATTACTGAATAGCGAAGTCG







AGCTTATCCCGGTTTGCGAAAGTATCTCTGGTGAGGAACTGTTCGACAACCATT







TCTCCGAATGCGATTTCGTCGTACTGTCCGCCGACTCTCCGTTCTTTGTTCACG







AATGGATTAACAATGCCGCGTTGAAATATGGCTTCTCCTACTCTAACGCAGGAT







ATATCGAAACCTATGGCGCGATCGGTCCACTGGTGATACCTGGGGAAACTGCCT







GCTACGAATGCTATAAAGACAAGGGCGATCTTTACTTGTACTCCGACAACAAGG







AAGAATTTTCTGTGAACCTGAATGAATCATTCCAAGCACCGAGCTATGGACCGC







TTAATGCGATGGTTAGTTCCATTCAGGCGAATGAAGTGATACGCCACCTCCTCG







GACTTAAAACCAAAACGTCCGGCAAACGGCTGCTGATCAACAGTGAAATCTACA







AAATCCACGAAGAGAACTTCGAGAAGAAGAACAACTGCCTGTGCTCGGATATTA







AGGGCGAGAAGCTGTCGAAGAACACCCTTAACTCCGATAAAGAGCTGCACGAAG







TGTATATCGAAGAACGCGAATCGGATTCTTTCAACTCCATTCTCTTGGATAAAA







CCATGAGCAAGCTGGTAAAAATTAACAAAGAGGAGACAAAAATCCTCGACATTG







GTTGCGCTACCGGCGAACAGGCTCTGTATTTCGCGAATAAAGGTGCTAAGGTGA







CCGCTGTCGACATTTCAGACGATATGTTGAAGGTGCTGGACAAGAAAGCAAGCA







ACATTAACGCGGGGAGTATCAAAACCATGCGTGGTAATATCGAATCCATCGAGG







TGAATGACACTTTTAATTACATCGTCTGTAACAACATCCTTGATTACCTGCCGG







AGATCGACCGCACGCTGAGAAAACTTAACATGTTTTTGAAAAATGACGGGACGC







TGATTGTGACGATTCCCCACCCCGTGAAGGATGGTGGAGGGTGGCGGAAAGATT







ATTATAACGGCAAATGGAACTACGAAGAGTTTATCCTGAAGGATTACTTCAACG







AGGGTCTGATCGAAAAGAGCCGCGAGGACAAAAATGGGGAAACGGTGATCAAAA







GCATTAAAACGTACCACAGAACCACCGAAACCTATTTCAATAGCTTTACTGACG







CTGGCTTCAAGGTAGTATCTCTGCTGGAACCGCAACCGCTTTCAACTGTTTCAG







AGACTCATCCAATTCTGTTCGAAAAGTGTTCGCGCATTCCGTACTTTCAAGTTT







TTGTGCTCAAGAAAGAGGATCGCCACGCCATTTAATAA







aIn each backbone sequence (labeled “bEG_SX”, where X is a number), the relevant part (encoding a peptide or RBS + enzyme) has GFP as a placeholder (RBS + GFP for enzyme plasmid) and is double underlined. This region can be replaced with an insert DNA (such as a peptide or RBS + enzyme, including those listed below each plasmid backbone sequence) to get a plasmid sequence. The full plasmid sequences used herein (labeled “pEG####”) for peptides and enzymes can be identified by replacing the double underlined portion of the backbone sequence found above a given peptide/RBS + enzyme sequence with the respective peptide/RBS + enzyme sequence (for example, the full pEG3045 plasmid sequence is provided by replacing the double underlined portion of the bEG_S2 backbone sequence with the HIS6-MdnA provided next to the pEG3045 label).




bText is formatted according to sequence components: promoters (lowercase), ribozyme





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(UNDERLINED), and plasmid backbone and spacers (REGULAR ALL CAPS).







OTHER EMBODIMENTS

All of the features disclosed in this specification may be combined in any combination. Each feature disclosed in this specification may be replaced by an alternative feature serving the same, equivalent, or similar purpose. Thus, unless expressly stated otherwise, each feature disclosed is only an example of a generic series of equivalent or similar features.


From the above description, one skilled in the art can easily ascertain the essential characteristics of the present invention, and without departing from the spirit and scope thereof, can make various changes and modifications of the invention to adapt it to various usages and conditions. Thus, other embodiments are also within the claims.


EQUIVALENTS

While several inventive embodiments have been described and illustrated herein, those of ordinary skill in the art will readily envision a variety of other means and/or structures for performing the function and/or obtaining the results and/or one or more of the advantages described herein, and each of such variations and/or modifications is deemed to be within the scope of the inventive embodiments described herein. More generally, those skilled in the art will readily appreciate that all parameters, dimensions, materials, and configurations described herein are meant to be exemplary and that the actual parameters, dimensions, materials, and/or configurations will depend upon the specific application or applications for which the inventive teachings is/are used. Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific inventive embodiments described herein. It is, therefore, to be understood that the foregoing embodiments are presented by way of example only and that, within the scope of the appended claims and equivalents thereto, inventive embodiments may be practiced otherwise than as specifically described and claimed. Inventive embodiments of the present disclosure are directed to each individual feature, system, article, material, kit, and/or method described herein. In addition, any combination of two or more such features, systems, articles, materials, kits, and/or methods, if such features, systems, articles, materials, kits, and/or methods are not mutually inconsistent, is included within the inventive scope of the present disclosure.


All definitions, as defined and used herein, should be understood to control over dictionary definitions, definitions in documents incorporated by reference, and/or ordinary meanings of the defined terms.


All references, patents and patent applications disclosed herein are incorporated by reference with respect to the subject matter for which each is cited, which in some cases may encompass the entirety of the document.


The indefinite articles “a” and “an,” as used herein in the specification and in the claims, unless clearly indicated to the contrary, should be understood to mean “at least one.”


The phrase “and/or,” as used herein in the specification and in the claims, should be understood to mean “either or both” of the elements so conjoined, i.e., elements that are conjunctively present in some cases and disjunctively present in other cases. Multiple elements listed with “and/or” should be construed in the same fashion, i.e., “one or more” of the elements so conjoined. Other elements may optionally be present other than the elements specifically identified by the “and/or” clause, whether related or unrelated to those elements specifically identified. Thus, as a non-limiting example, a reference to “A and/or B”, when used in conjunction with open-ended language such as “comprising” can refer, in one embodiment, to A only (optionally including elements other than B); in another embodiment, to B only (optionally including elements other than A); in yet another embodiment, to both A and B (optionally including other elements); etc.


As used herein in the specification and in the claims, “or” should be understood to have the same meaning as “and/or” as defined above. For example, when separating items in a list, “or” or “and/or” shall be interpreted as being inclusive, i.e., the inclusion of at least one, but also including more than one, of a number or list of elements, and, optionally, additional unlisted items. Only terms clearly indicated to the contrary, such as “only one of” or “exactly one of,” or, when used in the claims, “consisting of,” will refer to the inclusion of exactly one element of a number or list of elements. In general, the term “or” as used herein shall only be interpreted as indicating exclusive alternatives (i.e. “one or the other but not both”) when preceded by terms of exclusivity, such as “either,” “one of,” “only one of,” or “exactly one of.” “Consisting essentially of,” when used in the claims, shall have its ordinary meaning as used in the field of patent law.


As used herein in the specification and in the claims, the phrase “at least one,” in reference to a list of one or more elements, should be understood to mean at least one element selected from any one or more of the elements in the list of elements, but not necessarily including at least one of each and every element specifically listed within the list of elements and not excluding any combinations of elements in the list of elements. This definition also allows that elements may optionally be present other than the elements specifically identified within the list of elements to which the phrase “at least one” refers, whether related or unrelated to those elements specifically identified. Thus, as a non-limiting example, “at least one of A and B” (or, equivalently, “at least one of A or B,” or, equivalently “at least one of A and/or B”) can refer, in one embodiment, to at least one, optionally including more than one, A, with no B present (and optionally including elements other than B); in another embodiment, to at least one, optionally including more than one, B, with no A present (and optionally including elements other than A); in yet another embodiment, to at least one, optionally including more than one, A, and at least one, optionally including more than one, B (and optionally including other elements); etc.


It should also be understood that, unless clearly indicated to the contrary, in any methods claimed herein that include more than one step or act, the order of the steps or acts of the method is not necessarily limited to the order in which the steps or acts of the method are recited.

Claims
  • 1. A non-naturally occurring peptide comprising: (A) AACX1X2X3X4X5X6MPPX7X8X9X10X11X12C (SEQ ID NO: 1) (scaffold L1), wherein: (i) X6 and X7 are each the amino acid S or T;(ii) X1-X5 and X8-X12 are each any amino acid; and(iii) the peptide comprises a thioether bridge that links C at position 3 in to S or T at position 9 in SEQ ID NO: 1 and a thioether bridge that links S or T at position 13 to C at position 19 in SEQ ID NO: 1;(B) X1PX2TTX3X4TX5X6X7EX8X9DX10DEX11X12X13 (SEQ ID NO: 2) (scaffold L2), wherein: (i) X2 is the amino acid H, Q, N, K, D, or E;(ii) X6 is the amino acid F, L, S, I, M, T, V, or A;(iii) X7 is the amino acid F, L, I, or V;(iv) X1, X3-X5 and X8-X13 are each any amino acid; and(v) the peptide comprises an ester bridge that links T at position 5 of SEQ ID NO: 2 to D at position 15 of SEQ ID NO: 2 and an ester bridge that links T at position 8 of SEQ ID NO: 2 to E at position 12 of SEQ ID NO: 2;(C) X1CX2X3X4X5X6CX7X8X9X10X11 (SEQ ID NO: 3) (scaffold L3), wherein: (i) X5 and X10 are each the amino acid D or E;(ii) X1-X4, X6-X9, and X11 are each any amino acid; and(iii) the peptide comprises a thioether bridge that links C at position 2 to D or E at position 6 of SEQ ID NO: 3 and a thioether bridge that links C at position 8 to D or E at position 12 of SEQ ID NO: 3;(D) X1CX2X3CX4X5X6X7X8X9 (SEQ ID NO: 4) (scaffold L4), wherein: (i) X4 and X7 are each the amino acid D or E;(ii) X1-X3, X5-X6, and X8-X9 are each any amino acid; and(iii) the peptide comprises a thioether bridge that links C at position 2 to D or E at position 6 of SEQ ID NO: 4 and a thioether bridge that links C at position 5 to D or E at position 9 of SEQ ID NO: 4; and/or(E) X1CX2X3X4X5X6CX7X8CX9X10X11X12X13 (SEQ ID NO: 5), wherein: (i) X5, X9, and X12 are each the amino acid D or E;(ii) X1-X4, X6-X8, X10-X11, and X13 are each any amino acid; and(iii) the peptide comprises a thioether bridge that links the C at position 2 to D or E at position 6 of SEQ ID NO: 5, a thioether bridge that links C at position 8 of SEQ ID NO: 5 with D or E at position 12 of SEQ ID NO: 5, and a thioether bridge that links C at position 11 with D or E at position 15 of SEQ ID NO: 5.
  • 2. The non-naturally occurring peptide of claim 1, comprising scaffold L5 and a sequence selected from SEQ ID NOS: 6-16; and/or scaffold L3 and a sequence selected from SEQ ID NOs: 17-25.
  • 3. The non-naturally occurring peptide of claim 1 or 2, wherein the non-naturally occurring peptide comprises scaffold L3 and SEQ ID NO: 24.
  • 4. A host cell comprising a heterologous nucleic acid encoding the non-naturally occurring peptide of any one of claims 1-3.
  • 5. The host cell of claim 4, wherein the heterologous nucleic acid further encodes SEQ ID NO: 46.
  • 6. The host cell of claim 4 or 5, wherein the heterologous nucleic acid comprises any one of SEQ ID NOs: 47-66.
  • 7. A host cell comprising: (a) a first fusion protein comprising (i) a first fragment of a transcription factor, (ii) a first split intein, and (iii) a target protein;(b) a second fusion protein comprising (i) a candidate peptide, (ii) a second split intein, and (iii) a second fragment of the transcription factor; wherein the first split intein and second split intein are complementary fragments; and(c) an inducible promoter operably linked to at least one reporter gene, wherein the transcription factor induces transcription of the at least one reporter gene when the transcription factor is present as a full-length transcription factor.
  • 8. The host cell of claim 7, wherein: (A) in (a), the first fusion protein comprises (i)-(iii) linked sequentially from the N-terminus to the C-terminus, the first fragment is an N-terminal fragment of the transcription factor and the first split intein is an N-terminal split intein; and(B) in (b), (i)-(iii) are linked sequentially from the N-terminus to the C-terminus, wherein the second split intein is a C-terminal split intein, and the second fragment is a C-terminal fragment of the transcription factor; or(C) in (a), from the N-terminus to the C-terminus, the first fusion protein comprises (iii) linked to (ii) linked to (i), wherein the first fragment is a C-terminal fragment of the transcription factor and the first split intein is a C-terminal split intein; and(D) in (b), from the N-terminus to the C-terminus, the second fusion protein comprises (iii) linked to (ii) linked to (i), wherein the second split intein is an N-terminal split intein and the second fragment is an N-terminal fragment of the transcription factor.
  • 9. The host cell of claim 7 or 8, wherein the cell is a eukaryotic or prokaryotic cell, optionally wherein the prokaryotic cell is a bacterial cell.
  • 10. The host cell of any one of claims 7-9, wherein the transcription factor is a sigma factor (a factor).
  • 11. The host cell of any one of claims 7-10, wherein the first fusion protein is encoded by a first heterologous nucleic acid and the second fusion is encoded by a second heterologous nucleic acid.
  • 12. The host cell of any one of claims 7-11, wherein the candidate peptide comprises a sequence selected from SEQ ID NOs: 6-25 or comprises the non-naturally occurring peptide of any one of claims 1 or 2, optionally wherein the candidate peptide further comprises SEQ ID NO: 46.
  • 13. The host cell of any one of claims 7-12, wherein the at least one reporter gene encodes a positive selection marker, a negative selection marker, and/or a fluorescent protein, optionally wherein the positive selection marker is an antibiotic resistance gene, optionally wherein the antibiotic resistance gene is chloramphenicol acetyltransferase (cat), optionally wherein the negative selection marker is the herpes simplex virus-thymidine kinase (hsvtk) gene.
  • 14. The host cell of any one of claims 7-13, wherein the inducible promoter is an ECF promoter.
  • 15. The host cell of any one of claims 7-14, wherein the target protein comprises a viral receptor binding domain (RBD) of the SARS-CoV-2 spike protein.
  • 16. The host cell of claim 15, wherein the RBD comprises SEQ ID NO: 71.
  • 17. The host cell of any one of claims 4-16, further comprising one or more enzymes selected from ProcM, LynD, TgnB, or PapB, optionally wherein the host cell comprises a heterologous nucleic acid encoding the enzyme, optionally wherein the heterologous nucleic acid encoding the enzyme comprises an inducible promoter.
  • 18. A method of identifying a peptide that binds a target protein comprising culturing the host cell of any one of claims 7-17 and detecting transcription of the at least one reporter gene, thereby identifying the candidate peptide as being capable of binding to the target protein.
  • 19. A method of identifying a peptide that binds a target protein comprising incubating in a reaction vessel: (a) a first fusion protein comprising (i) a first fragment of a transcription factor, (ii) a first split intein, and (iii) a target protein;(b) a second fusion protein comprising (i) a candidate peptide, (ii) a second split intein, and (iii) a second fragment of the transcription factor; wherein the first and second split inteins belong to the same intein; and(c) an inducible promoter operably linked to at least one reporter gene, wherein the transcription factor induces transcription of the at least one reporter gene when the transcription factor is present as a full-length transcription factor, and detecting transcription of the reporter gene, thereby identifying the candidate peptide as being capable of binding to the target protein.
  • 20. A method of treating a subject having or suspected of having a SARS-CoV-2 infection comprising administering an effective amount of the non-naturally occurring peptide of any one of claims 1-3.
  • 21. The method of claim 18 or 19, wherein the method comprises: repeating the method with a plurality of candidate peptides.
  • 22. The method of claim 18, or 21, wherein culturing comprises positive and/or negative selection of the host cell.
  • 23. The method of claim 21 or 22, wherein the method further comprises sequencing.
  • 24. A library comprising a plurality of peptides, wherein each peptide of the plurality of peptides has a length of n amino acids and has an amino acid sequence defined by a motif X1X2X3X4 . . . Xn, wherein n is 5-100, wherein each of X1-Xn is independently selected from a group consisting of up to 20 amino acids and at least one of X1-Xn within each peptide is an amino acid selected from a group consisting of 19 or fewer amino acids, and wherein the motif X1X2X3X4 . . . Xn is determined to be susceptible to post-translational modification by at least 2 distinct protein modification enzymes.
  • 25. The library of claim 24, wherein less than 80% of the plurality of peptides are capable of being fully modified by the at least 2 distinct protein modification enzymes.
  • 26. The library of claim 24 or 25, wherein at least one of X1-Xn is defined to be a single amino acid.
  • 27. A composition comprising a plurality of host cells, each host cell of the plurality comprising a peptide of the library of any one of claims 24-26, wherein the peptide comprised by each host cell is independent of the peptide comprised by each other host cell.
  • 28. The composition of claim 27, wherein the composition comprises each peptide of the plurality of peptides.
  • 29. The composition of claim 27 or claim 28, wherein the host cells are bacterial cells.
  • 30. The composition of any one of claims 27-29, wherein the peptide is encoded by a first nucleic acid sequence in the host cell.
  • 31. The composition of any one of claims 27-30, wherein each host cell further comprises at least one protein modifying enzyme.
  • 32. The composition of claim 31, wherein the at least one protein modifying enzyme is encoded by a second nucleic acid sequence in the host cell.
  • 32. A method of designing an amino acid motif, the method comprising: (i) selecting one or more protein modifying enzymes;(ii) identifying a recognition site (RS) sequence for each of the one or more protein modifying enzymes;(iii) constructing a plurality of nucleic acid molecules, each nucleic acid molecule encoding a leader amino acid sequence comprising the RS sequence for each of the one or more protein modifying enzymes;(iv) assigning a score to each of the plurality of nucleic acid molecules; and(v) selecting one of the plurality of nucleic acid molecules based on step (iv),to design the amino acid motif, wherein each RS sequence facilitates interaction of the corresponding protein modifying enzyme to a peptide defined by the amino acid motif, and wherein the leader amino acid sequence encoded by the nucleic acid molecule selected in step (v) is comprised within each peptide defined by the amino acid motif.
  • 33. The method of claim 32, wherein each peptide defined by the amino acid motif further comprises a core sequence.
  • 34. The method of claim 33, wherein the core sequence comprises one or more amino acids susceptible to modification by the one or more protein modifying enzymes.
RELATED APPLICATION

This application claims the benefit under 35 U.S.C. § 119(e) of U.S. provisional application No. 63/038,394, filed Jun. 12, 2020, which is incorporated by reference herein in its entirety.

FEDERALLY SPONSORED RESEARCH

This invention was made with Government support under Grant No. HR0011-15-C-0084 awarded by the Defense Advanced Research Projects Agency (DARPA). The Government has certain rights in this invention.

PCT Information
Filing Document Filing Date Country Kind
PCT/US2021/037120 6/11/2021 WO
Provisional Applications (1)
Number Date Country
63038394 Jun 2020 US