Patent Publication Number: US-2023151062-A1

Title: Genetically encoded system for constructing and detecting biologically active agents

Description:
CROSS-REFERENCE 
     This application is a Divisional of U.S. application Ser. No. 17/141,321, filed Jan. 5, 2021, which is a Continuation of International Application No.: PCT/US2019/040896, filed Jul. 8, 2019, which claims benefit of U.S. Provisional Application No. 62/694,838, filed Jul. 6, 2018, which are incorporated herein by reference in their entirety. 
    
    
     STATEMENT OF GOVERNMENT SUPPORT 
     This invention was made with government support under Award 1750244 and 1804897 awarded by the National Science Foundation. The government has certain rights in the invention. 
    
    
     SEQUENCE LISTING 
     The instant application contains a Sequence Listing which has been submitted electronically in XML, file format and is hereby incorporated by reference in its entirety. Said XML copy, created on Dec. 9, 2022, is named 57123-701_401_SL.xml and is 196,880 bytes in size. 
     FIELD OF THE INVENTION 
     This invention relates to the field of genetic engineering. Specifically, the invention relates to the construction of operons to produce biologically active agents. For example, operons may be constructed to produce agents that control the function of biochemical pathway proteins (e.g, protein phosphatases, kinases and/or proteases). Such agents may include inhibitors and modulators that may be used in studying or controlling phosphatase function associated with abnormalities in a phosphatase pathway or expression level. Fusion proteins, such as light activated protein phosphatases, may be genetically encoded and expressed as photoswitchable phosphatases. Systems are provided for use in controlling phosphatase function within living cells or in identifying small molecule inhibitors/activator/modulator molecules of protein phosphatases associated with cell signaling. 
     BACKGROUND 
     Protein phosphorylation is involved with cell signaling as in part it controls the location and timing of cellular differentiation, movement, proliferation, and death 1-4 ; its misregulation is implicated in cancer, diabetes, obesity, and Alzheimer&#39;s disease, among other disorders 5-9 . Optical tools to exert spatiotemporal control over the activity of phosphorylation-regulating enzymes in living cells could elucidate the mechanisms by which cells transmit, filter, and integrate chemical signals 10,11 , reveal links between seemingly disparate physiological processes (e.g., memory 12  and metabolism 13 ), and facilitate the identification of new targets for phosphorylation-modulating therapeutics (a class of pharmaceuticals 14 ). Therefore, there is a need for developing tools to control, reduce, or enhance the activity of phosphorylation-regulating enzymes in living cells. 
     SUMMARY OF THE INVENTION 
     This invention relates to the field of genetic engineering. Specifically, the invention relates to the construction of operons to produce biologically active agents. For example, operons may be constructed to produce agents that control the function of biochemical pathway proteins (e.g, protein phosphatases, kinases and/or proteases). Such agents may include inhibitors and modulators that may be used in studying or controlling phosphatase function associated with abnormalities in a phosphatase pathway or expression level. Fusion proteins, such as light activated protein phosphatases, may be genetically encoded and expressed as photoswitchable phosphatases. Systems are provided for use in controlling phosphatase function within living cells or in identifying small molecule inhibitors/activator/modulator molecules of protein phosphatases associated with cell signaling. 
     In one embodiment, the present invention contemplates a genetic operon comprising: a) providing; i) a first gene encoding a first fusion protein, the first fusion protein comprising a substrate recognition domain and either a DNA-binding domain or an anchoring unit for RNA polymerase; ii) a second gene encoding a second fusion protein, the second fusion protein comprising an enzyme substrate domain and either an anchoring unit for RNA polymerase or a DNA binding domain; iii) a first DNA sequence comprising a binding site for said DNA-binding domain; iv) a second DNA sequence comprising a binding site, proximal to the first, for said anchoring unit and for said RNA polymerase; v) a third gene encoding a first enzyme, wherein said first enzyme is capable of modifying said substrate domain, thereby changing the affinity of said substrate recognition domain; vi) a fourth gene encoding a second enzyme, wherein said second enzyme is capable unmodifying said substrate domain; vii) a reporter gene encoding at least one capable of having a detectable output when said RNA polymerase and said anchoring unit binds to said second DNA sequence binding site after association of the two fusion proteins. In one embodiment, said substrate domain is a peptide substrate of a protein kinase. In one embodiment, said substrate domain is a peptide substrate of a protein tyrosine kinase. In one embodiment, said substrate domain is a peptide substrate of Src kinase (a protein tyrosine kinase). In one embodiment, said substrate recognition domain is capable of binding to said substrate domain in its phosphorylated state. In one embodiment, said substrate recognition domain is capable of binding to said substrate domain in its unphosphorylated state. In one embodiment, said DNA-binding domain is the 434 cI repressor and said DNA binding site is the binding sequence for that repressor. In one embodiment, said anchoring unit is the omega subunit of RNA polymerase and said second DNA binding site is the binding site for RNA polymerase. In one embodiment, said substrate domain is a peptide substrate of a protein kinase. In one embodiment, said operon further comprises a system of proteins. In one embodiment, said first enzyme is a protein phosphatase. In one embodiment, said first enzyme is a protein tyrosine phosphatase. In one embodiment, said first enzyme is protein tyrosine phosphatase 1B. In one embodiment, said second enzyme is a protein kinase. In one embodiment, said second enzyme is a protein tyrosine kinase. In one embodiment, said second enzyme is Src kinase. In one embodiment, said reporter protein yields a detectable output. In one embodiment, said reporter protein that yields a detectable output is a LuxAB bioreporters (e.g., output is a luminescence). In one embodiment, said reporter protein that yields a detectable output is a fluorescent protein. In one embodiment, said reporter protein that yields a detectable output is mClover. In one embodiment, said reporter protein that yields a detectable output confers antibiotic resistance. In one embodiment, said antibiotic resistance is to spectinomycin. In one embodiment, said operon further comprises a gene encoding a decoy protein fusion comprising: (i) a second enzyme substrate domain that is different from the first enzyme substrate domain and (ii) a protein that that does not bind specifically to DNA and/or to RNA polymerase, and a fifth gene encoding a third enzyme, wherein said third enzyme is capable of being active on the decoy substrate domain. In one embodiment, both said first enzyme substrate domain (of the base system) and said second enzyme substrate domain (of the decoy) are substrates of a protein kinases. In one embodiment, both said first enzyme substrate domain (of the base system) and said second enzyme substrate domain (of the decoy) are substrates of a protein tyrosine kinase. In one embodiment, both said first enzyme substrate domain (of the base system) and said second enzyme substrate domain (of the decoy) are substrates of Src kinase. In one embodiment, both said first enzyme substrate domain (of the base system) and said second substrate domain (of the decoy) are substrates of a protein phosphatase. In one embodiment, both said first enzyme substrate domain (of the base system) and said second substrate domain (of the decoy) are substrates of a protein tyrosine phosphatase. In one embodiment, both said first enzyme substrate domain (of the base system) and said second substrate domain (of the decoy) are substrates of protein tyrosine phosphatase 1B. In one embodiment, said first enzyme is a light modulated enzyme. In one embodiment, said first enzyme is a protein-LOV2 chimera. In one embodiment, said first enzyme is a PTP1B-LOV2 chimera. In one embodiment, said proteins that yield a detectable output include a protein that generates a toxic product in the presence of a non-essential substrate. In one embodiment, said additional protein is SacB, which converts sucrose to a nonstructural polysaccharide that is toxic in  E. coli . In one embodiment, said operon further comprises an expression vector and a bacterial cell. 
     In one embodiment, the present invention contemplates a system for detecting inhibitors of an enzyme, comprising: a) providing; i) an operon comprising a gene encoding an enzyme; ii) a bacterium cell; iii) a small molecule test compound; and b) contacting said bacterium with said operon such that said contacted bacterium is capable of producing a detectable output; c) growing said contacted bacterium in the presence of said test compound under conditions allowing said detectable output; and d) assessing the influence of the test compound on said detectable output. In one embodiment, said enzyme is a protein phosphatase. In one embodiment, said enzyme is a protein tyrosine phosphatase. In one embodiment, said enzyme, is protein tyrosine phosphatase 1B. 
     In one embodiment, the present invention contemplates a method for evolving inhibitors of an enzyme, comprising: a) providing: i) an operon comprising a gene encoding an enzyme; a library of bacteria cells, wherein each said bacteria cells has at least one mutated metabolic pathway; b) growing said library of bacteria cells; and c) screening said library of bacterial cells for a detectable output. In one embodiment, said operon further comprises an expression vector. 
     In one embodiment, the present invention contemplates a method for detecting selective inhibitors of a first enzyme over a second enzyme, comprising: a) providing; i) a system as described above comprising a library of bacterial cells; and ii) a small molecule test compound; b) growing said library of bacterial cells in the presence of the test compound; and c) assessing an influence of the test compound on a detectable output. In one embodiment, the system further provides an operon comprising a gene encoding a decoy fusion protein, said decoy fusion protein comprising; (i) a second enzyme substrate domain that is different from the first enzyme substrate domain and (ii) a protein that that does not bind specifically to DNA and/or RNA polymerase. In one embodiment, said operon further comprises an expression vector. 
     In one embodiment, the present invention contemplates a method for evolving selective inhibitors of a first enzyme over a second enzyme, comprising; a) providing; a system as described herein comprising a library of bacterial cells having mutated metabolic pathways; b) growing said bacterial cell library; and b) screening the bacterial cell library for a detectable output. In one embodiment, the method further provides an operon comprising a gene encoding a decoy fusion protein, the decoy fusion protein comprising; (i) a second enzyme substrate domain that is different from the first enzyme substrate domain and (ii) a protein that that does not bind specifically to DNA and/or RNA polymerase. In one embodiment, said operon further comprises an expression vector. 
     In one embodiment, the present invention contemplates a method for evolving photoswitchable enzymes, comprising; a) providing; i) a system as described herein comprising a bacterial cell library having mutated photoswitchable enzymes; b) growing the bacterial cell library under at least two different light conditions; and c) comparing differences in detectable output for each cell between each of said two different light conditions. In one embodiment, said operon further comprises an expression vector. 
     In one embodiment, the present invention contemplates a method for evolving photoswitchable enzymes, comprising: a) providing; i) a system as described herein comprising a library of bacterial cells have mutated photoswitchable enzymes; b) growing the library of bacterial cells under a first light source in which activity is desired; c) subsequently growing the library of bacterial cells from step b) in the presence of: (i) a non-essential substrate; and (ii) a second light source in which activity is not desired; d) subsequently screening survivors of step c) for a mutant bacterial cell; and e) examining the mutant bacterial cell for activity under the first light source and the second light source. In one embodiment, the method further comprises an operon comprising a gene encoding a decoy fusion protein, the decoy fusion protein comprising; (i) a second enzyme substrate domain that is different from the first enzyme substrate domain; and (ii) a protein that that does not bind specifically to DNA and/or RNA polymerase. In one embodiment, said operon further comprises an expression vector. 
     In one embodiment, the present invention contemplates a method for evolving selective mutants of an enzyme, comprising: a) providing; a system as described above comprising a library of bacterial cells having a mutant enzyme; b) growing the library of bacterial cells; and c) comparing a detectable output between the cells to identify the mutant enzyme. In one embodiment, the method further comprises an operon comprising a gene encoding a decoy fusion protein, the decoy fusion protein comprising; (i) a second enzyme substrate domain that is different from the first enzyme substrate domain; and (ii) a protein that that does not bind specifically to DNA and/or RNA polymerase. In one embodiment, said operon further comprises an expression vector. 
     In one embodiment, the present invention contemplates a method for evolving substrate domains selective for an enzyme, comprising: a) providing; a method as described above comprising a library of bacterial cells comprising substrate domains fused to DNA binding domains; b) growing the library of bacterial cells in the presence of an inducer for a first enzyme and a non-essential substrate; c) subsequently growing the library of bacterial cells from step b) in the presence of an inducer for a second enzyme; and d) subsequently screening for survivor bacterial cells, thereby identifying substrates that bind to the first enzyme but not to the second enzyme. In one embodiment, said system comprises a reporter protein that yields a detectable output. In one embodiment, the reporter protein generates a toxic product in the presence of a non-essential substrate. In one embodiment, the system further comprises an operon comprising a gene selected from the group consisting of a first inducible promoter for a first enzyme and a second inducible promoter for a second enzyme, wherein the second enzyme has a similar activity to the first enzyme. 
     In one embodiment, the present invention contemplates a method of using a microbial biosensor comprising an operon, wherein said operon comprises; a) providing a reporter gene and a sensor fusion protein gene; and b) expressing said sensor fusion protein with a post-translational modification and the reporter gene. In one embodiment, said expressed sensor fusion protein has a protein tyrosine phosphatase substrate domain and is capable of binding to said DNA binding sequences in the presence of at least one expressible sensor fusion protein as a recognition domain (SH2) for said protein tyrosine phosphatase substrate domain attached to a phosphate molecule. In one embodiment, said operon further comprises gene segments encoding: i) a first expressible sensor fusion protein as a protein tyrosine phosphatase substrate domain capable of attaching to said phosphate molecule, said first expressible sensor fusion protein is in an operable combination with a DNA-binding protein; and ii) a second expressible sensor fusion protein as a recognition domain (SH2) for said protein tyrosine phosphatase substrate domain when attached to a phosphate molecule, said second expressible sensor fusion protein is in operable combination with a subunit of an RNA polymerase; and iii) individual expressible fragments including, but not limited to, a Src kinase protein; a protein tyrosine phosphatase 1B (PTP1B) and conjugated to said transcriptionally active binding sequences capable of binding to said DNA-binding protein of sensor fusion protein and said subunit of an RNA polymerase in operable combination with said reporter gene. 
     In one embodiment, the present invention contemplates a method of using a microbial biosensor comprising; a) providing; i) an operon, wherein said operon comprises a reporter gene and a sensor fusion protein gene; ii) a living bacterium; and iii) a test small molecule inhibitor of said protein tyrosine phosphatase enzyme; b) expressing said sensor fusion protein with a post-translational modification and a reporter gene; c) contacting said bacterium with said test small molecule; and d) determining whether said test small molecule is an inhibitor for said protein phosphatase enzyme by expression of said reporter gene. In one embodiment, said expressed sensor fusion protein has a protein tyrosine phosphatase substrate domain that is capable of binding to a DNA binding sequence in the presence of at least one expressible sensor fusion protein as a recognition domain (SH2) for said protein tyrosine phosphatase substrate domain attached to a phosphate molecule. In one embodiment, said expressed sensor fusion protein has a protein tyrosine phosphatase 1B substrate domain that is capable of binding to said DNA binding sequences in the presence of at least one expressible sensor fusion protein as a recognition domain (SH2) for said protein tyrosine phosphatase substrate domain attached to a phosphate molecule. In one embodiment, said operon further comprises gene segments encoding: i) said first expressible sensor fusion protein as said protein tyrosine phosphatase substrate domain capable of attaching to said phosphate molecule that is in operable combination with a DNA-binding; and ii) said second expressible sensor fusion protein as a recognition domain (SH2) for said protein tyrosine phosphatase substrate domain when attached to a phosphate molecule that is in operable combination with a subunit of an RNA polymerase; and iii) individual expressible fragments including but not limited to, a Src kinase protein; a protein tyrosine phosphatase 1B (PTP1B) and conjugated to said transcriptionally active binding sequences capable of binding to said DNA-binding protein of sensor fusion protein and said subunit of an RNA polymerase in operable combination with said reporter gene. In one embodiment, said biosensor further comprises an operon component for expressing a second gene. In one embodiment, said biosensor further comprises an operon component for expressing a second PTP that is different from the first PTP for identifying a said inhibitor selective for one of the TPT enzymes. In one embodiment, said test small molecule inhibitor includes, but is not limited to, abietane-type diterpenes, abietic acid (AA), dihydroabietic acid and structural variants thereof. 
     In one embodiment, the present invention contemplates a method of using a microbial biosensor, comprising: a) providing; i) an operon, wherein said operon comprises a reporter gene and a sensor fusion protein gene; ii) a living bacterium; and iii) a test small molecule inhibitor of said protein tyrosine phosphatase enzyme; b) expressing said sensor fusion protein with a post-translational modification and the reporter gene; c) expressing said expressible sensor fusion proteins in said bacterium; d) contacting said bacterium with said test small molecule; and e) determining whether said test small molecule is an inhibitor for said protein phosphatase enzyme by expression of said reporter gene. In one embodiment, said expressed sensor fusion protein has a protein tyrosine phosphatase substrate domain and is capable of binding to said DNA binding sequences in the presence of at least one expressible sensor fusion protein as a recognition domain (SH2) for said protein tyrosine phosphatase substrate domain attached to a phosphate molecule. In one embodiment, the expressed sensor fusion protein has a protein tyrosine phosphatase 1B substrate domain and capable of binding to said DNA binding sequences in the presence of at least one expressible sensor fusion protein as a recognition domain (SH2) for said protein ty rosin phosphatase substrate domain attached to a phosphate molecule, and an individual expressible fragment for a photoswitchable protein tyrosine phosphatase 1B. In one embodiment, said operon comprises gene segments encoding: i) said first expressible sensor fusion protein as said protein tyrosine phosphatase substrate domain that is capable of attaching to said phosphate molecule in operable combination with a DNA-binding protein; ii) said second said expressible sensor fusion protein as a recognition domain (SH2) for said protein tyrosine phosphatase substrate domain when attached to a phosphate molecule that is in operable combination with a subunit of an RNA polymerase; and iii) individual expressible fragments including, but not limited to, a Src kinase protein; a protein tyrosine phosphatase 1B (PTP1B) and conjugated to said transcriptionally active binding sequences capable of binding to said DNA-binding protein of sensor fusion protein and said subunit of an RNA polymerase in operable combination with said reporter gene. 
     In one embodiment, the present invention contemplates a method for providing variants of chemical structures for use as a potential therapeutic, comprising: a) providing; i) an  E. coli  bacterium comprising a metabolic terpenoid chemical structure-producing pathway providing an altered chemical structure, wherein said metabolic pathway comprises a synthetic enzyme, wherein said  E. coli  further comprises a microbial biosensor operon for detecting PTP inhibition; and ii) a mutated synthetic enzyme of system of enzymes; a) introducing said mutated synthetic enzyme of system of enzymes; c) expressing said mutated synthetic enzyme under conditions wherein said mutated synthetic enzyme or system of enzymes alters/alter the chemical structure of said terpenoid chemical structure; and d) determining whether said altered chemical structure is an inhibitor for said PTP as a test inhibitor for use as a potential therapeutic. In one embodiment, said metabolic pathway comprises synthetic enzymes including, but not limited to, terpene synthases, cytochrome P450s, halogenases, methyl transferases, or terpenoid-functionalizing enzymes. In one embodiment, said terpenoid includes, but is not limited to, labdane-related diterpenoids. In one embodiment, said terpenoid includes but is not limited to, abietane-type diterpenoids. In one embodiment, said terpenoid is abietic acid. 
     In one embodiment, the present invention contemplates a fusion protein DNA construct, comprising a protein phosphatase gene and a protein light switch gene conjugated within said phosphatase gene, wherein said protein phosphatase gene encodes a protein with a C-terminal domain and said protein light switch gene encodes a protein with an N-terminal alpha helical region such that said C-terminal domain is conjugated to said N-terminal alpha helical region. In one embodiment, said construct further comprises an expression vector and a living cell. In one embodiment, said protein phosphatase is a protein tyrosine phosphatase. In one embodiment, said protein phosphatase is protein tyrosine phosphatase 1B (PTP1B). In one embodiment, said C-terminal domain encodes an α7 helix of PTP1B. In one embodiment, said construct encodes PTP1B PS -A. In one embodiment, said construct encodes PTP1B PS -B. In one embodiment, said protein phosphatase is T-Cell protein tyrosine phosphatases (TC-PTP). In one embodiment, said protein light switch is a light-oxygen-voltage (LOV) domain. In one embodiment, said protein light switch is the LOV2 domain of phototropin 1 form  Avena sativa . In one embodiment, said LOV2 domain comprises an A′a helix of LOV2. In one embodiment, said LOV2 has at least one mutation resulting in an amino acid mutation. It is not meant to limit such mutations. In fact, a mutation may include but is not limited to a nucleotide substitution, the addition of a nucleotide, and the deletion of a nucleotide from said gene. In one embodiment, said mutation is a substitution of a nucleotide. In one embodiment, said A′a helix of LOV2 has a T406A mutation. In one embodiment, said protein light switch is a phytochrome protein. In one embodiment, said phytochrome protein is a bacterial phytochrome protein. In one embodiment, said bacterial phytochrome protein is a bacterial phytochrome protein 1 (BphP1) from  Rhodopseudomonas palustris . In one embodiment, said protein light switch is a light-oxygen-voltage (LOV) domain with an artificial chromophore. In one embodiment, said protein light switch is a phytochrome protein with an artificial chromophore. 
     In one embodiment, the present invention contemplates a fusion protein, comprising a protein phosphatase and a protein light switch conjugated within said phosphatase, wherein said protein phosphatase has a C-terminal domain and said protein light switch has a N-terminal alpha helical region such that said C-terminal domain is conjugated to said N-terminal alpha helical region. In one embodiment, said fusion protein further comprises an expression vector and a living cell. In one embodiment, said protein phosphatase is a protein tyrosine phosphatase. In one embodiment, said protein phosphatase is protein tyrosine phosphatase 1B (PTP1B). In one embodiment, said C-terminal domain encodes an α7 helix. In one embodiment, said fusion protein is PTP1B PS -A. In one embodiment, said fusion protein is PTP1B PS -B. In one embodiment, said protein phosphatase is T-Cell protein tyrosine phosphatases (TC-PTP). In one embodiment, said protein light switch is a light-oxygen-voltage (LOV) domain. In one embodiment, said protein light switch is the LOV2 domain of phototropin 1 form  Avena sativa . In one embodiment, said LOV2 domain comprises an A′a helix of LOV2. In one embodiment, said A′a helix of LOV2 has a T406A mutation. In one embodiment, said protein light switch is a light-oxygen-voltage (LOV) domain with an artificial chromophore. In one embodiment, said protein light switch is a phytochrome protein with an artificial chromophore. In one embodiment, said protein light switch is a phytochrome protein. In one embodiment, said phytochrome protein is a bacterial phytochrome protein. In one embodiment, said bacterial phytochrome protein is a bacterial phytochrome protein 1 (BphP1) from  Rhodopseudomonas palustris . In one embodiment, said protein light switch is a light-oxygen-voltage (LOV) domain with an artificial chromophore. In one embodiment, said protein light switch is a phytochrome protein with an artificial chromophore. 
     In one embodiment, the present invention contemplates a method of using a fusion protein, comprising; a) providing; i) a fusion protein; ii) a protein phosphatase, and iii) a living cell; and b) introducing said fusion protein in said a living cell such that illumination of said light switch alters a feature in said living cell. In one embodiment, said feature includes but is not limited to controlling cell movement, morphology, controlling cell signaling and having a modulatory effect. In one embodiment, said modulatory effect includes but is not limited to inactivation, activation, reversible inactivation and reversible activation. In one embodiment, said modulatory effect is dose dependent. In one embodiment, said illumination is light within the range of 450-500 nm. In one embodiment, said illumination is light within the range of 600-800 nm. In one embodiment, said protein light switch undergoes light-induced conformational change and said protein phosphatase has allosterically modulated catalytic activity that is altered by said conformational change. In one embodiment, said altering is enhanced or reduced. In one embodiment, said protein light switch is a light-oxygen-voltage (LOV) domain with an artificial chromophore. In one embodiment, said protein light switch is a phytochrome protein with an artificial chromophore. In one embodiment, said living cell has an activity. In one embodiment, said living cell is in vivo. In one embodiment, said method further comprises a step of controlling said cellular activity in vivo. 
     In one embodiment, the present invention contemplates a method for detecting a small molecule modulator of a protein phosphatase, comprising: a) providing; i) a fusion protein comprising a protein phosphatase and protein light switch; ii) a visual readout for phosphatase activity; iii) an optical source, wherein said source is capable of emitting light radiation; iv) a living cell; and v) a small molecule test compound; b) expressing said fusion protein in said living cell; c) contacting said living cell with said small molecule test compound; d) illuminating said fusion protein within said cell with said optical source; e) measuring a visual readout for a change in phosphatase activity for identifying said small molecule test compound as a modulator of said activity of said phosphatase; and f) using said modulatory small molecule test compound for treating a patient exhibiting at least one symptom of a disease associated with said phosphatase. In one embodiment, said method further comprises identifying said small molecule test compound as an inhibitor of the activity of said phosphatase. In one embodiment, said method further comprises identifying said small molecule test compound as an activator of the activity of said phosphatase. In one embodiment, said disease includes but is not limited to diabetes, obesity, cancer, anxiety, autoimmunity, or neurodegenerative diseases. In one embodiment, said protein light switch is a light-oxygen-voltage (LOV) domain with an artificial chromophore. In one embodiment, said protein light switch is a phytochrome protein with an artificial chromophore. In one embodiment, said method further provides a fluorescence-based biosensor, and comprises a step of introducing said fluorescence-based biosensor into said cell. In one embodiment, said method further comprises a step of controlling said cellular activity in vivo. In one embodiment, said visual readout for phosphatase activity is selected from the group consisting of a fluorescence-based biosensor; changes in cell morphology; and changes in cell motility. 
     In one embodiment, the present invention contemplates a photoswitchable protein tyrosine phosphatase enzyme construct comprising an N-terminal alpha helix of a protein light switch conjugated to a C-terminal allosteric domain region. In one embodiment, said protein tyrosine phosphatase enzyme is protein tyrosine phosphatase 1B (PTP1B). In one embodiment, said protein light switch is a LOV2 domain of phototropin 1 derived from  Avena sativa  (wild oats). In one embodiment, said enzyme construct further comprises an expression vector. In one embodiment, the present invention contemplates a biosensor for enzyme activity, comprising; a) a substrate domain as described above; b) a substrate recognition domain; c) a first fluorescent protein; and d) a second fluorescent protein. 
     In one embodiment, the invention provides a genetically encoded system for detecting small molecules that modulate enzyme activity, comprising, a. a first region in operable combination comprising: i. a first promoter; ii. a first gene encoding a first fusion protein comprising a substrate recognition domain linked to a DNA-binding protein; iii. a second gene encoding a second fusion protein comprising a substrate domain linked to a protein capable of recruiting RNA polymerase to DNA; iv. a second promoter; v. a third gene for a protein kinase; vi. a fourth gene for a molecular chaperone; vii. a fifth gene for a protein phosphatase; b. a second region in operable combination comprising: i. a first DNA sequence encoding an operator for said DNA-binding protein; ii. a second DNA sequence encoding a binding site for RNA polymerase; and iii. one or more genes of interest (GOI). In one embodiment, said first promoter is Prol. In one embodiment, said substrate recognition domain is a substrate homology 2 (SH2) domain from  H. sapiens . In one embodiment, said DNA-binding protein is the 434 phage cI repressor. In one embodiment, said substrate domain is a peptide substrate of both said kinase and said phosphatase. In one embodiment, said second promoter is ProD. In one embodiment, said protein capable of recruiting RNA polymerase to DNA is the omega subunit of RNA polymerase (i.e., RpoZ or RP ω ). In one embodiment, said protein kinase is Src kinase from  H. sapiens . In one embodiment, said molecular chaperone is CDC37 (i.e., the Hsp90 co-chaperone) from  H. sapiens . In one embodiment, said protein phosphatase is protein tyrosine phosphatase 1B (PTP1B) from  H. sapiens . In one embodiment, said operator is the operator for 434 phage cI repressor. In one embodiment, said binding site for RNA polymerase is the −35 to −10 region of the lacZ promoter. In one embodiment, said gene of interest is SpecR, a gene that confers resistance to spectinomycin. In one embodiment, said genes of interest are LuxA and LuxB, two genes that yield a luminescent output. In one embodiment, said gene of interest is a gene that confers resistance to an antibiotic. In one embodiment, said protein phosphatase is PTPN6 from  H. sapiens . In one embodiment, said protein phosphatase is a protein tyrosine phosphatase (PTP). In one embodiment, said protein phosphatase is the catalytic domain of a PTP. In one embodiment, an alignment of the X-ray crystal structures of (i) the catalytic domain of said protein phosphatase and (ii) the catalytic domain of PTP1B yields a root-mean-square deviation (RMSD) of less than or equal to 0.95 Å (as defined by a function similar to the PyMol function align). In one embodiment, said catalytic domain of said protein phosphatase has at least 34.1% sequence identity with the catalytic domain of PTP1B. In one embodiment, said catalytic domain of said phosphatase has at least 53.5% sequence similarity with the catalytic domain of PTP1B. In one embodiment, said protein kinase is a protein tyrosine kinase (PTK). In one embodiment, said protein kinase is the catalytic domain of a PTK. In one embodiment, said first promoter is a constitutive promoter. In one embodiment, said second promoter is a constitutive promoter. In one embodiment, said first promoter is an inducible promoter. In one embodiment, said second promoter is an inducible promoter. In one embodiment, said binding site for RNA polymerase comprises part of a third promoter. In one embodiment, said first region lacks a gene for a molecular chaperone. In one embodiment, said first fusion protein consists of a substrate recognition domain linked a protein capable of recruiting RNA polymerase to DNA, and said second fusion protein consists of a substrate domain linked to a DNA-binding protein. In one embodiment, said first region further contains a third fusion protein (i.e., a “decoy”) comprising a second substrate domain, which is distinct from the first substrate domain, linked to a protein that is incapable of recruiting RNA polymerase to DNA. In one embodiment, said substrate domain of said third fusion protein is a peptide substrate of both said kinase and said phosphatase. In one embodiment, said substrate domain of said third fusion protein is a peptide substrate of said kinase but is a poor substrate of said phosphatase. In one embodiment, said first region further contains a sixth gene for a second protein phosphatase, which is distinct from the first protein phosphatase and which acts on said substrate domain of said third fusion protein. 
     In one embodiment, the invention provides a method for using both (i) a genetically encoded system for detecting small molecules that modulate enzyme activity and (ii) a genetically encoded pathway for terpenoid biosynthesis to identify and/or build terpenoids that modulate enzyme activity, comprising, a. providing, i. a genetically encoded system for detecting small molecules that modulate enzyme activity, comprising, 1. a first region in operable combination comprising: a. a first promoter; b. a first gene encoding a first fusion protein comprising a substrate recognition domain linked to a DNA-binding protein; c. a second gene encoding a second fusion protein comprising a substrate domain linked to a protein capable of recruiting RNA polymerase to DNA; d. a second promoter; e. a third gene for a protein kinase; f. a fourth gene for a molecular chaperone; g. a fifth gene for a protein phosphatase; 2. a second region in operable combination comprising: a. a first DNA sequence encoding an operator for said DNA-binding protein; b. a second DNA sequence encoding a binding site for RNA polymerase; c. one or more genes of interest (GOI); ii. a genetically encoded pathway for terpenoid biosynthesis comprising: 1. a pathway that generates linear isoprenoid precursors; 2. a gene for a terpene synthase (TS); 3. a plurality of  E. coli  bacteria; b. transforming said bacteria with both (i) said genetically encoded system for detecting small molecules and (ii) said genetically encoded pathway for terpenoid biosynthesis, and allowing said transformed bacteria to replicate; c. observing the expression of a gene of interest through a measurable output. In one embodiment, said pathway that generates linear isoprenoid precursors generates farnesyl pyrophosphate (FPP). In one embodiment, said pathway that generates linear isoprenoid precursors is all or part of the mevalonate-dependent isoprenoid pathway of  S. cerevisiae . In one embodiment, said pathway that generates linear isoprenoid precursors is carried by the plasmid pMBIS. In one embodiment, said gene of interest is SpecR, a gene that confers resistance to spectinomycin. In one embodiment, said TS gene is carried on a separate plasmid (pTS) from the rest of the terpenoid pathway. In one embodiment, said TS gene encodes for amorphadiene synthase (ADS) from  Artemisia annua . In one embodiment, said TS gene encodes for γ-humulene synthase (GHS) from  Abies grandis . In one embodiment, said TS gene encodes for abietadiene synthase (ABS) from  Abies grandis , and this gene is carried in operable combination with a gene for geranylgeranyl diphosphate synthase (GPPS). In one embodiment, said TS gene encodes for taxadiene synthase (TXS) from  Taxus brevifolia , and this gene is carried in operable combination with a gene for GGPPS. In one embodiment, the method further comprises, d. extracting terpenoids that enable the highest measurable output (e.g., growth at the highest concentration of spectinomycin); e. identifying said terpenoids; f. purifying said terpenoids. In one embodiment, the method further comprises, providing, g. a mammalian cell culture, h. treating said cell cultures with purified terpenoids, i. measuring a biochemical effect that results from changes in the activity of a protein phosphatase or protein kinase. In one embodiment, the method further comprises, j. providing, a purified enzyme target, k. measuring the modulatory effect of purified terpenoids on the enzyme target, l. quantifying that modulatory effect (e.g., by calculating an IC 50 ). In one embodiment, said TS gene has at least one mutation. In one embodiment, said TS gene is in operable combination with a gene for an enzyme that functionalizes terpenoids. In one embodiment, said TS gene is in operable combination with a gene for a cytochrome P450. In one embodiment, said TS gene is in operable combination with a gene for cytochrome P450 BM3 from  Bacillus megaterium . In one embodiment, said TS gene is in operable combination with a gene for a halogenase. In one embodiment, said TS gene is in operable combination with a gene for 6-halogenase (SttH) from  Streptomyces toxytricini . In one embodiment, said TS gene is in operable combination with a gene for vanadium haloperoxidase (VHPO) from  Acaryochloris marina . In one embodiment, said mammalian cell is a HepG2, Hela, Hek393t, MCF-7, and/or Cho-hIR cell. In one embodiment, said cells are BT474, SKBR3, or MCF-7 and MDA-MB-231 cells. In one embodiment, said biochemical effect is insulin receptor phosphorylation, which can be measured by a western blot or enzyme-linked immunosorbent assay (ELISA). In one embodiment, said cells are triple negative (TN) cell lines. In one embodiment, said cells are TN cells from the American Type Culture Collection (ATCC). In one embodiment, said cells are TN cells from ATCC TCP-1002. In one embodiment, said biochemical effect is cellular migration. In one embodiment, said biochemical effect is cellular viability. In one embodiment, said biochemical effect is cellular proliferation. In one embodiment, said protein phosphatase is PTP1B from  H. sapiens . In one embodiment, said protein kinase is Src kinase from  H. sapiens . In one embodiment, said gene of interest confers resistance to an antibiotic. In one embodiment, said gene of interest is SacB, a gene that confers sensitivity to sucrose. In one embodiment, said gene of interest confers conditional toxicity (i.e., toxicity in the presence of an exogenously added molecule). In one embodiment, said genes of interest are SpecR and SacB. In one embodiment, said protein phosphatase is the wild-type enzyme. In one embodiment, said protein phosphatase has at least one mutation. In one embodiment, said protein phosphatase has at least one mutation that reduces its sensitivity to a small molecule that modulates the activity of the wild-type protein phosphatase. In one embodiment, said protein kinase is the wild-type enzyme. In one embodiment, said protein kinase has at least one mutation. In one embodiment, said protein kinase has at least one mutation that reduces its sensitivity to a small molecule that modulates the activity of the wild-type protein kinase. In one embodiment, said at least one of said terpenoids inhibit a protein phosphatase. In one embodiment, said at least one of said terpenoids inhibit a PTP. In one embodiment, said least one of said terpenoids inhibit PTP1B. In one embodiment, said at least one of said terpenoids activate a protein phosphatase. In one embodiment, said least one of said terpenoids activates a PTP. In one embodiment, said at least one of aid terpenoids activate protein tyrosine phosphatase non-receptor type 12 (PTPN12). In one embodiment, said at least one of said terpenoids inhibit a protein kinase. In one embodiment, said at least one of said terpenoids inhibit a PTK. In one embodiment, said at least one of said terpenoid inhibit Src kinase. In one embodiment, said at least one of said terpenoids activate a protein kinase. In one embodiment, said at least one of said terpenoids activate a PTK. In one embodiment, said genetically encoded system for detecting small molecules further contains both (i) a third fusion protein comprising a second substrate domain, which is distinct from the first substrate domain, linked to a protein that is incapable of recruiting RNA polymerase to DNA and (ii) a sixth gene for a second protein phosphatase, which is distinct from the first protein phosphatase. In one embodiment, said genetically encoded system for detecting small molecules further contains both (i) a third fusion protein comprising a second substrate domain, which is distinct from the first substrate domain, linked to a protein that is incapable of recruiting RNA polymerase to DNA and (ii) a sixth gene for a second protein kinase, which is distinct from the first protein kinase. In one embodiment, said genetically encoded pathway for terpenoid biosynthesis comprises, instead, a library of pathways that differ in the identity of the TS gene such that upon transformation, the majority of cells contain a distinct TS gene (i.e., a gene that differs by at least one mutation). In one embodiment, said genetically encoded pathway for terpenoid biosynthesis comprises, instead, a library of pathways that differ in the identity of a gene that functionalizes terpenoids (e.g., a cytochrome P450 or halogenase), in operable combination with the SI gene, such that upon transformation, the majority of cells contain a distinct gene that functionalizes terpenoids (i.e., a gene that differs by at least one mutation). In one embodiment, said genetically encoded pathway for terpenoid biosynthesis comprises, instead, a library of pathways in which the TS gene has been replaced by a component of a eukaryotic complementary DNA (cDNA) library such that upon transformation, the majority of cells contain a distinct gene in place of the TS gene. In one embodiment, said genetically encoded pathway for terpenoid biosynthesis comprises, instead, a library of pathways in which the TS gene accompanied by a component of a eukaryotic complementary DNA (cDNA) library such that upon transformation, the majority of cells contain a distinct gene in operable combination with the TS gene (e.g., a gene that may encode for a terpenoid-functionalizing enzyme). In one embodiment, said genetically encoded system for detecting small molecules comprises, instead, a library of such systems that differ in the identity of the protein phosphatase gene such that upon transformation, the majority of cells contain a distinct protein phosphatase gene (i.e., a gene that differs by at least one mutation). In one embodiment, said genetically encoded pathway for terpenoid biosynthesis generates a terpenoid that modulates the activity of the wild-type form of said protein phosphatase, thereby enabling the growth study to isolate a mutant of said protein phosphatase that is less sensitive to the modulatory effect of the small molecule. In one embodiment, said genetically encoded system for detecting small molecules comprises, instead, a library of such systems that differ in the identity of the protein kinase gene, such that upon transformation, the majority of cells contain a separate protein kinase gene (i.e., a gene that differs by at least one mutation). In one embodiment, said genetically encoded pathway for terpenoid biosynthesis generates a terpenoid that modulates the activity of the wild-type form of said protein kinase, thereby enabling the growth study to isolate a mutant of said protein kinase that is less sensitive to the modulatory effect of the small molecule. In one embodiment, said at least one of said terpenoids modulates the activity of the wild-type form of said protein phosphatase, but not a mutated form of said protein phosphatase. In one embodiment, said at least one of said terpenoids modulates the activity of the said first protein phosphatase, but not the activity of said second protein phosphatase. In one embodiment, said at least one of said terpenoids modulates the activity of the wild-type form of said protein kinase, but not a mutated form of said protein kinase. In one embodiment, said at least one of said terpenoids modulates the activity of said first protein kinase, but not the activity of said second protein kinase. 
     In one embodiment, the invention provides an inhibitor detection operon comprising A: a first region in operable combination under control of a first promoter including: i. a first DNA sequence encoding a first fusion protein comprising a substrate recognition homology 2 domain (SH2) and a repressor; ii. a second DNA sequence encoding a second fusion protein comprising a phosphate molecule binding domain of a substrate recognition domain, said substrate recognition domain and an omega subunit of RNA polymerase (RpoZ or RP ω ); iii. a third DNA sequence encoding a Cell Division Cycle 37 protein (CDC37); iv. a protein phosphatase; and B: a second region in operable combination under control of a second promoter comprising: i. an operator comprising a repressor binding domain said repressor, ii. a ribosome binding site (RB); and iii. a gene of interest (GOI). In one embodiment, said SH2 domain is a substrate recognition domain of said protein phosphatase. In one embodiment, said repressor is a 434 phage cI repressor. In one embodiment, said substrate recognition domain binds said protein phosphatase. In one embodiment, said decoy substrate domain is a Src kinase gene. In one embodiment, said operator is a 434cI operator. In one embodiment, said gene of interest encodes an antibiotic protein. In one embodiment, said protein phosphatase is a protein tyrosine phosphatase. In one embodiment, said first promoter is constitutive promoter. In one embodiment, said second promoter is an inducible promoter. 
     In one embodiment, the invention provides a method of using an inhibitor detection operon, comprising, a. providing, i. a detection operon, comprising A: a first region in operable combination under control of a first promoter including: 1. a first DNA sequence encoding a first fusion protein comprising a protein phosphatase enzyme&#39;s substrate recognition homology 2 domain (SH2) and a repressor binding domain; 2. a second DNA sequence encoding a second fusion protein comprising a phosphate molecule binding domain of a protein phosphatase enzyme&#39;s substrate recognition domain, said protein phosphatase enzyme&#39;s substrate recognition domain and an omega subunit of RNA polymerase (RpoZ or RP ω ); 4. a third DNA sequence encoding a Cell Division Cycle 37 (CDC37) protein; 5. a protein phosphatase enzyme; and B: a second region in operable combination under control of a second promoter comprising: 6. an operator comprising a repressor binding domain biding said repressor, 7. a ribosome binding site (RB); and 8. a gene of interest (GOI); and ii. a mevalonate pathway operon having a missing gene, such that said pathway operon does not contain at least one gene in said pathway for producing said terpenoid compound, under control of a third promoter comprising a second gene of interest for producing a terpenoid compound, iii. a fourth DNA sequence under control of a fourth promoter comprising said missing gene from said mevalonate pathway operon and a third gene of interest; and iv. a plurality of  E. coli  bacteria, and b. transfecting said  E. coli  bacteria with said first operon for expressing said first gene of interest; c. transfecting said  E. coli  bacteria with said mevalonate pathway operon for expressing said first and said second gene of interest; d. transfecting said  E. coli  bacteria with said fourth DNA sequence for expressing said first and said second and said third gene of interest; e. growing said cells wherein said inhibitor terpenoid compounds for protein phosphatase enzymes are produced by said cells. In one embodiment, said method further comprising step e. isolating said protein phosphatase inhibitor molecules and providing a mammalian cell culture for step f. treating said cell cultures for reducing activity of said protein phosphatase enzyme. In one embodiment, said method further providing an inducer compound for inducing said inducible promoter and a step of contacting said bacteria with said compound. In one embodiment, said method wherein reducing activity of said protein phosphatase enzyme reduces growth of said mammalian cells. In one embodiment, said protein phosphatase enzyme is human PTP1B. In one embodiment, said protein phosphatase enzyme is wild-type. In one embodiment, said protein phosphatase enzyme has at least one mutation. In one embodiment, said missing enzyme is a terpene synthase enzyme. In one embodiment, said terpene synthase enzyme is selected from the group consisting of amorphadiene synthase (ADS) and γ-humulene synthase (GHS). In one embodiment, said fourth DNA sequence further comprises a geranylgeranyl diphosphate synthase (GPPS) and said missing enzyme is selected from the group consisting of abietadiene synthase (ABS) and taxadiene synthase (TXS). In one embodiment, said terpene synthase enzyme is wild-type. In one embodiment, said terpene synthase enzyme has at least one mutation. In one embodiment, said terpenoid compounds are structural variants of terpenoid compounds. In one embodiment, said genes of interest are antibiotic genes. In one embodiment, said genes of interest are each different antibiotic genes. 
     In one embodiment, said genetically encoded detection operon system, comprising; Part A: a first region of DNA in operable combination comprising: a region of DNA encoding a first promoter; a first gene encoding a first fusion protein comprising a substrate recognition domain linked to a DNA-binding protein; a second gene encoding a second fusion protein comprising a substrate domain linked to a protein capable of recruiting RNA polymerase to DNA; a region of DNA encoding a second promoter; a third gene for a protein kinase; a fourth gene for a molecular chaperone; a fifth gene fora protein phosphatase; Part B: a second region of DNA in operable combination under control of a second promoter comprising: a first DNA sequence encoding an operator for said DNA-binding protein; a second DNA sequence encoding a binding site for RNA polymerase; and at least one gene of interest (GOI). In one embodiment, said substrate recognition domain is a substrate homology 2 (SH2) domain. In one embodiment, said DNA-binding protein is the 434 phage cI repressor. In one embodiment, said substrate domain is a peptide substrate of both said kinase and said phosphatase. In one embodiment, said protein capable of recruiting RNA polymerase to DNA is the omega subunit of RNA polymerase (RP ω ). In one embodiment, said gene for a kinase is a Src kinase gene. In one embodiment, said molecular chaperone is CDC37. In one embodiment, said molecular chaperone is the Hsp90 co-chaperone) from  H. sapiens . In one embodiment, said operator is a 434 phage cI operator. In one embodiment, said gene of interest is a gene for antibiotic resistance. In one embodiment, said gene for antibiotic resistance produces an enzyme that allow the bacteria to degrade an antibiotic protein. In one embodiment, said protein phosphatase enzyme is protein tyrosine phosphatase 1B. In one embodiment, said first and second promoters of part A are constitutive promoters. In one embodiment, said second promoter of Part B is an inducible promoter. 
     In one embodiment, the invention provides a method of using a genetically encoded detection operon system, comprising, a. providing, i. an inhibitor detection operon, comprising Part A: a first region of DNA in operable combination comprising: 1. a region of DNA encoding a first promoter; 2. a first gene encoding a first fusion protein comprising a substrate recognition domain linked to a DNA-binding protein; 3. a second gene encoding a second fusion protein comprising a substrate domain linked to a protein capable of recruiting RNA polymerase to DNA; 4. a region of DNA encoding a second promoter; 5. a third gene fora protein kinase; 6. a fourth gene for a molecular chaperone; 7. a fifth gene for a protein phosphatase; Part B: a second region of DNA in operable combination under control of a second promoter comprising: 8. a first DNA sequence encoding an operator for said DNA-binding protein; 9. a second DNA sequence encoding a binding site for RNA polymerase; and 10. at least one gene of interest (GOI). ii. a mevalonate-terpene pathway operon not containing a terpene synthase gene, under control of a fourth promoter comprising a second gene of interest for producing a terpenoid compound, iii. a fourth DNA sequence under control of a fifth promoter comprising said terpene synthase gene and a third gene of interest; and iv. a plurality of bacteria, and b. transfecting said bacteria with said inhibitor detection operon for expressing said first gene of interest; c. transfecting said bacteria with said mevalonate pathway operon for expressing said said second gene of interest; d. transfecting said bacteria with said fourth DNA sequence for expressing said third gene of interest; e. growing said bacteria cells expressing said three genes of interest wherein said inhibitor terpenoid compounds are produced by said bacteria cells inhibiting said protein phosphatase enzyme. In one embodiment, said method further comprising step e. isolating said protein phosphatase inhibitor molecules and providing a mammalian cell culture for step f. treating said cell cultures for reducing activity of said protein phosphatase enzyme. In one embodiment, said method wherein reducing activity of said protein phosphatase enzyme reduces growth of said mammalian cells. In one embodiment, said protein phosphatase enzyme is human PTP1B. In one embodiment, said protein phosphatase enzyme is wild-type. In one embodiment, said protein phosphatase enzyme has at least one mutation. In one embodiment, said mevalonate pathway operon comprises genes for expressing mevalonate kinase (ERG12), phosphomevalonate kinase (ERGS), mevalonate pyrophosphate decarboxylatse (MVD1), Isopentenyl pyrophosphate isomerase (IDI gene), and Farnesyl pyrophosphate (FPP) synthase (ispA). In one embodiment, said missing enzyme is a terpene synthase enzyme. In one embodiment, said terpene synthase enzyme is selected from the group consisting of amorphadiene synthase (ADS) and γ-humulene synthase (GHS). In one embodiment, said fourth DNA sequence further comprises a geranylgeranyl diphosphate synthase (GPPS) and said terpene synthase is selected from the group consisting of abietadiene synthase (ABS) and taxadiene synthase (TXS). In one embodiment, said terpene synthase enzyme is wild-type. In one embodiment, said terpene synthase enzyme has at least one mutation. In one embodiment, said terpenoid compounds are structural variants of terpenoid compounds. In one embodiment, said genes of interest are antibiotic genes. In one embodiment, said genes of interest are each different antibiotic genes. In one embodiment, said method further provides an inducer compound for inducing said inducible promoter and a step of contacting said bacteria with said compound. 
     In one embodiment, the invention provides a method for using both (i) a genetically encoded system for detecting small molecules that modulate enzyme activity and (ii) a genetically encoded pathway for polyketide biosynthesis to identify and/or build polyketides that modulate enzyme activity, comprising, providing, A genetically encoded system for detecting small molecules that modulate enzyme activity, comprising, a first region in operable combination comprising: a first promoter; a first gene encoding a first fusion protein comprising a substrate recognition domain linked to a DNA-binding protein; a second gene encoding a second fusion protein comprising a substrate domain linked to a protein capable of recruiting RNA polymerase to DNA; a second promoter; a third gene for a protein kinase; a fourth gene for a molecular chaperone; a fifth gene for a protein phosphatase; a second region in operable combination comprising: a first DNA sequence encoding an operator for said DNA-binding protein; a second DNA sequence encoding a binding site for RNA polymerase; one or more genes of interest (GOI); a genetically encoded pathway for polyketide biosynthesis comprising; a gene fora polyketide synthase; a plurality of  E. coli  bacteria. In one embodiment, said polyketide synthase is 6-deoxyerythronolide B synthase (DEBS). In one embodiment, said polyketide synthase (PKS) is a modular combination of different PKS components. 
     In one embodiment, the invention provides a method for using both (i) a genetically encoded system for detecting small molecules that modulate enzyme activity and (ii) a genetically encoded pathway for polyketide biosynthesis to identify and/or build alkaloids that modulate enzyme activity, comprising, a. providing, a genetically encoded system for detecting small molecules that modulate enzyme activity, comprising, a first region in operable combination comprising: a first promoter; a first gene encoding a first fusion protein comprising a substrate recognition domain linked to a DNA-binding protein; a second gene encoding a second fusion protein comprising a substrate domain linked to a protein capable of recruiting RNA polymerase to DNA; a second promoter; a third gene for a protein kinase; a fourth gene for a molecular chaperone; a fifth gene for a protein phosphatase; a second region in operable combination comprising: a first DNA sequence encoding an operator for said DNA-binding protein; a second DNA sequence encoding a binding site for RNA polymerase; one or more genes of interest (GOI); a genetically encoded pathway for polyketide biosynthesis comprising, a pathway for alkaloid biosynthesis. a plurality of  E. coli  bacteria. In one embodiment, said pathway for alkaloid biosynthesis described herein. 
     In one embodiment, the invention provides an engineered bacteria cell line comprising expression plasmid 1, plasmid 2, plasmid 3 and plasmid 4. 
     In one embodiment, the invention provides a phosphatase inhibitor molecule produced by a bacterium expressing a plasmid 1 in contact with an inducer molecule for inducing a promoter expressing a terpenoid synthesis pathway operon in plasmid 2 and a terpene synthase enzyme in plasmid 3, wherein said plasmid 2 and plasmid 3 are coexpressed in said bacteria with plasmid 1. In one embodiment, said plasmid 2 and said plasmid 3 are under control of an inducible promoter. In one embodiment, said bacterium is contacted by an inducible molecule for inducing said promoter. 
     In one embodiment, the invention provides a bacteria strain producing a phosphatase inhibitor molecule. In one embodiment, said inhibitor is a terpenoid molecule. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
       The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee. 
         FIG.  1 A-G  illustrates embodiments and shows exemplary results of developing a photoswitchable phosphatase, e.g. PTP1B PS . 
         FIG.  1 A  illustrates one embodiment of a design of PTP1B PS : Light-induced unwinding of the A′α helix of LOV2 destabilizes the α7 helix of PTP1B and, thus, inhibits catalysis.  FIG.  1 B  illustrates one embodiment of Elaboration: In the competitively inhibited structure of PTP1B (orange), the α7 helix is stable, and the WPD loop (black) adopts a closed, catalytically competent conformation. In the apo structure (yellow), the α7 helix is disordered, and the WPD loop (blue) adopts an open, inactive conformation. We attached the C-terminal α7 helix of PTP1B (SEQ ID NO: 1) to the N-terminal A′α (SEQ ID NO: 2) helix of LOV2 at homologous crossover points (1-7) to create a chimera for which the photoresponsive of LOV2 destabilizes the α7 helix.  FIG.  1 C  shows exemplary results of optimization of one embodiment: Construct 7 exhibited the largest dynamic range of the crossover variants; 7.1 had an improved activity over 7, while 7.1(T406A) had an improved dynamic range over 7.1.  FIG.  1 D  shows an exemplary analysis of the activity of PTP1B PS  on pNPP indicates that light affects k cat , but not K m .  FIG.  1 E  shows the dynamic range of PTP1B PS  is similar for substrates of different sizes.  FIG.  1 F  shows exemplary illustrations of two small molecules: p-nitrophenyl-phosphate (or pNPP), and 4-methylumbelliferyl phosphate (or 4MU) and a peptide domain from EGFR.  FIG.  1 G  shows exemplary activity of PTP1B-LOV2 chimeras that differ in (A-D) crossover location and (E-E4) linker composition in the presence and absence of 455 nm light. Substrate: 4-methylumbelliferyl phosphate. 
         FIG.  2 A-J  shows exemplary biophysical characterizations of PTP1B PS . 
         FIG.  2 A  shows exemplary mutations that (i) prevent the formation of the cysteine adduct in LOV2 (C450M), (ii) destabilize the A′α and Jα helices if LOV2 (I532E, I539E, and ΔJα), or (iii) disrupt the allosteric network of PTP1B (Y152A/Y153A) reduced the photosensitivity of 7.1 and, with the exception of I532E and C450M, lowered its specific activity.  FIG.  2 B  shows exemplary exposure of PTP1B PS  to 455 nm light reduces its α-helical content (CD 222 nm ).  FIG.  2 C  shows exemplary optical modulation of α-helical content (i.e., δ 222 =CD 222-dark −CD 222-light ) is necessary, but not sufficient for optical modulation of catalytic activity. The dashed line denotes δ 222  for an equimolar solution of PTP1B WT  and LOV2 WT .  FIG.  2 D  shows exemplary fluorescence of six tryptophan residues in the catalytic domain of PTP1B which enables optical monitoring of its conformational state.  FIG.  2 E-F  shows exemplary thermal recovery of ( FIG.  2 E ) α-helical content and ( FIG.  2 F ) tryptophan fluorescence of PTP1B PS .  FIG.  2 G  shows exemplary kinetic constants for thermal resetting are larger for α-helical content than for tryptophan fluorescence, suggesting that LOV2 resets more quickly than the PTP1B domain. This discrepancy is smallest for the most photosensitive variant: 7.1(T406A).  FIG.  2 H  shows exemplary alignments of the crystal structures of PTP1B PS  (blue) and apo PTP1B WT  (orange) indicate that LOV2 does not distort the structure of the catalytic domain. The LOV2 domain of PTP1B PS  could not be resolved; a flexible loop at the beginning of the α7 helix likely causes LOV2 to adopt variable orientations in the crystal lattice. The α6 and α7 helices of an inhibited structure of PTP1B (yellow) are shown for reference.  FIG.  2 I  shows an exemplary gap in the crystal structure of PTP1B PS  that can accommodate LOV2.  FIG.  2 J  shows where exemplary crystals of a PTP1B-LOV2 fusion are green and turn clear when illuminated with 455 nm light; LOV2 is, thus, unequivocally present Error bars for A, C, and G denote standard error (n&gt;3). Note: PTP1B PS  corresponds to construct 7.1(T406A) from  FIG.  1   . 
         FIG.  3 A-D  demonstrates exemplary Fluorescence-based Biosensors having PTP1B activity. 
         FIG.  3 A  shows one embodiment of a sensor for PTP1B activity. This sensor consists of a kinase substrate domain, a short flexible linker, and a phosphorylation recognition domain, sandwiched between two fluorescent proteins (e.g., a cyan fluorescent protein and a yellow fluorescent protein). When the sensor is in its unphosphorylated state, Förster resonance energy transfer (FRET) between the two fluorophores causes a decrease in CFP fluorescence and an increase in YFP fluorescence; when the sensor is in its phosphorylated state, the absence of FRET causes the opposite effect.  FIG.  3 B  shows an exemplary increase in the ratio of donor fluorescence (CFP) to acceptor fluorescence (YPet) evidences the presence of Src kinase (i.e., a tyrosine kinase). When either (i) EDTA, which chelates a metal cofactor of Src, or (ii) PTP1B, which dephosphorylates the substrate domain, are additionally added, this increase does not occur.  FIG.  3 C  shows one embodiment as another variety of the FRET sensor for A; this one uses mClover3 and mRuby3. The excitation and emission wavelengths of these proteins make them compatible with LOV2-based imaging experiments.  FIG.  3 D  shows an exemplary repeat of the experiment from B with the sensor from C. 
         FIG.  4 A-H  demonstrates exemplary Evidence of phosphatase activity within living cells using photoconstructs and fluorescent tags. 
         FIG.  4 A-C  shows embodiments of three constructs are expressed in Cos-7 cells: ( FIG.  4 A ) GFP-PTP1B PS , ( FIG.  4 B ) GFP-PTP1B PS -A, and ( FIG.  4 C ) GFP-PTP1B PS -B. Here, GFP-PTP1B PS  is a fusion of green fluorescent protein (GFP) and the N-terminus of 7.1(T406A) from  FIG.  1 B-C  (without the histidine tag); GFP-PTP1B PS -A is a fusion of GFP-PTP1B PS  and the C-terminal domain of full-length PTP1B; and GFP-PTP1B PS -B is fusion of GFP-PTP1B PS  and the C-terminal endoplasmic reticulum (ER) anchor of full-length PTP1B (see below). GFP-PTP1B PS  localizes to the cytosol and nucleus, while GFP-PTP1B PS -A and GFP-PTP1B PS -B localize to the ER.  FIG.  4 D-H  shows exemplary results of cell-based studies of PTP1B PS . We transformed Cos-7 cells with a plasmid containing (i) the FRET sensor from  FIGS.  3 C- 3 D  and (ii) PTP1B PS  or PTP1B PS /C450M (a light-insensitive mutant). In this experiment, we illuminated individual cells with 447 nm light and immediately imaged them with 561 nm light. Light-modulated changes in FRET ratio (as defined in  FIG.  3   ) allowed us to detect light-modulated changes in PTP1B activity.  FIG.  4 D-E  shows an exemplary Cos-7 cell transformed with PTP1B PS  at two time points: ( FIG.  4 D ) immediately after excitation with 447 nm light and ( FIG.  4 E ) after 1 min. A slight increase in FRET ratio (dark green to lighter green) evidences photoactivation of PTP1B. (F-G). A Cos-7 cell transformed with PTP1B PS  (C450M) at two time points: ( FIG.  4 F ) immediately after excitation with 447 nm light and (G) after 1 min. The absence of a detectable change in FRET-ratio indicates that the change observed in D-E results from light-induced changes in PTP1B activity.  FIG.  4 H  shows an exemplary average fractional change in FRET ratio observed in the nucleus (nuc) and cytosol (cyt) after 1 min and 2.67 min. The change is higher for PTP1B PS  than for PTP1B PS (C450M), the light-insensitive mutant. Error bars indicate standard error. 
         FIG.  5 A-C  illustrates embodiments of drug discovery. 
         FIG.  5 A  shows an exemplary use of a phosphatase, i.e. drug target (upper left depiction of PTP1B) for identifying a synthetic enzyme (lower right depiction) where the enzyme is then used for providing an inhibitor or modulatory molecule for the phosphatase, thus showing a general framework for using enzymes to build inhibitors of chosen protein targets.  FIG.  5 B  shows an exemplary analysis of structural relationships between binding pockets. A matrix compares individual properties (e.g., volume) between binding pocket 1 and all other binding pockets (2 to n) capable of functionalizing (e.g., P450) or binding to (e.g., PTP1B) ligands synthesized within pocket 1.  FIG.  5 C  shows an exemplary comparison of the ability of binding pockets in a biosynthetic pathway to bind to intermediates. 
         FIG.  6    illustrates PTP1B showing an overlay of allosterically inhibited (green) and competitively inhibited (orange) structures of PTP1B (PDB entries 1t4j and 2f71, respectively) show activity-modulating conformational changes: Unwinding of the α7 helix of LOV2 (blue) causes its catalytically essential WPD loop (right) to adopt an open, catalytically compromised conformation. Competitive (red) and allosteric (yellow) inhibitors highlight the active site and allosteric site, respectively. 
         FIG.  7 A-B  shows and exemplary analysis of binding affinity.  FIG.  7 A  shows embodiments of two binding partners of PTP1B: LMO4 and Stat3.  FIG.  7 B  shows an exemplary binding isotherm based on binding-induced changes in the tryptophan fluorescence of PTP1B (the ligand isTCS 401, a competitive inhibitor). 
         FIG.  8 A-B  illustrates exemplary structural alignment of PTP1B (light blue) and STEP (orange),  FIG.  8 A , which have only 31% sequence identity, shows remarkable structural similarity.  FIG.  8 B  illustrates an exemplary structure of PTK6. Both STEP and PTK6 possess a C-terminal alpha-helix that is compatible with actuation by the N-terminal helix of LOV2 (i.e., an photomodulatory architecture similar to that depicted in  FIG.  1   ). 
         FIG.  9 A-B  illustrates an exemplary framework for building an enzyme modulated by red light We will attach the C-terminal α-helix of PTP1B to the N-terminal α-helix of BphP1. 
         FIG.  10 A-B  illustrates an exemplary operon for screening photoswitchable variants of PTP1B.  FIG.  10 A  shows an exemplary illustration where in its active state (here the far-red state), PTP1B dephosphorylates the substrate domain, prevents substrate-SH2 association, and, thus, prevents transcription.  FIG.  10 B  shows an exemplary illustration where in its inactive state (here, the red state), the phosphorylated substrate domain binds SH2, permitting transcription of a gene for antibiotic resistance. 
         FIG.  11 A-B  illustrates an exemplary strategy for evolution of photoswitchable proteins.  FIG.  11 A  illustrates where we will compare the growth of colonies on replicate plates exposed to red and infrared light and select colonies that exhibit differential growth.  FIG.  11 B  illustrates where we will further characterize the photosensitivity of top hits in liquid culture. 
         FIG.  12 A-B  illustrates an exemplary FRET-based sensor developed for measuring intracellular phosphatase or kinase activity. Binding of the substrate and SH2 domain either ( FIG.  12 A ) enhance or ( FIG.  12 B ) reduce FRET, depending on architecture. 
         FIG.  13    shows a cartoon of imaging experiments. We will inactivate PTP1B PS within sub cellular regions (1-10 μm) containing different amounts of plasma membrane, ER, and cytosol, and we will use fluorescence lifetime imaging to examine the phosphorylation state of our FRET-based sensor (from  FIG.  12   ) throughout the cell. 
         FIG.  14 A-D  illustrates an exemplary starting point for lead drug design and discovery.  FIG.  14 A  illustrates Abietic acid.  FIG.  14 B  demonstrates inhibition of PTP1B by abietic acid at concentrations (dark to light) of 0-400 uM. Analysis of different fits suggests noncompetitive or mixed-type inhibition.  FIG.  14 C  illustrates Abietic acid (green) docked in the allosteric site of PTP1B. We have since shown that abietic acid binds to the active site of PTP1B. Inset highlights active site in black.  FIG.  14 D  shows an exemplary X-ray crystal structure of a known allosteric inhibitor (blue). 
         FIG.  15 A-D  illustrates an exemplary  FIG.  15 A  Pathway for the synthesis of terpenoids (mevalonate can be synthesized through pMevT or added to the media).  FIG.  15 B  shows exemplary Abietadiene titers generated by  E. Coli  DH5a transformed with the plasmids from A (with no P450).  FIG.  15 C-D  shows exemplary GC-MS analysis of products of  FIG.  15 C ) abietadiene-producing strain and  FIG.  15 D  abietic-acid-producing strain: (1) abietadiene, (2) levopimaradiene, and (3) abietic acid (ion counts in 10,000 for C and 1,000 for  FIG.  15 D ). Note:  E. coli  DH5a avoids protein overexpression is commonly used in metabolic engineering* 4 . 
         FIG.  16 A-B  illustrates exemplary terpenoids showing differences in stereochemistry, shape, size, and chemical functionality.  FIG.  16 A  illustrates clockwise from abietic acid (1), neoabietic acid (2), levopimaric acid (3), dihydroabietic acid (4).  FIG.  16 B  shows exemplary initial rates in PTP1B on 10 mM of p-NP phosphate in the presence of 200 uM inhibitor. No inhibitor. Error bars=standard error (n&gt;5). 
         FIG.  17 A-C  shows results from exemplary studies.  FIG.  17 A  N-HSQC spectra of PTP1B (red) and PTP1B bound to abietic acid (blue). Inset: Crystal structure of PTP1B.  FIG.  17 B-C  shows exemplary Tryptophan (W) fluorescence of PTP1B in the presence of  FIG.  17 B  culture extract of control (ABS X ), abietadiene-producing (ABS), and abietic-acid producing (ABS/BM3) strains and ( FIG.  17 C ) various concentrations of abietic acid and 25 uM of known allosteric inhibitor (BBR). Error bars represent standard error (n&gt;5). 
         FIG.  18 A-B  illustrates exemplary terpenoids that differ in  FIG.  18 A  stereochemistry and  FIG.  18 B  shape. Inset: residues targeted for mutagenesis in class I site of ABS. 
         FIG.  19 A-E  illustrates exemplary terpenoids  FIG.  19 A  carboxylated,  FIG.  19 B  hydroxylated,  FIG.  19 C  and halogenated diterpenoids.  FIG.  19 D-E  shows exemplary residues targeted for mutagenesis in  FIG.  19 D  P450 BM3 and  FIG.  19 E  SttH. 
         FIG.  20    illustrates an exemplary WaterMap analysis of UPPS. Colors of water molecules correspond to free energies, relative to bulk water. 
         FIG.  21 A-E  illustrates an exemplary high-throughput screens for PTP1B inhibitors. 
         FIG.  21 A  Growth-coupled (i.e., selection; strategy 1).  FIG.  21 B ) FRET sensor for PTP1B activity (strategy 2).  FIG.  21 C ) FRET sensor and  FIG.  21 D ) tryptophan fluorescence for changes in PTP1B conformation (strategies 3 and 4).  FIG.  21 E . Results for an operon similar to that shown in  FIG.  21 A , where Amp is replaced with Lux. Error bars=SD (n≥3). 
         FIG.  22 A-D  illustrates exemplary inhibition of PTP1B. Error bars in  FIG.  22 C  denote SE (n≥3 independent reactions). 
         FIG.  22 A  shows exemplary alignments of the backbone of PTP1B in competitively inhibited (yellow and orange, PDB entry 2F71) and allosterically inhibited (gray and black, PDB entry 1T4J) poses. The binding of substrates and competitive inhibitors to the active site causes the WPD loop to adopt a closed (orange) conformation that stabilizes the C-terminal alpha7 helix through an allosteric network; this helix is unresolvable in allosterically inhibited, noncompetitively inhibited, and uninhibited structures, which exhibit WPD-open conformations (black).  FIG.  22 B  shows an exemplary illustration of a chemical structure of abietic acid (AA).  FIG.  22 C  shows exemplary initial rates of PTP1B-catalyzed hydrolysis of pNPP in the presence of increasing concentrations of AA. Lines show a fit to a model for mixed inhibition.  FIG.  22 D  an exemplary illustration of this model, where the inhibitor (I) binds to the enzyme (E) and enzyme-substrate complex (ES) with different affinities. 
         FIG.  23 A-C  illustrates an exemplary NMR analysis of PTP1B-AA association. 
         FIG.  23 A  shows exemplary weighted differences in chemical shifts (Δδ) between 1H-15 N-HSQC spectra collected in the absence and presence of AA (PTP1B:AA of 10:1). The dashed red line delineates the threshold for values of Δδ larger than two standard deviations (σ) above the mean; gray bars mark residues for which chemical shifts broadened beyond recognition.  FIG.  23 B  illustrates an exemplary crystal structure of PTP1B (PDB entry 3A5J, gray) highlights the locations of assigned residues (blue); inhibitors in the allosteric site (PDB entry 1T4J, green) and active site (PDB entry 3EB1, yellow) are overlaid for reference. Residues with significant CSPs (i.e., Δδ&gt;Δδ mean+2σ) are distributed across the protein (red) and, with the exception of two residues in the WPD loop, outside of known binding sites.  FIG.  23 C  illustrates an exemplary detail of the active site (upper panel) and known allosteric site (lower panel) with inhibitors from ( FIG.  23 B ) overlaid. 
         FIG.  24 A-C  illustrates an exemplary mutational analysis of the AA binding site. 
         FIG.  24 A  illustrates an exemplary crystal structure of PTP1B (gray, PDB entry 3A5J) shows the location of mutations introduced at five sites: the active site (red), the allosteric site (green), site 1 (orange), site 2 (yellow), and the L11 loop (blue). The bound configurations of BBR (allosteric site, PDB entry 1 T4J) and TCS401 (active site, PDB entry 1C83) are overlaid for reference.  FIG.  24 B  illustrates exemplary disruptive mutations introduced at each site. Mutations were designed to alter the size and/or polarity of targeted residues. The mutation denoted “YAYA” (Y152A/Y153A), which was identified in a previous study, attenuates allosteric communication between the C-terminus and the WPD loop.  FIG.  24 C  illustrates exemplary fractional change in inhibition (F in Eq. 1) caused by the mutations from (B). Five mutations distributed across the protein reduced inhibition by AA and TCS401, but had negligible effect on inhibition by BBR. The similar effects of most mutations on AA and TCS401 suggest that both inhibitors bind to the active site. Error bars denote SE (propagated from n≥9 independent measurements of each V in Eq. 1). 
         FIG.  25 A-D  illustrates exemplary computational analysis of AA binding. 
         FIG.  25 A-B  illustrates exemplary results of molecular dynamics simulations: backbone traces of PTP1B in (A) AA-free and  FIG.  25 B  illustrates exemplary amino acid (AA)-bound states. The thickness of traces indicates the amplitude and direction of local motions (Methods). The binding of AA increases the flexibility of the WPD, E, and L10 loops. The WPD and L10 loops contain residues with significant CSPs (red), suggesting consistency between the results of MD and NMR analyses.  FIG.  25 C  illustrates an exemplary representative bound conformation if AA (green). Upon binding to the active site, AA (i) forms a hydrogen bond with R221 that weakens a bond between R221 and E115 and (ii) prevents the formation of a hydrogen bond (red) between W179 and R221 that forms when the WPD loop closes. Both effects enhance the conformational dynamics of the WPD loop.  FIG.  25 D  shows exemplary results of docking calculations are consistent with mixed-type inhibition: the binding of AA prevents the WPD loop from closing and disrupts, but does not preclude, the binding of pNPP (blue spheres). 
         FIG.  26 A-C  illustrates exemplary terpenoids showing differences in stereochemistry, shape, size, and chemical functionality.  FIG.  26 A ) Structural analogues of abietic acid (AA): continentalic acid (CA), isopimaric acid (IA), dehydroabietic acid (DeAA), and dihydroabietic acid (DiAA).  FIG.  26 B ) Differences in degree of saturation yield pronounced differences in potency (i.e., IC 50), but not selectivity. Error bars represent 95% confidence intervals.  FIG.  26 C  shows binding of three of the analogues depicted in  FIG.  26 A . 
         FIG.  27 A-C  Analysis of pathologically relevant mutations. 
         FIG.  27 A  illustrates an exemplary Histogram of kinetically characterized mutations. All mutations proximal (&lt;4 A) to five or more network residues were “influential” (i.e., they altered k cat  or K M  by &gt;50% or had a detectable influence on inhibition); non-consequential mutations, by contrast, had fewer neighboring network residues.  FIG.  27 B  illustrates an exemplary crystal structure of PTP IB (gray, PDB entry 3A5J) highlights the locations of influential mutations on network residues; colors indicate whether they were introduced in biophysical studies or found in diseases.  FIG.  27 C  illustrates an exemplary two cumulative distribution functions describe numbers of network residues proximal to (i) mutations identified in diseases and (ii) a random selection of sites. The two distributions are indistinguishable from one another (P&lt;0.05), suggesting that disease-associated mutations do not occur preferentially near the allosteric network. 
         FIG.  28 A-D  illustrates and shows exemplary data using a Genetic operon linking PTP activity to the output of a gene of interest (GOI). 
         FIG.  28 A  shows embodiments of Operon A. An example of the operon. S, tyrosine substrate; P, phosphate group; cI, the 434 phage cI repressor; RpoZ and RP ω , the omega subunit of RNA polymerase; cI OP, the binding sequence for the 434 phage cI repressor; and RB, the binding site for RNA polymerase (RNAP). Phosphorylation of the tyrosine substrate (by c-Src kinase) causes binding of the substrate-RP ω , fusion to the SH2-cI fusion; this binding event, in turn, localizes the RNA polymerase to RB, triggering transcription of the GOI. PTP1B dephosphorylates the substrate domain, preventing the association of substrate-RP ω  fusion and the SH2-cI, thereby, halting transcription of the GOI. Inactivation of PTP1B, in turn, re-enables transcription of the GOI.  FIG.  28 B  illustrates one embodiment of a proposed medium-throughput screen for membrane-permeable inhibitors: A strain of the  E. coli  is transformed with the operon and grown in the presence of small molecules; small-molecule inhibitors of PTP1B modulate transcription of the GOI (e.g., a gene for luminescence, fluorescence, or antibiotic resistance) in a dose-dependent manner. The bar graph shows a predicted trend in data.  FIG.  28 C  shows embodiments of Operon B. An operon that enables screens for selective inhibitors. This operon comprises operon A with (i) a second substrate-protein fusion (red), a “decoy”, that can bind to the SH2-cI fusion but not specifically to DNA or RNA polymerase, and (ii) a second PTP (e.g., TC-PTP) that is active on the substrate domain of the decoy. Because complexes between the decoy and SH2-cI do not trigger transcription, the decoy inhibits transcription by competing with cI-substrate for binding sites. Accordingly, molecules that inhibit PTP1B, but not TC-PTP (which dephosphorylates the decoy)—that is, selective inhibitors—cause the greatest transcriptional activation. Molecules that inhibit both enzymes, by contrast, cause less activation.  FIG.  28 D  shows embodiments of Operon C. This operon enables screens for photoswitchable enzymes. This operon comprises a version of operon A in which PTP1B has been replaced with a photoswitchable version of PTP1B. In this case, transcription of the GOI is different (e.g., higher or lower) under different sources of light. In the example shown, light inhibits the activity of a PTP1B-LOV2 chimera and, thus, enhances transcription of the GOI. 
         FIG.  29 A-B  shows exemplary Preliminary results showing phosphorylation-dependent expression of a GOI.  FIG.  29 A  shows one embodiment of Operon A in which the GOI is a bacterial luciferase (LuxAB). PTP1B inhibits luminescence (i.e., reduces transcription of the GOI), while a catalytically inactive version of PTP1B (a mimic for an inhibited version of PTP1B) enhances luminescence.  FIG.  29 B  shows one embodiment of Operon A in which the GOI is a gene for spectinomycin resistance (SpecR). PTP1B inhibits growth on spectinomycin, while a catalytically inactive version of PTP1B (a mimic for an inhibited version of PTP1B) enhances growth. The MidT substrate is used herein. 
         FIG.  30 A-B  illustrates Optimization of operon. 
         FIG.  30 A  shows one embodiment of operon from A in which the GOI is a bacterial luciferase (LuxAB), the PTP1B is missing, and the substrate is a peptide from Kras, midT, ShcA, or EGFR. Although all substrates can be phosphorylated by Src kinase, only two substrates bind to the SH2 domain tightly enough to enable significant luminescence over background (0% arabinose).  FIG.  30 B  shows one embodiment of operon from A (here, contained on a single plasmid) in which the GOI is a bacterial luciferase (LuxAB) and PTP1B is missing. The Y/F mutation on the substrate domain (blue) prevents it from being phosphorylated. The RBS sites toggle expression of the Src kinase. 
         FIG.  31 A-D  illustrates Applications of operons. 
         FIG.  31 A  illustrates an exemplary conceptualization of a screen for microbially synthesizable inhibitors of PTP1B. When transformed with one embodiment of Operon A (or operon B), a cell capable of synthesizing PTP1B-inhibiting metabolites will produce a different GOI output than a cell that does not produce such metabolites. Because abietane-type diterpenoids can both (i) inhibit PTP1B and (ii) be synthesized in  E. coli , we believe that a strain of  E. coli  that contains both Operon A and a pathway for building abietane-type diterpenoids could be “evolved” to build inhibitors of PTP1B. Here, the GOI could be a gene for luminescence or fluorescence (low throughput) or antibiotic resistance (high throughput).  FIG.  31 B  illustrates an exemplary conceptualization of a screen for photoswitchable enzymes. Consider a fusion of PTP1B to LOV2 or BphP1 (here, the highlighted helices show N-terminal connection points on these two proteins). For this example, illumination of the PTP1B-LOV2 with 455 nm light reduces its activity; illumination of the PTP1B-BphP1 fusion with 650 nm light reduces its activity, while illumination of the PTP1B-BphP1 fusion with 750 nm light enhances its activity. When transformed with operon C (which would contain one of these fusions), a cell will produce a different GOI output under different illumination conditions.  FIG.  31 C  illustrates an exemplary conceptualization of a screen for selective mutants of enzymes. When transformed with a version of operon B where (i) PTP1B is also active on the decoy and (ii) the second PTP (TC-PTP in our example) is missing a cell containing a mutant of PTP1B will most effectively transcribe the GOI when PTP1B is only active on the decoy substrate.  FIG.  31 D  illustrates an exemplary conceptualization of a screen for selective substrates. When transformed with a version of operon B where (i) the decoy is missing, (ii) the first enzyme (PTP1B in our example) is under an inducible promoter, (iii) a second PTP (TC-PTP in our example) is under a second inducible promoter, and (iv) the GOI includes a gene for antibiotic resistance and a gene that produces a toxic product in the presence of a non-essential substrate, a cell containing a mutated substrate domain will grow under both condition 1 (inducer of PTP1B and non-essential substrate) and condition 2 (inducer of TC-PTP), when it binds to PTP1B, but not to TC-PTP. 
         FIG.  32 A-B  presents exemplary evidence of an evolutionarily conserved allosteric network.  FIG.  32 A  refers to an exemplary results of a statistical coupling analysis. The orange and blue clusters represent two groups of interconnected residues, termed “sectors”, that exhibit strong intragroup correlations in nonrandom distributions of amino acids. The allosteric site (green inhibitor, PDB entry 1T4J), WPD loop (purple spheres), and active site (red inhibitor, 3EB1) are highlighted for reference.  FIG.  32 B  refers to an exemplary analysis of crosstalk between pockets of PTP1B modeled with MD simulations. Pockets are represented as spheres, colored according to their persistency along the MD trajectory; the size of each sphere indicates its average volume in MD simulations. Links have thicknesses proportional to the frequency of inter-pocket merging and splitting events (i.e., communication). Two independent sets of interconnected pockets map closely to the sectors identified in SCA and, thus, suggest that these two sectors represent distinct domains of an evolutionarily conserved allosteric network. In the PTP1B-LOV2 fusions of  FIG.  1   , LOV2 modulates the activity of PTP1B by tapping into the allosteric network defined by sector A. Identification of sector A with a statistical coupling analysis of the PTP family thus indicates that the architecture for photocontrol described in  FIG.  1    is broadly applicable to all protein tyrosine phosphatases. 
         FIG.  33 A-E  illustrates an embodiment of a genetically encoded system that links the activity of an enzyme to the expression of a gene of interest (GOI). Error bars in  FIG.  33 B-E  denote standard deviation with n=3 biological replicates. 
         FIG.  33 A  illustrates an embodiment of a bacterial two-hybrid system that detects phosphorylation-dependent protein-protein interactions. Components include (i) a substrate domain fused to the omega subunit of RNA polymerase (yellow), (ii) an SH2 domain fused to the 434 phage cI repressor (light blue), (iii) an operator for 434cI (dark green), (iv) a binding site for RNA polymerase (purple), (v) Src kinase, and (vi) PTP1B. Src-catalyzed phosphorylation of the substrate domain enables a substrate-SH2 interaction that activates transcription of a gene of interest (GOI, black). PTP1B-catalyzed dephosphorylation of the substrate domain prevents that interaction; inhibition of PTP1B re-enables it.  FIG.  33 B  refers to an embodiment of the two-hybrid system from  FIG.  33 A  that (i) lacks PTP1B and (ii) contains luxAB as the GOI. We used an inducible plasmid to increase expression of specific components; overexpression of Src enhanced luminescence.  FIG.  33 C  refers to an embodiment of the two-hybrid system from  FIG.  33 A  that (i) lacks both PTP1B and Src and (ii) includes a “superbinder” SH2 domain (SH2*, i.e., an SH2 domain with mutations that enhance its affinity for phosphopeptides), a variable substrate domain, and LuxAB as the GOI. We used an inducible plasmid to increase expression of Src; luminescence increased most prominently for p130cas and MidT, suggesting that Src acts on both substrate domains.  FIG.  33 D  refers to an embodiment of a two-hybrid system from  FIG.  33 C  with one of two substrates: p130cas or MidT. We used a second plasmid to overexpress either (i) Src and PTP1B or (ii) Src and an inactive variant of PTP1B (C215S). The difference in luminescence between systems containing PTP1B or PTP1B (C215S) was greatest for MidT, suggesting that PTP1B acts on this substrate. Right: An optimized version of the two-hybrid system (with bb030 as the RBS for PTP1B) appears for reference.  FIG.  33 E  displays the results of an exemplary growth-coupled assay performed using an optimized B2H including SH2*, a midT substrate, optimized promoters and ribosome binding sites (bb034 for PTP1B), and SpecR as the GOI. This system is illustrated at the top of the figure. Exemplary growth results demonstrate that inactivation of PTP1B enables strain of  E. coli  harboring this system to survive at high concentrations of spectinomycin (&gt;250 μg/ml). 
         FIG.  34    illustrates exemplary experiments used to optimized the B2H system depicted in  FIG.  33   . 
         FIG.  35    illustrates exemplary experiments used to optimize the B2H system depicted in  FIG.  33    for growth-coupled assays. 
         FIG.  36 A-C  depicts an exemplary metabolic pathway for the biosynthesis of terpenoids. 
         FIG.  36 A  depicts a plasmid-borne pathway for terpenoid biosynthesis: (i) pMBIS, which harbors the mevalonate-dependent isoprenoid pathway of  S. cerevisiae , converts mevalonate to isopentyl pyrophosphate (IPP) and farnesyl pyrophosphate (FPP). (ii) pTS, which encodes a terpene synthase (TS) and, when necessary, a geranylgeranyl diphosphate synthase (GPPS), converts IPP and FPP to sesquiterpenes and/or diterpenes. 
         FIG.  36 B  depicts exemplary terpene synthases: amorphadiene synthase (ADS) from  Artemisia annua , γ-humulene synthase (GHS) from  Abies grandis , abietadiene synthase (ABS) from  Abies grandis , and taxadiene synthase (TXS) from  Taxus brevifolia.    
         FIG.  36 C  shows the results of an exemplary growth-coupled assay of strain of  E. coli  that contains both (i) an embodiment of the optimized bacterial two-hybrid (B2H) system (i.e., the B2H system from  FIG.  33 E ) and (ii) an embodiment of a pathway for terpenoid biosynthesis (i.e., the pathway from  FIG.  35 A ). 
         FIG.  37 A-C  provides an exemplary analysis of the inhibitory effects of terpenoids generated by different strains of  E. coli.    
         FIG.  37 A  depicts the results of our analysis of the inhibitory effect of DMSO containing (i) no inhibitor and (ii) extracted compounds from the culture broth of the ADS-containing strain.  FIG.  37 B  depicts the results of our analysis of the inhibitory effect of DMSO containing (i) extracted compounds from the culture broth of the GHS-containing strain (gHUM) or (ii) extracted compounds from the culture broth of the strain including the L450Y mutant of GHS.  FIG.  37 C  depicts the results of our analysis of the inhibitory effect of DMSO containing (i) no inhibitor, (ii) extracted compounds from the culture broth of the ABS-containing strain, (iii) extracted compounds from the culture broth of the TXS-containing strain, and (iv) extracted compounds from the culture broth of the train strain containing a catalytically inactive variant of ABS. 
         FIG.  38    shows exemplary analysis of the product profiles of mutants of GHS that enabled growth in the presence of spectinomcyin. 
         FIG.  39    shows an analysis of an exemplary B2H systems that link the inhibition of other PTPs to cell survival. 
         FIG.  40 A-E  depicts exemplary embodiments of genetically encoded systems that link the activity of an enzyme to the expression of a gene of interest, and the application of those embodiments to (i) the prediction of resistance mutations, (ii) the construction of inhibitors that combat resistance mutations, and (ii) the evolution of inhibitors of kinases. 
         FIG.  40 A  depicts an exemplary first step in examining potential resistance mutations. By evolving a metabolic pathway to produce molecules that inhibit a known drug target (e.g., PTP1B); these molecules will permit expression of a gene of interest (GOI) that confers survival in the presence of a selection pressure (e.g., the presence of spectinomycin, an antibiotic).  FIG.  40 B  depicts an exemplary second step in examining potential resistance mutations. In a second strain of  E. coli , we will replace the original gene of interest with a second (GOI2) that confers conditional toxicity (e.g., SacB, which converts sucrose to levan, a toxic product); we will evolve the drug target to become resistant to the endogenous inhibitors, while still retaining its activity. This mutant will prevent expression of the toxic gene.  FIG.  40 C  depicts an exemplary third step in combating resistance mutations. In a third strain of  E. coli , we will evolve a metabolic pathway that produces molecules that inhibit the mutated drug target. In this way, we will both predict—and, through our second evolved pathway, address—mutations that might cause resistance to terpenoid-based drugs.  FIG.  40 D  depicts an exemplary genetically encoded system that detects inhibitors of an Src kinase. In brief, Src activity enables expression of a toxic gene (GOI2); inhibition of Src, in turn, would confer survival.  FIG.  40 E  demonstrates one embodiment of a roof of principle for the B2H system describe in  FIG.  40 B . The system shown here includes two GOIs: SpecR and SacB. Expression of the GOIs confers survival in the presence of spectinomycin; expression of the GOIs causes toxicity in the presence of sucrose. The images depict the results of a growth-coupled assay performed on a strain of  E. coli  in the presence of various concentrations of sucrose. The strain harboring an active form of PTP1B (WT) grows better at high sucrose concentrations that the strain harboring an inactive form of PTP1B (C215 S). 
         FIG.  41 A  depicts an exemplary strategy for the evolution of inhibitors of PTP1B. 
         FIG.  41 A  depicts an exemplary structural analysis used to identify targets for mutagenesis in the active sites of terpene synthases. It shows an alignment of the class I active site of ABS (gray, PDB entry 3s9v) and TXS (blue, PDB entry 3p5r) with the locations of sites targeted for site-saturation mutagenesis (SSM) highlighted on ABS (red). A substrate analogue (yellow) of TXS appears for reference.  FIG.  41 B  depicts an exemplary strategy for introducing diversity into libraries of metabolic pathways: An iterative combination of SSM of key sites on a terpene synthase (as in a), error-prone PCR (ePCR) of the entire terpene synthase gene, SSM of sites on a terpene-functionalizing enzyme (e.g., P450), and ePCR of the entire terpene-functionalizing enzyme.  FIG.  41 C  depicts an exemplary quantification the total terpenoids present in DMSO samples with extracts of various TS-containing strains. In brief, we performed site-saturation mutagenesis of six sites on ADS (analogous to the sites shown in  FIG.  41 A ); we plated the SSM library on agar plates containing different concentrations of spectinomycin; we picked colonies that grew on a plate containing a high concentration (800 μg/ml) of spectinomycin and used each colony to inoculate a separate culture; we used a hexane overlay to extract the terpenoids secreted into each culture broth; we dried the hexane extract in a rotary evaporator and re-suspended the solid in DMSO; and we used a GC-MS to quantify the total amount of terpenoids present in the DMSO.  FIG.  41 D  depicts an exemplary analysis of the inhibitory effect of various extracts on PTP1B. In brief, the figure shows initial rates of PTP1B-catalyzed hydrolysis of p-nitrophenyl phosphate (pNPP) in the presence of terpenoids quantified in  FIG.  41 C . Two mutants of ADS (G439A and G400L) generate particularly potent inhibitors of PTP1B. 
         FIG.  42    depicts an exemplary analysis of the link between B2H activation and cell survival. An exemplary strain of  E. coli  that contains both (i) the optimized bacterial two-hybrid (B2H) system ( FIG.  33 E ) and (ii) the terpenoid pathway depicted in  FIG.  36 A . Note: pTS includes GGPPS only when ABS or TXS are present; the “Y/F” operon corresponds to a B2H system in which the substrate domain cannot be phosphorylated. Survival at high concentrations of spectinomycin requires activation of the B2H system (i.e., phosphorylation of the substrate domain, a process facilitated by inhibition of PTP1B). 
         FIG.  43    provides exemplary product profiles of strains of  E. coli  harboring various terpene synthases. For this figure, the strain of  E. coli  harbored (i) the optimized B2H system ( FIG.  33 E ) and (ii) the terpenoid pathway ( FIG.  36 A ). The pathways corresponding to each profile differ only in the composition of the pTS plasmid, which contains TXS (taxadiene synthase from  Taxus brevifolia  and a geranylgeranyl diphosphate synthase from  Taxus Canadensis ); GHS (γ-humulene synthase from  Abies grandis ); ADS (amorphadiene synthase from  Artemisia annua ); ABS (abietadiene synthase from  Abies grandis  and a geranylgeranyl diphosphate synthase from  Taxus Canadensis ); G400A (the G400A mutant of amorphadiene synthase from  Artemisia annua ); and G439L (the G439L mutant of amorphadiene synthase from  Artemisia annua ). Note that the two mutants of ADS yield different product profiles than the wild-type enzyme (ADS); our results indicate that products generated by these two mutants are more inhibitory than those generated by the wild-type enzyme ( FIG.  41 E ). 
         FIG.  44 A-D  provides exemplary structural and sequence-based evidence that supports the extension the B2H system to other protein tyrosine phosphatases (PTPs). 
         FIG.  44 A  provides an exemplary structural alignment PTP1B and PTPN6, two PTPs that are compatible with the B2H system (see  FIGS.  1   e    and  7  of Update A for evidence of compatibility). We used the align function of PyMol to align each structure of PTPN6 with either (i) the ligand-free (3A5J) or (ii) ligand-bound (2F71) structure of the catalytic domain of PTP1B. The align function carries out a sequence alignment followed by a structural superposition and, thus, effectively aligns the catalytic domains of both proteins.  FIG.  44 B  provides an exemplary structural comparison of PTP1B and PTPN6; the root-mean-square deviations (RMSD) of aligned structures of PTP1B and PTPN6 range from 0.75 to 0.94 Å.  FIG.  44 C  proves an exemplary sequence alignment of the catalytic domains of PTP1B (SEQ ID NO: 3) and PTPN6 (SEQ ID NO: 4) (EMBOSS Needle 1 ).  FIG.  44 D  provides an exemplary sequence comparison of the catalytic domains of PTP1B and TPPN6. The sequences share 34.1% sequence identity and 53.5% sequence similarity. In summary, the results of this figure indicate that our B2H system can be readily extended to PTPs that possess catalytic domains that are (i) structurally similar to the catalytic domain of PTP1B (here, we define structural similarity as two structures that when aligned, have with an RMSD of ≤0.94 Å RMSD with the framework similar to the one used by the align function of PyMol) and/or (ii) sequence similar to the catalytic domain of PTP1B (here, we define sequence similarity as ≥34% sequence identity or ≥53.5% sequence similarity as defined by the EMBOSS Needle algorithm). 
     
    
    
     DEFINITIONS 
     As used herein, the use of the term “operon” may refer to a cluster of genes under the control of a single promoter (as in a classical definition of an operon) and may also refer to a genetically encoded system comprising multiple operons (e.g., the bacterial two-hybrid system). 
     As used herein, “phosphorylation-regulating enzymes” refer to proteins that regulate phosphorylation. 
     As used herein, “phosphorylation” refers to a biochemical process that involves the addition of phosphate to an organic compound. 
     As used herein, “optogenetic actuator” refers to a genetically encodable protein that undergoes light-induced changes in conformation. 
     As used herein, “dynamic range” refers to the ratio of activity in dark and light state (i.e., the initial rate in the dark/the initial rate in the presence of 455 nm light). 
     As used herein, “operon” refers to a unit made up of multiple genes that regulate other genes responsible for protein synthesis, 
     As used herein, “operably linked” refers to one or more genes (i.e. DNA sequences) suitably positioned and oriented in a DNA molecule for transcription to be initiated from the same promoter. DNA sequences that are operably linked to a promoter means that expression of the DNA sequence(s) is under transcriptional initiation regulation of the promoter. 
     As used herein, “construct” refers to an engineered molecule, e.g. ligated pieces of DNA as a DNA construct; a RNA construct as one contiguous sequence resulting from the expression of a DNA construct. 
     As used herein, “fusion” refers to an expressed product of an engineered construct i.e. a combination of several ligated sequences as one molecule or a single gene that encodes for a protein-protein fusion originally encoded by two genes. 
     As used herein, “expression vector” or “expression construct” refers to an operon, plasmid or virus designed for DNA expression of a construct in host cells, typically containing a promoter sequence operable within the host cell. 
     As used herein, “promoter” refers to a region of DNA that initiates transcription of a particular DNA sequence. Promoters are located near the transcription start sites of, towards the 5′ region of the sense strand. Promoters may be constitutive promoters, such as cytomegalovirus (CMV) promoters in mammalian cells, or inducible promoters, such as tetracycline-inducible promoters in mammalian cells. 
     As used herein, “transformation” refers to a foreign nucleic acid sequence or plasmid delivery into a prokaryotic host cell, for example, an expression plasmid (e.g. a plasmid expression construct) inserted into or taken up by a host cell. 
     As used herein, “transfection” refers to the insertion of a nucleic acid sequence into a eukaryotic cell. 
     Transformation and transfection may be transient, such that the nucleic acid sequence or plasmid introduced into the host cell is not permanently incorporated into the cellular genome. A stable transformation and transfection refers to a host cell retaining the foreign nucleic acid sequence or plasmid for multip generations regardless of whether the nucleic acid or plasmid was integrated into the genome of the host cell. 
     As used herein, “host” in reference to a cell refers to a cell intended for receiving a nucleic acid sequence or plasmid or already harboring a a nucleic acid sequence or plasmid, eg. a bacterium. 
     As used herein, “conjugate” refers to a covalently attachment of at least two compounds, for example, a photosensing element attached to a phosphatase protein. 
     As used herein, “decoy” in reference to a protein construct that cannot bind to DNA and/or RNA polymerase. 
     DETAILED DESCRIPTION OF INVENTION 
     This invention relates to the field of genetic engineering. Specifically, the invention relates to the construction of operons to produce biologically active agents. For example, operons may be constructed to produce agents that control the function of biochemical pathway proteins (e.g, protein phosphatases, kinases and/or proteases). Such agents may include inhibitors and modulators that may be used in studying or controlling phosphatase function associated with abnormalities in a phosphatase pathway or expression level. Fusion proteins, such as light activated protein phosphatases, may be genetically encoded and expressed as photoswitchable phosphatases. Systems are provided for use in controlling phosphatase function within living cells or in identifying small molecule inhibitors/activator/modulator molecules of protein phosphatases associated with cell signaling. 
     The invention also relates to the assembly of genetically encoded systems (e.g., one or more operons) for detecting and/or constructing biologically active agents. For example, systems may be assembled in order to accomplish one or more goals, e.g. (i) to detect and/or synthesize small molecules that affect the activity of regulatory enzymes (e.g., protein phosphatases, kinases, and/or proteases); (ii) to detect and/or evolve regulatory enzymes modulated by light (e.g., light-responsive protein phosphatases, kinases, or proteases), etc. Small molecule modulators may include inhibitors of phosphatases known to be associated with human diseases or implicated with causing or perpetuating human diseases; activators of phosphatases implicated or known to be associated in human diseases (e.g., diabetes, obesity, and cancer); such small molecules may serve as chemical probes in studies of cell signaling; as structural starting points (i.e., leads); etc., for the development of pharmaceutical compounds for use in treating a human disease. Light-sensitive enzymes may include protein tyrosine phosphatases fused to optogenetic actuators (e.g., a LOV domain if phototropin 1). Such fusions could serve as tools for exerting spatiotemporal control over protein tyrosine phosphorylation in living cells 
     Further, microbial operons are provided that are designed for use in identifying either small molecule inhibitors, activators, or modulator molecules, photoswitchable enzymes, or biological components, including intracellularly expressed molecules, including, for examples, operons having components for use in whole cell microbial screening assay systems. Inhibitors/modulator molecules discovered using compositions, systems and methods described herein are contemplated for use in treating diseases such as diabetes, type II diabetes, obesity, cancer, and Alzheimer&#39;s disease, among other disorders associated with protein phosphatase enzymes. 
     In one embodiment, the present invention relates to a Protein tyrosine phosphatase 1B (PTP1B). PTP1B represents a valuable starting point for this study for four reasons: (i) It is implicated in diabetes 5 , obesity 6 , cancer 30 , anxiety 31 , inflammation 32 , the immune response 7 , and neural specification in embryonic stem cells 33 , (ii) The mechanisms underlying its subcellular localization are well understood (a short C-terminal anchor connects it to the ER; proteolysis of this anchor releases it to the cytosol) 2934 . (iii) It can be expressed, purified, and assayed with ease 35 , (iv) It is a member of a class of structurally similar enzymes (PTPs) that could facilitate the rapid extension of architectures for making it photoswitchable. PTP1B represents both an experimentally tractable model system for testing strategies for optical control, and an enzyme for which optical modulation is contemplated to permit detailed analyses of a wide range of diseases and physiological processes. 
     Specifically related to exemplary Figures:  FIGS.  1 ,  2 ,  3 ,  4 ,  8 ,  9 ,  12 , and  13    describe optogenetic and imaging technologies (i.e., light-sensitive enzymes and genetically encodable biosensors) that could be evolved, improved, or optimized with the operon;  FIGS.  10  and  11    describe strategies for using the operon to evolve, improve, or optimize light-sensitive enzymes;  FIGS.  5 ,  6 ,  14 ,  15 ,  16 ,  17 ,  18 ,  19 ,  20 ,  28 ,  29 ,  30 , and  31    support both (i) the development of an operon for detecting and/or evolving small molecules that inhibit known drug targets and (ii) the subsequent characterization of those molecules;  FIGS.  22 ,  23 ,  24 ,  25 ,  26 ,  27 , and  32    provide examples of kinetic and biophysical characterizations of a microbially synthesizable molecule that inhibits PTP1B. 
     I. Protein Tyrosine Phosphatases (PTPs) and Protein Tyrosine Kinases (PTKs) in Relation to Disease. 
     Protein tyrosine phosphatases (PTPs) and protein tyrosine kinases (PTKs) are two classes of enzymes contributing to anomalous signaling events in a wide range of diseases (e.g., diabetes, cancer, atherosclerosis, and Alzheimer&#39;s disease, among others) and understanding disease progression 14,36 . Further, they are involved with regulating memory, fear, appetite, energy expenditure, and metabolism, thus use of such phosphorylation regulating enzymes may reveal links between seemingly disparate physiological processes 14,22,13 . 
     Embodiments for using light as photoswitchable constructs for controlling PTPs and PTKs is described herein. Accordingly, examples of photoswitchable constructs of PTPs and PTKs developed as described herein, should be broadly useful to biomedical researchers interested in understanding how healthy and diseased cells process chemical signals in addition to use for identifying specific alleles of PTPs and/or PTKs (i.e. gene sequences or proteins)—or other enzymes that they regulate—linked to specific diseases, such as diabetes, etc., including subtypes of diseases, i.e. early onset, late onset, etc., and specific types of cancer, and for screening and testing molecules, including small molecules, for treating diseases associated with these alleles. 
     Although other references describe photocontrol of proteins, including using LOV2 conjugates, these references do not mention using phosphatases. Fan, et al., “Optical Control Of Biological Processes By Light-Switchable Proteins.” Wiley Interdiscip Rev Dev Biol. 4(5): 545-554. 2015. This reference describes blue light-oxygen-voltage-sensing (LOV) domains including the LOV2 C-terminal α-helix, termed Jα, from  Avena sativa  phototropin. Linkage to the LOV domain can cage a protein of interest (POI), while light-induced conformational change in the LOV domain results in its uncaging. As one example, peptide kinase inhibitors can be caged by fusion to the C-terminus of LOV2. Exposure to light results in uncaging of the inhibitors for light modulating protein kinase activities in cells. WO2011133493. “Allosteric regulation of kinase activity.” Published Oct. 27, 2011. This reference describes fusion proteins comprising a kinase, including as examples, a tyrosine kinase (Src), a serine/threonine kinase (p38), and a ligand binding domain, e.g. a light-regulated LOV domain (where illumination is considered “ligand binding), inserted in the N-terminal and/or C-terminal end or near the catalytic domain to produce allosteric regulation using a light-dependent kinase. Further, a LOV domain includes a LOV2 domain and/or Jα domain from  A. sativa  phototropin I. WO2012111772 (A1) In Japanese with an English abstract. This reference abstract describes a polypeptide for the optical control of calcium signaling comprising an amino acid sequence including: a LOV2 domain composed of SEQ ID NO: 1 or an amino acid sequence having at least 80% sequence identity with SEQ ID NO: 1. The construct has a LOV2 domain followed by a LOV2-Jalpha optical switch at the N terminus of the construct. U.S. Pat. No. 8,859,232. “Genetically encoded photomanipulation of protein and peptide activity.” Issued Oct. 14, 2014. This reference describes fusion proteins comprising protein light switches and methods of photomanipulating the activity of the fusion proteins to study protein function and analyze subcellular activity, as well as diagnostic and therapeutic methods. More specifically, a fusion protein comprising a protein of interest fused to a protein light switch comprising a light, oxygen or voltage (LOV2) domain of  Avena sativa  (oat) phototropin 1, wherein illumination of the fusion protein activates or inactivates the protein of interest. The protein of interest is a functional domain of a human protein. As an example, a LOV2-Jα sequence of phototropin1 (404-547) was fused to the N-terminus of RacI so that the LOV domain in its closed conformation would reversibly block the binding of effectors to RacI. 
     A. Protein Tyrosine Phosphatases (PTPs). 
     Protein tyrosine phosphatases (PTPs) are a class of regulatory enzymes that exhibit aberrant activities in a wide range of diseases. A detailed mapping of allosteric communication in these enzymes could, thus, reveal the structural basis of physiologically relevant—and, perhaps, therapeutically informative—perturbations (i.e., mutations, post-translational modifications, or binding events) that influence their catalytic states. This study combines detailed biophysical studies of protein tyrosine phosphatase IB (PTP IB) with large-scale bioinformatic analyses to examine allosteric communication in PTPs. Results of X-ray crystallography, molecular dynamics simulations, and sequence-based statistical analyses indicate that PTP D3 possesses a broadly distributed allosteric network that is evolutionarily conserved across the PTP family, and findings from kinetic studies show that this network is functionally intact in sequence-diverse PTPs. The allosteric network resolved in this study reveals new sites for targeting allosteric inhibitors of PTPs and helps explain the functional influence of a diverse set of disease-associated mutations. 
     In one embodiment, a tyrosine phosphatase and photosensitive protein as described herein may be attached to a drug for use in medical treatments. In contrast to EP2116263, “Reversibly light-switchable drug-conjugates.” Published Nov. 11, 2009 which does not mention tyrosine phosphatase, and which describes photoswitchable conjugates of protein phosphatase calcineurin attached to a photoisomerizable group B and also attached to a drug for use in medical treatments (neither of these groups are genetically encodable). As one example in EP2116263, tumor growth is suppressed by inhibition of the protein phosphatase calcineurin. A photoisomerizable group B, for near UV (e.g. 370 nm) or near IR (e.g. 740 nm) induced activity, does not include a light responsive plant protein phototropin 1 LOV2 N-terminal alpha helix. 
     Receptor PTPs are contemplated for conjugation to light sensing proteins, as described herein. In contrast, Karunarathne, et al., “Subcellular optogenetics—controlling signaling and single-cell behavior.” J Cell Sci. 128(1):15-25, 2015, describes photosensitive domains, such as bacteria light-oxygen-voltage-sensing (LOV and LOV2) domains including a C-terminal helical Jα region, tagged to receptor tyrosine kinases (RTKs), there were no specific examples, there was no mention of a tyrosine phosphatase nor a plant phototropin 1 LOV2 N-terminal alpha helix. Optical activation of an inositol 5-phosphatase was shown, but inositol 5-phosphatase is not a protein phosphatase. 
     B. Enzymatic Phosphorylation of Tyrosine Residues. 
     Enzymatic phosphorylation of tyrosine residues has a role in cellular function and is anomalously regulated in an enormous range of diseases (e.g., diabetes, cancer, autoimmune disorders, and Noonan syndrome. It is controlled by the concerted action of two classes of structurally flexible—and dynamically regulatable—enzymes: protein tyrosine kinases (PTKs), which catalyze the ATP-dependent phosphorylation of tyrosine residues, and protein tyrosine phosphatases (PTPs), which catalyze the hydrolytic dephosphorylation of phosphotyrosines (5, 6). A detailed understanding of the mechanisms by which these enzymes respond to activity-modulating structural perturbations (i.e., mutations, post-translational modifications, or binding events) can, thus, illuminate their contributions to various diseases and facilitate the design of new PTK- or PTP-targeted therapeutics. 
     Over the last several decades, many biophysical studies have dissected the catalytic mechanisms and regulatory functions of PTKs (7, 8), which are common targets of pharmaceuticals. (9) Detailed analyses of PTPs, by contrast, have lagged behind. (10) These enzymes represent an underdeveloped source of biomedical insight and therapeutic potential (no inhibitors of PTPs have cleared clinical trials); they are, thus, the focus of this study. 
     PTPs uses two loops to dephosphorylate tyrosine residues. The eight-residue P-loop binds phosphate moieties through a positively charged arginine, which enables nucleophilic attack by a nearby cysteine, and the ten-residue WPD loop contains a general acid catalyst—an aspartate—that protonates the tyrosine leaving group and hydrolyzes the phosphoenzyme intermediate{circumflex over ( )}11-13) During catalysis, the P-loop remains fixed, while the WPD loop moves ˜10A between open and closed states; nuclear magnetic resonance (NMR) analyses suggest this movement controls the rate of catalysis. (14) 
     Recent analyses of protein tyrosine phosphatase IB (PTP IB) a drug target for the treatment of diabetes, obesity, and breast cancer, indicate that motions of its WPD loop are regulated by an allosteric network that extends to its C-terminus ( FIG.  1 B ) (15, 16). This network is susceptible to modulation by both (i) inhibitors that displace its C-terminal α7 helix (17, 18) and (ii) mutations that disrupt communication between the a(alpha)7 helix and the WPD loop (15); the specific collection of residues that enable allosteric communication in PTP1B and other PTPs has yet to be fully resolved. 
     Protein tyrosine phosphatase 1B (PTP1B). PTP1B represents a valuable tool for use in identifying potential therapeutics for at least four reasons: (i) It is implicated in diabetes 5 , obesity 6 , cancer 30 , anxiety 31 , inflammation 32 , the immune response 7 , and neural specification in embryonic stem cells 33 , (ii) The mechanisms underlying its subcellular localization are well understood (a short C-terminal anchor connects it to the ER; proteolysis of this anchor releases it to the cytosol) 2934 . (iii) It can be expressed, purified, and assayed with ease 35 , (iv) It is a member of a class of structurally similar enzymes (PTPs) that could facilitate the rapid extension of architectures for making it photoswitchable. PTP1B, thus, represents both an experimentally tractable model system for testing strategies for optical control, and an enzyme for which optical modulation will permit detailed analyses of a wide range of diseases and physiological processes. 
     Spatial regulation and intracellular signaling. PTP1B demonstrates, by example, the value of photoswitchable enzymes for studying spatial regulation in intracellular signaling. It is hypothesized to inactivate receptor tyrosine kinases through (i) contacts between endosomes and the ER 37,38 , (ii) contacts between the plasma membrane and extended regions of the ER 39 , and (iii) direct protein-protein interactions enabled by its partial proteolysis and release into the cytosol 34 . The role of different mechanisms (or locations) of PTP2B-substrate interaction in determining the outcomes of those interactions is poorly understood. Evidence suggesting a relationship between the location of PTP1B and its role in signaling has arisen in studies of tumorigenesis. Inhibition of PTP1B can suppress tumor growth and metastasis in breast 30,40 , lung 3,41 , colorectal 9 , and prostate cancers, 42,43  while its upregulation has similar effects in lymphoma 3,44 . Recent evidence suggest that the former effect may result from inhibition of cytosolic PTP1B 45 ; the cause of the latter is unclear. At present, there are no tools to investigate the differential influence of spatially distinct subpopulations of PTP1B on tumor-associated signaling events within the same cell. Photoswitchable variants of PTP1B represent such a tool. 
     Network biology. Signaling networks are often represented as nodes (proteins) connected by lines (interactions) 46 . Such maps capture the connectivity of biochemical relay systems, but obscure spatial context—the ability of a single interaction to occur in multiple locations and, perhaps, to stimulate multiple signaling outcomes. This study develops a set of tools that will enable detailed studies of the role of spatial context in guiding the propagation of signals through biochemical networks; such an examination contributes to understanding the role of PTP1B in cell signaling (and processes associated with tumorigenesis), and generally relevant to the study of any enzyme that exists in spatially distinct subpopulations within the cell. 
     II. Optogenetic Actuators. 
     Optogenetic actuators (genetically encodable proteins that undergo light-induced changes in conformation) provide a convenient means of placing biochemical events under optical control. Alone, or when fused to other proteins, they have enabled optical manipulation of biomolecular transport, binding, and catalysis with millisecond and submicron resolution in living cells. Our approach addresses two major deficiencies in existing technologies: Observational interference and illuminating half the story. Existing strategies to control the activity of enzymes with light interfere with native patterns of protein production, localization, and interaction (often by design) and, thus, make direct interrogation and/or control of those patterns—which determine how biochemical signals are processed—difficult. There are several methods to control protein kinases with light, but no analogous methods for controlling protein phosphatases. As signaling networks are regulated by the concerted action of both classes of enzyme, comprehensive control and/or detailed dissections of those networks require methods for controlling both. 
     Embodiments described herein comprise (i) an approach for controlling the activity of proteins with light without disrupting their wild-type activities and (ii) a demonstration of this approach on a protein of particular importance: protein tyrosine phosphatase 1B (PTP1B), a regulator of cell signaling and a validated drug target for the treatment of diabetes, obesity, and cancer. There are no known photoswitchable protein tyrosine phosphatases. The PTP1B-LOV2 construct reported in this filing is the first. (ii) The N-terminal alpha helix of LOV2 is ignored in most studies (even reviews of optical switches) and has not been used as an exclusive connection point for optical modulation of enzymes. 
     We have developed a photoswitchable version of PTP1B by fusing the C-terminal allosteric domain of this enzyme to the N-terminal alpha helix of a protein light switch (i.e., the LOV2 domain of phototropin 1 from  Avena sativa ). We present evidence that this general architecture—which is unique in the placement of LOV2 away from the active site of PTP1B (minimally disruptive)—can be extended to other PTPs and, perhaps, PTKs. For example, we used a statistical coupling analysis to show that the allosteric network exploited in our PTP1B design is preserved across the PTP family. 
     Alone, or when fused to other proteins, optogenetic actuators have enabled optical manipulation of biomolecular transport, binding, and catalysis with millisecond and submicron resolution 15,16 . At least three deficiencies limit their use in detailed studies of signaling networks: Observational interference. Existing strategies to control the activity of enzymes with light interfere with native patterns of protein production, localization, and interaction 16,17  (often by design) and, thus, make direct interrogation of those patterns—which determine how biochemical signals are processed 10  difficult. Illuminating half the story. There are several methods to control protein kinases with light 18,19 , but no analogous methods for controlling protein phosphatases. As signaling networks are regulated by the concerted action of both classes of enzyme, detailed dissections of those networks require methods for controlling both. A limited palette of actuators. Optogenetic actuators that enable subcellular control of enzyme activity require the use of blue or green light&#39;s. These wavelengths exhibit significant phototoxicity 20 , suffer from short biological penetration depths 21 , and, as a result of their spectral similarity, limit actuation to individual signaling events, rather than multiple events simultaneously. 
     A. Photoswitchable Constructs: Advantages Over Other Exemplary Technologies. 
     As described herein, a photoswitch describes a protein-protein architecture (e.g., a PTP1B-LOV2 fusion) that is optically active in its monomeric form. A reference, WO2013016693. “Near-infrared light-activated proteins.” Publication Date Jan. 31, 2013, relies on homodimerization. In contrast, optical control as described herein is over a larger range of proteins, including both those that require homodimerization and those that do not, unlike in WO2013016693. Further, this reference describes types of photosensory modules including blue light-sensitive flavoproteins found in plants; photoreceptors of blue-light using flavin adenine dinucleotide (BLUF); Light, Oxygen, or Voltage sensing (LOV) types, which includes plant and bacterial photoreceptors; and plant/microbe phytochromes, sensitive to light, i.e. light-induced helix rotation in the red-to-NIR region. More specifically described with examples are bacteriophytochrome (Bph)-based photoactivated fusion proteins, using light-responsive alpha helixes from  Rhodobacter sphaeroides  (BphG) fused to proteins such as protein phosphatases, protein kinases, membrane receptors, etc.  E. coli , are modified so as to exhibit the level of photoactivity of these expressed fusion proteins, i.e. in the presence or absence of red-to-NIR light. Although blue color changes in  E. coli  expressing fusion proteins are described in response to light, these blue bacteria are the result of using far-red/NIR-light for photoactivating a fusion protein that in turn activates lacZ expression in the presence of Xgal, not a photoresponse to exposure to blue light. However, there is no specific mention of a tyrosine phosphatase or a plant phototropin 1 LOV2 N-terminal alpha helix. In fact, reviews on optogenetics tend to depict LOV2 as having one terminal helix: The C-terminal Jalpha helix. While there are studies/patents indicating that simple insertion of the LOV2 domain enables photocontrol they rely on the underlying assumption that the Jalpha helix is unwinding to produce the controlling effect, not the A alpha helix as described herein. 
     B. A “Cage-Free” Approach to Control Protein Tyrosine Phosphatases and Protein Tyrosine Kinases with Light. 
     Current strategies for using light to control the activity of enzymes (as opposed to their concentration or location) rely on cage-based systems: a light-responsive protein, when fused to an enzyme of interest, controls access to its active site 16,47 . Unfortunately, such architectures can alter the affinity of enzymes for binding partners and change their susceptibility to activity modulating modifications (e.g., phosphorylation) 16,18 . These effects complicate the use of optogenetics to study signaling. This study will develop a “cage-free”, allostery-based approach for optical control that minimizes interference between enzymes and their substrates (and other binding partners). This approach will help preserve native patterns of protein localization, interaction, and post-translational modification and, thus, facilitate studies of the influence of those patterns on intracellular signaling. 
     2. A genetically encoded photoswitchable phosphatase. There are no genetically encodable photoswitchable phosphatases; the chimeras developed in this proposal will be the first. Photoswitchable variants of PTP1B will enable detailed studies of a wide range of interesting PTP1B-regulated processes (e.g., insulin, endocannabinoid, and epidermal growth factor signaling 49,51 , and cell adhesion and migration 52 ). Photoswitchable phosphatases, in general, will provide a useful class of tools for studying cell biology (particularly in concert with photoswitchable kinases, which could enable complementation experiments). 
     Hypothesis: The catalytic domains of PTPs and PTKs possess C-terminal a-helices that are distal to their active sites, yet capable of modulating their catalytic activities (for at least a subset of enzymes—the generality of this function is not known) 23,24 . We hypothesize that the fusion of this helix to the N-terminal a-helix of the light-oxygen voltage 2 (LOV2) domain of phototropin 1 from  Avena sativa —a photosensory domain with terminal helices that unwind in response to blue light 2526 —will yield enzyme-LOV2 chimeras that exhibit light-dependent catalytic activities, yet retain their native substrate specificities and binding affinities. 
     Experimental approach: We will attach the C-terminal a-helix of PTP1B to the N-terminal a-helix of LOV2 at homologous crossover points, and we will assess the influence of photoactivation on the catalytic activity of the resulting chimeras. This effort will involve the use of (i) kinetic assays and binding studies to characterize the substrate specificities and binding affinities of photoswitchable constructs and (ii) crystallographic and spectroscopic analyses to examine the structural basis of photocontrol. Informed by these studies, we will extend our approach to striatal-enriched protein tyrosine phosphatase (STEP) and protein tyrosine kinase 6 (PTK6), enzymes implicated in Alzheimer&#39;s disease and triple-negative breast cancer, respectively. 
     We will combine sophisticated biophysical studies, synthetic biology, and fluorescence microscopy to (i) develop protein architectures that enable optical control of protein tyrosine phosphatases (PTPs) and protein tyrosine kinases (PTKs) without interfering with their wild-type activities or binding specificities, (ii) evolve PTPs and PTKs modulated by red light, and (iii) develop an imaging methodology to study spatially localized signaling events in living cells. 
     We will begin our study with PTP1B, a validated drug target for the treatment of diabetes, obesity, and breast cancer, and an enzyme for which optogenetic tools will be particularly useful to address current gaps in knowledge (e.g., the role of spatially distinct subpopulations of PTP1B in promoting or suppressing the growth of tumors 22 ). Using it as a model, we will establish the generality of our methods by extending them to other PTPs and PTKs. 
     C. A Photo Switchable Variant of PTP1B. 
     Our first objective seeks to use LOV2, a protein with terminal helices that unwind in response to blue light, to control the activity of PTP1B, an enzyme for which unwinding of the C-terminal a-helix disrupts activity by distorting its catalytically essential WPD loop ( FIG.  1 AB ,  FIG.  6   ). To assess the feasibility of this goal, we constructed five PTP1B-LOV2 chimeras (joined at homologous crossover points): three chimeras showed light-dependent catalytic activity on 4-methylumbelliferyl phosphate (4M) ( FIG.  1 G ). A subsequent mutational analysis of one chimera indicated that mutations in the α-helix that links PTP1B to LOV2 can improve catalytic activity and dynamic range (DR, the ratio of dark/light activities;  FIG.  1 G ). Our ability to build—and begin optimizing—a photoswitchable PTP1B-LOV2 chimera by screening a small number of constructs suggests that rational design will allow us to build a chimera sufficient for intracellular signaling studies. We note: Our most photoswitchable chimera has a DR of 2.2; previous imaging studies suggest that a DR of 3-10 is sufficient to control intracellular signaling 18,19 . 
     More specifically,  FIG.  1 C  demonstrates some of differences over other types of optical control. The y-axis of the top plot indicates the activity of each construct in the dark (i.e., the initial rate of PTP1B-catalyzed hydrolysis of p-nitrophenyl phosphate); the y-axis of the bottom plot indicates the ratio of activity in dark and light state (i.e., the initial rate in the dark/the initial rate in the presence of 455 nm light), i.e. dynamic range. 
     Black bars show the activity and dynamic range for a set of eight initial constructs that differ in the crossover point (see the bottom of  FIG.  1 B ). Some of these constructs are photoswitchable, and some are not. Version 7 shows the greatest photoswitchability—the dynamic range is approximately 1.8. 
     More specifically, colors are associated with different types of constructs. Black: different crossover point (see  FIG.  1 B  for crossover points); Gray: different partitioning of the linker (see, Linker section below); Light blue: the Jalpha helix—this is at the C-terminus of the LOV2 domain; Dark blue: the A′alpha helix—this is at the N-terminus of the LOV2 domain and, thus, on the region that links it to PTP1B; Yellow: the alpha7 helix of PTP1B—this is at the C-terminus of PTP1B and, thus, on the region that links PTP1B to LOV2; Orange: combination: a combination of sites from the previous colors, see below for additional information. 
     These results were surprising, in part, because a recent review on optogenetics shows that that photocontrol of activity requires the Jα helix of LOV2, where Jα is a C-terminal helix which resides in a folded state against the LOV domain core, to be attached to a protein of interest, see Repina, N. A., Rosenbloom, A., Mukherjee, A., Schaffer, D. V. &amp; Kane, R. S. At Light Speed: Advances in Optogenetic Systems for Regulating Cell Signaling and Behavior.  Annu. Rev. Chem. Biomol. Eng.  8, 13-39 (2017). Photoactivation with blue light converts the noncovalent interaction between the LOV core and its bound flavin chromophore, FMN, into a covalent one through a conserved cysteine residue. The accompanying light-induced conformational change displaces the Jα helix away from the protein core, leading to uncaging of a fused effector domain (e.g., the kinase domain of phot1). Jα helix reverts to its dark-state caged conformation within minutes owing to spontaneous decay of the protein-cofactor bond. 
     Several limitations of the native AsLOV2 domain have motivated efforts to engineer improved variants. First, when fused to foreign protein domains, spontaneous undocking of the Jα helix can lead to a relatively high dark-state activity, resulting in a low dynamic range upon AsLOV2 uncaging (26). For example, the light-inducible DNA-binding system LovTAP has only a fivefold change in DNA affinity between the dark and illuminated states (27). To address this issue, Strickland et al. (26) used rational design to introduce four mutations into AsLOV2 that stabilized the docking of Jα to the LOV core. This increased the dynamic range of LovTAP from 5-fold to 70-fold, an approach that can be applied to other LOV domain optogenetic systems to reduce dark-state activity. AsLOV2 fusions are also particularly sensitive to linker lengths and the size and structure of attached domains (28, 29), and as a result, each new fusion protein switch requires optimization to achieve low dark-state and high light-state activity in mammalian cells. 
     In contrast to the Jα helix-protein chimers, as shown herein, the A′α helix not the Jα helix is attached to the protein of interest to form photoswitchable constructs, e.g. PTPB1. 
     Exemplary Linkers. 
     Gray bars of  FIG.  1 C  show the activity and dynamic range of mutants of version 7 in which the linker has been re-partitioned. In other words, version 7 has the following linker region: LSHEDLATTL (SEQ ID NO: 5), where the underlined region “LSHED” (SEQ ID NO: 6) corresponds to the C-terminus of PTP1B, and the region “LATTL” (SEQ ID NO: 7) corresponds to the N-terminus of LOV2. Version 7.1 has sequence LSHEDATTL (SEQ ID NO: 8); version 7.2 has sequence LSHEDTTL (SEQ ID NO: 9), and so on. Here, we find that version 7.1 has the same dynamic range as version 7, but a higher activity. We, thus, used version 7.1 for further optimization. 
     Exemplary Mutations. 
     Light blue bars show the activity and dynamic range of mutants of version 7.1 in which the Jα helix contains helix-stabilizing mutations. Curiously, these improve the activity of 7.1, but do not improve its dynamic range. 
     Dark blue bars show the activity and dynamic range for mutants of version 7.1 in which the A′α helix contains helix-stabilizing mutations. One of these mutations (T406A) improves dynamic range; we used this version for further studies. 
     Yellow bars show the activity and dynamic range of mutants of version 7.1 in which the α7 of PTP1B has helix-stabilizing mutations; the orange bars show the activity and dynamic range for mutants of version 7.1 in which the multiple mutations are combined. Neither of the constructs associated with yellow and orange bars show improved characteristics of 7.1 (T406A). 
     A minimally disruptive approach. Two kinetic studies indicate that our architecture for photocontrol does not interfere with the native substrate specificity or binding behavior of PTP1B: (i) An analysis of the activity of chimera E3 (from  FIG.  1 D ) on p-nitrophenyl phosphate (pN) indicates that light affects k cat , but not K m  ( FIGS.  2 K  and L). (ii) An analysis of activities on three substrates of different sizes (4M, pN, and a peptide) shows that DR is the same for all three ( FIG.  2 L-K ). The results of both studies are consistent with our hypothesized mechanism of photocontrol: LOV2-induced unwinding of the C-terminal a-helix of PTP1B disrupts the movement of its catalytically essential WPD loop, which controls the rate of catalysis, but has little influence on substrate binding affinity. 
     Biophysical studies. Photoswitchable chimeras express at titers (−100 mg/L) sufficient to carry out detailed biophysical analyses. We performed a preliminary set of these analyses on chimera E3. (i) We use circular dichroism (CD) to examine the influence of photoactivation on its secondary structure; spectral measurements indicate that photoactivation reduces a-helical content (222 nm;  FIG.  2 B ). (ii) We used the amplitude at 222 nm to measure a post-activation recovery time for a-helical content: T r —30 s ( FIG.  2 E ). This value is similar to the recovery times of previously developed LOV2-based photoswitchable constructs, (iii) We used tryptophan fluorescence to measure a post-activation recovery time of tryptophan residues: T r -50 s ( FIG.  2 F ). Tryptophan fluorescence is a rough metric for the conformation of PTP1B (which has seven tryptophan residues, compared to one in LOV2); this slower recovery time, thus, suggests that PTP1B takes longer than LOV2 to refold, (iv) We identified a set of crystallization conditions (those previously used to crystallize PTP1B W T) to grow crystals of E3 ( FIG.  2 F ). (V) We collected a two-dimensional  1 - 15 N HSQC spectrum of PTP1B W T, and assigned-65% of non-proline peaks. These NMR experiments, which are recent, have yet to include PTP1B-LOV2 chimeras; but the ease with which we carried them out (a single try) suggests that similar analyses of chimeras will be straightforward. The experimental tractability of PTP1B-LOV2 chimeras will enable a comprehensive biophysical analysis of variants with different photophysical properties. 
     Example 1. To develop a “cage-free” approach to control protein tyrosine phosphatases and kinases with light. This section develops an approach for placing enzymes under optical control without disrupting their native interactions. We will demonstrate this approach with PTP1B and, then, extend it to STEP and PTK6. We will know that we are successful when we have a PTP1B-LOV2 chimera that exhibits a three- to ten-fold change in activity between light and dark states, and when we have identified structure-based design rules that facilitate fine-tuning of the photophysical properties of photoswitchable variants of PTP1B, STEP, and PTK6. 
     D. Development of a Photoswitchable Variant of PTP1B. 
     The efforts in this section assume—and with crystallographic, kinetic, and binding studies, attempt to confirm—that optogenetic actuation systems located far from active sites are less likely to disrupt wild-type behaviors that actuation systems located nearby. Kinetic studies of preliminary PTP1B-LOV2 chimeras (i.e., chimeras in which the C-terminal helix of PTP1B is connected to the N-terminal helix of the LOV2 domain of phototropin 1 from  Avena sativa ) support this hypothesis: light inhibits their activity by affecting k cat , not K m , and they show wild-type kinetics on 4-methylumbelliferyl phosphate (4M), a model substrate ( FIG.  1 G  and  FIG.  2 K ). Photomodulation of k cat , but not K m  suggests that LOV2 exploits an allosteric network to distort the WPD loop ( FIG.  6   ). 
     Our initial constructs, which represent the first reported examples photoswitchable protein phosphatases, will facilitate a systematic study of the functional advantages of different chimera architectures. We are particularly interested in understanding how (i) the length of the linker that connects PTP1B and LOV2 and (ii) the stability of the terminal helices of LOV2 affect catalytic activity and dynamic range. We will study these relationships by combing spectroscopic analyses with kinetic studies. Spectroscopic analyses will show how different PTP1B-LOV2 chimeras rearrange under illumination (e.g., we will use CD and fluorescence spectroscopy to measure photomodulation of a-helical content and tryptophan fluorescence), and kinetic studies will reveal the influence of those rearrangements on catalytic activity and dynamic range. 
     The results of our biophysical analyses will facilitate the optimization of our chimera for in vitro cell studies. We will target a chimera—hereafter, referred to as PTP1B PS —with the following properties: a dynamic range (DR) of 3-10, a recovery time of T r ˜15-60 s, and wild-type activity (in its activated state). Previous optogenetic studies suggest that these attributes enable optical control of cell signaling 2,18,19 . We note: Biophysical studies of PTP1B indicate that the removal of its C-terminal a-helix can reduce its activity by a factor of four 57 ; accordingly, we believe that LOV2 can modulate the activity of PTP1B by at least fourfold (of course, LOV2 may trigger structural distortions more pronounced than those of a simple truncation). 
     E. Characterization of PTP1B-Substrate and PTP1B-Protein Interactions. 
     We will assess the influence of LOV2 on the substrate specificity of PTP1B by using kinetic analyses. Specifically, we will compare the activities of PTP1B W T and PTP1B PS  on three substrates: (i) p-nitrophenyl phosphate, a general substrate for tyrosine phosphatases, (ii) ETGTEEpYMKMDLG (SEQ ID NO: 10), a substrate of PTPs closely related to PTP1B, and (iii) RRLIEDAEpYAARG (SEQ ID NO: 11), a substrate specific to PTP1B. A comparison of values of k cat  and K m  on these substrates ( FIG.  2 K  shows an example kinetic study) will reveal differences in the catalytic activities and specificities of PTP1B W T and PTP1B PS . These studies will also allow us to assess the substrate-dependence of photoswitchability (i.e., DR). Photomodulation is often assumed to be independent of substrate; there is, however, no biochemical basis for this assumption (particularly in cage-based systems, where substrates may bind with different affinities and, thus, have different abilities to compete with the caging protein). We will test it. 
     We will assess the ability of PTP1B PS  to engage in the same protein-protein interactions as PTP1B W T by measuring the affinity of both enzymes for two native binding partners of PTP1B WT : LM04 and Stat3. Binding isotherms based on changes in tryptophan fluorescence of PTP1B will facilitate this study ( FIG.  7   ). 
     Our biochemical comparison of PTP1B WT  and PTP1B PS  may seem tedious, but we believe that this analysis is necessary to establish the relevance of future optogenetic observations to wild-type processes. 
     Biostructural characterization. We will investigate the structural basis of photocontrol in PTP1B PS  by using X-ray crystallography and NMR spectroscopy. X-ray crystal structures will show how LOV2 affects the structure of PTP1B (and vice versa); NMR spectroscopy will show how LOV2 modulates catalytic activity. For crystallographic studies, we will crystallize PTP1B PS  in its dark state (we will use the C450S mutation, which prevents formation of the cysteine adduct 2,26 ) by screening crystallization conditions previously used for LOV2, PTP1B, and LOV2-protein chimeras (all of which have crystal structures 2,35,58 ); preliminary results suggest that those used to grow crystals of PTP1B W T also yield crystals of PTP1B-LOV2 chimeras ( FIG.  2 J ). For NMR studies, we will use heteronuclear single quantum coherence (HSQC) spectroscopy and transverse relaxation-optimized spectroscopy (TROSY) to monitor changes in the conformation and backboned dynamics of PTP1B PS  before and after illumination. (We note: Backbone  1 H,  13 C, and  15 N chemical shifts have been assigned for PTP1B and LOV2 59,60 ). 
     G. Exemplary Imaging Methodology to Study Subcellular Signaling Events in Living Cells. 
     This section uses PTP1B PS  (a PTP1B-LOV2 chimera) to develop an approach for using confocal microscopy to probe—and study—subcellular signaling events. We will know that this objective is successful when we can inactivate a within subcellular regions, monitor the effect of that inactivation with an FRET-based sensor, and isolate the contributions of different subpopulations of PTP1B (e.g., ER-bound and cytosolic) to sensor phosphorylation. 
     Hypothesis. The sub cellular localization of PTPs and PTKs is controlled by domains proximal to their catalytic cores 23,24 . We hypothesize that the attachment of these domains to photoswitchable chimeras will give them wild-type localization patterns, and enable the use of confocal microscopy to study the contribution of spatially distinct subpopulations of PTPs and PTKs to cell signaling. Experimental approach: Within the cell, PTP1B exists in two spatially distinct subpopulations: attached to the cytosolic face of the endoplasmic reticulum, and free in the cytosol—a result of proteolysis of its short (−80 residue) C-terminal ER anchor 29 . We will (i) attach the ER anchor of wild-type PTP1B (PTP1B W T) to our PTP1B-LOV2 chimera, (ii) compare the subcellular localization of the resulting chimera with that of PTP1B W T, (iii) use confocal microscopy—in conjunction with a FRET-based sensor for phosphatase activity—to control and monitor PTP1B activity within the cell, and (iv) develop a reaction-diffusion model to assess the contributions of spatially distinct subpopulations of PTP1B to changes in sensor pho sphorylation over time and space. This work will yield a general approach for studying spatially localized signaling events in living cells. 
     Localization of PTP1B PS . 
     To examine the localization of PTP1B PS  in living cells, we will express three variants in COS-7 cells: (i) PTP1B PS_C 45os, (ii) PTP1B PS_ c45os attached to a short segment (−20 amino acids 29 ) of the C-terminal ER anchor of PTP1B W T that contains only the transmembrane domain (but not the proteolysis site), and (iii) PTP1B PS -c45os attached to the full C-terminal ER anchor of PTP1B W T (˜80 amino acids 29 ). We hypothesize that these constructs will have (i) cytosolic, ER-bound, and (iii) both cytosolic and ER-bound (i.e., wild-type) localization patterns, respectively. Using confocal microscopy, we will test this hypothesis by using the fluorescence of LOV2 to locate each chimera 70 . (In these studies, we will locate the ER with fluorescently-labeled SEC61B, an ER-associated transport complex 71 . The C450S mutation, which locks LOV2 in its fluorescent state, will prevent photoactivation during imaging). 
     COS-7 cells, fibroblast-like cells derived from the kidney tissue of the African green monkey, are particularly compatible with the aforementioned analysis for three reasons: (i) They are large and flat and, thus, facilitate imaging of spatially segregated subcellular regions 72 , (ii) They are compatible with commercially available transfection reagents 73 , (iii) Methods for inducing endocytosis 71  and calpain expression 74 , two processes that influence the subcellular activity and localization of PTP1B, are well developed for these cells. 
     Control of PTP1B PS  in living cells. We will examine the activity of PTP1B within subcellular regions by pairing confocal microscopy with a FRET-based sensor for protein phosphorylation (developed by the Umezawa group 54 ;  FIG.  12   ). This sensor will consist of a kinase substrate domain, a short flexible linker, and a phosphorylation recognition domain—all sandwiched between two fluorescent proteins (Clover, a green fluorescent protein, and mRuby2, a red fluorescent protein). Phosphorylation of the substrate domain will cause it to bind to the recognition domain, modulating (i.e., enhancing or reducing) FRET between the two fluorescent proteins. Our preliminary sensor, which uses substrate and SH2 domains compatible with PTP1B and src 23,55 , exhibits a 20% change in FRET in response to phosphorylation. We will attempt to optimize our sensor further by screening different substrate domains, SH2 domains, and linker lengths. Ouyang et al. built a FRET sensor for Src kinase activity that exhibits a −120% change in FRET when phosphorylated 55 ; we will use the architecture of this sensor—or, perhaps the sensor itself—to inform our designs. 
     In our imaging experiments, we will use a 455-nm laser to inactivate PTP1B within sub cellular regions (1-10 urn circles) and fluorescence lifetime imaging microscopy (FLIM) to monitor changes in sensor phosphorylation that result from that inactivation ( FIG.  13   ). For these experiments, we will use siRNA to deplete PTP1B W T and SEC61B to label the ER. The output will be a series of images in which the intensity of a pixel is proportional to the fluorescence lifetime of Clover (and, thus, the extent of sensor phosphorylation). 
     With this study, we are particularly interested in examining relationships between (i) the location of PTPIB PS  activation/inactivation, (ii) the size of the region of activation/inactivation, and (iii) the location and timing of changes in the phosphorylation state of the sensor. We will investigate these relationships by using a reaction-diffusion model. Equation 1 provides a simple example of a governing equation: 
     
       
         
           
             
               
                 
                   
                     
                       ∂ 
                         
                       
                         
                           S 
                           p 
                         
                         ( 
                         
                           r 
                           , 
                           t 
                         
                         ) 
                       
                     
                     
                       ∂ 
                         
                       t 
                     
                   
                   = 
                   
                     
                       
                         D 
                         S 
                       
                       ⁢ 
                       
                         
                           ∇ 
                           2 
                         
                         
                           S 
                           p 
                         
                       
                     
                     + 
                     
                       
                         k 
                         cat 
                         K 
                       
                       [ 
                       KS 
                       ] 
                     
                     - 
                     
                       
                         k 
                         cat 
                         P 
                       
                       [ 
                       
                         PS 
                         p 
                       
                       ] 
                     
                     - 
                     
                       
                         
                           k 
                           on 
                           K 
                         
                         [ 
                         P 
                         ] 
                       
                       [ 
                       
                         S 
                         p 
                       
                       ] 
                     
                   
                 
               
               
                 
                   ( 
                   
                     Eq 
                     . 
                         
                     l 
                   
                   ) 
                 
               
             
           
         
       
     
     for the phosphorylated sensor (S P ). Here, D s  is the diffusion coefficient for the sensor; KS is the concentration of tyrosine kinase bound to unphosphorylated sensor; PS p  is the concentration of PTP1B bound to phosphorylated sensor; P and S p  are the concentrations of free PTP1B and free phosphorylated sensor, respectively; k{circumflex over ( )} at  and k{circumflex over ( )} at  are the catalytic constants for the tyrosine kinase and PTP1B, respectively; and k % n  is the kinetic constant for sensor-PTP1B association. The kinase and phosphatase are assumed to bind only weakly with their products (an assumption that can be easily re-examined later). We may also supplement this model with tools such as BioNetGen, a web-based platform for generating biochemical reaction networks from user-specified rules for the mechanisms and locations of biomolecular interactions 75 ; such a tool, which can accommodate cellular heterogeneity (e.g., organelles and other compartments), will help to support and expand our kinetic model. 
     We hypothesize that a version of our kinetic model in which the phosphatase diffuses freely will more accurately capture the phosphorylation state of the sensor (at a specified time and position from the irradiation region) in the presence of cytosolic PTP1B PS . By contrast, a version of the model in which phosphatase does not diffuse freely will more accurately capture the behavior of sensors in the presence of ER-bound PTP1B PS . Regression of either model against imaging data will enable estimation of the extent to which cytosolic and ER-bound PTP1B contribute to changes in sensor phosphorylation over time and space. 
     Image analysis. The ER exists as a vesicular network that is spread throughout the cell; inactivation of sub cellular regions that are entirely ER or entirely cytosol is difficult. To enable analysis of spatially distinct subpopulations of PTP1B, we must, thus, estimate the amount of ER in different regions of irradiation. The discrepancy in length scales of ER heterogeneity (−20-100 pm) and irradiation (−1-10 pm) will permit such an estimation. We will work with two metrics: (i) the total fluorescence of labeled ER, and (ii) the anisotropy of labeled ER. Both metrics, by facilitating estimates of the populations of cytosolic and ER-bound PTP1B in an illuminated region, will help us to assess the contributions of those populations to changes in sensor phosphorylation. 
     Spatial Regulation and Intracellular Signaling. 
     PTP1B demonstrates, by example, the value of photoswitchable enzymes for studying spatial regulation in intracellular signaling. It is hypothesized to inactivate receptor tyrosine kinases through (i) contacts between endosomes and the ER 37,38 , (ii) contacts between the plasma membrane and extended regions of the ER 39 , and (iii) direct protein-protein interactions enabled by its partial proteolysis and release into the cytosol 34 . The role of different mechanisms (or locations) of PTP1B-substrate interaction in determining the outcomes of those interactions is poorly understood. Evidence suggesting a relationship between the location of PTP1B and its role in signaling has arisen in studies of tumorigenesis. Inhibition of PTP1B can suppress tumor growth and metastasis in breast 30,40 , lung 3,41 , colorectal 9 , and prostate cancers, 42,43  while its upregulation has similar effects in lymphoma 3,44 . Recent evidence suggests that the former effect may result from inhibition of cytosolic PTP1B 45 ; the cause of the latter is unclear. At present, there are no tools to investigate the differential influence of spatially distinct subpopulations of PTP1B on tumor-associated signaling events within the same cell. Photo switchable variants of PTP1B represent such a tool. 
     Network biology. Signaling networks are often represented as nodes (proteins) connected by lines (interactions) 46 . Such maps capture the connectivity of biochemical relay systems, but obscure spatial context—the ability of a single interaction to occur in multiple locations and, perhaps, to stimulate multiple signaling outcomes. This study develops a set of tools that will enable detailed studies of the role of spatial context in guiding the propagation of signals through biochemical networks; e.g. understanding the role of PTP1B in cell signaling (and processes associated with tumorigenesis), and generally relevant to the study of any enzyme that exists in spatially distinct subpopulations within the cells. 
     Generalization of Approach to Protein Tyrosine Phosphatases and Kinases. 
     Two observations suggest that our architecture for photocontrol (i.e., attachment of the N-terminus of LOV2 to the C-terminal a-helix of an enzyme) is broadly applicable to PTPs and PTKs. (i) Structural alignments show that all PTPs possess, or, with a few mutations, can possess—the same allosteric communication network as PTP1B ( FIG.  8 A ) 23 . (ii) PTKs contain a C-terminal a-helix that is distal to their active sites, yet capable of modulating their catalytic activities ( FIG.  8 B ) 61 . 
     We will assess the generalizability of our approach by building photoswitchable variants of striatal-enriched protein tyrosine phosphatase (STEP) and protein tyrosine kinase 6 (PTK6; 
       FIG.  8 A ). STEP is a neuron-specific phosphatase that is overactive in several neurological disorders, prominently Alzheimer&#39;s disease, schizophrenia, and drug addiction 62,63 . PTK6, which may function orthogonally to PTP1B in some signaling pathways, is expressed in approximately 70% of triple-negative breast cancers and promotes metastasis 50,64 . Photoswitchable variants of STEP and PTK6, both of which exist in multiple spatially distinct subpopulations within cells 50,62 , will enable detailed studies of their intracellular signaling roles, which remain poorly characterized. 
     For STEP and PTK6, we will develop—and measure the substrate specificities of—photoswitchable chimeras by using several kinetic assays. For STEP, we will use assays analogous to those employed with PTP1B. For PTK6, we will use the ADP-Glo kit developed by Promega, Inc. 65 . This assay, which is compatible with any peptide substrate, converts ADP produced by PTK-catalyzed peptide phosphorylation to a luminescent signal. For both enzymes, we will collect crystal structures of optimal chimeras. 
     Exemplary photoswitch construct sequences for use in expressing in mammalian cells or within an operon for microbial cells. In some embodiments, the sequences may be optimized for microbial expression. 
     
       
         
           
               
               
            
               
                 PPTP1B-LOV2, version 7.1 (T406A): DNA sequence SEQ ID NO: 12: 
                   
               
               
                 ATGGAGATGGAAAAGGAGTTCGAGCAGATCGACAAGTCCGGGAGCTGGGCGGCC 
               
               
                   
               
               
                 ATTTACCAGGATATCCGACATGAAGCCAGTGACTTCCCATGTAGAGTGGCCAAGCT 
               
               
                   
               
               
                 TCCTAAGAACAAAAACCGAAATAGGTACAGAGACGTCAGTCCCTTTGACCATAGTC 
               
               
                   
               
               
                 GGATTAAACTACATCAAGAAGATAATGACTATATCAACGCTAGTTTGATAAAAATGG 
               
               
                   
               
               
                 AAGAAGCCCAAAGGAGTTACATTCTTACCCAGGGCCCTTTGCCTAACACATGCGGT 
               
               
                   
               
               
                 CACTTTTGGGAGATGGTGTGGGAGCAGAAAAGCAGGGGTGTCGTCATGCTCAACA 
               
               
                   
               
               
                 GAGTGATGGAGAAAGGTTCGTTAAAATGCGCACAATACTGGCCACAAAAAGAAGAA 
               
               
                   
               
               
                 AAAGAGATGATCTTTGAAGACACAAATTTGAAATTAACATTGATCTCTGAAGATATC 
               
               
                   
               
               
                 AAGTCATATTATACAGTGCGACAGCTAGAATTGGAAAACCTTACAACCCAAGAAAC 
               
               
                   
               
               
                 TCGAGAGATCTTACATTTCCACTATACCACATGGCCTGACTTTGGAGTCCCTGAAT 
               
               
                   
               
               
                 CACCAGCCTCATTCTTGAACTTTCTTTTCAAAGTCCGAGAGTCAGGGTCACTCAGC 
               
               
                   
               
               
                 CCGGAGCACGGGCCCGTTGTGGTGCACTGCAGTGCAGGCATCGGCAGGTCTGGA 
               
               
                   
               
               
                 ACCTTCTGTCTGGCTGATACCTGCCTCTTGCTGATGGACAAGAGGAAAGACCCTTC 
               
               
                   
               
               
                 TTCCGTTGATATCAAGAAAGTGCTGTTAGAAATGAGGAAGTTTCGGATGGGGCTGA 
               
               
                   
               
               
                 TCCAGACAGCCGACCAGCTGCGCTTCTCCTACCTGGCTGTGATCGAAGGTGCCAA 
               
               
                   
               
               
                 ATTCATCATGGGGGACTCTTCCGTGCAGGATCAGTGGAAGGAGCTTTCCCACGAG 
               
               
                   
               
               
                 GACGCTGCTACACTTGAACGTATTGAGAAGAACTTTGTCATTACTGACCCAAGGTT 
               
               
                   
               
               
                 GCCAGATAATCCCATTATATTCGCGTCCGATAGTTTCTTGCAGTTGACAGAATATAG 
               
               
                   
               
               
                 CCGTGAAGAAATTTTGGGAAGAAACTGCAGGTTTCTACAAGGTCCTGAAACTGATC 
               
               
                   
               
               
                 GCGCGACAGTGAGAAAAATTAGAGATGCCATAGATAACCAAACAGAGGTCACTGTT 
               
               
                   
               
               
                 CAGCTGATTAATTATACAAAGAGTGGTAAAAAGTTCTGGAACCTCTTTCACTTGCAG 
               
               
                   
               
               
                 CCTATGCGAGATCAGAAGGGAGATGTCCAGTACTTTATTGGGGTTCAGTTGGATG 
               
               
                   
               
               
                 GAACTGAGCATGTCCGAGATGCTGCCGAGAGAGAGGGAGTCATGCTGATTAAGAA 
               
               
                   
               
               
                 AACTGCAGAAAATATTGATGAGGCGGCAAAAGAACTT CTCGAGCACCACCACCAC   
               
               
                   
               
               
                 
                   CACCACTGA 
                 
               
               
                   
               
               
                 Protein sequence: SEQ ID NO: 13: 
               
               
                 MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKL 
               
               
                   
               
               
                 HQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEK 
               
               
                   
               
               
                 GSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHY 
               
               
                   
               
               
                 TTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMD 
               
               
                   
               
               
                 KRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELS 
               
               
                   
               
               
                 HEDAATLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRATV 
               
               
                   
               
               
                 RKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVR 
               
               
                   
               
               
                 DAAEREGVMLIKKTAENIDEAAKEL LEHHHHHH   
               
               
                   
               
               
                 PTP1B-LOV2, version 7.1(S286A): DNA sequence: SEQ ID NO: 14: 
               
               
                 ATGGAGATGGAAAAGGAGTTCGAGCAGATCGACAAGTCCGGGAGCTGGGCGGCCAT 
               
               
                   
               
               
                 TTACCAGGATATCCGACATGAAGCCAGTGACTTCCCATGTAGAGTGGCCAAGCTTCC 
               
               
                   
               
               
                 TAAGAACAAAAACCGAAATAGGTACAGAGACGTCAGTCCCTTTGACCATAGTCGGA 
               
               
                   
               
               
                 TTAAACTACATCAAGAAGATAATGACTATATCAACGCTAGTTTGATAAAAATGGAA 
               
               
                   
               
               
                 GAAGCCCAAAGGAGTTACATTCTTACCCAGGGCCCTTTGCCTAACACATGCGGTCAC 
               
               
                   
               
               
                 TTTTGGGAGATGGTGTGGGAGCAGAAAAGCAGGGGTGTCGTCATGCTCAACAGAGT 
               
               
                   
               
               
                 GATGGAGAAAGGTTCGTTAAAATGCGCACAATACTGGCCACAAAAAGAAGAAAAA 
               
               
                   
               
               
                 GAGATGATCTTTGAAGACACAAATTTGAAATTAACATTGATCTCTGAAGATATCAAG 
               
               
                   
               
               
                 TCATATTATACAGTGCGACAGCTAGAATTGGAAAACCTTACAACCCAAGAAACTCG 
               
               
                   
               
               
                 AGAGATCTTACATTTCCACTATACCACATGGCCTGACTTTGGAGTCCCTGAATCACC 
               
               
                   
               
               
                 AGCCTCATTCTTGAACTTTCTTTTCAAAGTCCGAGAGTCAGGGTCACTCAGCCCGGA 
               
               
                   
               
               
                 GCACGGGCCCGTTGTGGTGCACTGCAGTGCAGGCATCGGCAGGTCTGGAACCTTCTG 
               
               
                   
               
               
                 TCTGGCTGATACCTGCCTCTTGCTGATGGACAAGAGGAAAGACCCTTCTTCCGTTGA 
               
               
                   
               
               
                 TATCAAGAAAGTGCTGTTAGAAATGAGGAAGTTTCGGATGGGGCTGATCCAGACAG 
               
               
                   
               
               
                 CCGACCAGCTGCGCTTCTCCTACCTGGCTGTGATCGAAGGTGCCAAATTCATCATGG 
               
               
                   
               
               
                 GGGACTCTGCCGTGCAGGATCAGTGGAAGGAGCTTTCCCACGAGGACGCTACTACA 
               
               
                   
               
               
                 CTTGAACGTATTGAGAAGAACTTTGTCATTACTGACCCAAGGTTGCCAGATAATCCC 
               
               
                   
               
               
                 ATTATATTCGCGTCCGATAGTTTCTTGCAGTTGACAGAATATAGCCGTGAAGAAATT 
               
               
                   
               
               
                 TTGGGAAGAAACTGCAGGTTTCTACAAGGTCCTGAAACTGATCGCGCGACAGTGAG 
               
               
                   
               
               
                 AAAAATTAGAGATGCCATAGATAACCAAACAGAGGTCACTGTTCAGCTGATTAATT 
               
               
                   
               
               
                 ATACAAAGAGTGGTAAAAAGTTCTGGAACCTCTTTCACTTGCAGCCTATGCGAGATC 
               
               
                   
               
               
                 AGAAGGGAGATGTCCAGTACTTTATTGGGGTTCAGTTGGATGGAACTGAGCATGTCC 
               
               
                   
               
               
                 GAGATGCTGCCGAGAGAGAGGGAGTCATGCTGATTAAGAAAACTGCAGAAAATATT 
               
               
                   
               
               
                 GATGAGGCGGCAAAAGAACTT CTCGAGCACCACCACCACCACCACTGA   
               
               
                   
               
               
                 Protein sequence: SEQ ID NO: 15: 
               
               
                 MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKL 
               
               
                   
               
               
                 HQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEK 
               
               
                   
               
               
                 GSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHY 
               
               
                   
               
               
                 TTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMD 
               
               
                   
               
               
                 KRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSAVQDQWKELS 
               
               
                   
               
               
                 HEDATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRATV 
               
               
                   
               
               
                 RKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVR 
               
               
                   
               
               
                 DAAEREGVMLIKKTAENIDEAAKEL LEHHHHHH   
               
               
                   
               
               
                 TCPTP-LOV2, best version: 
               
               
                 DNA sequence: SEQ ID NO: 16: 
               
               
                 ATGCCCACCACCATCGAGCGGGAGTTCGAAGAGTTGGATACTCAGCGTCGCTGGCA 
               
               
                   
               
               
                 GCCGCTGTACTTGGAAATTCGAAATGAGTCCCATGACTATCCTCATAGAGTGGCCAA 
               
               
                   
               
               
                 GTTTCCAGAAAACAGAAATCGAAACAGATACAGAGATGTAAGCCCATATGATCACA 
               
               
                   
               
               
                 GTCGTGTTAAACTGCAAAATGCTGAGAATGATTATATTAATGCCAGTTTAGTTGACA 
               
               
                   
               
               
                 TAGAAGAGGCACAAAGGAGTTACATCTTAACACAGGGTCCACTTCCTAACACATGC 
               
               
                   
               
               
                 TGCCATTTCTGGCTTATGGTTTGGCAGCAGAAGACCAAAGCAGTTGTCATGCTGAAC 
               
               
                   
               
               
                 CGC GTGATGGAGAAAGGTTCGTTA AAATGTGCACAGTACTGGCCAACAGATGACCA 
               
               
                   
               
               
                 AGAGATGCTGTTTAAAGAAACAGGATTCAGTGTGAAGCTCTTGTCAGAAGATGTGA 
               
               
                   
               
               
                 AGTCGTATTATACAGTACATCTACTACAATTAGAAAATATCAATAGTGGTGAAACCA 
               
               
                   
               
               
                 GAACAATATCTCACTTTCATTATACTACCTGGCCAGATTTTGGAGTCCCTGAATCACC 
               
               
                   
               
               
                 AGCTTCATTTCTCAATTTCTTGTTTAAAGTGAGAGAATCTGGCTCCTTGAACCCTGAC 
               
               
                   
               
               
                 CATGGGCCTGCGGTGATCCACTGTAGTGCAGGCATTGGGCGCTCTGGCACCTTCTCT 
               
               
                   
               
               
                 CTGGTAGACACTTGTCTT TTGCTGATGGACAAGAGGAAAGACCCTTCTTCCGTTG   
               
               
                   
               
               
                 
                   ATATCAAGAAAGTGCTGTTAGAAATGAGGAAGTTTCGGATGGGGCTGATCCAG 
                 
               
               
                   
               
               
                 
                   ACAGCCGACCAGCTGCGCTTCTCCTACCTGGCTGTGATCGAAGGTGCCAAATT 
                 
               
               
                   
               
               
                 
                   CATCATGGGGGACTCTTCCGTGCAGGATCAGTGGAAGGAGCTTTCCCACGAGG 
                 
               
               
                   
               
               
                   AC GCTGCTACACTTGAACGTATTGAGAAGAACTTTGTCATTACTGACCCAAGGTTGC 
               
               
                   
               
               
                 CAGATAATCCCATTATATTCGCGTCCGATAGTTTCTTGCAGTTGACAGAATATAGCC 
               
               
                   
               
               
                 GTGAAGAAATTTTGGGAAGAAACTGCAGGTTTCTACAAGGTCCTGAAACTGATCGC 
               
               
                   
               
               
                 GCGACAGTGAGAAAAATTAGAGATGCCATAGATAACCAAACAGAGGTCACTGTTCA 
               
               
                   
               
               
                 GCTGATTAATTATACAAAGAGTGGTAAAAAGTTCTGGAACCTCTTTCACTTGCAGCC 
               
               
                   
               
               
                 TATGCGAGATCAGAAGGGAGATGTCCAGTACTTTATTGGGGTTCAGTTGGATGGAAC 
               
               
                   
               
               
                 TGAGCATGTCCGAGATGCTGCCGAGAGAGAGGGAGTCATGCTGATTAAGAAAACTG 
               
               
                   
               
               
                 CAGAAAATATTGATGAGGCGGCAAAAGAACTTCTCGAGCACCACCACCACCACCA 
               
               
                   
               
               
                 CTGA 
               
               
                   
               
               
                 The underlined letters indicate sequence fromPTPIB. Protein 
               
               
                 sequence: SEQ ID NO: 17: 
               
               
                 MPTTIEREFEELDTQRRWQPLYLEIRNESHDYPHRVAKFPENRNRNRYRDVSPYDHSRV 
               
               
                   
               
               
                 KLQNAENDYINASLVDIEEAQRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNR VM   
               
               
                   
               
               
                   EKGSLK CAQYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHLLQLENINSGETRTISHF 
               
               
                   
               
               
                 HYTTWPDFGVPESPASFLNFLFKVRESGSLNPDHGPAVIHCSAGIGRSGTFSLVDTCLLL 
               
               
                   
               
               
                 MDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYL AVIEGAKFIMGDSSVQDQWK   
               
               
                   
               
               
                   ELSHED AATLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDR 
               
               
                   
               
               
                 ATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTE 
               
               
                   
               
               
                 HVRDAAEREGVMLIKKTAENIDEAAKEL LEHHHHHH   
               
               
                   
               
               
                 TCPTP-LOV2 V2: DNA sequence: SEQ ID NO: 18: 
               
               
                 ATGCCCACCACCATCGAGCGGGAGTTCGAAGAGTTGGATACTCAGCGTCGCTGGCA 
               
               
                   
               
               
                 GCCGCTGTACTTGGAAATTCGAAATGAGTCCCATGACTATCCTCATAGAGTGGCCAA 
               
               
                   
               
               
                 GTTTCCAGAAAACAGAAATCGAAACAGATACAGAGATGTAAGCCCATATGATCACA 
               
               
                   
               
               
                 GTCGTGTTAAACTGCAAAATGCTGAGAATGATTATATTAATGCCAGTTTAGTTGACA 
               
               
                   
               
               
                 TAGAAGAGGCACAAAGGAGTTACATCTTAACACAGGGTCCACTTCCTAACACATGC 
               
               
                   
               
               
                 TGCCATTTCTGGCTTATGGTTTGGCAGCAGAAGACCAAAGCAGTTGTCATGCTGAAC 
               
               
                   
               
               
                 CGCATTGTGGAGAAAGAATCGGTTAAATGTGCACAGTACTGGCCAACAGATGACCA 
               
               
                   
               
               
                 AGAGATGCTGTTTAAAGAAACAGGATTCAGTGTGAAGCTCTTGTCAGAAGATGTGA 
               
               
                   
               
               
                 AGTCGTATTATACAGTACATCTACTACAATTAGAAAATATCAATAGTGGTGAAACCA 
               
               
                   
               
               
                 GAACAATATCTCACTTTCATTATACTACCTGGCCAGATTTTGGAGTCCCTGAATCACC 
               
               
                   
               
               
                 AGCTTCATTTCTCAATTTCTTGTTTAAAGTGAGAGAATCTGGCTCCTTGAACCCTGAC 
               
               
                   
               
               
                 CATGGGCCTGCGGTGATCCACTGTAGTGCAGGCATTGGGCGCTCTGGCACCTTCTCT 
               
               
                   
               
               
                 CTGGTAGACACTTGTCTT TTGCTGATGGACAAGAGGAAAGACCCTTCTTCCGTTGAT   
               
               
                   
               
               
                 
                   ATCAAGAAAGTGCTGTTAGAAATGAGGAAGTTTCGGATGGGGCTGATCCAGACAGC 
                 
               
               
                   
               
               
                 
                   CGACCAGCTGCGCTTCTCCTACCTGGCTGTGATCGAAGGTGCCAAATTCATCATGGG 
                 
               
               
                   
               
               
                   GGACTCTTCCGTGCAGGATCAGTGGAAGGAGCTTTCCCACGAGGAC GCTGCTACACT 
               
               
                   
               
               
                 TGAACGTATTGAGAAGAACTTTGTCATTACTGACCCAAGGTTGCCAGATAATCCCAT 
               
               
                   
               
               
                 TATATTCGCGTCCGATAGTTTCTTGCAGTTGACAGAATATAGCCGTGAAGAAATTTT 
               
               
                   
               
               
                 GGGAAGAAACTGCAGGTTTCTACAAGGTCCTGAAACTGATCGCGCGACAGTGAGAA 
               
               
                   
               
               
                 AAATTAGAGATGCCATAGATAACCAAACAGAGGTCACTGTTCAGCTGATTAATTATA 
               
               
                   
               
               
                 CAAAGAGTGGTAAAAAGTTCTGGAACCTCTTTCACTTGCAGCCTATGCGAGATCAGA 
               
               
                   
               
               
                 AGGGAGATGTCCAGTACTTTATTGGGGTTCAGTTGGATGGAACTGAGCATGTCCGAG 
               
               
                   
               
               
                 ATGCTGCCGAGAGAGAGGGAGTCATGCTGATTAAGAAAACTGCAGAAAATATTGAT 
               
               
                   
               
               
                 GAGGCGGCAAAAGAACTT CTCGAGCACCACCACCACCACCACTGA   
               
               
                   
               
               
                 Protein sequence: SEQ ID NO: 19: 
               
               
                 MPTTIEREFEELDTQRRWQPLYLEIRNESHDYPHRVAKFPENRNRNRYRDVSPYDHSRV 
               
               
                   
               
               
                 KLQNAENDYINASLVDIEEAQRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRIVE 
               
               
                   
               
               
                 KESVKCAQYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHLLQLENINSGETRTISHFH 
               
               
                   
               
               
                 YTTWPDFGVPESPASFLNFLFKVRESGSLNPDHGPAVIHCSAGIGRSGTFSLVDTCLLLM 
               
               
                   
               
               
                 DKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYL AVIEGAKFIMGDSSVQDQWKEL   
               
               
                   
               
               
                   SHED AATLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRAT 
               
               
                   
               
               
                 VRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHV 
               
               
                   
               
               
                 RDAAEREGVMLIKKTAENIDEAAKEL LEHHHHHH   
               
            
           
         
       
     
     FRET sensors. Forster resonance energy transfer (FRET) is contemplated for use to monitor the activity of PTP1B in living cells. Sensor exhibits a 20% reduction in FRET signal when treated with Src kinase ( FIG.  21 B ). Previous imaging studies indicate that a 20% change in FRET is sufficient to monitor intracellular kinase activity 54-56 . To enhance spatial resolution in imaging studies, we will attempt to optimize our sensor further (and use it to measure the activity of PTP1B in vitro). 
     Exemplary FRET sensors: underlined  mClover3-SH2 -Linker-Bold Substrate—underlined and Bold  mRuby3 . 
     
       
         
           
               
               
            
               
                 mClover3-mRuby3: DNA sequence: SEQ ID NO: 20: 
                   
               
               
                 
                   ATGCATCATCATCATCATCAT 
                   GTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGG 
                 
               
               
                   
               
               
                 
                   TGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTCCGC 
                 
               
               
                   
               
               
                 
                   GGCGAGGGCGAGGGCGATGCCACCAACGGCAAGCTGACCCTGAAGTTCATCTGCAC 
                 
               
               
                   
               
               
                 
                   CACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCTTCGGCTACGGCGT 
                 
               
               
                   
               
               
                 
                   GGCCTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGC 
                 
               
               
                   
               
               
                 
                   CATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTCTTTCAAGGACGACGGTACCT 
                 
               
               
                   
               
               
                 
                   ACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAG 
                 
               
               
                   
               
               
                 
                   CTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTA 
                 
               
               
                   
               
               
                 
                   CAACTTCAACAGCCACTACGTCTATATCACGGCCGACAAGCAGAAGAACTGCATCA 
                 
               
               
                   
               
               
                 
                   AGGCTAACTTCAAGATCCGCCACAACGTTGAGGACGGCAGCGTGCAGCTCGCCGAC 
                 
               
               
                   
               
               
                 
                   CACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCA 
                 
               
               
                   
               
               
                 
                   CTACCTGAGCCATCAGTCCAAGCTGAGCAAAGACCCCAACGAGAAGCGCGATCACA 
                 
               
               
                   
               
               
                 
                   TGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATTACACATGGCATGGACGAGCTGT 
                 
               
               
                   
               
               
                 
                   ACAAGTGGTATTTTGGGAAGATCACTCGTCGGGAGTCCGAGCGGCTGCTGCTCAACC 
                 
               
               
                   
               
               
                 
                   CCGAAAACCCCCGGGGAACCTTCTTGGTCCGGGAGAGCGAGACGACAAAAGGTGCC 
                 
               
               
                   
               
               
                 
                   TATTGCCTCTCCGTTTCTGACTTTGACAACGCCAAGGGGCTCAATGTGAAGCACTAC 
                 
               
               
                   
               
               
                 
                   AAGATCCGCAAGCTGGACAGCGGCGGCTTCTACATCACCTCACGCACACAGTTCAG 
                 
               
               
                   
               
               
                 
                   CAGCCTGCAGCAGCTGGTGGCCTACTACTCCAAACATGCTGATGGCTTGTGCCACCG 
                 
               
               
                   
               
               
                   CCTGACTAACGTCTGT GGGTCTACATCTGGATCTGGGAAGCCGGGTTCTGGTGAGGG 
               
               
                   
               
               
                 TTCT TGGATGGAGGACTATGACTACGTCCACCTACAGGGGG AGCTC   GTGTCTAA     
               
               
                   
               
               
                 
                   
                     GGGCGAAGAGCTGATCAAGGAAAATATGCGTATGAAGGTGGTCATGGAAGGTT 
                   
                 
               
               
                   
               
               
                 
                   
                     CGGTCAACGGCCACCAATTCAAATGCACAGGTGAAGGAGAAGGCAGACCGTAC 
                   
                 
               
               
                   
               
               
                 
                   
                     GAGGGAACTCAAACCATGAGGATCAAAGTCATCGAGGGAGGACCCCTGCCATT 
                   
                 
               
               
                   
               
               
                 
                   
                     TGCCTTTGACATTCTTGCCACGTCGTTCATGTATGGCAGCCGTACTTTTATCAA 
                   
                 
               
               
                   
               
               
                 
                   
                     GTACCCGGCCGACATCCCTGATTTCTTTAAACAGTCCTTTCCTGAGGGTTTTAC 
                   
                 
               
               
                   
               
               
                 
                   
                     TTGGGAAAGAGTTACGAGATACGAAGATGGTGGAGTCGTCACCGTCACGCAGG 
                   
                 
               
               
                   
               
               
                 
                   
                     ACACCAGCCTTGAGGATGGCGAGCTCGTCTACAACGTCAAGGTCAGAGGGGTA 
                   
                 
               
               
                   
               
               
                 
                   
                     AACTTTCCCTCCAATGGTCCCGTGATGCAGAAGAAGACCAAGGGTTGGGAGCC 
                   
                 
               
               
                   
               
               
                 
                   
                     TAATACAGAGATGATGTATCCAGCAGATGGTGGTCTGAGAGGATACACTGACA 
                   
                 
               
               
                   
               
               
                 
                   
                     TCGCACTGAAAGTTGATGGTGGTGGCCATCTGCACTGCAACTTCGTGACAACTT 
                   
                 
               
               
                   
               
               
                 
                   
                     ACAGGTCAAAAAAGACCGTCGGGAACATCAAGATGCCCGGTGTCCATGCCGTT 
                   
                 
               
               
                   
               
               
                 
                   
                     GATCACCGCCTGGAAAGGATCGAGGAGAGTGACAATGAAACCTACGTAGTGCA 
                   
                 
               
               
                   
               
               
                 
                   
                     ACGCGAAGTGGCAGTTGCCAAATACAGCAACCTTGGTGGTGGCATGGACGAGC 
                   
                 
               
               
                   
               
               
                 
                   
                     TGTACAAGTAA 
                   
                 
               
               
                   
               
               
                 Protein sequence: SEQ ID NO: 21: 
               
               
                 
                   MHHHHHH 
                   VSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTG 
                 
               
               
                   
               
               
                 
                   KLPVPWPTLVTTFGYGVACFSRYPDHMKQHDFFKSAMPEGYVQERTISFKDDGTYKTR 
                 
               
               
                   
               
               
                 
                   AEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHYVYITADKQKNCIKANFKIRH 
                 
               
               
                   
               
               
                 
                   NVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSHQSKLSKDPNEKRDHMVLLEFVTAA 
                 
               
               
                   
               
               
                 
                   GITHGMDELYKWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAK 
                 
               
               
                   
               
               
                   GLNVKHYKIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVC GSTSGSGKP 
               
               
                   
               
               
                 GSGEGS WMEDYDYVHLQG EL VSKGEELIKENMRMKVVMEGSVNGHQFKCTGEGE   
               
               
                   
               
               
                 
                   GRPYEGTQTMRIKVIEGGPLPFAFDILATSFMYGSRTFIKYPADIPDFFKQSFPEGFT 
                 
               
               
                   
               
               
                 
                   WERVTRYEDGGVVTVTQDTSLEDGELVYNVKVRGVNFPSNGPVMQKKTKGWEP 
                 
               
               
                   
               
               
                 
                   NTEMMYPADGGLRGYTDIALKVDGGGHLHCNFVTTYRSKKTVGNIKMPGVHAVD 
                 
               
               
                   
               
               
                 
                   HRLERIEESDNETYVVQREVAVAKYSNLGGGMDELYK 
                 
               
            
           
         
       
     
     Exemplary Mammalian expression vector(s) for expressing a photoswitch construct in a mammalian cell. 
     For insertion into a mammalian expression vector, e.g. lentiviral vector, pAcGFP1-C1 (Clontech); PTP1B-LOV2 (above), a promoter, e.g. CMV: SEQ ID NO: 22: GCAAATGGGCGGTAGGCGTGTACGGTGGGAGGTCTATATAAGCAGAGCTGGTTTAG TGAACCGTCAGATC; a RBS, e.g. Kozak consensus translation initiation site: GCCACCATG; an Intergenic spacer (e.g. P2A: DNA sequence: SEQ ID NO: 23: GGCAGCGGCGCCACCAACTTCTCCCTGCTGAAGCAGGCCGGCGACGTGGAGGAGAA CCCCGGCCCC; a protein sequence: SEQ ID NO: 24: GSGATNFSLLKQAGDVEENPGP, etc. 
     An exemplary FRET Sensor included: a Promoter: Same as above; a RBS: Same as above, etc. 
     Exemplary FRET sensors are contemplated to avoid overlap between the excitation/emission wavelengths of LOV2 (455/495, we note that LOV2 is only weakly fluorescent 70 ) and our FRET pair (505/515 for Clover and 560/605 for mRuby2), while we still expect to see some crosstalk during imaging, previous three-color imaging studies 71  suggest that it will not interfere with our ability to carry out the experiments described in this section. 
     Contemplative Embodiments Include but at not Limited to Invadopodia Formation and EGFR Regulation. 
     A photoswitchable variant of PTP1B is contemplated to determine if cytosolic PTP1B, released from the ER by proteolysis, is exclusively responsible for regulating the formation of invadopodia, or if ER-bound PTP1B can function similarly. Cancer cell invasion and metastasis is facilitated by the formation of invadopodia, actin-rich protrusions that enable matrix degradation 45 . 
     Both PTP1B and PTK6 regulate epidermal growth factor receptor (EGFR), a regulator of cell proliferation and migration that exhibits aberrant activity in numerous cancers and inflammatory diseases 51,76 . We will use a variant of PTP1B stimulated by red light and a variant of PTK6 stimulated by blue light (or vice versa) to carry out a combinatorial analysis of the cooperative contribution of PTP1B and PTK6 to EGFR regulation within different regions of the cell. 
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     III. Genetically Encoded System for Constructing and Detecting Biologically Active Agents: Microbial Inhibitor Screening Systems. 
     Several types of operons were developed as described herein, each for a specific purpose, including but not limited to testing small molecules for their ability to inhibit, activate, or otherwise modulate a chosen PTP and/or PTK; operons for testing intracellularly provided small molecules for inhibiting, activating, or modulating effects on a chosen PTP and/or PTK; and evolving one or more proteins or small molecules of interest. More specifically, genetic operons were contemplated for insertion, using transfection and breeding techniques well known in the art, for providing microbial cells wherein the activity of an enzyme of interest (e.g., protein tyrosine phosphatase 1B, a drug target for the treatment of diabetes, obesity, and cancer) is linked to (i) cellular luminescence, (ii) cellular fluorescence, or (iii) cellular growth. In some embodiments, such operons are modified for use in detecting and/or evolving biologically active metabolites. When modified and/or induced to build various metabolites, the cell will be used for detection of metabolites that inhibit/activate a protein of interest (e.g., PTP1B). 
     These operons allow operon-containing microbial cells to be used to carry out the following tasks: Detecting biologically active molecules and non-native biologically active metabolites. When grown in the presence of biologically active molecules as a small molecule that is both (i) cell permeable and (ii) capable of inhibiting a protein of interest (e.g., PTP1B), the cell will enable detection of that molecule. That is, it will exhibit a concentration-dependent response in luminescence, fluorescence, or growth. Many non-native biologically active metabolites have useful pharmaceutical properties. Examples include paclitaxel and artemisinin, plant-derived terpenoids that are used to treat cancer and malaria, respectively. When the metabolic pathways responsible for making such natural metabolites are installed into microbial cells that also contain our operon, those cells will enable detection of interesting metabolite-based biological activities (e.g., the ability to inhibit PTP1B). 
     Genetic operons that, when installed into microbial cells, link the activity of an enzyme of interest (e.g., protein tyrosine phosphatase 1B, a drug target for the treatment of diabetes, obesity, and cancer) to (i) cellular luminescence, (ii) cellular fluorescence, or (iii) cellular growth. 
     Detect and/or evolve biologically active metabolites. When modified and/or induced to build various metabolites, the cell will enable detection of metabolites that inhibit/activate a protein of interest (e.g., PTP1B). 
     These operons allow operon-containing microbial cells to be used to carry out the following tasks: Detecting biologically active molecules and non-native biologically active metabolites. When grown in the presence of a biologically active molecules as a small molecule that is both (i) cell permeable and (ii) capable of inhibiting a protein of interest (e.g., PTP1B), the cell will enable detection of that molecule. That is, it will exhibit a concentration-dependent response in luminescence, fluorescence, or growth. Many non-native biologically active metabolites have useful pharmaceutical properties. Examples include paclitaxel and artemisinin, plant-derived terpenoids that are used to treat cancer and malaria, respectively. When the metabolic pathways responsible for making such natural metabolites are installed into microbial cells that also contain our operon, those cells will enable detection of metabolite-based biological activities (e.g., the ability to inhibit PTP1B). 
     In some embodiments, methods of evolving molecules may be modified from Moses, et al., “Bioengineering of plant (tri)terpenoids: from metabolic engineering of plants to synthetic biology in vivo and in vitro.” New Phytologist, Volume 200, Issue 1, where this reference describes synthesis of artemisinic acid, the precursor of the antimalarial drug artemisinin, as diterpenoids expressed in  E. coli . Further, enzyme engineering or directed evolution of terpenoid biosynthetic enzymes, e.g. engineer enzymes to accept unnatural substrates and to catalyze regions and stereospecific reactions with an efficiency comparable with that of the natural enzymes is described, along with discussions on enhancing the production of terpenoids in  Escherichia coli . In some embodiments, methods of evolving molecules may be modified from Badran, et al., “Continuous evolution of  Bacillus thuringiensis  toxins overcomes insect resistance”. Nature, Vol 533:58, 2016, where this reference describes a phage-assisted continuous evolution selection that rapidly evolves high-affinity protein-protein interactions, and applied this system to evolve variants of the Bt toxin Cry1Ac that bind a cadherin-like receptor from the insect pest  Trichoplusia ni  (TnCAD) that is not natively bound by wild-type Cry1Ac. 
     A. Protein Evolving Systems and Evolving Biologically Active Metabolites. 
     In some embodiments, methods of evolving molecules may be used to construct drug leads that can be readily synthesized in microbial hosts. It addresses a longstanding challenge—the development of low-cost pharmaceuticals—by using a sophisticated set of biophysical tools and analytical methodologies to narrow the molecular search space in lead discovery, and by explicitly considering the biosynthetic accessibility of therapeutic molecules. The approach, which departs from contemporary efforts to use microbial systems for the synthesis of clinically approved drugs and their precursors, is unique in its focus on using biology for the systematic construction of new molecules. It will accelerate the rate—and lower the cost—of pharmaceutical development. 
     The development of a drug requires optimization of many of its pharmacological properties—affinity, absorption, distribution, metabolism, excretion, toxicology, pharmacokinetics, and pharmacodynamics 1 . The first of these properties—protein-ligand binding affinity—generally determines whether the others are worth measuring or enhancing, and, thus, represents a property of drug leads 2 . Despite advances in computational chemistry and structural biology, the rational design of ligands that bind tightly to proteins—ligands, henceforth, referred to collectively as inhibitors—remains exceptionally difficult 3 ; as a result, the development of drugs often begins with screens of large libraries of molecules 4 . An inhibitor, once discovered, must be synthesized in quantities sufficient for subsequent analysis, optimization, formulation, and clinical evaluation. 
     The difficulties associated with developing protein inhibitors are particularly problematic for natural products. These molecules, which account for over 50% of clinically approved drugs, tend to have favorable pharmacological properties (e.g., membrane permeability) 5 . Unfortunately, their low natural titers—which hamper the extraction of testable quantities from natural sources and their chemical complexity—which complicates chemical synthesis—make the preparation of quantities sufficient for post-screen analyses time-consuming and expensive 6 . 
     In some embodiments, enzymes are contemplated for use to construct terpenoid inhibitors that can be synthesized in  ESCHERICHIA COLI ; such an approach takes advantage of the chemical diversity (and generally favorable pharmacological properties) of natural products without the constraints of their natural scarcity. In some embodiments, detailed biophysical study of the molecular-level origin and thermodynamic basis of affinity and activity in protein-terpenoid interactions are included for the rapid construction of high-affinity inhibitors. In some embodiments, development of selective inhibitors of protein tyrosine phosphatase 1B (PTP1B), a target for the treatment of diabetes, obesity, and cancer is contemplated in part for using enzymes to evolve readily synthesizable drug leads. 
     Structurally Varied Terpenoids with Different Affinities for the Allosteric Binding Pocket of Protein Tyrosine Phosphatase 1B (PTP1B). 
     Hypothesis. Results indicate that abietic acid, a mono-carboxylated variant of abietadiene, is an allosteric inhibitor of PTP1B. Derivatives or structural analogs of abietadiene that differ in stereochemistry, shape, size, and/or chemical functionality (including carboxylation position) are likely to have different affinities for the allosteric binding pocket of PTP1B. 
     In some embodiments, (i) mutants of abietadiene synthase, cytochrome P450s, and halogenases are contemplated for use to make structural variants of abietadiene, (ii) GC/MS to identify those variants, (iii) preparative HPLC and flash chromatography to isolate them, and (iii) isothermal titration calorimetry to determine their free energies, enthalpies, and entropies of binding. In some embodiments, a set of structurally varied inhibitors with (i) affinities that differ by 100-fold and/or (ii) enthalpies and entropies of binding that suggest alternative binding geometries is contemplated. 
     To Examine the Molecular Basis and Thermodynamic Origin of Affinity and Activity in Enzyme-Terpenoid Interactions. 
     Hypothesis. Enzymes that bind, functionalize, and/or synthesize terpenoids possess large nonpolar binding pockets. We hypothesize that both (i) the affinity of an enzyme for terpenoids and (ii) the activity of an enzyme ON terpenoids is determined by the general shape and hydration structure of its binding pocket, not the position of specific protein-terpenoid contacts. 
     In some embodiments, a sophisticated set of biophysical tools (isothermal titration calorimetry, X-ray crystallography, molecular dynamics (MD) simulations, and NMR spectroscopy) are contemplated for use to (i) determine how protein-ligand contacts, rearrangements of water, and conformational constraints contribute to differences in affinity between terpenoid inhibitors and to (ii) develop a set of empirical relationships that predict how mutations in terpene synthases and terpene-functionalizing enzymes influence general attributes (e.g., shape) of their products. 
     To Evolve High-Affinity Terpenoid Inhibitors of PTP1B. 
     Hypothesis. Mutants from secondary metabolism (e.g., terpene synthases, cytochrome P450s, and halogenases) are highly promiscuous; a single mutation in or near their active sites can dramatically alter their product profiles. Mutagenesis of a small number (i.e., 2-4) of such enzymes, selected for their ability to synthesize and/or functionalize diterpenoids, will enable the development of inhibitors of PTP1B with sub-micromolar affinities. 
     In some embodiments, high-affinity inhibitors of PTP1B by pairing (i) high-throughput methods for detecting inhibitors with (ii) site-saturation and random mutagenesis is contemplated. For (i) we will develop four alternative fluorescence or growth-coupled assays to screen libraries of mutated pathways (and their respective products). For (ii) we use biostructural analyses and sequence alignments to identify residues likely to yield enzymes with favorable product profiles. 
     To Identify Structure-Activity Relationships that Enable the Evolution of Terpenoid Inhibitors of Arbitrary Protein Targets. 
     Hypothesis. Proteins that interact with similar classes of molecules (through binding or catalysis) have structurally similar binding pockets. Methods for evaluating these structural similarities—and their implications for enzyme activity—may enable the identification of enzymes capable of synthesizing inhibitors of ANY specified protein. 
     In some embodiments, a biophysical framework for using the crystal structure of a protein as a starting point to identify enzymes capable of synthesizing inhibitors of that protein is contemplated. We will examine (and formalize) structural relationships between (i) the active sites of enzymes used to synthesize allosteric inhibitors of PTP1B and (ii) the allosteric binding pocket of PTP1B, and we will validate these relationships by using them to identify—and, then, test new enzymes capable of synthesizing inhibitors of PTP1B and (separately) undecaprenyl diphosphate synthase, a target for the treatment of antibiotic-resistant bacterial infections. 
     Diabetes, Obesity, and Cancer. 
     Protein tyrosine phosphatase 1B (PTP1B) contributes to insulin resistance in type 2 diabetes 7 , leptin resistance in obesity 8 , and tumor growth in breast, colorectal, and lung cancers 9,11 . To date, the development of selective, tight-binding inhibitors of PTP1B (i.e., treatments for diabetes, obesity, and cancer) has been hindered by the structure of its active site, where polar residues limit tight binding to charged, membrane-impermeable molecules, and where structural similarities to the active sites of other protein tyrosine phosphatases (PTPs) lead to off-target interactions 12,14 . In this proposal, we will construct selective inhibitors of PTP1B that bind to its C-terminal allosteric site, a largely nonpolar region that is not conserved across phosphatases 15 . Previous screens of large molecular libraries have identified several ligands that bind to this site, but have yet to yield clinically approved drugs 16,13 . The identification of new molecular alternatives—a feat tackled in this proposal—remains a goal in efforts to develop selective PTP1B-inhibiting therapeutics. 
     Development of pharmaceuticals. The development of enzyme inhibitors—or leads represents an expensive part of drug development; for each successful drug, lead identification and optimization takes an average of 3 years and $250M to complete (−20-30% of the total time and cost to bring a drug to market) 17 . By narrowing the molecular search space in lead discovery, by enabling rapid construction of structurally-varied leads (often referred to as “backups” 18 ), and by facilitating scale-up of molecular synthesis, the technology developed in this proposal could accelerate the rate—and lower the cost—of pharmaceutical development. 
     Molecular recognition. The hydrophobic effect—the free energetically favorable association of nonpolar species in aqueous solution—is, on average, responsible for −75% of the free energy of protein-ligand association 19 . Unfortunately, hydrophobic interactions between ligands and proteins—which differ dramatically in rigidity, topography, chemical functionality, and hydration structure—remain difficult to predict 20 . This study uses detailed biophysical analyses and explicit-water calculations to examine the thermodynamic basis of hydrophobic interactions between terpenoids and protein binding pockets. It will develop a model system—and corresponding conceptual framework—for studying the hydrophobic effect in the context of structurally varied protein-ligand complexes, for accounting for that effect in the design of biosynthetic pathways, and for exploiting it in the construction of new drug leads. 
     Biosynthesis of New Natural Products. 
     Synthetic biology offers a promising route to the discovery and production of natural products. When the metabolic machinery of one organism is installed into a genetically tractable production host (e.g.,  S. CEREVISIAE  or  E. COLI ), it enables the synthesis of complex compounds at high titers (relative to the native host). This approach has enabled the efficient production of pharmaceutically relevant metabolites from unculturable or low-yielding organisms 21,22 , but, unfortunately, requires large investments of time and resources in pathway discovery and optimization; its use, as a result, is generally limited to the low-throughput characterization of newly discovered gene clusters or to the production of known, pharmaceutically relevant molecules (e.g., paclitaxel, artemisinin, or opioids) 22,24 . 
     In some embodiments, a strategy for using synthetic biology to build new molecular function is contemplated. It begins with a pathologically relevant protein target and engineers pathway enzymes to produce molecules that selectively inhibit that target. This approach will yield molecules that can be produced in microbial hosts without extensive pathway optimization (it relies on enzymes that are expressible by default); it will, thus, expand the use of synthetic biology to the production of leads and backups. It is not a replacement for conventional approaches to the synthesis of complex natural products, but rather, a complementary strategy for constructing new compounds that will enhance the efficiency with which pharmaceuticals are developed. 
     In the presence of mutated metabolic pathways (e.g., version of a plant-based terpenoid-producing pathway in which the terpene synthase has been mutated), our operon will enable screens of large numbers of metabolites for their ability to inhibit our protein of interest (e.g., PTP1B). Such a platform could be used to evolve metabolites with specific biological activities. 
     Detect and/or evolve highly selective molecules. We have developed an idea for a version of our operon to detect molecules that inhibit one protein over a highly similar protein. Screens for molecular selectivity are, at present, remain very difficult. 
     Advantages of methods and systems described herein, over some other systems for detecting small molecule inhibitors includes but is not limited to enabling the detection of molecules that modulate or change the catalytic activity of an enzyme. Moreover, some embodiments of the systems described herein allow for the detection of test molecules that change the activity of an enzyme by binding anywhere on its surface. As one example, detection of an inhibitor is contemplated that inactivates PTP1B by binding to its C-terminal allosteric site; this binding event, which distorts catalytically essential motions of the WPD loop, would not necessarily prevent enzyme-substrate association. U.S. Pat. No. 6,428,951, herein incorporated by reference in its entirety, in contrast, enables the detection of molecules that prevent enzyme-substrate binding by competing for substrate binding sites (i.e., the active site). As another example, detection of molecules that activate an enzyme of interest is contemplated as an embodiment. U.S. Pat. No. 6,428,951, herein incorporated by reference in its entirety, in contrast, has methods that merely detect molecules that prevent enzymes from binding to their substrates, or that otherwise change the affinity of enzymes for their substrates. As another example, detection of molecules that do not require an enzyme and substrate to interact with any particular affinity, orientation, or half-life is contemplated as an embodiment. U.S. Pat. No. 6,428,951, herein incorporated by reference in its entirety, in contrast, requires an enzyme and substrate to bind one another with an affinity and orientation that enable assembly of a split reporter. As a result, it may require modifications to the enzyme; in contrast, the inventors use a “substrate trapping” mutant of PTP1B to improve its affinity for a substrate domain. 
     As another example, some embodiments enables the detection of inhibitors of wild-type enzymes. Tu S., U.S. Pat. No. 6,428,951, herein incorporated by reference in its entirety, in contrast, requires enzymes to be fused to one-half of a split reporter. 
     Further, the following two publications are examples of methods that for detecting molecules that merely disrupt the binding of an enzyme to a substrate. This characteristic, among others, is in contrast to U.S. Pat. No. 6,428,951. “Protein fragment complementation assays for the detection of biological or drug interactions.” Pub. Date: Jan. 31, 2008, herein incorporated by reference in its entirety, which describes a high throughput bacteria based protein-fragment complementation assays (PCAs) wherein when two protein fragments derived from the enzyme dihydrofolate reductase (DHFR), coexpressed as fusion molecules in  Escherichia coli , that interact in the absence of an inhibitor, then concentration dependent colony growth was observed. This reference states that PCA can be adapted to detecting interactions of proteins small molecules and provide examples, including complementary fragment fusions and a bait-fused fragment. In fact, protein tyrosine phosphatase PTP1B was provided in an example for detecting enzyme substrate interactions and an example of survival assay for detecting protein substrate interactions using aminoglycoside kinase (AK), an example of antibiotic resistance marker used for dominant selection of an  E. coli ,-based PCA. Further, a PCA is described as being applied to identify small molecule inhibitors of enzymes; natural products or small molecules from compound libraries of potential therapeutic value; may be used as survival assay for library screening; for detecting endogenous DHFR inhibitors, e.g. rapamycin; and for protein-drug interactions. Expression of PCA complementary fragments and fused cDNA libraries/target genes can be assembled on single plasmids as individual operons under the control of separate inducible or constitutive promoters with interceding region sequences, e.g. derived from a mel operon, or have polycistronic expression. The PCA can be adapted to detecting interactions of proteins with small molecules. In this conception, two proteins are fused to PCA complementary fragments, but the two proteins do not interact with each other. The interaction must be triggered by a third entity, which can be any molecule that will simultaneously bind to the two proteins or induce an interaction between the two proteins by causing a conformational change in one or both of the partners. Moreover, exemplary applications of the PCA Strategy in bacteria to protein engineering/evolution to generate peptides or proteins with novel binding properties that may have therapeutic value using phage display technology. One example of evolution produced novel zipper sequences; other examples of evolutions were described to produce endogenous toxins. 
     WO2004048549. Dep-1 Receptor Protein Tyrosine Phosphatase Interacting Proteins And Related Methods. Published Jun. 10, 2004, herein incorporated by reference in its entirety; describes screening assays for inhibitors that alter the interaction between a PTP and a tyrosine phosphorylated protein that is a substrate of the PTP, e.g. dephosphorylation by Density Enhanced Phosphatase-1 (DEP-1) of a DEP-1 substrate. DEP-1 polypeptides can be expressed in bacteria cells, including  E. coli , under the control of appropriate promoters, e.g.  E. coli  arabinose operon (P BAD  or P ARA ). This reference is similarly limited in focus as U.S. Pat. No. 6,428,951, herein incorporated by reference in its entirety; it enables the detection of molecules that disrupt the binding of a substrate to an enzyme, rather than the detection of molecules that modulate (i.e., enhance or reduce) the activity of an enzyme. 
     Advantages of methods and systems described herein, over some other systems for detecting small molecule inhibitors includes but is not limited to enabling the evolution of metabolites that change the catalytic activity of an enzyme. The technology described in Badran, et al., “Continuous evolution of  Bacillus thuringiensis  toxins overcomes insect resistance”. Nature, Vol 533:58, 2016, herein incorporated by reference in its entirety; and the platform of continuous evolution in general, has been used to evolve proteins with different affinities for other proteins/peptide substrates. It has not, however, been used to evolve enzymes that produce small molecules (i.e., metabolites) that alter the activities of enzymes or the strength of protein-protein interactions. 
     Another advantage of methods and systems described herein, over some other systems for detecting small molecule inhibitors includes the discovery of metabolites with targeted biological activities but unknown structures (e.g., the ability to inhibit protein tyrosine phosphatase 1B). There are many inventions relevant to the production of terpenoids in  E. coli  or  S. cerevisiae  (e.g., Moses, et al., “Bioengineering of plant (tri)terpenoids: from metabolic engineering of plants to synthetic biology in vivo and in vitro.” New Phytologist, Volume 200, Issue 1, where this reference describes synthesis of artemisinic acid, the precursor of the antimalarial drug artemisinin, as diterpenoids expressed in  E. coli . Further, enzyme engineering or directed evolution of terpenoid biosynthetic enzymes, e.g. engineer enzymes to accept unnatural substrates and to catalyze regions and stereospecific reactions with an efficiency comparable with that of the natural enzymes is described, along with discussions on enhancing the production of terpenoids in  Escherichia coli .); in many cases, the metabolic pathways responsible for making these terpenoids are mutated to improve production levels. However, the use of biosensors (i.e., constructs that report on the concentrations of various metabolites) has focused on the detection of specific intermediates (e.g., farnesyl pyrophosphate, a precursor to terpenoids) not for combining (i) mutagenesis of a metabolic pathway and (ii) a biosensor for specific biological activity (e.g., the ability to inhibit PTP1B) for the discovery of new biologically active molecules (which may possess unknown structures). 
     High-Throughput Metabolic Engineering. 
     Microbial pathways are most efficiently optimized with high-throughput screens. Unfortunately, at present, such screens are sparse, and those available rely on signals (e.g., absorbance or fluorescence, association with a product-specific transcription factor, or growth permitted by an essential metabolite) that are difficult to extend to broad classes of molecules (e.g, those without distinct optical or metabolic properties) 27 . The proposed work develops high-throughput screens for terpenoids with a targeted activity—the ability to inhibit PTP1B—rather than a targeted structure; these activity-focused screens could be broadly useful for building (i.e., evolving) new biologically active small molecules. 
     Identification of new inhibitors: a starting point. We recently discovered that abietic acid, the primary component of resin acid, is an allosteric inhibitor of PTP1B ( FIG.  22   ). We will use abietadiene, the immediate precursor of this molecule, as a starting point for the design of inhibitors. Abietadiene has several attributes that make it particularly compatible with our approach: (i) It can be synthesized in E.  COLI  at titers (200 mg/L) that permit purification, NMR analysis, and calorimetric studies 28 , (ii) Mutants of its associated terpene synthase—abietadiene synthase—yield a range of hydrocarbon scaffolds that differ in stereochemistry, shape, and size (and that still enable analysis and purification) 29-31 , (iii) It—and similar molecules—can be functionalized by cytochrome P450s and halogenases 32-34 . 
     Metabolic engineering. We have engineered a strain of  E. COLI  to produce abietadiene at titers (&gt;150 mg/L) sufficient to permit the analytical methods (i.e., GC/MS, ITC, and NMR). Our biosynthetic pathway has two requisite operons: MBIS, which converts (RJ-mevalonate to farnesyl pyrophosphate (FPP), and TS, which converts farnesyl pyrophosphate to abietadiene. One optional operon—MevT, which converts acetyl-CoA to (RJ-mevalonate—is necessary when mevalonate is not included in the media 35 . The plasmids pMevT and pMBIS were developed by the Keasling Laboratory 36 . The plasmid pTS, which contains abietadiene synthase (ABS) from  ABIES GRANDIS , was developed as in Morrone 28  with a gene for geranylgeranyl diphosphate synthase from Ajikumar 37 . 
     Improved inhibitors. We assessed the ability of minor structural perturbations of abietadiene derivatives to yield improved inhibitors by comparing four structurally related (and commercially available) molecules ( FIG.  16   ): abietic, neoabietic, levopimaric, and dihydroabietic acid. Surprisingly, dihydroabietic acid was ten times more inhibitory than abietic acid (K, ˜25 uM vs. 250 uM). Our ability to find an improved inhibitor in this small screen suggests that the kinds of structural variations explored in this study—and the sizes of molecular libraries generated—are likely yield improved inhibitors. 
     Functionalization of abietadiene. We assessed the ability of mutants of cytochrome P450 b m3 to functionalize abietadiene-like molecules by installing five readily available mutants (G3, KSA-4, 9-1 OA, 139-3, and J, which were engineered for activity on amorphadiene 38  and steroids 39 ) into our heterologous pathway; three mutants yielded hydroxylated and/or carb oxylated products, generating up to 0.3 mg/L of abietic acid ( FIG.  17   ). The abietadiene-functionalizing activity of mutants originally engineered for other targets suggests that we will be able to develop mutants of P450 b m3 with even higher activities on abietadiene-like molecules. 
     Biostructural analyses. We have crystallized PTP1B in our lab, collected X-ray diffraction data in collaboration with Peter Zwart at Lawrence Berkeley National Lab (LBNL), and solved its crystal structure ( FIG.  17 A  inset). We have also co-crystallized PTP1B with abietic acid; we will analyze these crystals in late July (first available beam time). 
     Recently, we expressed N 15 -labeled PTP1B and used it to collect two-dimensional  1 H- 15 N HSQC spectra in collaboration with Haribabu Arthanari at Harvard Medical School ( FIG.  17 A  main). The spectra include PTP1B bound (separately) to abietic acid and known inhibitors; at present, we are processing the data. Preliminary results (X-ray and NMR) suggest that biostructural studies of PTP1B bound to different inhibitors will be straightforward. 
     High-throughput screens. Upon binding to inhibitors (both competitive and allosteric), PTP1B exhibits changes in conformation that quench its tryptophan fluorescence (the basis of one of our four high-throughput screens).  FIG.  17 B  indicates that such quenching can be used to distinguish between inhibitory extract (i.e., a hexane overlay) from an abietadiene-producing strain of  E. COLI  and non-inhibitory extract from a control strain (i.e., one with a catalytically inactive ABS).  FIG.  17 C  indicates that such changes can also be used to detect 50 uM (15 mg/L) of abietic acid. Our ability to detect (i) abietadiene in culture extract and (ii) abietic acid at low concentrations (i.e., tenfold lower than our titers of abietadiene) suggests that we will be able to detect improved inhibitors of PTP1B, even if they are accompanied by reductions in titer. 
     Providing structurally varied terpenoids with different affinities for the allosteric binding pocket. This section describes developing a set of inhibitors with incremental differences in affinity that result from systematic differences in structure. The goal (metric for success): a minimum of −15 structurally varied inhibitors with (i) affinities for PTP1B that differ by 100-fold and/or (ii) enthalpies and entropies of binding that suggest alternative binding geometries. 
     Research plan. In the sections that follow, we use enzymes to build selective terpenoid inhibitors of PTP1B. This enzyme is the initial focus of our work because it is a therapeutic target for diabetes, obesity, and cancer, and it can be expressed, crystallized, and assayed with ease 15 . It, thus, serves as a pharmaceutically relevant model system with which to develop a general approach for the enzymatic construction of drug leads. 
     Hypothesis for structural changes. In this section, we use promiscuous enzymes to construct terpenoids that differ in stereochemistry, shape, size, and chemical functionality. We believe that these modifications will affect the affinity of ligands for PTP1B by altering (i) their ability to engage in van der Waals interactions with nonpolar residues (e.g., F280, L192, and F196) in the allosteric binding pocket, (ii) their ability to engage in direct or water-mediated hydrogen bonds with proximal polar residues (e.g., N193, E200, and E276), (iii) their ability to engage in halogen bonds with either set of residues, (iv) their influence on molecular conformational constraints, and, (v) their ability to reorganize water during binding. This hypothesis (which is supported, in part, by  FIG.  16   ) motivates the synthetic strategy described herein. 
     Stereochemistry, shape, and size. We will begin by using mutants of ABS to generate diterpenoids that differ in stereochemistry and shape  FIG.  18 A ). ABS uses two active sites to catalyze sequential class II (protonation-dependent) and class I (ionization-dependent) cyclization of geranylgeranyl pyrophosphate (GGPP, C 2 o) into abietadiene 29 . Previous studies indicate that amino acid substitutions in its active sites can alter the stereochemistry or shape of its products 29,31 . We will use mutations (new and previously identified) that affect the position of deprotonation, intramolecular protein transfer, or carbocation stability ( FIG.  8 B ). After installing these mutants into  E. COLI , we will use GC/MS to search for new products (fragmentation tools such as MetFrag 40  or ACD/MS Fragmenter 41  will facilitate identification of novel compounds). 
     We will generate terpenoids that differ in size by using mutations that increase/decrease the volume of the active sites of ABS. Previous attempts to change the substrate specificities of terpene synthases 42,43  suggest that such mutations could enable enhanced activity on farnesyl pyrophosphate (FPP, CI 5 ) and farnesylgeranyl pyrophosphate (FGPP, C 2 s). To synthesize FGPP, we will incorporate an FGPP synthase previously expressed in  E. COLI   44 . 
     We will isolate a subset of new terpenoids with particularly high titers by using flash chromatography and HPLC (a task for which feasibility has been established in several studies 28,31,45 ), and we will use ITC to measure the free energy (AG° birid ), enthalpy (AH° bind ), and entropy (−TAS° bind ) of binding to PTP1B. Differences in AG° b ind between ligands will reveal how structural changes affect the strength of binding; differences in AH° bin d and −TAS° b i nd  will reveal their influence on binding geometry 46,47 . 
     Hydroxylation and halogenation. For each of the three ligands selected in 6.1.2, we will use mutants of cytochrome P450 BM3 (P450 b m3) from  BACILLUS MEGATERIUM  and/or CYP720B4 (P450 72 o) from  PICEA SITCHENSIS  to construct five variants with hydroxyl or carboxyl groups at different positions ( FIGS.  19 A and  19 B ). P450 b m3 can hydroxylate a wide range of substrates, including terpenoids 48 ; P450 72 o can carboxylate over 20 diterpenoids, including abietadiene 49 . Both enzymes can be expressed in  E. COLI   ,4A . 
     We will work with several sets of mutations: For P450 bm 3, we will use (i) three (V78A, F87A, and A328L) that permit the stereoselective hydroxylation of sesquiterpenes and diterpenes 50 , (ii) five (L75A, M177A, L181A, and L437A) that enable hydroxylation of alkaloids and steroids 51 ), and (iii) two (F87V and A82F) that permit carboxylation of heteroaromatics ( FIG.  18 D ) 52 . For P450 72 o, we will examine −10 similar mutations likely to alter the position of oxidation. We will, again, screen each mutant in  E. COLI , isolate interesting products, and use ITC to analyze them. 
     For each of two high-affinity oxygenated ligands, we will construct six variants with bromide or iodide at different positions ( FIG.  18 C ). These two halogens can engage in halogen bonds with oxygen, nitrogen, or sulfur acceptors in proteins 53 , and can bind small nonpolar declivities on their surfaces 54 . The energetic contribution associated with both interactions tends to increase from Br to I 54,55  and, thus, lends itself to systematic analysis (i.e., a physical organic approach). To generate halogenated ligands, we will use mutants of tryptophan 6-halogenase (SttH) from  STREPTOMYCES TOXYTRICINI  and vanadium haloperoxidase (VHPO) from  ACARYOCHLORIS MARINA . These enzymes can introduce halogens (chloride, bromide, or iodide) into sp 2 -hybridized carbons of alkaloids or terpenoids (before or after cyclization) 56,57 . For each enzyme, we will examine several mutations known to change regioselectivity (e.g., L460F, P461E, and P452T for SttH 56 ) and 5-10 mutations likely to change the orientation of bound  FIG.  19    Examples: ( FIG.  19 A ) carboxylated, (B) hydroxylated, ligands ( FIG.  19 E ). We will, again, screen ( FIG.  19 C ) and halogenated diterpenoids. ( FIG.  19 D-E ) Residues each mutant in  E. COLI  and use ITC to targeted for mutagenesis in ( FIG.  19 D ) P450 bm 3 and ( FIG.  19 E ) SttH. 
     IV. Evolving High-Affinity Terpenoid Inhibitors of PTP1B. 
     This section develops four high-throughput screens for rapidly evaluating the strength of PTP1B inhibitors, and it uses those methods, in conjunction with site-saturation and random mutagenesis, to evolve new inhibitors. The goal: a set of evolved inhibitors with particularly high affinities (K D {circumflex over ( )}1 uM) and/or unpredictable structures (i.e., structures inconsistent with rational design). 
     Biological selection. A selection method (i.e., a growth-coupled screen) in which the survival of  E. COLI  is linked to inhibitor potency will enable rapid screening of extremely large libraries of molecules (10 10 ) 66 . In this section, we develop such a method. 
     PTP1B catalyzes the dephosphorylation—and inactivation—of several cell surface receptors. We will use the tyrosine-containing regions of these receptors to build an operon that links inhibition of PTP1B to cell growth. This operon will require six components ( FIG.  21 A ): (i) a substrate domain (the tyrosine-containing region of a receptor) tethered to a DNA-binding protein, (ii) a substrate recognition domain (a protein that binds the tyrosine-containing region after its phosphorylation) tethered to the co subunit of an RNA polymerase, (iii) a tyrosine kinase, (iv) PTP1B, (v) a gene for antibiotic resistance, and (vi) an operator for that gene. With this system, inhibitors of PTP1B will enable binding of the substrate and substrate recognition domains, recruitment of RNA polymerase to the DNA, and transcription of the gene for antibiotic resistance. Previous groups have used similar operons to evolve protein-protein binding partners; here, we take the additional steps of (i) using a protein-protein interaction mediated by enzymes (PTP1B and a kinase) and of (ii) screening that interaction in the presence of potential inhibitors of one of those enzymes. 
     We will develop our operon by starting with a luminescence-based system, and we will add an antibiotic resistance gene as a final step. In our preliminary work with a system optimized by Liu et al. 67 , we obtained a tenfold difference in Lux-based luminescence between a strain expressing two binding partners and a strain expressing one ( FIG.  21 E ; arabinose induces expression of the second partner). We now plan to introduce—and test—different substrate domains, recognition domains, and kinases (eGFR and Src). 
     A FRET sensor for PTP1B activity. A high-throughput screen in which inhibition of PTP1B is linked to cell fluorescence will enable rapid screening via fluorescence-activated cell sorting (FACS). This technique tends to produce more false positives than selection and limits libraries to sizes of 10 7 -10 8 , but it requires fewer heterologous genes 27,66 . 
     For this strategy, we will make use of FRET (Forster resonance energy transfer) sensors commonly used to monitor kinase and phosphatase activity in mammalian cells 68,69 . These sensors consist of a kinase substrate domain, a short flexible linker, and a phosphorylation recognition domain—all sandwiched between two fluorescent proteins. Phosphorylation of the substrate domain causes it to bind to the recognition domain, inducing FRET between the two fluorescent proteins. In a PTP1B-compatible sensor, inhibitors of PTP1B will increase FRET ( FIG.  21 B ). We have begun to develop such a sensor by trying different combinations of substrate domains, recognition domains, and kinases. (Note: FACS enables FRET-based screens 70,71 ). 
     A FRET sensor for changes in the conformation of PTP1B. A FACS-based screen in which changes in cell fluorescence result from binding-induced changes in the conformation of PTP1B would be less generalizable than strategies 2 and 3 (which could be used for any kinase or phosphatase), but would require only one heterologous gene. 
     For this strategy, we will make use of a FRET experiment carried out by the Tonks Group 13 . These researchers sought to show that the binding of trodusquemine to PTP1B caused the protein to become more compact. To do so, they attached members of a FRET pair to each terminus of the PTP1B ( FIG.  21 C ); upon protein-ligand association, an increase in FRET signal indicated that its termini approached one another. We hypothesize that this construct could be used as a sensor for identifying other molecules that bind to the allosteric site of PTP1B. We will begin by testing it with a variety of known inhibitors (a step the Tonks group did not take). 
     Binding-induced changes in the tryptophan fluorescence of PTP1B. A screen in which inhibition of PTP1B is linked to changes in tryptophan fluorescence ( FIG.  21 D ) will enable rapid screening of moderately sized libraries (10 3 -10 4 ) 27  in microtiter plates. Our use of binding-induced changes in tryptophan fluorescence is described in 5.6. In future work, we plan to extend this approach to other protein tyrosine phosphatases, many of which are allosteric and possess many tryptophans (e.g., SHP-2, a target for Noonan syndrome 72 ) 
     Mutagenesis. To use our high-throughput screens to evolve inhibitors of PTP1B, we will build libraries of mutated terpenoid pathways by using (i) site-saturation mutagenesis (SSM; we will target binary combinations of sites) and (ii) error-prone PCR (ep-PCR). 
     For SSM, we will identify “plastic” residues likely to accommodate useful mutations by developing functions similar to Eq. 1. This function scores residues based on their ability to accommodate mutations that influence the volume and hydration structure of an active site; S is a metric for the propensity of a residue to permit mutations, cr 2  is the variance in volume of 
         s= 4+ RTW   (EQ 1}
 
     similarly positioned residues in the active sites of other enzymes, A{circumflex over ( )} W  is the variance in hydrophilicity of those residues, and N V  and N HW  are normalization factors. In our preliminary analysis of ABS, we successfully used Eq. 1 (and structure/sequence information from Taxadiene, y-humulene, 5-selenine, and epi-isozizaene synthases) to identify residues for which mutations are known to yield new products (e.g., H348 of ABS) 31 . We note: Previous attempts to identify plastic residues have scanned each site near the bound substrate 73 ; our approach will be unique in its inclusion of biophysical considerations from (i) our study of optimal ligand attributes (6.2.1) and (ii) our study of the types of mutations that bring them about (6.2.2).
 
For library construction, we will explore mutating our pathway (i) enzyme-by enzyme (e.g., ABS, then P450 b m3, and then VttH) or (ii) at random. The second approach could give us access to structures that might be difficult to find with conventional approaches to lead design.
 
     To identify structure-activity relationships that enable the evolution of terpenoid inhibitors of arbitrary protein targets. This section develops a biophysical framework for using a crystal structure of a protein to identify enzymes capable of making inhibitors of that protein. The goal: the use of that framework to identify—and, then, test—enzymes capable of synthesizing new inhibitors of PTP1B and (separately) undecaprenyl diphosphate synthase (UPPS), a target for antibiotic-resistant bacterial infections. 
     Relationships between binding pockets. We will begin by determining how similarities in specific properties of binding pockets (e.g., volume, polarity, and shape) enable enzymes to synthesize, functionalize, and/or bind similar molecules. This effort will involve comparisons of the allosteric binding pocket of PTP1B with the binding pockets (i.e., active sites) of enzymes involved in inhibitor synthesis. For these comparisons, we will construct two matrices: matrix A in which each element (ay) represents the similarity of a specific property between binding pockets i and j ((0&lt;aij&lt;1, where 1 is highly similar) and matrix B in which each element (by) describes the ability of binding pockets i and j to bind similar molecules (0&lt;by&lt;1, where 1 represents identical binding specificities). The rank of the matrix formed by the product of these two matrices (AB) will suggest the number of independent variables (i.e., active site attributes) necessary to determine the functional compatibility of enzymes in a metabolic pathway; the eigenvalue will suggest the relative importance of the property under study (described by matrix A). 
     We will construct matrix A with PyMol- and MD-based analyses of protein crystal structures. We will construct matrix B by examining the binding of functionalized terpenoids and their precursors to each enzyme involved in terpenoid synthesis. Binding affinities for some of these ligand/protein combinations will be measured with ITC; most will be estimated with docking calculations (OEDocking 78 ). 
     The result of this section will be an equation similar to Eq. 2, where J is a metric for an active site&#39;s ability to synthesize 
         J=w   v   V+w   p   P+WiL+w   w   W   (Eq. 2)
 
     terpenoids that bind a particular binding pocket V, P, L, and W represent specific properties of that active site (volume, polarity, longest diameter, and shortest diameter); and w&#39;s represent weighting factors. The final number of variables—and their respective weights—will be determined through the above analysis. In parameterizing the equation, we plan to examine different metrics for properties of binding pockets (e.g. shape) and to explore/develop different matrix manipulations. 
     Validation and Extension. 
     The identification of promising active site motifs for inhibitor synthesis will require a search of available protein structural data. We will perform such a search by using PROBIS (probis.nih.gov 79 ), an alignment-based platform that uses a specified binding site to find similar binding sites on other proteins in the Protein Data Bank. PROBIS can identify similarly shaped binding pockets, even when the protein folds that surround those pockets are different (i.e., it detects similar constellations of amino acids). 
     To begin, we will use a PROBIS-based search to identify enzymes with active sites that have some level of structural similarity (we will explore different thresholds) to either (i) the allosteric binding site of PTP1B or (ii) the active sites of enzymes capable of synthesizing inhibitors of PTP1B. Using Eq. 2, we will select enzymes with the most favorable active sites and test them with our platform for inhibitor development). 
     We will assess the generalizability of our approach by attempting to construct inhibitors of UPPS, a protein known to bind terpenoids and polycyclic molecules 80 . Structure-based searches will use two starting points: (i) UPPS and (ii) mutants of ABS, P450 b m3, or similar enzymes that our biophysical analyses suggest might yield UPPS inhibitors. We will, again, select a subset of enzymes to test with our platform. 
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V. Specific Embodiments of Bacterial Systems for Identifying Small Molecules that Modulate the Activity of Enzymes.
 
       
    
     As described herein, a strain of  Escherichia coli  was developed comprising both (i) a genetically encoded system (i.e., a “bacterial two-hybrid” or B2H system) that links cell survival to the modulation inhibition of a pathologically relevant enzyme from  Homo sapiens  (i.e., a drug target) and (ii) a pathway for metabolite biosynthesis. The genetically encoded system described herein contains more genetic elements than would traditionally constitute a single operon (e.g. it has more than one promoter), but it is sometimes referred to as an operon. 
     More specifically, as described herein, host organisms, e.g.  Escherichia  ( E. )  coli , were transformed with up to four plasmids, including a first plasmid (plasmid 1) an expression plasmid comprising a genetically encoded system that links the inhibition of a target enzyme to cell survival, wherein the target enzyme may be chosen for the purpose of identifying molecules that inhibit a specific target enzyme; a second plasmid (plasmid 2) an expression plasmid comprising an operon for expressing at least some of the genes necessary to synthesize products of a metabolic pathway, e.g. a mevalonate-dependent pathway for terpenoid biosynthesis derived from  Saccharomyces cerevisiae  for providing terpenoid product compounds; a third plasmid (plasmid 3) an expression plasmid comprising at least one additional gene, not present in plasmid (plasmid 2), e.g. a terpene synthase, such as ADS, GHS, ABS, or TXS, for providing desired products, e.g. terpenoid products, such that when the host bacterial expresses plasmids 1 and 2, desired products are not produced until the host bacterial expresses plasmid 3 for completing the pathway for desired compounds; and a fourth plasmid (plasmid 4) comprising additional genetic components specific to the strain of  E. coli , e.g., the F-plasmid of 51030 (Addgene 105063). 
     Examples of plasmid 1 embodiments are shown in  FIG.  33 A,  33 B,  33 D,  33 E ,  FIG.  34   ,  FIG.  35   ,  FIG.  40 A,  40 B,  40 C,  40 D , etc. 
     In some embodiments, a strain of  E. coli  used as a host for transformation possesses the ΔrpoZ mutation, which enable the system encoded by plasmid 1 to control the expression of a gene for antibiotic resistance. 
     In some embodiments, plasmids 2 and/or 3 constitute a pathway for terpenoid biosynthesis. In some embodiments, plasmids 2 and/or 3 constitute a pathway for alkaloid biosynthesis. In some embodiments, plasmids 2 and/or 3 constitute a pathway for polyketide biosynthesis. 
     In some embodiments, plasmid 3 further comprises a GGPPS gene in combination with either ABS or TXS. Examples of GGPPS genes provide substrates for terpene synthase genes, i.e. ABS, or TXS. In some embodiments, terpene synthase genes are wild-type genes. In some preferred embodiments, terpene synthase genes contain mutations for producing variants of terpenoid products, as described and shown herein. In some embodiments, plasmid 3 further comprises a gene for terpenoid functionalizing enzymes, e.g., cytochromes P450. 
     In some preferred embodiments, plasmid 1 is under control of constitutive promoters. Thus, in some preferred embodiments, at least some of the genes that are part of the operon in plasmid 1 are constitutively expressed. In some preferred embodiments, at least some of the genes that are part of the operon in plasmid 1 are expressed when contacted with an inducible compound, i.e. under control of an inducible promoter, such as a lacZ promoter turned on when in contact with X-gal. 
     In some preferred embodiments, plasmids 2 and 3 are under control of inducible promoters. Thus, in some preferred embodiments, at least some of, and in some cases the entire set of genes contained in a metabolic pathway operon in plasmid 2 are expressed when contacted with an inducible compound. In some preferred embodiments, some genes expressed in plasmid 3 are under inducible control. 
     In some preferred embodiments, plasmid 4 is under the control of constitutive promoters. Thus, in some embodiments, at least one gene in plasmid 4 is under control of a constitutive promoter. In some embodiments, at least one gene in plasmid 4 is under control of an inducible promoter. 
     In some preferred embodiments, a host bacterium undergoes at least 2 rounds of transformation, e.g. first to transform plasmids 1 and 2 simultaneously into a strain that already harbors plasmid 4 (e.g., a 51030 strain which already comprises this accessory plasmid), followed by transformation with plasmid 3. In some preferred embodiments, a host bacterium undergoes at least 3 rounds of transformation, e.g. first to transfect plasmid 1, then transfect plasmid 2, followed by transfection of plasmid 3. 
     In some preferred embodiments, each plasmid has an antibiotic resistance gene (or other type of selective gene) for identifying successfully transformed bacteria for that plasmid, i.e. antibiotic resistance genes may be different for each plasmid. Thus, when an antibiotic resistance gene is expressed, instead of a bacteria stopped from normal replication when in contact with the antibiotic, a bacteria has resistance so is able to replicate at normal or near normal rates. 
     Thus, as described herein, laboratory stains of  E. coli  were engineered to comprise up to three types of expression plasmids by first transfecting with plasmid 1, then selecting for transformants (growing colonies) on/in antibiotic containing media wherein nontransformants do not grow, then transfecting transformants with plasmid 2 and selecting for double transformants, e.g. media containing antibiotics for allowing the growth of double transformants, then transfecting double transformants with plasmid 3 and selecting for triple transformants, e.g. media containing antibiotics for allowing the growth of triple transformants. In one embodiment, triple transformants are grown in media containing an inducer(s) for the inducible plasmids (2 and 3) in combination with the three antibiotics for producing products having at least some inhibitory activity for the chosen enzyme of plasmid 1, made by the enzymes provided by the combination of enzymes expressed by plasmids 2 and 3. 
     Further, as described herein, laboratory stains of  E. coli  were engineered to comprise up to four types of expression plasmids by first transforming host cells with plasmids 1 and 2, simultaneously, into a strain that already harbors plasmid 4, then selecting for triple transformants (growing colonies) on/in antibiotic containing media wherein non-transformants do not grow, then further transforming successful triple transformants with plasmid 3 and selecting for quadruple transformants, e.g. media containing antibiotics that allow for the growth of quadruple transformants. In one embodiment, quadruple transformants are grown in media containing (i) an inducer(s) for the inducible plasmids (2 and 3), (ii) a metabolic precursor for metabolite biosynthesis, e.g., mevalonate, and (iii) five antibiotics (i.e., one for each plasmid and one under control of the genetically encoded system in plasmid 1) for producing products having at least some inhibitory activity on the chosen enzyme of plasmid 1, made by the combination of enzymes expressed by plasmids 2 and 3. 
     In some embodiments, a terpenoid operon pathway intended for insertion into or already within plasmid 2, may be altered by swapping in a different gene for terpene synthases (i.e., in each row of  FIG.  36   , the metabolic pathway differs in the identity of the gene for a terpene synthase; when ADS or TXS are present, GGPPS is also present). 
     In  FIGS.  41 A,  41 B,  41 C, and  41 D , for examples, we mutate (rather than swap) a single gene of a metabolic pathway: e.g. induce at least one mutation in a gene encoding amorphadiene synthase. After doing so, we show that a metabolic pathway can be mutated to generate a library of pathways, and that these pathways can be screened to identify pathways that generate more potent inhibitors of PTP1B than the unmutated parent pathway. 
     To summarize, we provided a demonstration that (i) the B2H system (detection operon) and (ii) a metabolic pathway for terpenoid biosynthesis can be combined within a host organism to identify genes involved with production of small-molecules and evolve genes related to production of small-molecules that may be inhibitors that the microbial synthesis of PTP1B inhibitors. 
     In preferred embodiments, small-molecule products are derived from one general metabolic pathway (the mevalonate-dependent pathway for terpenoid biosynthesis from  Saccharomyces cerevisiae ), and one host organism ( Escherichia coli ). These small-molecule products produced as described herein, are contemplated for use as treatments of type 2 diabetes, obesity, and breast cancer, among other diseases. 
     Without being bound by theory, when a genetically encoded system for detecting the activity of a specified test enzyme is located within a host bacterium, a constitutive promoter expresses part A of the detection system (e.g. detection operon). So long as the phosphatase (or other test enzyme) expressed by part A is active, an expressed kinase enzyme, e.g. Src kinase, attaches a phosphate (P) group to the expressed second fusion protein comprising a substrate recognition domain (S) attached to a protein capable of recruiting RNA polymerase to DNA (e.g., the RP ω  subunit of RNA polymerase), and the phosphatase removes that phosphate group so that few molecules of phosphorylated fusion protein 2 stay bound to fusion protein 1 and, thus, few complexes between fusion proteins 2 and 1 form to initiate transcription of a gene of interest (GOI). 
     Thus, transcription of part B is off and the expression of a GOI is low, e.g. as observed when a GOI is a luminescent protein, so long as the placZ inducible promoter is not being induced. In this embodiment of an operon, the placZ inducible promoter is induced in order to allow the expression of a gene of interest in the absence of an inhibitor when not testing for inhibitor molecules. 
     However, in the presence of a small molecule that inhibits the phosphatase, a molecule either made endogenously from a metabolic pathway harbored by plasmids 2 and 3, or added to the growth media, then an excess of phosphorylated fusion protein 2 within the substrate binding region attaches to the substrate recognition domain of fusion protein 1 then when both are bound to the operator and the RB binding site then the GOI is expressed indicating the presence of a phosphatase inhibitor. 
     For practical purposes, it does not matter which fusion protein possesses a DNA-binding protein and which possesses a protein capable of recruiting RNA polymerase to DNA, so long as the DNA-binding protein constitutes part of one fusion protein and the protein that recruits RNA polymerase constitutes part of the other fusion protein, see  FIG.  40   ,  FIG.  10   , for examples. 
       E. coli  DH10B was used for molecular cloning and for preliminary analyses of terpenoid production;  E. coli  s1030′ was used for luminescence studies and for experiments involving terpenoid-mediated selection (e.g., molecular evolution); and  E. coli  B121 was used for experiments involving the heterologous expression and subsequent purification of proteins. However, it is not intended to limit the host bacteria strain to these  E. coli  strains. Indeed, any bacteria strain that supports the expression of the operons, DNA sequences and plasmids as described herein may be used as a host bacteria strain. 
     In preferred embodiments, small molecule products are derived from one general metabolic pathway (the mevalonate-dependent pathway for terpenoid biosynthesis from  Saccharomyces cerevisiae ), and one host organism ( Escherichia coli ). These small molecule products produced as described herein, are contemplated for use as treatments of type 2 diabetes, obesity, and breast cancer, among other diseases. 
     A. Bacterial Two-Hybrid (B2H) Systems (Operons) for the Identification of Microbially Synthesizable Inhibitors of PTP1B. 
     In one embodiment, an application of the B2H system to the evolution of genes that enable the microbial synthesis of molecules that (i) inhibit PRI B and (ii) may be identified (i.e., structurally characterized) with standard analytical methods. In brief, the B2H system links the inactivation of PIM B to the expression of a gene for antibiotic resistance. Accordingly, when a strain of  E. coli  (or other host bacterium) harbors both (i) the 132E1 system and (ii) a metabolic pathway for terpenoid biosynthesis, it will survive in the presence of antibiotics when it produces terpenoids that inhibit PTP1B. 
     A bacterial two-hybrid (B2H) system as described herein comprises one embodiment of an operon as described herein. Data displayed on left side of the plot in  FIG.  33 D  (i.e., p130cas [also called. Kras] and NUT substrates) is the same data displayed in  FIG.  29 A  with the addition of providing more details of the B2H system in light of development. 
     We propose to use directed evolution to evolve new inhibitors; that is, we will manually introduce mutations into specific genes (or sets of genes) within a metabolic pathway to generate a library of metabolic pathways that can be screened alongside the B2H system.  FIG.  41 A  describes a general approach to introduce mutations; Example C provides a very specific approach represented by  FIG.  41 A . To screen our library, we transform it into B2H-containing cells, and we grow them on plates containing various concentrations of spectinomycin; colonies that form on plates with high concentrations of spectinomycin contain a pathway capable of generating molecules that activate the B2H system (i.e., inhibit PTP1B). This pathway will not naturally evolve on its own. We can, thus, remove it from the first host cell, and transform it into another strain of  E. coli  to make high concentrations of inhibitors, 
     Embodiments of the system described herein enables the rapid identification of drug leads that can be readily synthesized in microbial hosts. It allows for a simultaneous solutions to two problems encountered during pharmaceutical development that are often examined separately 1) the identification of leads and 2) subsequent synthesis of those leads identified in 1). 
     Systems described herein have at least five uses:
         1. Enables the identification of genes for proteins that generate inhibitors of the drug target. In brief, when the pathway for terpenoid biosynthesis generates target-inhibiting molecules, the cell survives at high antibiotic concentrations. By swapping out genes for terpene synthesizing and/or functionalizing enzymes, we can identify genes for enzymes that build such inhibitors.   2. Enables the construction of novel—and, perhaps, unnatural—inhibitors. By mutating the pathway for terpenoid biosynthesis, we can generate pathways that confer survival at high antibiotic concentrations. These pathways contain mutated (i.e., unnatural) genes and, thus, can generate inhibitor molecules not found in Nature.   3. Enables the construction of inhibitors that overcome drug resistance. Briefly, after building a strain that generates a target-inhibiting molecule, we can carry out two steps: (i) We can mutate the drug target until it becomes resistant to that inhibitor. (ii) We can mutate the metabolic pathway until it generates an inhibitor of the mutated drug target. In this way, we can both (i) predict drug-resistance mutations and (ii) address those mutations by generating new inhibitors that overcome them.   4. Enables the construction of inhibitors of protein tyrosine kinases. Using a selection strategy similar to that described in 3.ii, we can mutate a metabolic pathway until it generates an inhibitor of Src kinase.       

     B. A Genetically Encoded System that Links the Inhibition of a Protein Tyrosine Phosphatase to Cell Survival. 
     In one preferred embodiment, a genetically encoded system was developed and used, as described herein, for detecting the presence of a small-molecule inhibitor of the catalytic domain of a chosen enzyme, e.g. a drug target enzyme, while allowing the survival of a host cell in the presence of a selective growth media. In other words, when the genetically encoded system is part of an expression plasmid in  E. coli.    
     In one embodiment, an exemplary drug target enzyme was chosen, e.g. protein tyrosine phosphatase enzyme, protein tyrosine phosphatase 1B (PTP1B), 
     In one embodiment, the genetically encoded system is part of an expression plasmid. In one embodiment, the sensing operon is operably linked to a constitutive promoter for expression in  E. coli.    
       FIG.  33 A-E  illustrates an embodiment of a genetically encoded system that links the activity of an enzyme to the expression of a gene of interest (GOI). Error bars in  FIG.  33 B-E  denote standard deviation with n=3 biological replicates. 
       FIG.  33 A  illustrates an embodiment of a bacterial two-hybrid system that detects phosphorylation-dependent protein-protein interactions. Components include (i) a substrate domain fused to the omega subunit of RNA polymerase (yellow), (ii) an SH2 domain fused to the 434 phage cI repressor (light blue), (iii) an operator for 434cI (dark green), (iv) a binding site for RNA polymerase (purple), (v) Src kinase, and (vi) PTP1B. Src-catalyzed phosphorylation of the substrate domain enables a substrate-SH2 interaction that activates transcription of a gene of interest (GOI, black). PTP1B-catalyzed dephosphorylation of the substrate domain prevents that interaction; inhibition of PTP1B re-enables it.  FIG.  33 B  refers to an embodiment of the two-hybrid system from  FIG.  33 A  that (i) lacks PTP1B and (ii) contains luxAB as the GOI. We used an inducible plasmid to increase expression of specific components; overexpression of Src enhanced luminescence.  FIG.  33 C  refers to an embodiment of the two-hybrid system from  FIG.  33 A  that (i) lacks both PTP1B and Src and (ii) includes a “superbinder” SH2 domain (SH2*, i.e., an SH2 domain with mutations that enhance its affinity for phosphopeptides), a variable substrate domain, and LuxAB as the GOI. We used an inducible plasmid to increase expression of Src; luminescence increased most prominently for p130cas and MidT, suggesting that Src acts on both substrate domains.  FIG.  33 D  refers to an embodiment of a two-hybrid system from  FIG.  33 C  with one of two substrates: p130cas or MidT. We used a second plasmid to overexpress either (i) Src and PTP1B or (ii) Src and an inactive variant of PTP1B (C215S). The difference in luminescence between systems containing PTP1B or PTP1B (C215S) was greatest for MidT, suggesting that PTP1B acts on this substrate. Right: An optimized version of the two-hybrid system (with bb030 as the RBS for PTP1B) appears for reference.  FIG.  33 E  displays the results of an exemplary growth-coupled assay performed using an optimized B2H including SH2*, a midT substrate, optimized promoters and ribosome binding sites (bb034 for PTP1B), and SpecR as the GOI. This system is illustrated at the top of the figure. Exemplary growth results demonstrate that inactivation of PTP1B enables strain of  E. coli  harboring this system to survive at high concentrations of spectinomycin (&gt;250 μg/ml). 
     1. Sequential Optimization of a Two-Hybrid System with LuxAB as the GM. 
     Phase 1: We examined two different promoters for Src in a system that lacked PTP1B. Phase 2: We examined two different ribosome binding sites (RBSs) for Src in a system that lacked PTP1B. Phase 3: We examined two different RBSs for PTP1B in a complete system. Note: In phases 1 and 2, the operon contains wild-type (WT) or non-phosphorylate-able (mutant, Y/F) versions of the substrate domain. In phase 3, the operon contains wild-type (WT) or catalytically inactive (mutant, C215S) version so PTP1B. See,  FIG.  34   . 
       FIG.  34    illustrates exemplary experiments used to optimize the B2H system depicted in  FIG.  33   . 
     2. Comparing RB Sites. 
     We grew strains of  E. coli  harboring versions of the bacterial two-hybrid that contained different RBSs for PTP1B (bb034 or bb030) on various concentrations of spectinomycin (left to right) and plated them on various concentrations of spectinomycin (top to bottom). We used bb034 for one embodiment of an “optimized” two-hybrid system shown in  FIG.  33 E . See,  FIG.  35   . 
       FIG.  35     FIG.  3    illustrates exemplary experiments used to optimize the B2H system depicted in  FIG.  33    for growth-coupled assays.
     Rice, P., Longden, L. &amp; Bleasby, A. EMBOSS: The European Molecular Biology Open Software Suite.  Trends Genet.  16, 276-277 (2000).   

     C. Biosynthesis of PTP1B-Inhibiting Terpenoids Enables Cell Survival. 
     When pTS contains ADS or GHS, it does not contain GGPPS; when pTS contains ABS or TXS, it also contains GGPPS; ABS D404A/D621A  refers to a catalytically inactive variant of ABS; and B2H* contains PTP1B (C215S). ADS and, marginally, ABS enabled survival in the presence of spectinomycin, a result suggestive of the ability of these to terpene synthases to generate inhibitors of PTP1B. 
       FIG.  36 A-C   FIG.  4   |shows an illustration of an operon ( FIG.  36 A ) used for providing exemplary results during biosynthesis of PTP1B-inhibiting terpenoids  FIG.  36 B  enabling cell survival  FIG.  36 C . 
       FIG.  36 A-C   FIG.  4    depicts an exemplary metabolic pathway for the biosynthesis of terpenoids. 
       FIG.  36 A  depicts a plasmid-borne pathway for terpenoid biosynthesis: (i) pMBIS, which harbors the mevalonate-dependent isoprenoid pathway of  S. cerevisiae , converts mevalonate to isopentyl pyrophosphate (IPP) and farnesyl pyrophosphate (FPP). (ii) pTS, which encodes a terpene synthase (TS) and, when necessary, a geranylgeranyl diphosphate synthase (GPPS), converts IPP and FPP to sesquiterpenes and/or diterpenes. 
       FIG.  36 B  depicts exemplary terpene synthases: amorphadiene synthase (ADS) from  Artemisia annua , γ-humulene synthase (GHS) from  Abies grandis , abietadiene synthase (ABS) from  Abies grandis , and taxadiene synthase (TXS) from  Taxus brevifolia.    
       FIG.  36 C  shows the results of an exemplary growth-coupled assay of strain of  E. coli  that contains both (i) an embodiment of the optimized bacterial two-hybrid (B2H) system (i.e., the B2H system from  FIG.  33 E ) and (ii) an embodiment of a pathway for terpenoid biosynthesis (i.e., the pathway from  FIG.  35 A ). 
     Briefly, we grew strains of  E. coli  that harbored (i) the same pathway for producing linear isoprenoid precursors and (ii) a different plasmid encoding a terpene synthase (pTS). The pTS plasmid contained on of the following: (i) amorphadiene synthase (ADS) from  Artemisia annua , (ii) γ-humulene synthase (GHS) from  Abies grandis , (iii) abietadiene synthase (ABS) from  Abies grandis  in operable combination with a geranylgeranyl diphosphate synthase (GGPPS, (iv) taxadiene synthase (TXS) from  Taxus brevifolia  in operable combination with a GGPPS, (v) a inactive variant of ABS (i.e., ABS XX , which corresponds to ABS D404A/D621A ), or (vi) the L450Y mutant of GHS. After growing these strains, we compared the ability of their products to inhibit PTP1B by carrying out the following steps: (i) We used a hexane overlay to extract hydrophobic products (e.g., terpene-like products) from each culture, we then dried the products in a rotary evaporator, we dissolved the dried extract in dimethyl sulfoxide (DMSO), and we measured PTP1B-catalyzed hydrolysis of p-nitrophenyl phosphate (pNPP) in the presence and absence of extract-containing DMSO. We note: The L450Y mutant of GHS was included in our analysis because the wild-type form of GHS does not permit B2H-mediated growth in the presence of an antibiotic, but our preliminary data indicate that the L450Y mutant of GHS does permit such growth. Accordingly, we hypothesized that this mutant produced a molecule that is a stronger inhibitor of PTP1B than the molecules generated by wild-type GHS. See,  FIG.  37 A-C  Demonstration of differential inhibition by structurally distinct terpenoids. 
     In examining  FIG.  37 A-C , we observed a trend: Extracts from strains containing terpene synthases that confer resistance to high concentrations of antibiotic (see  FIG.  36   ) where ADS and GHS L450Y  were more inhibitory than extracts from strains that did not confer resistance, e.g., TXS and ABS xx . We note: strains containing ADS and GHS also included the optimized bacterial two-hybrid (B2H) system, but selection was not performed in the experiments used to product terpenoids for the experiments described by these figures. 
       FIG.  37 A-C  provides an exemplary analysis of the inhibitory effects of terpenoids generated by different strains of  E. coli.    
       FIG.  37 A  depicts the results of our analysis of the inhibitory effect of DMSO containing (i) no inhibitor and (ii) extracted compounds from the culture broth of the ADS-containing strain.  FIG.  37 B  depicts the results of our analysis of the inhibitory effect of DMSO containing (i) extracted compounds from the culture broth of the GHS-containing strain (gHUM) or (ii) extracted compounds from the culture broth of the strain including the L450Y mutant of GHS.  FIG.  37 C  depicts the results of our analysis of the inhibitory effect of DMSO containing (i) no inhibitor, (ii) extracted compounds from the culture broth of the ABS-containing strain, (iii) extracted compounds from the culture broth of the TXS-containing strain, and (iv) extracted compounds from the culture broth of the train strain containing a catalytically inactive variant of ABS. 
     Briefly, we grew strains of  E. coli  containing both (i) the optimized bacterial two-hybrid system and (ii) a terpenoid pathway with mutants γ-humulene synthase (GHS; 1 mutant/cell) on varying concentrations of spectinomycin. Above: product profiles of strains with GHS mutants that conferred survival at high antibiotic concentrations. See,  FIG.  38   . 
       FIG.  38    shows exemplary analysis of the product profiles of mutants of GHS that enabled growth in the presence of spectinomcyin. 
     In brief, we constructed versions of the bacterial two-hybrid system that include SH2*, the midT substrate, optimized promoters and ribosome binding sites, SpecR, and alternative PTPs: the catalytic domain of PTPN6 (e.g., SHP-1) and PTP1B 405  (the full-length version of PTP1B). Note: these systems are identical to the B2H system depicted in  FIG.  33 E , except they possess only one of the following PTP genes: PTP1B (as in  FIG.  33 E ), PTPN6 (different from  FIG.  33 E ), or full-length PTP1B. Inactivation of the catalytic domain of both PTPN6 and the full-length PTP1B enabled strains of  E. coli  harboring corresponding operons to survive at high concentrations of spectinomycin (&gt;400 μg/ml). To extend our operon to other PTPs, we plan on modifying the substrate, SH2, and/or kinase domains. See,  FIG.  39   . 
       FIG.  39    An analysis of exemplary B2H systems that link the inhibition of other PTPs to cell survival. 
     We also generated versions of the bacterial two-hybrid system that include SH2*, the midT substrate, optimized promoters and ribosome binding sites, SpecR, and alternative PTPs: the catalytic domain of PTPN6 (e.g., SHP-1) and PTP1B 405  (the full-length version of PTP1B). Inactivation of the catalytic domain of PTPN6 and the full-length PTP1B enabled strains of  E. coli  harboring corresponding operons to survive at high concentrations of spectinomycin (&gt;400 μg/ml). To extend our operon to other PTPs, we plan on modifying the substrate, SH2, and/or kinase domains. 
       FIG.  40 A-E  depicts exemplary embodiments of genetically encoded systems that link the activity of an enzyme to the expression of a gene of interest, and the application of those embodiments to (i) the prediction of resistance mutations, (ii) the construction of inhibitors that combat resistance mutations, and (ii) the evolution of inhibitors of kinases. 
       FIG.  40 A  depicts an exemplary first step in examining potential resistance mutations. By evolving a metabolic pathway to produce molecules that inhibit a known drug target (e.g., PTP1B); these molecules will permit expression of a gene of interest (GOI) that confers survival in the presence of a selection pressure (e.g., the presence of spectinomycin, an antibiotic).  FIG.  40 B  depicts an exemplary second step in examining potential resistance mutations. In a second strain of  E. coli , we will replace the original gene of interest with a second (GOI2) that confers conditional toxicity (e.g., SacB, which converts sucrose to levan, a toxic product); we will evolve the drug target to become resistant to the endogenous inhibitors, while still retaining its activity. This mutant will prevent expression of the toxic gene.  FIG.  40 C  depicts an exemplary third step in combating resistance mutations. In a third strain of  E. coli , we will evolve a metabolic pathway that produces molecules that inhibit the mutated drug target. In this way, we will both predict—and, through our second evolved pathway, address—mutations that might cause resistance to terpenoid-based drugs. We note:  FIG.  40 A- 40 C  describe the use of our genetically encoded system to evolve inhibitors, but the steps 2 and 3 could be used to predict mutations that permit resistance to endogenously supplied inhibitors and, subsequently, to identify new endogenously supplied inhibitors that might combat that resistance.  FIG.  40 D  depicts an exemplary genetically encoded system that detects inhibitors of an Src kinase. In brief, Src activity enables expression of a toxic gene (GOI2); inhibition of Src, in turn, would confer survival. 
     One embodiment of a configuration of the B2H architecture that enables survival when PTP1B is active, that is, when the activity of Src kinase is successfully canceled out. in the absence of PTP1B, this configuration could be used to evolve inhibitors of Src kinase; such an inhibitor would act similarly to PTP1B by preventing the phosphorylation of the substrate domain (as shown in  FIG.  40 E ), Src kinase is a validated drug target; tyrosine kinases are targets of over 40 FDA-approved drugs. 
       FIG.  40 E  demonstrates one embodiment of a roof of principle for the B2H system describe in  FIG.  40 B . The system shown here includes two GOIs: SpecR and SacB. Expression of the GOIs confers survival in the presence of spectinomycin; expression of the GOIs causes toxicity in the presence of sucrose. The images depict the results of a growth-coupled assay performed on a strain of  E. coli  in the presence of various concentrations of sucrose. The strain harboring an active form of PTP1B (WT) grows better at high sucrose concentrations that the strain harboring an inactive form of PTP1B (C215S). 
       FIG.  41 A  depicts an exemplary strategy for the evolution of inhibitors of PTP1B. 
       FIG.  41 A  depicts an exemplary structural analysis used to identify targets for mutagenesis in the active sites of terpene synthases. It shows an alignment of the class I active site of ABS (gray, PDB entry 3s9v) and TXS (blue, PDB entry 3p5r) with the locations of sites targeted for site-saturation mutagenesis (SSM) highlighted on ABS (red). A substrate analogue (yellow) of TXS appears for reference.  FIG.  41 B  depicts an exemplary strategy for introducing diversity into libraries of metabolic pathways: An iterative combination of SSM of key sites on a terpene synthase (as in a), error-prone PCR (ePCR) of the entire terpene synthase gene, SSM of key sites on a terpene-functionalizing enzyme (e.g., P450), and ePCR of the entire terpene-functionalizing enzyme.  FIG.  41 C  depicts an exemplary quantification the total terpenoids present in DMSO samples with extracts of various TS-containing strains. In brief, we performed site-saturation mutagenesis of six sites on ADS (analogous to the sites shown in a); we plated the SSM library on agar plates containing different concentrations of spectinomycin; we picked colonies that grew on a plate containing a high concentration (800 μg/ml) of spectinomycin and used each colony to inoculate a separate culture; we used a hexane overlay to extract the terpenoids secreted into each culture broth; we dried the hexane extract in a rotary evaporator and re-suspended the solid in DMSO; and we used a GC-MS to quantify the total amount of terpenoids present in the DMSO. 
     “ADS WT”, “ADS F514E”, “ADS F370L”, “ADS G400A”, “ADS G439A”, and “ADS G4001,” describe mixtures of molecules generated by strains of  E. coli  harboring mutants of amorphadiene synthase (ADS): The labels describe the mutant: “G439A” corresponds to a mutant of abietadiene synthase in which glycine 439 has been mutated to alanine, and so on. In future work, we plan on (i) purifying different terpenoids from these mixtures, (ii) assessing their inhibitory effect on PTP1B in vitro, (iii) assaying their inhibitory effect on other PTPs (notably TC-PTP and PTPN11) in vitro, and (iv) assaying their influence on mammalian cells. See,  FIG.  41 D . 
       FIG.  41 D  depicts an exemplary analysis of the inhibitory effect of various extracts on PTP1B. In brief, the figure shows initial rates of PTP1B-catalyzed hydrolysis of p-nitrophenyl phosphate (pNPP) in the presence of terpenoids quantified in  FIG.  41 C . Two mutants of ADS (G439A and G400L) generate particularly potent inhibitors of PTP1B. 
       FIG.  42    depicts an exemplary analysis of the link between B2H activation and cell survival. An exemplary strain of  E. coli  that contains both (i) the optimized bacterial two-hybrid (B2H) system ( FIG.  33 E ) and (ii) the terpenoid pathway depicted in  FIG.  36 A . Note: pTS includes GGPPS only when ABS or TXS are present; the “Y/F” operon corresponds to a B2H system in which the substrate domain cannot be phosphorylated. Survival at high concentrations of spectinomycin requires activation of the B2H system (i.e., phosphorylation of the substrate domain, a process facilitated by inhibition of PTP1B). 
       FIG.  43    provides exemplary product profiles of strains of  E. coli  harboring various terpene synthases. For this figure, the strain of  E. coli  harbored (i) the optimized B2H system ( FIG.  33 E ) and (ii) the terpenoid pathway ( FIG.  36 A ). The pathways corresponding to each profile differ only in the composition of the pTS plasmid, which contains TXS (taxadiene synthase from  Taxus brevifolia  and a geranylgeranyl diphosphate synthase from  Taxus Canadensis ); GHS (γ-humulene synthase from  Abies grandis ); ADS (amorphadiene synthase from  Artemisia annua ); ABS (abietadiene synthase from  Abies grandis  and a geranylgeranyl diphosphate synthase from  Taxus Canadensis ); G400A (the G400A mutant of amorphadiene synthase from  Artemisia annua ); and G439L (the G439L mutant of amorphadiene synthase from  Artemisia annua ). Note that the two mutants of ADS yield different product profiles than the wild-type enzyme (ADS); our results indicate that products generated by these two mutants are more inhibitory than those generated by the wild-type enzyme ( FIG.  41 E ). 
     D. Identification of Sites for Site Saturation Mutagenesis (SSM). 
     The active sites of terpene synthases and cytochrome P450s contain constellations of amino acids that guide catalysis in two ways: (i) They control the conformation space available to reacting substrates, and (ii) they alter the organization of water that surrounds substrates 8-10 . We identified “plastic” residues likely to modulate these attributes in the class I active sites of terpene synthase by carrying out the following steps: (i) We aligned the crystal structure of ABS with the crystal structure of TXS. (ii) We selected all residues within 8 angstroms of the substrate analog (2-fluoro-geranylgeranyl diphosphate) of the class I active site of TXS, and we identified a subset of sites that differed between ABS and TXS. (iii) We aligned the sequences of ABS, 
     
       
         
           
             S 
             = 
             
               
                 
                   σ 
                   V 
                   2 
                 
                 
                   n 
                   v 
                 
               
               + 
               
                 
                   σ 
                   HW 
                   2 
                 
                 
                   n 
                   HW 
                 
               
             
           
         
       
     
     GHS, delta-selenine synthase (DSS), and epi-isozizaene synthase (EIS). (iv) We used Eq. S1 to score each site based on its variability in size and hydrophilicity across the five enzymes analyzed. In this equation, σ v   z  is the variance in volume, σ HW   z  is the variance in Hopp-Woods index, and n v  and n HW  are normalization factors (based on the highest variances measured in this study). (v) We ranked each site according to S and selected the six highest-scoring sites. We note: For this analysis, we chose ABS and TXS because they are structurally similar enzymes (i.e., both possess α, β, and γ domains) with crystal structures; we chose GHS, DSS, and EIS because they have been shown to exhibit mutation-responsive product profiles. 
       FIG.  44 A-D  provides exemplary structural and sequence-based evidence that supports the extension the B2H system to other protein tyrosine phosphatases (PTPs). 
       FIG.  44 A  provides an exemplary structural alignment PTP1B and PTPN6, two PTPs that are compatible with the B2H system (see  FIGS.  1   e    and  7  of Update A for evidence of compatibility). We used the align function of PyMol to align each structure of PTPN6 with either (i) the ligand-free (3A5J) or (ii) ligand-bound (2F71) structure of the catalytic domain of PTP1B. The align function carries out a sequence alignment followed by a structural superposition and, thus, effectively aligns the catalytic domains of both proteins.  FIG.  44 B  provides an exemplary structural comparison of PTP1B and PTPN6; the root-mean-square deviations (RMSD) of aligned structures of PTP1B and PTPN6 range from 0.75 to 0.94 Å.  FIG.  44 C  proves an exemplary sequence alignment of the catalytic domains of PTP1B (SEQ ID NO: 3) and PTPN6 (SEQ ID NO: 4) (EMBOSS Needle 1 ).  FIG.  44 D  provides an exemplary sequence comparison of the catalytic domains of PTP1B and TPPN6. The sequences share 34.1% sequence identity and 53.5% sequence similarity. In summary, the results of this figure indicate that our B2H system can be readily extended to PTPs that possess catalytic domains that are (i) structurally similar to the catalytic domain of PTP1B (here, we define structural similarity as two structures that when aligned, have with an RMSD of ≤0.94 Å RMSD with the framework similar to the one used by the align function of PyMol) and/or (ii) sequence similar to the catalytic domain of PTP1B (here, we define sequence similarity as ≥34% sequence identity or ≥53.5% sequence similarity as defined by the EMBOSS Needle algorithm). 
     To identify “plastic” residues capable of adjusting the activity of P450 BM3 , we carried out an approach similar to that described above: (i) We used the mutant database 11  (http://www.MuteinDB org) to identify the 25 most commonly mutated sites in functional variants of P450 BM3 . (ii) We used Eq. 51 to score each site based on its variability in size and hydrophobicity across different mutants. (iii) We ranked each site according to S and selected the 7 highest-scoring sites. Site S1024 scored highly based on S but was omitted due to its location on the P450 reductase domain. 
     E. Exemplary Purification of Products. 
     See section relating to flash chromatography and HPLC 1-3 . 
     F. Exemplary Concentration Range for Testing Products. 
     We plan on incubating mammalian cells with 1-400 μM of inhibitors; we will assess the biochemical influence of those inhibitors by using the assays described below. 
     G. Exemplary Cell-Based Assays. 
     We will characterize the biological activity of newly developed inhibitors in at least two ways: 
     1. We will assay the influence of inhibitors on insulin receptor phosphorylation. In brief, we will expose HepG2, Hela, Hek393t, MCF-7, and/or Cho-hIR cells to insulin shock in the presence and absence of inhibitors, and we will use a western blot and/or an enzyme-linked immunosorbent assay (ELISA) to measure the influence of the inhibitors on insulin receptor phosphorylation. In some embodiments we may use cell-permeable inhibitors of PTP1B to enhance insulin receptor phosphorylation.
 
2. We will examine the morphological and/or growth effects inhibitors identified in a system described herein on cellular models of HER2(+) and TN breast cancer.
 
In brief, we will examine the relevance of inhibitors to HER2(+) breast cancer by evaluating their ability to inhibit the migration of BT474 and SKBR3 cells, which are HER2(+), but not MCF-7 and MDA-MB-231 cells, which are HER2(−). We will examine the relevance of inhibitors to triple negative breast cancer, in turn, by carrying out viability and proliferation assays on panels of TN cell lines (e.g., ATCC TCP-1002). All cell lines are available from the ATCC (ATCC.org) and have been used previously to characterize potential therapeutics for HER2(+) and TN subtypes 4,5 .
 
     It is not meant to limit a pathway to terpenoid synthesis. Indeed, an alkaloid biosynthesis pathway is contemplated for use to identify, 
     An exemplary pathway for alkaloid biosynthesis consists of three modules (Nakagawa, A. et al. A bacterial platform for fermentative production of plant alkaloids. Nat. Commun. (2011). doi:10.1038/ncomms1327, herein incorporated by reference) (i) the first enables the overexpression of our enzymes for L-tyrosine overproduction: TKT, PEPS, fbr-DAHPS, and fbr-CM/PDH; (ii) the second enables the expression of three enzymes necessary for the construction of dopamine and 3,4-DHPAA: TYR, DODC, and MAO; and (iii) the third enable the expression of four enzymes for the construction of (S) reticuline from 3,4-DHPAA and dopamine: NCS, 6OMT, CNMT, and 4′OMT. Enzymes are as follows: TKT, transketolase (tktA, GenBank accession number X68025); PEPS, phosphoenolpyruvate (PEP) synthetase (ppsA, GenBank accession number X59381); fbr-DAHPS, feedback-inhibition resistant 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (aroGfbr, GenBank accession number J01591); fbr-CM/PDH, feedback-inhibition resistant chorismate mutase/prephenate dehydrogenase (tyrAfbr, GenBank accession number M10431); TYR, tyrosinase of  Streptomyces castaneoglobisporus  (ScTYR containing tyrosinase and its adaptor protein, ORF378, GenBank accession numbers AY254101 and AY254102); DODC, DOPA decarboxylase of  Pseudomonas putida  (GenBank accession number AE015451); MAO, monoamine oxidase of  Micrococcus luteus  (GenBank accession number AB010716); NCS, norcoclaurine synthetase of  C. japonica  (GenBank accession number AB267399); 6OMT, norcoclaurine 6-O-methyltransferase of  C. japonica  (GenBank accession number D29811); CNMT, coclaurine-N-methyltransferase of Coptis  japonica  (GenBank accession number AB061863); 4′OMT, 3′-hydroxy-N-methylcodaurine 4′-O-methyltransferase of  C. japonica  (GenBank accession number D29812). We note; these three modules may be encoded by two plasmids. 
     REFERENCES FOR SECTION V, HEREIN INCORPORATED BY REFERENCE IN THEIR ENTIRETY 
     
         
         1. Jia, M., Potter, K. C. &amp; Peters, R. J. Extreme promiscuity of a bacterial and a plant diterpene synthase enables combinatorial biosynthesis.  Metab. Eng.  37, 24-34 (2016). 
         2. Criswell, J., Potter, K., Shephard, F., Beale, M. H. &amp; Peters, R. J. A single residue change leads to a hydroxylated product from the class II diterpene cyclization catalyzed by abietadiene synthase.  Org. Lett.  14, 5828-5831 (2012). 
         3. Morrone, D. et al. Increasing diterpene yield with a modular metabolic engineering system in  E. coli : Comparison of MEV and MEP isoprenoid precursor pathway engineering.  Appl. Microbiol. Biotechnol.  85, 1893-1906 (2010). 
         4. Dagliyan, O. et al. Engineering extrinsic disorder to control protein activity in living cells.  Science  (80-.). 354, 1441-1444 (2016). 
         5. Lehmann, B. D. et al. Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies.  J. Clin. Invest.  (2011). doi:10.1172/JCI45014 
         6. Dempke, W. C. M., Uciechowski, P., Fenchel, K. &amp; Chevassut, T. Targeting SHP-1, 2 and SHIP Pathways: A novel strategy for cancer treatment?  Oncology  ( Switzerland ) (2018). doi:10.1159/000490106 
         7 Nakagawa, A. et al. A bacterial platform for fermentative production of plant alkaloids.  Nat. Commun.  (2011). doi:10.1038/ncomms1327 
         8. Christianson, D. W. Structural biology and chemistry of the terpenoid cyclases.  Chem. Rev.  106, 3412-3442 (2006). 
         9. Fasan, R. Tuning P450 enzymes as oxidation catalysts.  ACS Catalysis  2, 647-666 (2012). 
         10. Jung, S. T., Lauchli, R. &amp; Arnold, F. H. Cytochrome P450: Taming a wild type enzyme.  Current Opinion in Biotechnology  22, 809-817 (2011). 
         11. Braun, A. et al. MuteinDB: The mutein database linking substrates, products and enzymatic reactions directly with genetic variants of enzymes.  Database  (2012). doi:10.1093/database/bas028 
       
    
     VI. Evolving Optogenetic Actuators: Photoswitchable Constructs. 
     A. Optical Control with Red and Infrared Light. 
     Contemporary efforts for using light to control enzyme activity have relied on at least two optogenetic actuators: LOV2, which has terminal helices that are destabilized by blue light (−450 nm) 2,18,48 , and Dronpa, which switches from a dimer to a monomer in response to green light (−500 nm) 19 . Unfortunately, blue and green light suffer from problems of phototoxicity, penetration depth, and spectral similarity that limit their use in signaling studies 21 . Thus, in one embodiment, photoswitchable enzymes stimulated by red or infrared light are contemplated for development. These wavelengths have lower phototoxicities and greater penetration depths than blue and green light 20,21 , and will permit multi-color actuation alongside blue or green light. 
     B. An Operon to Evolve Photoswitchable Constructs. 
     In one embodiment, an operon that links the activity of PTP1B to cell growth is contemplated. In brief, this operon is based on the following control strategy (some additional details in  FIG.  10   ): A kinase stimulates the binding of two proteins, which in turn, promote transcription of an essential gene; PTP1B suppresses the binding of these two proteins and, thus, inhibits transcription. This operon allows cells in possession of photoswitchable variants of PTP1B to grow faster in the presence of one light source than in the present of another (e.g., 750 nm vs. 650 nm). The difference in growth rates enables the identification of functional chimeras. Initial experiments with an operon based on Lux-based luminescence (based on a system developed by Liu and colleagues 53 ) show a 20-fold difference in luminescence between a strain expressing two model binding partners and a strain expressing one ( FIG.  3 E ). We will continue to develop this operon by adding a protein-protein interaction that is modulated by a PTP and PTK (see below). 
     This operon allows cells in possession of photoswitchable variants of PTP1B to grow faster in the presence of one light source than in the present of another (e.g., 750 nm vs. 650 nm). The difference in growth rates enables the identification of functional chimeras. Initial experiments with an operon based on Lux-based luminescence (based on a system developed by Liu and colleagues 53) show a 20-fold difference in luminescence between a strain expressing two model binding partners and a strain expressing one ( FIG.  3 E ). We will continue to develop this operon by adding a protein-protein interaction that is modulated by a PTP and PTK. 
     FRET sensors. We will use Forster resonance energy transfer (FRET) to monitor the activity of PTP1B in living cells. Our preliminary sensor exhibits a 20% reduction in FRET signal when treated with Src kinase ( FIG.  3 F ). Previous imaging studies indicate that a 20% change in FRET is sufficient to monitor intracellular kinase activity54″56. To enhance spatial resolution in imaging studies, we will attempt to optimize our sensor further (and use it to measure the activity of PTP1B in vitro). 
     1. To Evolve Phosphatases and Kinases Modulated by Red and Infrared Light. 
     This section uses directed evolution to build enzymes that can be turned “on” and “off” with red and infrared light. We will know that we are successful when we have (i) built a genetic operon that links the activity of PTP1B to antibiotic resistance, (ii) A used that operon to build a PTP1B-phytochrome chimera that exhibits a three- to ten-fold change in activity in response to red and infrared light, and (iii) built similar phytochrome chimeras of STEP and PTK6. 
     Hypothesis. Phytochrome proteins exhibit global conformational changes when exposed to red and infrared light 27,28 , but to date, have eluded rational integration into photoswitchable enzymes. We hypothesize that a genetic operon that links PTP or PTK activity to cell growth will enable the evolution of PTP- or PTK-phytochrome chimeras stimulated by red or infrared light. 
     Experimental approach: We will build an operon that links PTP1B inhibition to antibiotic resistance, and we will use that operon to evolve photoswitchable PTP1B-phytochrome chimeras. This effort will involve (i) the construction a library of PTP1B-phytochrome chimeras that differ in linker composition and/or linker length, (ii) the use of our operon to screen that library for functional mutants, (iii) a kinetic and biostructural characterization of the most photoswitchable mutants, and (iv) the extension of this approach to STEP and PTK6. This effort has two major goals: a variant of PTP1B modulated by red and/or infrared light, and a general approach for using directed evolution to extend optical control to new enzymes and different wavelengths of light. 
     2. Development of a Synthetic Operon for Evolving PTP1B-Phytochrome Chimeras. 
     We will build a variant of PTP1B that can be modulated by red and infrared light by attaching its C-terminal a-helix to the N-terminal a-helix of bacterial phytochrome protein 1 (BphP1) from  Rhodopseudomonas palustris  ( FIG.  9   ); this protein undergoes a reversible conformational change when exposed to 650 nm and 750 nm light. Phytochromes such as BphP1 are valuable for photocontrol because they can be actively toggled between conformations (i.e., turned “on” and “off”). Their structures, however, are not compatible with cage-based actuation (they do not undergo large-scale “unwinding”); they have, thus, been overlooked in previous efforts to develop photoswitchable enzymes. 
     We will evolve photoswitchable PTP1B-BphP1 chimeras by using a genetic operon that links PTP1B activity to antibiotic resistance. This operon will consist of six components ( FIG.  10 A-B ): (i) a PTP1B substrate domain tethered to a DNA-binding protein, (ii) a substrate recognition domain (i.e., a substrate homology 2 domain, or SH2) tethered to the subunit of an RNA polymerase, (iii) an Src kinase (a kinase capable of phosphorylating a wide range of substrates), (iv) PTP1B (or a potentially photoswitchable variant of PTP1B), (v) a gene for antibiotic resistance, and (vi) an operator for that gene. 
     With this system, light-induced inactivation of PTP1B will enable transcription of the gene for antibiotic resistance. Previous groups have used similar operons to evolve protein-protein binding partners (our system is based on an operon used by Liu et al. to evolve insecticidal proteins 53 ); here, we take the additional (new) steps of (i) using a protein-protein interaction mediated by enzymes (phosphatases and kinases) and (ii) screening that interaction in the presence and absence of light. 
     We have begun to develop our operon by using a Lux-based luminescence as an output. Preliminary results show that model protein-protein binding partners can elicit a 20-fold change in luminescence ( FIG.  3 E ). We plan to swap out these binding partners with substrate and SH2 domains, and test the new system alongside simultaneously expressed PTP1B and Src kinase (which have some complementary activities, and can be expressed in  E. coli   68,69 ). 
     Advantages of using operons expressing photosensitive phosphatases includes but is not limited to enabling high-throughput screens of mutants of photoswitchable enzymes and provides a method for screening the libraries of enzymes that they motivate, see,  FIG.  5 A  for example. In contrast, have shown that mutagenesis a photoswitchable enzyme can adjust (i.e., improve) its dynamic range (i.e., ratio of dark-state activity to light-state activity); while some published studies, such as WO2011002977. Genetically Encoded Photomanipulation Of Protein And Peptide Activity. Published Jan. 6, 2011, have proposed, but not shown, that mutagenesis of protein light switches might enable spectral tuning of photoswitchable enzymes. WO2011002977, provides a list of sites that could be mutated to modify the flavin-binding pocket of LOV2 to accept flavins that absorb light at alternative wavelengths. However, their construct is described as a LOV2 domain of  Avena sativa  (oat) phototropin 1 (404-546), including the C-terminal helical extension J alpha where Ja unwinds instead of the A alpha helix described herein. Nonetheless, there is no available method for carrying out high-throughput screens of mutants with modified binding pockets for which the invention described herein provides a platform for doing so. Further, in contrast to WO2013016693. “Near-infrared light-activated proteins.” Publication Date Jan. 31, 2013, inventions described herein provide a platform for screening potentially improved/modified variants of photoswitchable proteins, such as a plant phototropin 1 LOV2. 
     Additionally, methods for screening the libraries of enzymes enable the detection of (i) molecules or (ii) photoswitchable domains that change the activity of any enzyme that, in turn, can modulate the affinity, or outcome associated with, a protein-protein interaction: protein tyrosine phosphatase (PTPs) and protein tyrosine kinases (PTKs) are demonstrated. Moreover, proteases are contemplated as proteins to add to this system. 
     C. Directed Evolution. 
     We will build libraries of PTP1B-BphP1 chimeras by pairing overlap extension PCR (oePCR) with error-prone PCR (epPCR). Specifically, we will use oePCR to build chimeras that differ in linker length (here, we define the linker as the −20 residue region comprised of the C-terminal a-helix of PTP1B and the N-terminal a-helix of BphP1), and we will use epPCR to vary linker composition. Depending on the results of this initial library, we may extend error-prone PCR into the BphP1 gene, but we will not mutate PTP1B beyond its C-terminal a-helix. 
     In the presence of a small amount of antibiotic (i.e. an amount that impedes the growth of  E. coli ), our genetic operon will cause cells that contain functional PTP1B-BphP1 chimeras to exhibit different growth rates under red and infrared light. We will exploit these differences to identify cells that harbor photoswitchable constructs. In brief, we will (i) generate two replicate plates of cell colonies, (ii) grow one under red light and one under infrared light ( FIG.  11 A ), and (iii) select a subset of colonies (top hits) that show differential growth. We will further characterize our top hits by growing them in small-scale liquid cultures (e.g., 96-well plates with ˜1 ml/well;  FIG.  11 B ) under red and infrared light, and by sequencing the PTP1B-BphP1 genes of colonies that show the greatest different in growth rates. 
     We will attempt to build enzyme-phytochrome chimeras of STEP and PTK6 by pursuing two strategies: (i) We will replace PTP1B in our final PTP1B-BphP1 chimera with STEP or PTK6; this strategy will allow us to assess the modularity of our final design, (ii) We will use our operon-based approach to evolve functional STEP-BphP1 and PTK6-BphP1 chimeras; this strategy will allow us to assess the generalizability of our approach to evolution. 
     Operons for evolving STEP-BphP1 and PTK6-BphP1 chimeras will closely resemble the PTP IB-specific operon. For STEP, we will use a STEP-specific substrate and SH2 domain (Src kinase, which has a broad substrate specificity, is likely to have complementary activities on a subset of STEP substrates); for PTK6, we will use a recognition process that is inhibited—not activated—by phosphorylation (here, we can use PTP1B W T as the complementary enzyme). 
     D. Extension of Approach. 
     We will attempt to build enzyme-phytochrome chimeras of STEP and PTK6 by pursuing two strategies: (i) We will replace PTP1B in our final PTP1B-BphP1 chimera with STEP or PTK6; this strategy will allow us to assess the modularity of our final design, (ii) We will use our operon-based approach to evolve functional STEP-BphP1 and PTK6-BphP1 chimeras; this strategy will allow us to assess the generalizability of our approach to evolution. 
     Operons for evolving STEP-BphP1 and PTK6-BphP1 chimeras will closely resemble the PTP IB-specific operon. For STEP, we will use a STEP-specific substrate and SH2 domain (Src kinase, which has a broad substrate specificity, is likely to have complementary activities on a subset of STEP substrates); for PTK6, we will use a recognition process that is inhibited—not activated—by phosphorylation (here, we can use PTP1BWT as the complementary enzyme) 
     F. Exemplary Contemplated Characterization: Biophysical Characterization of Enzyme-Phytochrome Chimeras. 
     We will examine the structural basis of photocontrol in the most photo switchable chimeras by using a subset of crystallographic and kinetic analyses. X-ray crystal structures will show how BphP1 affects the structures of PTP1B, STEP, and PTK6. Kinetic studies will show how BphP1 affects substrate specificity and binding affinity (or more specifically, Km, which is affected by binding affinity). 
     
       
         
           
               
             
               
                 TABLE 1 
               
             
            
               
                   
               
               
                 Exemplary Promoters. 
               
            
           
           
               
               
               
            
               
                   
                   
                 SEQ ID 
               
               
                 Name 
                 DNA Sequence 
                 NO.# 
               
               
                   
               
               
                 Pro1 
                 TTCTAGAGCACAGCTAACACCACGTCGTCCCTATCTGCTGCCCTAGGTCTA 
                 SEQ ID NO. 
               
               
                   
                 TGAGTGGTTGCTGGATAACTTTACGGGCATGCATAAGGCTCGGTATCTATA 
                 25 
               
               
                   
                 TTCAGGGAGACCACAACGGTTTCCCTCTACAAATAATTTTGTTTAACTTTT 
                   
               
               
                   
                 ACTAGAG 
                   
               
               
                   
               
               
                 ProD 
                 GCACAGCTAACACCACGTCGTCCCTATCTGCTGCCCTAGGTCTATGAGTGG 
                 SEQ ID NO. 
               
               
                   
                 TTGCTGGATAACTTTACGGGCATGCATAAGGCTCGTATAATATATTCAGGG 
                 26 
               
               
                   
                 AGACCACAACGGTTTCCCTCTACAAATAATTTTGTTTAACTTTTACTAGAG 
                   
               
               
                   
               
               
                 pBAD 
                 AGAAACCAATTGTCCATATTGCATCAGACATTGCCGTCACTGCGTCTTTTA 
                 SEQ ID NO. 
               
               
                   
                 CTGGCTCTTCTCGCTAACCAAACCGGTAACCCCGCTTATTAAAAGCATTCT 
                 27 
               
               
                   
                 GTAACAAAGCGGGACCAAAGCCATGACAAAAACGCGTAACAAAAGTGTC 
                   
               
               
                   
                 TATAATCACGGCAGAAAAGTCCACATTGATTATTTGCACGGCGTCACACTT 
                   
               
               
                   
                 TGCTATGCCATAGCATTTTTATCCATAAGATTAGCGGATCCTACCTGACGC 
                   
               
               
                   
                 TTTTTATCGCAACTCTCTACTGTTTCTCCATACCCGTTTTTTTGGGCTAGC 
                   
               
               
                   
               
               
                 pLacZOpt 
                   ACAAGAAAGTTTGT TCATTAGGCACCCCGGGCTTTACTCGTAAAGCTTCC 
                 SEQ ID No. 
               
               
                 (cI operate 
                 GGCGCGTATGTTGTGTCGACCG 
                 28 
               
               
                 bolded) 
                   
                   
               
               
                   
               
               
                 pTrc 
                 CGACTGCACGGTGCACCAATGCTTCTGGCGTCAGGCAGCCATCGGAAGCT 
                 SEQ ID No. 
               
               
                   
                 GTGGTATGGCTGTGCAGGTCGTAAATCACTGCATAATTCGTGTCGCTCAAG 
                 29 
               
               
                   
                 GCGCACTCCCGTTCTGGATAATGTTTTTTGCGCCGACATCATAACGGTTCT 
                   
               
               
                   
                 GGCAAATATTCTGAAATGAGCTGTTGACAATTAATCATCCGGCTCGTATAA 
                   
               
               
                   
                 TGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAG 
                   
               
               
                   
               
               
                 T7 
                 CCTATAGTGAGTCGTATTA 
                 SEQ ID No. 
               
               
                   
                   
                 30 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                 Exemplary Ribosome Binding Sites. 
               
            
           
           
               
               
               
            
               
                   
                   
                 SEQ ID 
               
               
                 Name 
                 DNA Sequence 
                 NO. # 
               
               
                   
               
               
                 proRBS 
                 TTAAAGAGGAGAAAGGTC 
                 SEQ ID 
               
               
                   
                   
                 NO. 31 
               
               
                   
               
               
                 Sal28 RBS 
                 CGAAAAAAAGTAAGGCGGTAATCC 
                 SEQ ID 
               
               
                   
                   
                 NO. 32 
               
               
                   
               
               
                 bb034 RBS 
                 TGCAGAAAGAGGAGAAATACTAG 
                 SEQ ID 
               
               
                   
                   
                 NO. 33 
               
               
                   
               
               
                 bb030 
                 ATTAAAGAGGAGAAATACTAG 
                 SEQ ID 
               
               
                   
                   
                 No. 34 
               
               
                   
               
               
                 RBS for GOI 
                 GTGCAGTAAGGAGGAAAAAAAA 
                 SEQ ID 
               
               
                 in B2H 
                   
                 No. 35 
               
               
                   
               
               
                 bbAH 
                 GCTAGCTTTAAGAAGGAGATATACC 
                 SEQ ID 
               
               
                   
                   
                 No. 36 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 3 
               
             
            
               
                   
               
               
                 Exemplary Protein Sequences (includes truncations). 
               
            
           
           
               
               
               
            
               
                   
                   
                 SEQ ID 
               
               
                 Name 
                 Amino Acid Sequence 
                 NO.# 
               
               
                   
               
               
                 RpoZ (linker 
                 MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTV 
                 SEQ ID 
               
               
                 bolded) 
                 IALREIEEGLINNQILDVRERQEQQEQEAAELQAVTAIAEGRR AAA   
                 NO. 37 
               
               
                   
               
               
                 cI (linker bolded) 
                 MSISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTKRPRFLPELAS 
                 SEQ ID 
               
               
                   
                 ALGVSVDWLLNGTSDSNVRFVGHVEPKGKYPLISMVRARSWCEACEPYD 
                 NO. 38 
               
               
                   
                 IKDIDEWYDSDVNLLGNGFWLKVEGDSMTSPVGQSIPEGHMVLVDTGRE 
                   
               
               
                   
                 PVNGSLVVAKLTDANEATFKKLVIDGGQKYLKGLNPSWPMTPINGNCKII 
                   
               
               
                   
                 GVVVEARVKFVD YKDDDDK   
                   
               
               
                   
               
               
                 SH2 
                 WYFGKITRRESERLLLNPENPRGTFLVRESETVKGAYALSVSDFDNAKGL 
                 SEQ ID 
               
               
                   
                 NVKHYLIRKLDSGGFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVC 
                 NO. 39 
               
               
                   
               
               
                 Kras Substrate 
                 WMEDYDYVHLQG 
                 SEQ ID 
               
               
                   
                   
                 NO. 40 
               
               
                   
               
               
                 MidT Substrate 
                 EPQYEEIPIYL 
                 SEQ ID 
               
               
                   
                   
                 NO. 41 
               
               
                   
               
               
                 ShcA Substrate 
                 DHQYYNDFPG 
                 SEQ ID 
               
               
                   
                   
                 NO. 42 
               
               
                   
               
               
                 EGFR Substrate 
                 PQRYLVIQGD 
                 SEQ ID 
               
               
                   
                   
                 NO. 43 
               
               
                   
               
               
                 Src 
                 MSKPQTQGLAKDAWEIPRESLRLEVKLGQGCFGEVWMGTWNGTTRVAI 
                 SEQ ID 
               
               
                   
                 KTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSEEPIYIVTEYMSKG 
                 NO. 44 
               
               
                   
                 SLLDFLKGETGKYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANIL 
                   
               
               
                   
                 VGENLVCKVADFGLARLIEDNEYTARQGAKFPIKWTAPEAALYGRFTIKS 
                   
               
               
                   
                 DVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYRMPCPPECPESLHD 
                   
               
               
                   
                 LMCQCWRKEPEERPTFEYLQAFLEDYFTSTEPQYQPGENL 
                   
               
               
                   
               
               
                 CDC37 
                 MVDYSVWDHIEVSDDEDETHPNIDTASLFRWRHQARVERMEQFQKEKEE 
                 SEQ ID 
               
               
                   
                 LDRGCRECKRKVAECQRKLKELEVAEGGKAELERLQAEAQQLRKEERSW 
                 NO. 45 
               
               
                   
                 EQKLEEMRKKEKSMPWNVDTLSKDGFSKSMVNTKPEKTEEDSEEVREQK 
                   
               
               
                   
                 HKTFVEKYEKQIKHFGMLRRWDDSQKYLSDNVHLVCEETANYLVIWCID 
                   
               
               
                   
                 LEVEEKCALMEQVAHQTIVMQFILELAKSLKVDPRACFRQFFTKIKTADR 
                   
               
               
                   
                 QYMEGFNDELEAFKERVRGRAKLRIEKAMKEYEEEERKKRLGPGGLDPV 
                   
               
               
                   
                 EVYESLPEELQKCFDVKDVQMLQDAISKMDPTDAKYHMQRCIDSGLWVP 
                   
               
               
                   
                 NSKASEAKEGEEAGPGDPLLEAVPKTGDEKDVSV 
                   
               
               
                   
               
               
                 PTP1B 
                 MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDV 
                 SEQ ID 
               
               
                   
                 SPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMV 
                 NO. 46 
               
               
                   
                 WEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISED 
                   
               
               
                   
                 IKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRE 
                   
               
               
                   
                 SGSLSPEHGPVVVHSSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLL 
                   
               
               
                   
                 EMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEP 
                   
               
               
                   
                 PPEHIPPPPRPPKRILEPHN 
                   
               
               
                   
               
               
                 MBP 
                 MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFP 
                 SEQ ID 
               
               
                   
                 QVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDA 
                 NO. 47 
               
               
                   
                 VRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKS 
                   
               
               
                   
                 ALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGL 
                   
               
               
                   
                 TFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKV 
                   
               
               
                   
                 NYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEG 
                   
               
               
                   
                 LEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMS 
                   
               
               
                   
                 AFWYAVRTAVINAASGRQTVDEALKDAQTRITK 
                   
               
               
                   
               
               
                 LuxAB 
                 MKFGNFLLTYQPPQFSQTEVMKRLVKLGRISEECGFDTVWLLEHHFTEF 
                 SEQ ID 
               
               
                   
                 GLLGNPYVAAAYLLGATKKLNVGTAAIVLPTAHPVRQLEDVNLLDQM 
                 NO. 48 
               
               
                   
                 SKGRFRFGICRGLYNKDFRVFGTDMNNSRALAECWYGLIKNGMTEGYM 
                   
               
               
                   
                 EADNEHIKFHKVKVNPAAYSRGGAPVYVVAESASTTEWAAQFGLPMIL 
                   
               
               
                   
                 SWIINTNEKKAQLELYNEVAQEYGHDIHNIDHCLSYITSVDHDSIKAKEIC 
                   
               
               
                   
                 RKFLGHWYDSYVNATTIFDDSDQTRGYDFNKGQWRDFVLKGHKDTNRR 
                   
               
               
                   
                 IDYSYEINPVGTPQECIDIIQKDIDATGISNICCGFEANGTVDEIIASMKLFQ 
                   
               
               
                   
                 SDVMPFLKEKQRSLLYYGGGGSGGGGSGGGGSGGGGSKFGLFFLNFINS 
                   
               
               
                   
                 TTVQEQSIVRMQEITEYVDKLNFEQILVYENHFSDNGVVGAPLTVSGFLL 
                   
               
               
                   
                 GLTEKIKIGSLNHIITTHHPVRIAEEACLLDQLSEGRFILGFSDCEKKDEMH 
                   
               
               
                   
                 FFNRPVEYQQQLFEECYEIINDALTTGYCNPDNDFYSFPKISVNPHAYTPG 
                   
               
               
                   
                 GPRKYVTATSHHIVEWAAKKGIPLIFKWDDSNDVRYEYAERYKAVADKY 
                   
               
               
                   
                 DVDLSEIDHQLMILVNYNEDSNKAKQETRAFISDYVLEMHPNENFENKLE 
                   
               
               
                   
                 EIIAENAVGNYTECITAAKLAIEKCGAKSVLLSFEPMNDLMSQKNVINIV 
                   
               
               
                   
                 DDNIKKYHTEYT 
                   
               
               
                   
               
               
                 SpecR 
                 MREAVIAEVSTQLSEVVGVIERHLEPTLLAVHLYGSAVDGGLKPHSDIDL 
                 SEQ ID 
               
               
                   
                 LVTVTVRLDETTRRALINDLLETSASPGESEILRAVEVTIVVHDDIIPWRY 
                 NO. 49 
               
               
                   
                 PAKRELQFGEWQRNDILAGIFEPATIDIDLAILLTKAREHSVALVGPAAE 
                   
               
               
                   
                 ELFDPVPEQDLFEALNETLTLWNSPPDWAGDERNVVLTLSRIWYSAVTG 
                   
               
               
                   
                 KIAPKDVAADWAMERLPAQYQPVILEARQAYLGQEEDRLASRADQLEE 
                   
               
               
                   
                 FVHYVKGEITKVVGK 
                   
               
               
                   
               
               
                 AgAs 
                 MVKREFPPGFWKDDLIDSLTSSHKVAASDEKRIETLISEIKNMFRCMGY 
                 SEQ ID 
               
               
                   
                 GETNPSAYDTAWVARIPAVDGSDNPHFPETVEWILQNQLKDGSWGEG 
                 NO. 50 
               
               
                   
                 FYFLAYDRILATLACIITLTLWRTGETQVQKGIEFFRTQAGKMEDEADSH 
                   
               
               
                   
                 RPSGFEIVFPAMLKEAKILGLDLPYDLPFLKQIIEKREAKLKRIPTDVLYA 
                   
               
               
                   
                 LPTTLLYSLEGLQEIVDWQKIMKLQSKDGSFLSSPASTAAVFMRTGNKKC 
                   
               
               
                   
                 LDFLNFVLKKFGNHVPCHYPLDLFERLWAVDTVERLGIDRHFKEEIKEAL 
                   
               
               
                   
                 DYVYSHWDERGIGWARENPVPDIDDTAMGLRILRLHGYNVSSDVLKTFR 
                   
               
               
                   
                 DENGEFFCFLGQTQRGVTDMLNVNRCSHVSFPGETIMEEAKLCTERYLRN 
                   
               
               
                   
                 ALENVDAFDKWAFKKNIRGEVEYALKYPWHKSMPRLEARSYIENYGPDD 
                   
               
               
                   
                 VWLGKTVYMMPYISNEKYLELAKLDFNKVQSIHQTELQDLRRWWKSSGF 
                   
               
               
                   
                 TDLNFTRERVTEIYFSPASFIFEPEFSKCREVYTKTSNFTVILDDLYDAHGSL 
                   
               
               
                   
                 DDLKLFTESVKRWDLSLVDQMPQQMKICFVGFYNTFNDIAKEGRERQGR 
                   
               
               
                   
                 DVLGYIQNVWKVQLEAYTKEAEWSEAKYVPSFNEYIENASVSIALGTVVL 
                   
               
               
                   
                 ISALFTGEVLTDEVLSKIDRESRFLQLMGLTGRLVNDTKTYQAERGQGEV 
                   
               
               
                   
                 ASAIQCYMKDHPKISEEEALQHVYSVMENALEELNREFVNNKIPDIYKRL 
                   
               
               
                   
                 VFETARIMQLFYMQGDGLTLSHDMEIKEHVKNCLFQPVA 
                   
               
               
                   
               
               
                 GGPPS 
                 MFDFNEYMKSKAVAVDAALDKAIPLEYPEKIHESMRYSLLAGGKRVRPA 
                 SEQ ID 
               
               
                   
                 LCIAACELVGGSQDLAMPTACAMEMIHTMSLIHDDLPCMDNDDFRRGKP 
                 NO. 51 
               
               
                   
                 TNHKVFGEDTAVLAGDALLSFAFEHIAVATSKTVPSDRTLRVISELGKTIG 
                   
               
               
                   
                 SQGLVGGQVVDITSEGDANVDLKTLEWIHIHKTAVLLECSVVSGGILGGA 
                   
               
               
                   
                 TEDEIARIRRYARCVGLLFQVVDDILDVTKSSEELGKTAGKDLLTDKATYP 
                   
               
               
                   
                 KLMGLEKAKEFAAELATRAKEELSSFDQIKAAPLLGLADYIAFRQN 
                   
               
               
                   
               
               
                 P450 
                 MTIKEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRVIR 
                 SEQ ID 
               
               
                   
                 YLSSQRLIKEACDESRFDKNLSQALKFVRDFAGDGLFTSWTHEKNWKKA 
                 NO. 52 
               
               
                   
                 HNILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRL 
                   
               
               
                   
                 TLDTIGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLQRANPDDPAY 
                   
               
               
                   
                 DENKRQFQEDIKVMNDLVDKIIADRKASGEQSDDLLTHMLNGKDPETGEP 
                   
               
               
                   
                 LDDENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLV 
                   
               
               
                   
                 DPVPSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLE 
                   
               
               
                   
                 KGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQR 
                   
               
               
                   
                 ACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKA 
                   
               
               
                   
                 KSKKIPLGGIPSPSTEQSAKKVRKKAENAHNTPLLVLYGSNMGTAEGTAR 
                   
               
               
                   
                 DLADIAMSKGFAPQVATLDSHAGNLPREGAVLIVTASYNGHPPDNAKQF 
                   
               
               
                   
                 VDWLDQASADEVKGVRYSVFGCGDKNWATTYQKVPAFIDETLAAKGAE 
                   
               
               
                   
                 NIADRGEADASDDFEGTYEEWREHMWSDVAAYFNLDIENSEDNKSTLSL 
                   
               
               
                   
                 QFVDSAADMPLAKMHGAFSTNVVASKELQQPGSARSTRHLEIELPKEASY 
                   
               
               
                   
                 QEGDHLGVIPRNYEGIVNRVTARFGLDASQQIRLEAEEEKLAHLPLAKTVS 
                   
               
               
                   
                 VEELLQYVELQDPVTRTQLRAMAAKTVCPPHKVELEALLEKQAYKEQVL 
                   
               
               
                   
                 AKRLTMLELLEKYPACEMKFSEFIALLPSIRPRYYSISSSPRVDEKQASITVS 
                   
               
               
                   
                 VVSGEAWSGYGEYKGIASNYLAELQEGDTITCFISTPQSEFTLPKDPETPLI 
                   
               
               
                   
                 MVGPGTGVAPFRGFVQARKQLKEQGQSLGEAHLYFGCRSPHEDYLYQEE 
                   
               
               
                   
                 LENAQSEGIITLHTAFSRMPNQPKTYVQHVMEQDGKKLIELLDQGAHFYI 
                   
               
               
                   
                 CGDGSQMAPAVEATLMKSYADVHQVSEADARLWLQQLEEKGRYAKDV 
                   
               
               
                   
                 WAG 
                   
               
               
                   
               
               
                 LOV2 
                 AATLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPET 
                 SEQ ID 
               
               
                   
                 DRATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRDQKGDVQ 
                 NO. 53 
               
               
                   
                 YFIGVQLDGTEHVRDAAEREGVMLIKKTAENIDEAAKEL 
                   
               
               
                   
               
               
                 BphP1 
                 MASVAGHASGSPAFGTADLSNCEREEIHLAGSIQPHGALLVVSEPDHRIIQ 
                 SEQ ID 
               
               
                   
                 ASANAAEFLNLGSVLGVPLAEIDGDLLIKILPHLDPTAEGMPVAVRCRIGN 
                 NO. 54 
               
               
                   
                 PSTEYDGLMHRPPEGGLIIELERAGPPIDLSGTLAPALERIRTAGSLRALCD 
                   
               
               
                   
                 DTALLFQQCTGYDRVMVYRFDEQGHGEVFSERHVPGLESYFGNRYPSSDI 
                   
               
               
                   
                 PQMARRLYERQRVRVLVDVSYQPVPLEPRLSPLTGRDLDMSGCFLRSMSP 
                   
               
               
                   
                 IHLQYLKNMGVRATLVVSLVVGGKLWGLVACHHYLPRFMHFELRAICEL 
                   
               
               
                   
                 LAEAIATRITALESFAQSQSELFVQRLEQRMIEAITREGDWRAAIFDTSQSIL 
                   
               
               
                   
                 QPLHAAGCALVYEDQIRTIGDVPSTQDVREIAGWLDRQPRAAVTSTASLG 
                   
               
               
                   
                 LDVPELAHLTRMASGVVAAPISDHRGEFLMWFRPERVHTVTWGGDPKKP 
                   
               
               
                   
                 FTMGDTPADLSPRRSFAKWHQVVEGTSDPWTAADLAAARTIGQTVADIV 
                   
               
               
                   
                 LQFRAVRTLIAREQYEQFSSQVHASMQPVLITDAEGRILLMNDSFRDMLP 
                   
               
               
                   
                 AGSPSAVHLDDLAGFFVESNDFLRNVAELIDHGRGWRGEVLLRGAGNRP 
                   
               
               
                   
                 LPLAVRADPVTRTEDQSLGFVLIFSDATDRRTADAARTRFQEGILASARPG 
                   
               
               
                   
                 VRLDSKSDLLHEKLLSALVENAQLAALEITYGVETGRIAELLEGVRQSML 
                   
               
               
                   
                 RTAEVLGHLVQHAARTAGSDSSSNGSQNKKEFDSAGSAGSAGTS 
                   
               
               
                   
               
               
                 TC-PTP 
                 MGMPTTIEREFEELDTQRRWQPLYLEIRNESHDYPHRVAKFPENRNRNRY 
                 SEQ ID 
               
               
                   
                 RDVSPYDHSRVKLQNAENDYINASLVDIEEAQRSYILTQGPLPNTCCHFW 
                 No. 55 
               
               
                   
                 LMVWQQKTKAVVMLNRIVEKESVKCAQYWPTDDQEMLFKETGFSVKLL 
                   
               
               
                   
                 SEDVKSYYTVHLLQLENINSGETRTISHFHYTTWPDFGVPESPASFLNFLFK 
                   
               
               
                   
                 VRESGSLNPDHGPAVIHCSAGIGRSGTFSLVDTCLVLMEKGDDINIKQVLL 
                   
               
               
                   
                 NMRKYRMGLIQTPDQLRFSYMAIIEGAKCIKGDSSIQKRWKELS 
                   
               
               
                   
               
               
                 PTP1B 1-435   
                 MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDV 
                 SEQ ID 
               
               
                   
                 SPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMV 
                 No. 56 
               
               
                   
                 WEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISED 
                   
               
               
                   
                 IKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRE 
                   
               
               
                   
                 SGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLL 
                   
               
               
                   
                 EMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEP 
                   
               
               
                   
                 PPEHIPPPPRPPKRILEPHNGKCREFFPNHQWVKEETQEDKDCPIKEEKGSP 
                   
               
               
                   
                 LNAAPYGIESMSQDTEVRSRVVGGSLRGAQAASPAKGEPSLPEKDEDHAL 
                   
               
               
                   
                 SYWKPFLVNMCVATVLTAGAYLCYRFLFNSNT 
                   
               
               
                   
               
               
                 SacB 
                 MNIKKFAKQATVLTFTTALLAGGATQAFAKETNQKPYKETYGISHITRHD 
                 SEQ ID 
               
               
                   
                 MLQIPEQQKNEKYQVPEFDSSTIKNISSAKGLDVWDSWPLQNADGTVAN 
                 No. 57 
               
               
                   
                 YHGYHIVFALAGDPKNADDTSIYMFYQKVGETSIDSWKNAGRVFKDSDK 
                   
               
               
                   
                 FDANDSILKDQTQEWSGSATFTSDGKIRLFYTDFSGKHYGKQTLTTAQVN 
                   
               
               
                   
                 VSASDSSLNINGVEDYKSIFDGDGKTYQNVQQFIDEGNYSSGDNHTLRDP 
                   
               
               
                   
                 HYVEDKGHKYLVFEANTGTEDGYQGEESLFNKAYYGKSTSFFRQESQKL 
                   
               
               
                   
                 LQSDKKRTAELANGALGMIELNDDYTLKKVMKPLIASNTVTDEIERANVF 
                   
               
               
                   
                 KMNGKWYLFTDSRGSKMTIDGITSNDIYMLGYVSNSLTGPYKPLNKTGL 
                   
               
               
                   
                 VLKMDLDPNDVTFTYSHFAVPQAKGNNVVITSYMTNRGFYADKQSTFAP 
                   
               
               
                   
                 SFLLNIKGKKTSVVKDSILEQGQLTVNK 
                   
               
               
                   
               
               
                 GalK 
                 MSLKEKTQSLFANAFGYPATHTIQAPGRVNLIGEHTDYNDGFVLPCAIDY 
                 SEQ ID 
               
               
                   
                 QTVISCAPRDDRKVRVMAADYENQLDEFSLDAPIVAHENYQWANYVRG 
                 No. 58 
               
               
                   
                 VVKHLQLRNNSFGGVDMVISGNVPQGAGLSSSASLEVAVGTVLQQLYHL 
                   
               
               
                   
                 PLDGAQIALNGQEAENQFVGCNCGIMDQLISALGKKDHALLIDCRSLGTK 
                   
               
               
                   
                 AVSMPKGVAVVIINSNFKRTLVGSEYNTRREQCETGARFFQQPALRDVTIE 
                   
               
               
                   
                 EFNAVAHELDPIVAKRVRHILTENARTVEAASALEQGDLKRMGELMAES 
                   
               
               
                   
                 HASMRDDFEITVPQIDTLVEIVKAVIGDKGGVRMTGGGFGGCIVALIPEEL 
                   
               
               
                   
                 VPAVQQAVAEQYEAKTGIKETFYVCKPSQGAGQC 
                   
               
               
                   
               
               
                 GHS 
                 MAQISESVSPSTDLKSTESSITSNRHGNMWEDDRIQSLNSPYGAPAYQERS 
                 SEQ ID 
               
               
                   
                 EKLIEEIKLLFLSDMDDSCNDSDRDLIKRLEIVDTVECLGIDRHFQPEIKLAL 
                 No. 59 
               
               
                   
                 DYVYRCWNERGIGEGSRDSLKKDLNATALGFRALRLHRYNVSSGVLENF 
                   
               
               
                   
                 RDDNGQFFCGSTVEEEGAEAYNKHVRCMLSLSRASNILFPGEKVMEEAK 
                   
               
               
                   
                 AFTTNYLKKVLAGREATHVDESLLGEVKYALEFPWHCSVQRWEARSFIEI 
                   
               
               
                   
                 FGQIDSELKSNLSKKMLELAKLDFNILQCTHQKELQIISRWFADSSIASLNF 
                   
               
               
                   
                 YRKCYVEFYFWMAAAISEPEFSGSRVAFTKIAILMTMLDDLYDTHGTLDQ 
                   
               
               
                   
                 LKIFTEGVRRWDVSLVEGLPDFMKIAFEFWLKTSNELIAEAVKAQGQDMA 
                   
               
               
                   
                 AYIRKNAWERYLEAYLQDAEWIATGHVPTFDEYLNNGTPNTGMCVLNLI 
                   
               
               
                   
                 PLLLMGEHLPIDILEQIFLPSRFHHLIELASRLVDDARDFQAEKDHGDLSCIE 
                   
               
               
                   
                 CYLKDHPESTVEDALNHVNGLLGNCLLEMNWKFLKKQDSVPLSCKKYSF 
                   
               
               
                   
                 HVLARSIQFMYNQGDGFSISNKVIKDQVQKVLIVPVPI* 
                   
               
               
                   
               
               
                 ADS 
                 MALTEEKPIRPIANFPPSIWGDQFLIYEKQVEQGVEQIVNDLKKEVRQLLK 
                 SEQ ID 
               
               
                   
                 EALDIPMKHANLLKLIDEIQRLGIPYHFEREIDHALQCIYETYGDNWNGDR 
                 No. 60 
               
               
                   
                 SSLWFRLMRKQGYYVTCDVFNNYKDKNGAFKQSLANDVEGLLELYEAT 
                   
               
               
                   
                 SMRVPGEIILEDALGFTRSRLSIMTKDAFSTNPALFTEIQRALKQPLWKRLP 
                   
               
               
                   
                 RIEAAQYIPFYQQQDSHNKTLLKLAKLEFNLLQSLHKEELSHVCKWWKAF 
                   
               
               
                   
                 DIKKNAPCLRDRIVECYFWGLGSGYEPQYSRARVFFTKAVAVITLIDDTYD 
                   
               
               
                   
                 AYGTYEELKIFTEAVERWSITCLDTLPEYMKPIYKLFMDTYTEMEEFLAKE 
                   
               
               
                   
                 GRTDLFNCGKEFVKEFVRNLMVEAKWANEGHIPTTEEHDPVVIITGGANL 
                   
               
               
                   
                 LTTTCYLGMSDIFTKESVEWAVSAPPLFRYSGILGRRLNDLMTHKAEQER 
                   
               
               
                   
                 KHSSSSLESYMKEYNVNEEYAQTLIYKEVEDVWKDINREYLTTKNIPRPLL 
                   
               
               
                   
                 MAVIYLCQFLEVQYAGKDNFTRMGDEYKHLIKSLLVYPMSI* 
                   
               
               
                   
               
               
                 TXS 
                 MSSSTGTSKVVSETSSTIVDDIPRLSANYHGDLWHHNVIQTLETPFRESSTY 
                 SEQ ID 
               
               
                   
                 QERADELVVKIKDMFNALGDGDISPSAYDTAWVARLATISSDGSEKPRFP 
                 No. 61 
               
               
                   
                 QALNWVFNNQLQDGSWGIESHFSLCDRLLNTTNSVIALSVWKTGHSQVQ 
                   
               
               
                   
                 QGAEFIAENLRLLNEEDELSPDFQIIFPALLQKAKALGINLPYDLPFIKYLST 
                   
               
               
                   
                 TREARLTDVSAAADNIPANMLNALEGLEEVIDWNKIMRFQSKDGSFLSSP 
                   
               
               
                   
                 ASTACVLMNTGDEKCFTFLNNLLDKFGGCVPCMYSIDLLERLSLVDNIEH 
                   
               
               
                   
                 LGIGRHFKQEIKGALDYVYRHWSERGIGWGRDSLVPDLNTTALGLRTLR 
                   
               
               
                   
                 MHGYNVSSDVLNNFKDENGRFFSSAGQTHVELRSVVNLFRASDLAFPDE 
                   
               
               
                   
                 RAMDDARKFAEPYLREALATKISTNTKLFKEIEYVVEYPWHMSIPRLEAR 
                   
               
               
                   
                 SYIDSYDDNYVWQRKTLYRMPSLSNSKCLELAKLDFNIVQSLHQEELKLL 
                   
               
               
                   
                 TRWWKESGMADINFTRHRVAEVYFSSATFEPEYSATRIAFTKIGCLQVLFD 
                   
               
               
                   
                 DMADIFATLDELKSFTEGVKRWDTSLLHEIPECMQTCFKVWFKLMEEVN 
                   
               
               
                   
                 NDVVKVQGRDMLAHIRKPWELYFNCYVQEREWLEAGYIPTFEEYLKTYA 
                   
               
               
                   
                 ISVGLGPCTLQPILLMGELVKDDVVEKVHYPSNMFELVSLSWRLTNDTKT 
                   
               
               
                   
                 YQAEKARGQQASGIACYMKDNPGATEEDAIKHICRVVDRALKEASFEYF 
                   
               
               
                   
                 KPSNDIPMGCKSFIFNLRLCVQIFYKFIDGYGIANEEIKDYIRKVYIDPIQV* 
                   
               
               
                   
               
               
                 TC-PTP 
                 MPTTIEREFEELDTQRRWQPLYLEIRNESHDYPHRVAKFPENRNRNRYRD 
                 SEQ ID 
               
               
                   
                 VSPYDHSRVKLQNAENDYINASLVDIEEAQRSYILTQGPLPNTCCHFWLM 
                 No. 62 
               
               
                   
                 VWQQKTKAVVMLNRIVEKESVKCAQYWPTDDQEMLFKETGFSVKLLSE 
                   
               
               
                   
                 DVKSYYTVHLLQLENINSGETRTISHFHYTTWPDFGVPESPASFLNFLFKV 
                   
               
               
                   
                 RESGSLNPDHGPAVIHCSAGIGRSGTFSLVDTCLVLMEKGDDINIKQVLLN 
                   
               
               
                   
                 MRKYRMGLIQTPDQLRFSYMAIIEGAKCIKGDSSIQKRWKELSKEDLSPAF 
                   
               
               
                   
                 DHSPNKIMTEKYNGNR 
                   
               
               
                   
               
               
                 PTPN5 
                 MSSGVDLGTENLYFQSMSRVLQAEELHEKALDPFLLQAEFFEIPMNFVDP 
                 SEQ ID 
               
               
                   
                 KEYDIPGLVRKNRYKTILPNPHSRVCLTSPDPDDPLSSYINANYIRGYGGEE 
                 No. 63 
               
               
                   
                 KVYIATQGPIVSTVADFWRMVWQEHTPIIVMITNIEEMNEKCTEYWPEEQ 
                   
               
               
                   
                 VAYDGVEITVQKVIHTEDYRLRLISLKSGTEERGLKHYWFTSWPDQKTPD 
                   
               
               
                   
                 RAPPLLHLVREVEEAAQQEGPHCAPIIVHCSAGIGRTGCFIATSICCQQLRQ 
                   
               
               
                   
                 EGVVDILKTTCQLRQDRGGMIQTCEQYQFVHHVMSLYEKQLSHQS* 
                   
               
               
                   
               
               
                 PTPN6 
                 MVRWFHRDLSGLDAETLLKGRGVHGSFLARPSRKNQGDFSLSVRVGDQV 
                 SEQ ID 
               
               
                   
                 THIRIQNSGDFYDLYGGEKFATLTELVEYYTQQQGVVQDRDGTIIHLKYPL 
                 No. 64 
               
               
                   
                 NCSDPTSERWYHGHMSGGQAETLLQAKGEPWTFLVRESLSQPGDFVLSV 
                   
               
               
                   
                 LSDQPKAGPGSPLRVTHIKVMCEGGRYTVGGLETFDSLTDLVEHFKKTGI 
                   
               
               
                   
                 EEASGAFVYLRQPYYATRVNAADIENRVLELNKKQESEDTAKAGFWEEF 
                   
               
               
                   
                 ESLQKQEVKNLHQRLEGQRPENKGKNRYKNILPFDHSRVILQGRDSNIPGS 
                   
               
               
                   
                 DYINANYIKNQLLGPDENAKTYIASQGCLEATVNDFWQMAWQENSRVIV 
                   
               
               
                   
                 MTTREVEKGRNKCVPYWPEVGMQRAYGPYSVTNCGEHDTTEYKLRTLQ 
                   
               
               
                   
                 VSPLDNGDLIREIWHYQYLSWPDHGVPSEPGGVLSFLDQINQRQESLPHA 
                   
               
               
                   
                 GPIIVHCSAGIGRTGTIIVIDMLMENISTKGLDCDIDIQKTIQMVRAQRSGM 
                   
               
               
                   
                 VQTEAQYKFIYVAIAQFIETTKKKLEVLQSQKGQESEYGNITYPPAMKNA 
                   
               
               
                   
                 HAKASRTSSKHKEDVYENLHTKNKREEKVKKQRSADKEKSKGSLKRK* 
                   
               
               
                   
               
               
                 PTPN11 
                 MTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGA 
                 SEQ ID 
               
               
                   
                 VTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELK 
                 No. 65 
               
               
                   
                 YPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVL 
                   
               
               
                   
                 SVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYK 
                   
               
               
                   
                 KNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFW 
                   
               
               
                   
                 EEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDP 
                   
               
               
                   
                 NEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQ 
                   
               
               
                   
                 ENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHD 
                   
               
               
                   
                 YTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHH 
                   
               
               
                   
                 KQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMV 
                   
               
               
                   
                 RSQRSGMVQTEAQYRFIYMAVQHYIETLQRRIEEEQKSKRKGHEYTNIKY 
                   
               
               
                   
                 SLADQTSGDQSPLPPCTPTPPCAEMREDSARVYENVGLMQQQKSFR* 
                   
               
               
                   
               
               
                 PTN12 
                 MEQVEILRKFIQRVQAMKSPDHNGEDNFARDFMRLRRLSTKYRTEKIYPT 
                 SEQ ID 
               
               
                   
                 ATGEKEENVKKNRYKDILPFDHSRVKLTLKTPSQDSDYINANFIKGVYGP 
                 No. 66 
               
               
                   
                 KAYVATQGPLANTVIDFWRMVWEYNVVIIVMACREFEMGRKKCERYWP 
                   
               
               
                   
                 LYGEDPITFAPFKISCEDEQARTDYFIRTLLLEFQNESRRLYQFHYVNWPD 
                   
               
               
                   
                 HDVPSSFDSILDMISLMRKYQEHEDVPICIHCSAGCGRTGAICAIDYTWNL 
                   
               
               
                   
                 LKAGKIPEEFNVFNLIQEMRTQRHSAVQTKEQYELVHRAIAQLFEKQLQL 
                   
               
               
                   
                 YEIHGAQKIADGVNEINTENMVSSIEPEKQDSPPPKPPRTRSCLVEGDAKEE 
                   
               
               
                   
                 ILQPPEPHPVPPILTPSPPSAFPTVTTVWQDNDRYHPKPVLQWFHQNNIQQT 
                   
               
               
                   
                 STETIVNQQNFQGKMNQQLNR 
                   
               
               
                   
               
               
                 PTPN22 
                 MDQREILQKFLDEAQSKKITKEEFANEFLKLKRQSTKYKADKTYPTTVAE 
                 SEQ ID 
               
               
                   
                 KPKNIKKNRYKDILPYDYSRVELSLITSDEDSSYINANFIKGVYGPKAYIAT 
                 No. 67 
               
               
                   
                 QGPLSTTLLDFWRMIWEYSVLIIVMACMEYEMGKKKCERYWAEPGEMQ 
                   
               
               
                   
                 LEFGPFSVSCEAEKRKSDYIIRTLKVKFNSETRTTYQFHYKNWPDHDVPSSI 
                   
               
               
                   
                 DPILELIWDVRCYQEDDSVPICIHCSAGCGRTGVICAIDYTWMLLKDGIIPE 
                   
               
               
                   
                 NFSVFSLIREMRTQRPSLVQTQEQYELVYNAVLELFKRQMDVIRD 
                   
               
               
                   
               
               
                 sfGFP 
                 MRKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTT 
                 SEQ ID 
               
               
                   
                 GKLPVPWPTLVTTLTYGVQCFARYPDHMKQHDFFKSAMPEGYVQERTIS 
                 No. 68 
               
               
                   
                 FKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHN 
                   
               
               
                   
                 VYITADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNH 
                   
               
               
                   
                 YLSTQSVLSKDPNEKRDHMVLLEFVTAAGITHGMDELYK* 
                   
               
               
                   
               
               
                 mClover 
                 MHHHHHHVSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKL 
                 SEQ ID 
               
               
                   
                 TLKFICTTGKLPVPWPTLVTTFGYGVACFSRYPDHMKQHDFFKSAMPEGY 
                 No. 69 
               
               
                   
                 VQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEY 
                   
               
               
                   
                 NFNSHNVYITADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPV 
                   
               
               
                   
                 LLPDNHYLSHQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 4 
               
             
            
               
                   
               
               
                 Exemplary Terminators. 
               
            
           
           
               
               
               
            
               
                   
                   
                 SEQ 
               
               
                   
                   
                 ID No. 
               
               
                 Name 
                 DNA Sequence 
                 # 
               
               
                   
               
               
                 T7 
                 ATCCGGATATAGTTCCTCCTTTCAGCAAAAAACCCCTCAAGACCCGTTTAGAGG 
                 SEQ ID 
               
               
                   
                 CCCCAAGGGGTTATGCTAGTTATTGCTCAGCGGTGGCAGCAGCCAACTCAGCTT 
                 No. 70 
               
               
                   
                 CCTTTCGGGCTTTGTTAGCAG 
                   
               
               
                   
               
               
                 rrnB 
                 GGCTGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAA 
                 SEQ ID 
               
               
                 T1/T2 
                 CGCAGAAGCGGTCTGATAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGT 
                 No. 71 
               
               
                   
                 CCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTA 
                   
               
               
                   
                 GTGTGGGGTCACCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATAAAACG 
                   
               
               
                   
                 AAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAA 
                   
               
               
                   
                 CGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGC 
                   
               
               
                   
                 AACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAA 
                   
               
               
                   
                 ATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCT 
                   
               
               
                   
               
               
                 TrrnB 
                 TGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAA 
                 SEQ ID 
               
               
                   
                 GTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGG 
                 No. 72 
               
               
                   
                 GAACTGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTT 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 5 
               
             
            
               
                   
               
               
                 Exemplary DNA Sequences (includes truncations): 
               
            
           
           
               
               
               
               
            
               
                   
                   
                   
                 SEQ 
               
               
                   
                   
                   
                 ID 
               
               
                 Comp. 
                 Organism 
                 DNA Sequence 
                 No. # 
               
               
                   
               
               
                 Src 
                 
                   H. sapiens 
                 
                 ATGGGCTCCAAGCCGCAGACTCAGGGCCTGGCCAAGGATGCCTGGGA 
                 SEQ 
               
               
                   
                   
                 GATCCCTCGGGAGTCGCTGCGGCTGGAGGTCAAGCTGGGCCAGGGCT 
                 ID 
               
               
                   
                   
                 GCTTTGGCGAGGTGTGGATGGGGACCTGGAACGGTACCACCAGGGTG 
                 No. 73 
               
               
                   
                   
                 GCCATCAAAACCCTGAAGCCTGGCACGATGTCTCCAGAGGCCTTCCTG 
                   
               
               
                   
                   
                 CAGGAGGCCCAGGTCATGAAGAAGCTGAGGCATGAGAAGCTGGTGCA 
                   
               
               
                   
                   
                 GTTGTATGCTGTGGTTTCAGAGGAGCCCATTTACATCGTCACGGAGTA 
                   
               
               
                   
                   
                 CATGAGCAAGGGGAGTTTGCTGGACTTTCTCAAGGGGGAGACAGGCA 
                   
               
               
                   
                   
                 AGTACCTGCGGCTGCCTCAGCTGGTGGACATGGCTGCTCAGATCGCCT 
                   
               
               
                   
                   
                 CAGGCATGGCGTACGTGGAGCGGATGAACTACGTCCACCGGGACCTTC 
                   
               
               
                   
                   
                 GTGCAGCCAACATCCTGGTGGGAGAGAACCTGGTGTGCAAAGTGGCC 
                   
               
               
                   
                   
                 GACTTTGGGCTGGCTCGGCTCATTGAAGACAATGAGTACACGGCGCGG 
                   
               
               
                   
                   
                 CAAGGTGCCAAATTCCCCATCAAGTGGACGGCTCCAGAAGCTGCCCTC 
                   
               
               
                   
                   
                 TATGGCCGCTTCACCATCAAGTCGGACGTGTGGTCCTTCGGGATCCTG 
                   
               
               
                   
                   
                 CTGACTGAGCTCACCACAAAGGGACGGGTGCCCTACCCTGGGATGGTG 
                   
               
               
                   
                   
                 AACCGCGAGGTGCTGGACCAGGTGGAGCGGGGCTACCGGATGCCCTG 
                   
               
               
                   
                   
                 CCCGCCGGAGTGTCCCGAGTCCCTGCACGACCTCATGTGCCAGTGCTG 
                   
               
               
                   
                   
                 GCGGAAGGAGCCTGAGGAGCGGCCCACCTTCGAGTACCTGCAGGCCT 
                   
               
               
                   
                   
                 TCCTGGAGGACTACTTCACGTCCACCGAGCCCCAGTACCAGCCCGGGG 
                   
               
               
                   
                   
                 AGAACCTCTAA 
                   
               
               
                   
               
               
                 CDC37 
                 
                   H. sapiens 
                 
                 ATGGTGGACTACAGCGTGTGGGACCACATTGAGGTGTCTGATGATGAA 
                 SEQ 
               
               
                   
                   
                 GACGAGACGCACCCCAACATCGACACGGCCAGTCTCTTCCGCTGGCGG 
                 ID 
               
               
                   
                   
                 CATCAGGCCCGGGTGGAACGCATGGAGCAGTTCCAGAAGGAGAAGGA 
                 No. 74 
               
               
                   
                   
                 GGAACTGGACAGGGGCTGCCGCGAGTGCAAGCGCAAGGTGGCCGAGT 
                   
               
               
                   
                   
                 GCCAGAGGAAACTGAAGGAGCTGGAGGTGGCCGAGGGCGGCAAGGC 
                   
               
               
                   
                   
                 AGAGCTGGAGCGCCTGCAGGCCGAGGCACAGCAGCTGCGCAAGGAGG 
                   
               
               
                   
                   
                 AGCGGAGCTGGGAGCAGAAGCTGGAGGAGATGCGCAAGAAGGAGAA 
                   
               
               
                   
                   
                 GAGCATGCCCTGGAACGTGGACACGCTCAGCAAAGACGGCTTCAGCA 
                   
               
               
                   
                   
                 AGAGCATGGTAAATACCAAGCCCGAGAAGACGGAGGAGGACTCAGAG 
                   
               
               
                   
                   
                 GAGGTGAGGGAGCAGAAACACAAGACCTTCGTGGAAAAATACGAGAA 
                   
               
               
                   
                   
                 ACAGATCAAGCACTTTGGCATGCTTCGCCGCTGGGATGACAGCCAAAA 
                   
               
               
                   
                   
                 GTACCTGTCAGACAACGTCCACCTGGTGTGCGAGGAGACAGCCAATTA 
                   
               
               
                   
                   
                 CCTGGTCATTTGGTGCATTGACCTAGAGGTGGAGGAGAAATGTGCACT 
                   
               
               
                   
                   
                 CATGGAGCAGGTGGCCCACCAGACAATCGTCATGCAATTTATCCTGGA 
                   
               
               
                   
                   
                 GCTGGCCAAGAGCCTAAAGGTGGACCCCCGGGCCTGCTTCCGGCAGTT 
                   
               
               
                   
                   
                 CTTCACTAAGATTAAGACAGCCGATCGCCAGTACATGGAGGGCTTCAA 
                   
               
               
                   
                   
                 CGACGAGCTGGAAGCCTTCAAGGAGCGTGTGCGGGGCCGTGCCAAGC 
                   
               
               
                   
                   
                 TGCGCATCGAGAAGGCCATGAAGGAGTACGAGGAGGAGGAGCGCAA 
                   
               
               
                   
                   
                 GAAGCGGCTCGGCCCCGGCGGCCTGGACCCCGTCGAGGTCTACGAGTC 
                   
               
               
                   
                   
                 CCTCCCTGAGGAACTCCAGAAGTGCTTCGATGTGAAGGACGTGCAGAT 
                   
               
               
                   
                   
                 GCTGCAGGACGCCATCAGCAAGATGGACCCCACCGACGCAAAGTACC 
                   
               
               
                   
                   
                 ACATGCAGCGCTGCATTGACTCTGGCCTCTGGGTCCCCAACTCTAAGG 
                   
               
               
                   
                   
                 CCAGCGAGGCCAAGGAGGGAGAGGAGGCAGGTCCTGGGGACCCATTA 
                   
               
               
                   
                   
                 CTGGAAGCTGTTCCCAAGACGGGCGATGAGAAGGATGTCAGTGTGTA 
                   
               
               
                   
                   
                 A 
                   
               
               
                   
               
               
                 PTP1B 1-435   
                 
                   H. sapiens 
                 
                 ATGGAGATGGAAAAGGAGTTCGAGCAGATCGACAAGTCCGGGAGCTG 
                 SEQ 
               
               
                   
                   
                 GGCGGCCATTTACCAGGATATCCGACATGAAGCCAGTGACTTCCCATG 
                 ID 
               
               
                   
                   
                 TAGAGTGGCCAAGCTTCCTAAGAACAAAAACCGAAATAGGTACAGAG 
                 No. 75 
               
               
                   
                   
                 ACGTCAGTCCCTTTGACCATAGTCGGATTAAACTACATCAAGAAGATA 
                   
               
               
                   
                   
                 ATGACTATATCAACGCTAGTTTGATAAAAATGGAAGAAGCCCAAAGG 
                   
               
               
                   
                   
                 AGTTACATTCTTACCCAGGGCCCTTTGCCTAACACATGCGGTCACTTTT 
                   
               
               
                   
                   
                 GGGAGATGGTGTGGGAGCAGAAAAGCAGGGGTGTCGTCATGCTCAAC 
                   
               
               
                   
                   
                 AGAGTGATGGAGAAAGGTTCGTTAAAATGCGCACAATACTGGCCACA 
                   
               
               
                   
                   
                 AAAAGAAGAAAAAGAGATGATCTTTGAAGACACAAATTTGAAATTAA 
                   
               
               
                   
                   
                 CATTGATCTCTGAAGATATCAAGTCATATTATACAGTGCGACAGCTAG 
                   
               
               
                   
                   
                 AATTGGAAAACCTTACAACCCAAGAAACTCGAGAGATCTTACATTTCC 
                   
               
               
                   
                   
                 ACTATACCACATGGCCTGACTTTGGAGTCCCTGAATCACCAGCCTCAT 
                   
               
               
                   
                   
                 TCTTGAACTTTCTTTTCAAAGTCCGAGAGTCAGGGTCACTCAGCCCGG 
                   
               
               
                   
                   
                 AGCACGGGCCCGTTGTGGTGCACTGCAGTGCAGGCATCGGCAGGTCTG 
                   
               
               
                   
                   
                 GAACCTTCTGTCTGGCTGATACCTGCCTCTTGCTGATGGACAAGAGGA 
                   
               
               
                   
                   
                 AAGACCCTTCTTCCGTTGATATCAAGAAAGTGCTGTTAGAAATGAGGA 
                   
               
               
                   
                   
                 AGTTTCGGATGGGGCTGATCCAGACAGCCGACCAGCTGCGCTTCTCCT 
                   
               
               
                   
                   
                 ACCTGGCTGTGATCGAAGGTGCCAAATTCATCATGGGGGACTCTTCCG 
                   
               
               
                   
                   
                 TGCAGGATCAGTGGAAGGAGCTTTCCCACGAGGACCTGGAGCCCCCA 
                   
               
               
                   
                   
                 CCCGAGCATATCCCCCCACCTCCCCGGCCACCCAAACGAATCCTGGAG 
                   
               
               
                   
                   
                 CCACACAATGGGAAATGCAGGGAGTTCTTCCCAAATCACCAGTGGGTG 
                   
               
               
                   
                   
                 AAGGAAGAGACCCAGGAGGATAAAGACTGCCCCATCAAGGAAGAAA 
                   
               
               
                   
                   
                 AAGGAAGCCCCTTAAATGCCGCACCCTACGGCATCGAAAGCATGAGT 
                   
               
               
                   
                   
                 CAAGACACTGAAGTTAGAAGTCGGGTCGTGGGGGGAAGTCTTCGAGG 
                   
               
               
                   
                   
                 TGCCCAGGCTGCCTCCCCAGCCAAAGGGGAGCCGTCACTGCCCGAGA 
                   
               
               
                   
                   
                 AGGACGAGGACCATGCACTGAGTTACTGGAAGCCCTTCCTGGTCAACA 
                   
               
               
                   
                   
                 TGTGCGTGGCTACGGTCCTCACGGCCGGCGCTTACCTCTGCTACAGGT 
                   
               
               
                   
                   
                 TCCTGTTCAACAGCAACACATAG 
                   
               
               
                   
               
               
                 LuxAB 
                 Bacterial 
                 ATGAAATTTGGAAACTTTTTGCTTACATACCAACCTCCCCAATTTTCCC 
                 SEQ 
               
               
                   
                   
                 AAACAGAGGTAATGAAACGTTTGGTTAAATTAGGTCGCATCTCTGAGG 
                 ID 
               
               
                   
                   
                 AGTGTGGTTTTGATACCGTATGGTTACTGGAGCATCATTTCACGGAGTT 
                 No. 76 
               
               
                   
                   
                 TGGTTTGCTTGGTAACCCTTATGTCGCTGCTGCATATTTACTTGGCGCG 
                   
               
               
                   
                   
                 ACTAAAAAATTGAATGTAGGAACTGCCGCTATTGTTCTTCCCACAGCC 
                   
               
               
                   
                   
                 CATCCAGTACGCCAACTTGAAGATGTGAATTTATTGGATCAAATGTCA 
                   
               
               
                   
                   
                 AAAGGACGATTTCGGTTTGGTATTTGCCGAGGGCTTTACAACAAGGAC 
                   
               
               
                   
                   
                 TTTCGCGTATTCGGCACAGATATGAATAACAGTCGCGCCTTAGCGGAA 
                   
               
               
                   
                   
                 TGCTGGTACGGGCTGATAAAGAATGGCATGACAGAGGGATATATGGA 
                   
               
               
                   
                   
                 AGCTGATAATGAACATATCAAGTTCCATAAGGTAAAAGTAAACCCCGC 
                   
               
               
                   
                   
                 GGCGTATAGCAGAGGTGGCGCACCGGTTTATGTGGTGGCTGAATCAGC 
                   
               
               
                   
                   
                 TTCGACGACTGAGTGGGCTGCTCAATTTGGCCTACCGATGATATTAAG 
                   
               
               
                   
                   
                 TTGGATTATAAATACTAACGAAAAGAAAGCACAACTTGAGCTTTATAA 
                   
               
               
                   
                   
                 TGAAGTGGCTCAAGAATATGGGCACGATATTCATAATATCGACCATTG 
                   
               
               
                   
                   
                 CTTATCATATATAACATCTGTAGATCATGACTCAATTAAAGCGAAAGA 
                   
               
               
                   
                   
                 GATTTGCCGGAAATTTCTGGGGCATTGGTATGATTCTTATGTGAATGCT 
                   
               
               
                   
                   
                 ACGACTATTTTTGATGATTCAGACCAAACAAGAGGTTATGATTTCAAT 
                   
               
               
                   
                   
                 AAAGGGCAGTGGCGTGACTTTGTATTAAAAGGACATAAAGATACTAA 
                   
               
               
                   
                   
                 TCGCCGTATTGATTACAGTTACGAAATCAATCCCGTGGGAACGCCGCA 
                   
               
               
                   
                   
                 GGAATGTATTGACATAATTCAAAAAGACATTGATGCTACAGGAATATC 
                   
               
               
                   
                   
                 AAATATTTGTTGTGGATTTGAAGCTAATGGAACAGTAGACGAAATTAT 
                   
               
               
                   
                   
                 TGCTTCCATGAAGCTCTTCCAGTCTGATGTCATGCCATTTCTTAAAGAA 
                   
               
               
                   
                   
                 AAACAACGTTCGCTATTATATTATTAA 
                   
               
               
                   
               
               
                 LuxB 
                 
                   V. fischeri 
                 
                 ATGAGCAAATTTGGATTGTTCTTCCTTAACTTCATCAATTCAACAACTG 
                 SEQ 
               
               
                   
                   
                 TTCAAGAACAGAGTATAGTTCGCATGCAGGAAATAACGGAGTATGTTG 
                 ID 
               
               
                   
                   
                 ATAAGTTGAATTTTGAACAGATTTTAGTGTATGAAAATCATTTTTCAGA 
                 No. 77 
               
               
                   
                   
                 TAATGGTGTTGTCGGCGCTCCTCTGACTGTTTCTGGTTTTCTGCTCGGT 
                   
               
               
                   
                   
                 TTAACAGAGAAAATTAAAATTGGTTCATTAAATCACATCATTACAACT 
                   
               
               
                   
                   
                 CATCATCCTGTCCGCATAGCGGAGGAAGCTTGCTTATTGGATCAGTTA 
                   
               
               
                   
                   
                 AGTGAAGGGAGATTTATTTTAGGGTTTAGTGATTGCGAAAAAAAAGAT 
                   
               
               
                   
                   
                 GAAATGCATTTTTTTAATCGCCCGGTTGAATATCAACAGCAACTATTTG 
                   
               
               
                   
                   
                 AAGAGTGTTATGAAATCATTAACGATGCTTTAACAACAGGCTATTGTA 
                   
               
               
                   
                   
                 ATCCAGATAACGATTTTTATAGCTTCCCTAAAATATCTGTAAATCCCCA 
                   
               
               
                   
                   
                 TGCTTATACGCCAGGCGGACCTCGGAAATATGTAACAGCAACCAGTCA 
                   
               
               
                   
                   
                 TCATATTGTTGAGTGGGCGGCCAAAAAAGGTATTCCTCTCATCTTTAA 
                   
               
               
                   
                   
                 GTGGGATGATTCTAATGATGTTAGATATGAATATGCTGAAAGATATAA 
                   
               
               
                   
                   
                 AGCCGTTGCGGATAAATATGACGTTGACCTATCAGAGATAGACCATCA 
                   
               
               
                   
                   
                 GTTAATGATATTAGTTAACTATAACGAAGATAGTAATAAAGCTAAACA 
                   
               
               
                   
                   
                 AGAAACGCGTGCATTTATTAGTGATTATGTTCTTGAAATGCACCCTAA 
                   
               
               
                   
                   
                 TGAAAATTTCGAAAATAAACTTGAAGAAATAATTGCAGAAAACGCTG 
                   
               
               
                   
                   
                 TCGGAAATTATACGGAGTGTATAACTGCGGCTAAGTTGGCAATTGAAA 
                   
               
               
                   
                   
                 AGTGTGGTGCGAAAAGTGTATTGCTGTCCTTTGAACCAATGAATGATT 
                   
               
               
                   
                   
                 TGATGAGCCAAAAAAATGTAATCAATATTGTTGATGATAATATTAAGA 
                   
               
               
                   
                   
                 AGTACCACACGGAATATACCTAA 
                   
               
               
                   
               
               
                 RpoZ 
                 
                   Escherichia 
                 
                 ATGGCACGCGTAACTGTTCAGGACGCTGTAGAGAAAATTGGTAACCGT 
                 SEQ 
               
               
                   
                 
                   coli 
                 
                 TTTGACCTGGTACTGGTCGCCGCGCGTCGCGCTCGTCAGATGCAGGTA 
                 ID 
               
               
                   
                   
                 GGCGGAAAGGATCCGCTGGTACCGGAAGAAAACGATAAAACCACTGT 
                 No. 78 
               
               
                   
                   
                 AATCGCGCTGCGCGAAATCGAAGAAGGTCTGATCAACAACCAGATCC 
                   
               
               
                   
                   
                 TCGACGTTCGCGAACGCCAGGAACAGCAAGAGCAGGAAGCCGCTGAA 
                   
               
               
                   
                   
                 TTACAAGCCGTTACCGCTATTGCTGAAGGTCGTCGTTAA 
                   
               
               
                   
               
               
                 cI 
                 Lambda 
                 ATGAGTATCAGCAGCAGGGTAAAAAGCAAAAGAATTCAGCTTGGACT 
                 SEQ 
               
               
                   
                 bacterio- 
                 TAACCAGGCTGAACTTGCTCAAAAGGTGGGGACTACCCAGCAGTCTAT 
                 ID 
               
               
                   
                 phage 
                 AGAGCAGCTCGAAAACGGTAAAACTAAGCGACCACGCTTTTTACCAG 
                 No. 79 
               
               
                   
                   
                 AACTTGCGTCAGCTCTTGGCGTAAGTGTTGACTGGCTGCTCAATGGCA 
                   
               
               
                   
                   
                 CCTCTGATTCGAATGTTAGATTTGTTGGGCACGTTGAGCCCAAAGGGA 
                   
               
               
                   
                   
                 AATATCCATTGATTAGCATGGTTAGAGCTCGTTCGTGGTGTGAAGCTT 
                   
               
               
                   
                   
                 GTGAACCCTACGATATCAAGGACATTGATGAATGGTATGACAGTGACG 
                   
               
               
                   
                   
                 TTAACTTATTAGGCAATGGATTCTGGCTGAAGGTTGAAGGTGATTCCA 
                   
               
               
                   
                   
                 TGACCTCACCTGTAGGTCAAAGCATCCCTGAAGGTCATATGGTGTTAG 
                   
               
               
                   
                   
                 TAGATACTGGACGGGAGCCAGTGAATGGAAGCCTTGTTGTAGCCAAA 
                   
               
               
                   
                   
                 CTGACTGACGCGAACGAAGCAACATTCAAGAAACTGGTCATAGATGG 
                   
               
               
                   
                   
                 CGGTCAGAAGTACCTGAAAGGCCTGAATCCTTCATGGCCTATGACTCC 
                   
               
               
                   
                   
                 TATCAACGGAAACTGCAAGATTATCGGTGTTGTCGTGGAAGCGAGGGT 
                   
               
               
                   
                   
                 AAAATTCGTAGACTAA 
                   
               
               
                   
               
               
                 SH2 
                 
                   Rous 
                 
                 ATGTGGTATTTTGGGAAGATCACTCGTCGGGAGTCCGAGCGGCTGCTG 
                 SEQ 
               
               
                   
                 
                   sarcoma 
                 
                 CTCAACCCCGAAAACCCCCGGGGAACCTTCTTGGTCCGGGAGAGCGA 
                 ID 
               
               
                   
                 virus 
                 GACGGTAAAAGGTGCCTATGCCCTCTCCGTTTCTGACTTTGACAACGC 
                 No. 80 
               
               
                   
                   
                 CAAGGGGCTCAATGTGAAACACTACCTGATCCGCAAGCTGGACAGCG 
                   
               
               
                   
                   
                 GCGGCTTCTACATCACCTCACGCACACAGTTCAGCAGCCTGCAGCAGC 
                   
               
               
                   
                   
                 TGGTGGCCTACTACTCCAAACATGCTGATGGCTTGTGCCACCGCCTGA 
                   
               
               
                   
                   
                 CCAACGTCTGCTAA 
                   
               
               
                   
               
               
                 MBP 
                   E .  coli   
                 ATGAAAATCGAAGAAGGTAAACTGGTAATCTGGATTAACGGCGATAA 
                 SEQ 
               
               
                   
                   
                 AGGCTATAACGGTCTCGCTGAAGTCGGTAAGAAATTCGAGAAAGATA 
                 ID 
               
               
                   
                   
                 CCGGAATTAAAGTCACCGTTGAGCATCCGGATAAACTGGAAGAGAAA 
                 No. 81 
               
               
                   
                   
                 TTCCCACAGGTTGCGGCAACTGGCGATGGCCCTGACATTATCTTCTGG 
                   
               
               
                   
                   
                 GCACACGACCGCTTTGGTGGCTACGCTCAATCTGGCCTGTTGGCTGAA 
                   
               
               
                   
                   
                 ATCACCCCGGACAAAGCGTTCCAGGACAAGCTGTATCCGTTTACCTGG 
                   
               
               
                   
                   
                 GATGCCGTACGTTACAACGGCAAGCTGATTGCTTACCCGATCGCTGTT 
                   
               
               
                   
                   
                 GAAGCGTTATCGCTGATTTATAACAAAGATCTGCTGCCGAACCCGCCA 
                   
               
               
                   
                   
                 AAAACCTGGGAAGAGATCCCGGCGCTGGATAAAGAACTGAAAGCGAA 
                   
               
               
                   
                   
                 AGGTAAGAGCGCGCTGATGTTCAACCTGCAAGAACCGTACTTCACCTG 
                   
               
               
                   
                   
                 GCCGCTGATTGCTGCTGACGGGGGTTATGCGTTCAAGTATGAAAACGG 
                   
               
               
                   
                   
                 CAAGTACGACATTAAAGACGTGGGCGTGGATAACGCTGGCGCGAAAG 
                   
               
               
                   
                   
                 CGGGTCTGACCTTCCTGGTTGACCTGATTAAAAACAAACACATGAATG 
                   
               
               
                   
                   
                 CAGACACCGATTACTCCATCGCAGAAGCTGCCTTTAATAAAGGCGAAA 
                   
               
               
                   
                   
                 CAGCGATGACCATCAACGGCCCGTGGGCATGGTCCAACATCGACACC 
                   
               
               
                   
                   
                 AGCAAAGTGAATTATGGTGTAACGGTACTGCCGACCTTCAAGGGTCAA 
                   
               
               
                   
                   
                 CCATCCAAACCGTTCGTTGGCGTGCTGAGCGCAGGTATTAACGCCGCC 
                   
               
               
                   
                   
                 AGTCCGAACAAAGAGCTGGCGAAAGAGTTCCTCGAAAACTATCTGCT 
                   
               
               
                   
                   
                 GACTGATGAAGGTCTGGAAGCGGTTAATAAAGACAAACCGCTGGGTG 
                   
               
               
                   
                   
                 CCGTAGCGCTGAAGTCTTACGAGGAAGAGTTGGCGAAAGATCCACGT 
                   
               
               
                   
                   
                 ATTGCCGCCACCATGGAAAACGCCCAGAAAGGTGAAATCATGCCGAA 
                   
               
               
                   
                   
                 CATCCCGCAGATGTCCGCTTTCTGGTATGCCGTGCGTACTGCGGTGATC 
                   
               
               
                   
                   
                 AACGCCGCCAGCGGTCGTCAGACTGTCGATGAAGCCCTGAAAGACGC 
                   
               
               
                   
                   
                 GCAGACTCGTATCACCAAGTAA 
                   
               
               
                   
               
               
                 p130cas 
                 
                   H. sapiens 
                 
                 TGGATGGAGGACTATGACTACGTCCACCTACAGGGG 
                 SEQ 
               
               
                 (or 
                   
                   
                 ID 
               
               
                 Kras) 
                   
                   
                 No. 82 
               
               
                 substrate 
                   
                   
                   
               
               
                   
               
               
                 MidT 
                 
                   Hamster 
                 
                 GAACCGCAGTATGAAGAAATTCCGATTTATCTG 
                 SEQ 
               
               
                 substrate 
                 
                   polyoma 
                 
                   
                 ID 
               
               
                   
                 virus 
                   
                 No. 83 
               
               
                   
               
               
                 EGFR 
                 
                   H. sapiens 
                 
                 CCGCAGCGCTATCTGGTGATTCAGGGCGAT 
                 SEQ 
               
               
                 substrate 
                   
                   
                 ID 
               
               
                   
                   
                   
                 No. 84 
               
               
                   
               
               
                 ShcA 
                 
                   H. sapiens 
                 
                 GATCATCAGTATTATAACGATTTTCCGGGC 
                 SEQ 
               
               
                 substrate 
                   
                   
                 ID 
               
               
                   
                   
                   
                 No. 85 
               
               
                   
               
               
                 MBIS 
                 
                   S. 
                 
                 ATGTCATTACCGTTCTTAACTTCTGCACCGGGAAAGGTTATTATTTTTG 
                 SEQ 
               
               
                   
                 
                   cerevisiae 
                 
                 GTGAACACTCTGCTGTGTACAACAAGCCTGCCGTCGCTGCTAGTGTGT 
                 ID 
               
               
                   
                 (from 
                 CTGCGTTGAGAACCTACCTGCTAATAAGCGAGTCATCTGCACCAGATA 
                 No. 86 
               
               
                   
                 pMBIS 
                 CTATTGAATTGGACTTCCCGGACATTAGCTTTAATCATAAGTGGTCCAT 
                   
               
               
                   
                 Addgene#: 
                 CAATGATTTCAATGCCATCACCGAGGATCAAGTAAACTCCCAAAAATT 
                   
               
               
                   
                 17817 
                 GGCCAAGGCTCAACAAGCCACCGATGGCTTGTCTCAGGAACTCGTTAG 
                   
               
               
                   
                   
                 TCTTTTGGATCCGTTGTTAGCTCAACTATCCGAATCCTTCCACTACCAT 
                   
               
               
                   
                   
                 GCAGCGTTTTGTTTCCTGTATATGTTTGTTTGCCTATGCCCCCATGCCA 
                   
               
               
                   
                   
                 AGAATATTAAGTTTTCTTTAAAGTCTACTTTACCCATCGGTGCTGGGTT 
                   
               
               
                   
                   
                 GGGCTCAAGCGCCTCTATTTCTGTATCACTGGCCTTAGCTATGGCCTAC 
                   
               
               
                   
                   
                 TTGGGGGGGTTAATAGGATCTAATGACTTGGAAAAGCTGTCAGAAAA 
                   
               
               
                   
                   
                 CGATAAGCATATAGTGAATCAATGGGCCTTCATAGGTGAAAAGTGTAT 
                   
               
               
                   
                   
                 TCACGGTACCCCTTCAGGAATAGATAACGCTGTGGCCACTTATGGTAA 
                   
               
               
                   
                   
                 TGCCCTGCTATTTGAAAAAGACTCACATAATGGAACAATAAACACAAA 
                   
               
               
                   
                   
                 CAATTTTAAGTTCTTAGATGATTTCCCAGCCATTCCAATGATCCTAACC 
                   
               
               
                   
                   
                 TATACTAGAATTCCAAGGTCTACAAAAGATCTTGTTGCTCGCGTTCGT 
                   
               
               
                   
                   
                 GTGTTGGTCACCGAGAAATTTCCTGAAGTTATGAAGCCAATTCTAGAT 
                   
               
               
                   
                   
                 GCCATGGGTGAATGTGCCCTACAAGGCTTAGAGATCATGACTAAGTTA 
                   
               
               
                   
                   
                 AGTAAATGTAAAGGCACCGATGACGAGGCTGTAGAAACTAATAATGA 
                   
               
               
                   
                   
                 ACTGTATGAACAACTATTGGAATTGATAAGAATAAATCATGGACTGCT 
                   
               
               
                   
                   
                 TGTCTCAATCGGTGTTTCTCATCCTGGATTAGAACTTATTAAAAATCTG 
                   
               
               
                   
                   
                 AGCGATGATTTGAGAATTGGCTCCACAAAACTTACCGGTGCTGGTGGC 
                   
               
               
                   
                   
                 GGCGGTTGCTCTTTGACTTTGTTACGAAGAGACATTACTCAAGAGCAA 
                   
               
               
                   
                   
                 ATTGACAGCTTCAAAAAGAAATTGCAAGATGATTTTAGTTACGAGACA 
                   
               
               
                   
                   
                 TTTGAAACAGACTTGGGTGGGACTGGCTGCTGTTTGTTAAGCGCAAAA 
                   
               
               
                   
                   
                 AATTTGAATAAAGATCTTAAAATCAAATCCCTAGTATTCCAATTATTTG 
                   
               
               
                   
                   
                 AAAATAAAACTACCACAAAGCAACAAATTGACGATCTATTATTGCCAG 
                   
               
               
                   
                   
                 GAAACACGAATTTNCCATGGACTTCATAGGAGGCAGATCAAATGTCA 
                   
               
               
                   
                   
                 GAGTTGAGAGCCTTCAGTGCCCCAGGGAAAGCGTTACTAGCTGGTGGA 
                   
               
               
                   
                   
                 TATTTAGTTTTAGATACAAAATATGAAGCATTTGTAGTCGGATTATCG 
                   
               
               
                   
                   
                 GCAAGAATGCATGCTGTAGCCCATCCTTACGGTTCATTGCAAGGGTCT 
                   
               
               
                   
                   
                 GATAAGTTTGAAGTGCGTGTGAAAAGTAAACAATTTAAAGATGGGGA 
                   
               
               
                   
                   
                 GTGGCTGTACCATATAAGTCCTAAAAGTGGCTTCATTCCTGTTTCGATA 
                   
               
               
                   
                   
                 GGCGGATCTAAGAACCCTTTCATTGAAAAAGTTATCGCTAACGTATTT 
                   
               
               
                   
                   
                 AGCTACTTTAAACCTAACATGGACGACTACTGCAATAGAAACTTGTTC 
                   
               
               
                   
                   
                 GTTATTGATATTTTCTCTGATGATGCCTACCATTCTCAGGAGGATAGCG 
                   
               
               
                   
                   
                 TTACCGAACATCGTGGCAACAGAAGATTGAGTTTTCATTCGCACAGAA 
                   
               
               
                   
                   
                 TTGAAGAAGTTCCCAAAACAGGGCTGGGCTCCTCGGCAGGTTTAGTCA 
                   
               
               
                   
                   
                 CAGTTTTAACTACAGCTTTGGCCTCCTTTTTTGTATCGGACCTGGAAAA 
                   
               
               
                   
                   
                 TAATGTAGACAAATATAGAGAAGTTATTCATAATTTAGCACAAGTTGC 
                   
               
               
                   
                   
                 TCATTGTCAAGCTCAGGGTAAAATTGGAAGCGGGTTTGATGTAGCGGC 
                   
               
               
                   
                   
                 GGCAGCATATGGATCTATCAGATATAGAAGATTCCCACCCGCATTAAT 
                   
               
               
                   
                   
                 CTCTAATTTGCCAGATATTGGAAGTGCTACTTACGGCAGTAAACTGGC 
                   
               
               
                   
                   
                 GCATTTGGTTGATGAAGAAGACTGGAATATTACGATTAAAAGTAACCA 
                   
               
               
                   
                   
                 TTTACCTTCGGGATTAACTTTATGGATGGGCGATATTAAGAATGGTTC 
                   
               
               
                   
                   
                 AGAAACAGTAAAACTGGTCCAGAAGGTAAAAAATTGGTATGATTCGC 
                   
               
               
                   
                   
                 ATATGCCAGAAAGCTTGAAAATATATACAGAACTCGATCATGCAAATT 
                   
               
               
                   
                   
                 CTAGATTTATGGATGGACTATCTAAACTAGATCGCTTACACGAGACTC 
                   
               
               
                   
                   
                 ATGACGATTACAGCGATCAGATATTTGAGTCTCTTGAGAGGAATGACT 
                   
               
               
                   
                   
                 GTACCTGTCAAAAGTATCCTGAAATCACAGAAGTTAGAGATGCAGTTG 
                   
               
               
                   
                   
                 CCACAATTAGACGTTCCTTTAGAAAAATAACTAAAGAATCTGGTGCCG 
                   
               
               
                   
                   
                 ATATCGAACCTCCCGTACAAACTAGCTTATTGGATGATTGCCAGACCT 
                   
               
               
                   
                   
                 TAAAAGGAGTTCTTACTTGCTTAATACCTGGTGCTGGTGGTTATGACG 
                   
               
               
                   
                   
                 CCATTGCAGTGATTACTAAGCAAGATGTTGATCTTAGGGCTCAAACCG 
                   
               
               
                   
                   
                 CTAATGACAAAAGATTTTCTAAGGTTCAATGGCTGGATGTAACTCAGG 
                   
               
               
                   
                   
                 CTGACTGGGGTGTTAGGAAAGAAAAAGATCCGGAAACTTATCTTGATA 
                   
               
               
                   
                   
                 AATAGGAGGTAATACTCATGACCGTTTACACAGCATCCGTTACCGCAC 
                   
               
               
                   
                   
                 CCGTCAACATCGCAACCCTTAAGTATTGGGGGAAAAGGGACACGAAG 
                   
               
               
                   
                   
                 TTGAATCTGCCCACCAATTCGTCCATATCAGTGACTTTATCGCAAGATG 
                   
               
               
                   
                   
                 ACCTCAGAACGTTGACCTCTGCGGCTACTGCACCTGAGTTTGAACGCG 
                   
               
               
                   
                   
                 ACACTTTGTGGTTAAATGGAGAACCACACAGCATCGACAATGAAAGA 
                   
               
               
                   
                   
                 ACTCAAAATTGTCTGCGCGACCTACGCCAATTAAGAAAGGAAATGGA 
                   
               
               
                   
                   
                 ATCGAAGGACGCCTCATTGCCCACATTATCTCAATGGAAACTCCACAT 
                   
               
               
                   
                   
                 TGTCTCCGAAAATAACTTTCCTACAGCAGCTGGTTTAGCTTCCTCCGCT 
                   
               
               
                   
                   
                 GCTGGCTTTGCTGCATTGGTCTCTGCAATTGCTAAGTTATACCAATTAC 
                   
               
               
                   
                   
                 CACAGTCAACTTCAGAAATATCTAGAATAGCAAGAAAGGGGTCTGGTT 
                   
               
               
                   
                   
                 CAGCTTGTAGATCGTTGTTTGGCGGATACGTGGCCTGGGAAATGGGAA 
                   
               
               
                   
                   
                 AAGCTGAAGATGGTCATGATTCCATGGCAGTACAAATCGCAGACAGCT 
                   
               
               
                   
                   
                 CTGACTGGCCTCAGATGAAAGCTTGTGTCCTAGTTGTCAGCGATATTA 
                   
               
               
                   
                   
                 AAAAGGATGTGAGTTCCACTCAGGGTATGCAATTGACCGTGGCAACCT 
                   
               
               
                   
                   
                 CCGAACTATTTAAAGAAAGAATTGAACATGTCGTACCAAAGAGATTTG 
                   
               
               
                   
                   
                 AAGTCATGCGTAAAGCCATTGTTGAAAAAGATTTCGCCACCTTTGCAA 
                   
               
               
                   
                   
                 AGGAAACAATGATGGATTCCAACTCTTTCCATGCCACATGTTTGGACT 
                   
               
               
                   
                   
                 CTTTCCCTCCAATATTCTACATGAATGACACTTCCAAGCGTATCATCAG 
                   
               
               
                   
                   
                 TTGGTGCCACACCATTAATCAGTTTTACGGAGAAACAATCGTTGCATA 
                   
               
               
                   
                   
                 CACGTTTGATGCAGGTCCAAATGCTGTGTTGTACTACTTAGCTGAAAA 
                   
               
               
                   
                   
                 TGAGTCGAAACTCTTTGCATTTATCTATAAATTGTTTGGCTCTGTTCCT 
                   
               
               
                   
                   
                 GGATGGGACAAGAAATTTACTACTGAGCAGCTTGAGGCTTTCAACCAT 
                   
               
               
                   
                   
                 CAATTTGAATCATCTAACTTTACTGCACGTGAATTGGATCTTGAGTTGC 
                   
               
               
                   
                   
                 AAAAGGATGTTGCCAGAGTGATTTTAACTCAAGTCGGTTCAGGCCCAC 
                   
               
               
                   
                   
                 AAGAAACAAACGAATCTTTGATTGACGCAAAGACTGGTCTACCAAAG 
                   
               
               
                   
                   
                 GAATAACTGCAGCCCGGGAGGAGGATTACTATATGCAAACGGAACAC 
                   
               
               
                   
                   
                 GTCATTTTATTGAATGCACAGGGAGTTCCCACGGGTACGCTGGAAAAG 
                   
               
               
                   
                   
                 TATGCCGCACACACGGCAGACACCCGCTTACATCTCGCGTTCTCCAGT 
                   
               
               
                   
                   
                 TGGCTGTTTAATGCCAAAGGACAATTATTAGTTACCCGCCGCGCACTG 
                   
               
               
                   
                   
                 AGCAAAAAAGCATGGCCTGGCGTGTGGACTAACTCGGTTTGTGGGCAC 
                   
               
               
                   
                   
                 CCACAACTGGGAGAAAGCAACGAAGACGCAGTGATCCGCCGTTGCCG 
                   
               
               
                   
                   
                 TTATGAGCTTGGCGTGGAAATTACGCCTCCTGAATCTATCTATCCTGAC 
                   
               
               
                   
                   
                 TTTCGCTACCGCGCCACCGATCCGAGTGGCATTGTGGAAAATGAAGTG 
                   
               
               
                   
                   
                 TGTCCGGTATTTGCCGCACGCACCACTAGTGCGTTACAGATCAATGAT 
                   
               
               
                   
                   
                 GATGAAGTGATGGATTATCAATGGTGTGATTTAGCAGATGTATTACAC 
                   
               
               
                   
                   
                 GGTATTGATGCCACGCCGTGGGCGTTCAGTCCGTGGATGGTGATGCAG 
                   
               
               
                   
                   
                 GCGACAAATCGCGAAGCCAGAAAACGATTATCTGCATTTACCCAGCTT 
                   
               
               
                   
                   
                 AAATAACCCGGGGGATCCACTAGTTCTAGAGCGGCCGCCACCGCGGA 
                   
               
               
                   
                   
                 GGAGGAATGAGTAATGGACTTTCCGCAGCAACTCGAAGCCTGCGTTAA 
                   
               
               
                   
                   
                 GCAGGCCAACCAGGCGCTGAGCCGTTTTATCGCCCCACTGCCCTTTCA 
                   
               
               
                   
                   
                 GAACACTCCCGTGGTCGAAACCATGCAGTATGGCGCATTATTAGGTGG 
                   
               
               
                   
                   
                 TAAGCGCCTGCGACCTTTCCTGGTTTATGCCACCGGTCATATGTTCGGC 
                   
               
               
                   
                   
                 GTTAGCACAAACACGCTGGACGCACCCGCTGCCGCCGTTGAGTGTATC 
                   
               
               
                   
                   
                 CACGCTTACTCATTAATTCATGATGATTTACCGGCAATGGATGATGAC 
                   
               
               
                   
                   
                 GATCTGCGTCGCGGTTTGCCAACCTGCCATGTGAAGTTTGGCGAAGCA 
                   
               
               
                   
                   
                 AACGCGATTCTCGCTGGCGACGCTTTACAAACGCTGGCGTTCTCGATT 
                   
               
               
                   
                   
                 TTAAGCGATGCCGATATGCCGGAAGTGTCGGACCGCGACAGAATTTCG 
                   
               
               
                   
                   
                 ATGATTTCTGAACTGGCGAGCGCCAGTGGTATTGCCGGAATGTGCGGT 
                   
               
               
                   
                   
                 GGTCAGGCATTAGATTTAGACGCGGAAGGCAAACACGTACCTCTGGA 
                   
               
               
                   
                   
                 CGCGCTTGAGCGTATTCATCGTCATAAAACCGGCGCATTGATTCGCGC 
                   
               
               
                   
                   
                 CGCCGTTCGCCTTGGTGCATTAAGCGCCGGAGATAAAGGACGTCGTGC 
                   
               
               
                   
                   
                 TCTGCCGGTACTCGACAAGTATGCAGAGAGCATCGGCCTTGCCTTCCA 
                   
               
               
                   
                   
                 GGTTCAGGATGACATCCTGGATGTGGTGGGAGATACTGCAACGTTGGG 
                   
               
               
                   
                   
                 AAAACGCCAGGGTGCCGACCAGCAACTTGGTAAAAGTACCTACCCTG 
                   
               
               
                   
                   
                 CACTTCTGGGTCTTGAGCAAGCCCGGAAGAAAGCCCGGGATCTGATCG 
                   
               
               
                   
                   
                 ACGATGCCCGTCAGTCGCTGAAACAACTGGCTGAACAGTCACTCGATA 
                   
               
               
                   
                   
                 CCTCGGCACTGGAAGCGCTAGCGGACTACATCATCCAGCGTAATAAAT 
                   
               
               
                   
                   
                 AA 
                   
               
               
                   
               
               
                 ADS 
                 
                   Artemisia 
                 
                 GCCCTGACCGAAGAGAAACCGATCCGCCCGATCGCTAACTTCCCGCCG 
                 SEQ 
               
               
                   
                 
                   annua 
                 
                 TCTATCTGGGGTGACCAGTTCCTGATCTACGAAAAGCAGGTTGAGCAG 
                 ID 
               
               
                   
                   
                 GGTGTTGAACAGATCGTAAACGACCTGAAGAAAGAAGTTCGTCAGCT 
                 No. 87 
               
               
                   
                   
                 GCTGAAAGAAGCTCTGGACATCCCGATGAAACACGCTAACCTGTTGAA 
                   
               
               
                   
                   
                 GCTGATCGACGAGATCCAGCGTCTGGGTATCCCGTACCACTTCGAACG 
                   
               
               
                   
                   
                 CGAAATCGACCACGCACTGCAGTGCATCTACGAAACCTACGGCGACA 
                   
               
               
                   
                   
                 ACTGGAACGGCGACCGTTCTTCTCTGTGGTTTCGTCTGATGCGTAAAC 
                   
               
               
                   
                   
                 AGGGCTACTACGTTACCTGTGACGTTTTTAACAACTACAAGGACAAGA 
                   
               
               
                   
                   
                 ACGGTGCTTTCAAACAGTCTCTGGCTAACGACGTTGAAGGCCTGCTGG 
                   
               
               
                   
                   
                 AACTGTACGAAGCGACCTCCATGCGTGTACCGGGTGAAATCATCCTGG 
                   
               
               
                   
                   
                 AGGACGCGCTGGGTTTCACCCGTTCTCGTCTGTCCATTATGACTAAAG 
                   
               
               
                   
                   
                 ACGCTTTCTCTACTAACCCGGCTCTGTTCACCGAAATCCAGCGTGCTCT 
                   
               
               
                   
                   
                 GAAACAGCCGCTGTGGAAACGTCTGCCGCGTATCGAAGCAGCACAGT 
                   
               
               
                   
                   
                 ACATTCCGTTTTACCAGCAGCAGGACTCTCACAACAAGACCCTGCTGA 
                   
               
               
                   
                   
                 AACTGGCTAAGCTGGAATTCAACCTGCTGCAGTCTCTGCACAAAGAAG 
                   
               
               
                   
                   
                 AACTGTCTCACGTTTGTAAGTGGTGGAAGGCATTTGACATCAAGAAAA 
                   
               
               
                   
                   
                 ACGCGCCGTGCCTGCGTGACCGTATCGTTGAATGTTACTTCTGGGGTCT 
                   
               
               
                   
                   
                 GGGTTCTGGTTATGAACCACAGTACTCCCGTGCACGTGTGTTCTTCACT 
                   
               
               
                   
                   
                 AAAGCTGTAGCTGTTATCACCCTGATCGATGACACTTACGATGCTTAC 
                   
               
               
                   
                   
                 GGCACCTACGAAGAACTGAAGATCTTTACTGAAGCTGTAGAACGCTGG 
                   
               
               
                   
                   
                 TCTATCACTTGCCTGGACACTCTGCCGGAGTACATGAAACCGATCTAC 
                   
               
               
                   
                   
                 AAACTGTTCATGGATACCTACACCGAAATGGAGGAATTCCTGGCAAAA 
                   
               
               
                   
                   
                 GAAGGCCGTACCGACCTGTTCAACTGCGGTAAAGAGTTTGTTAAAGAA 
                   
               
               
                   
                   
                 TTCGTACGTAACCTGATGGTTGAAGCTAAATGGGCTAACGAAGGCCAT 
                   
               
               
                   
                   
                 ATCCCGACTACCGAAGAACATGACCCGGTTGTTATCATCACCGGCGGT 
                   
               
               
                   
                   
                 GCAAACCTGCTGACCACCACTTGCTATCTGGGTATGTCCGACATCTTTA 
                   
               
               
                   
                   
                 CCAAGGAATCTGTTGAATGGGCTGTTTCTGCACCGCCGCTGTTCCGTTA 
                   
               
               
                   
                   
                 CTCCGGTATTCTGGGTCGTCGTCTGAACGACCTGATGACCCACAAAGC 
                   
               
               
                   
                   
                 AGAGCAGGAACGTAAACACTCTTCCTCCTCTCTGGAATCCTACATGAA 
                   
               
               
                   
                   
                 GGAATATAACGTTAACGAGGAGTACGCACAGACTCTGATCTATAAAG 
                   
               
               
                   
                   
                 AAGTTGAAGACGTATGGAAAGACATCAACCGTGAATACCTGACTACT 
                   
               
               
                   
                   
                 AAAAACATCCCGCGCCCGCTGCTGATGGCAGTAATCTACCTGTGCCAG 
                   
               
               
                   
                   
                 TTCCTGGAAGTACAGTACGCTGGTAAAGATAACTTCACTCGCATGGGC 
                   
               
               
                   
                   
                 GACGAATACAAACACCTGATCAAATCCCTGCTGGTTTACCCGATGTCC 
                   
               
               
                   
                   
                 ATCTGA 
                   
               
               
                   
               
               
                 GHS 
                 
                   Abies 
                 
                 ATGGCTCAAATCAGCGAATCAGTGTCTCCAAGCACCGACCTTAAAAGC 
                 SEQ 
               
               
                   
                 
                   grandis 
                 
                 ACGGAATCTTCTATTACCAGCAACCGCCACGGTAACATGTGGGAAGAT 
                 ID 
               
               
                   
                   
                 GACCGCATTCAGAGCTTAAACAGCCCATATGGCGCACCCGCTTATCAG 
                 No. 88 
               
               
                   
                   
                 GAACGTAGCGAAAAATTGATTGAAGAAATTAAGCTCCTGTTTCTGTCC 
                   
               
               
                   
                   
                 GATATGGACGATAGTTGCAATGATTCGGATCGCGACTTGATCAAACGC 
                   
               
               
                   
                   
                 CTGGAGATCGTAGATACGGTTGAGTGTCTGGGCATTGATCGTCATTTC 
                   
               
               
                   
                   
                 CAACCTGAAATTAAGCTGGCGCTGGATTACGTGTACCGTTGCTGGAAT 
                   
               
               
                   
                   
                 GAGCGTGGCATCGGAGAAGGTAGCCGTGATAGCTTAAAAAAGGACCT 
                   
               
               
                   
                   
                 GAATGCGACCGCCTTGGGCTTTCGGGCTTTACGCTTACACCGTTATAAT 
                   
               
               
                   
                   
                 GTAAGCTCAGGAGTGCTGGAGAACTTCCGTGATGACAATGGTCAATTC 
                   
               
               
                   
                   
                 TTTTGCGGTTCTACTGTGGAGGAGGAAGGCGCGGAGGCCTACAATAAA 
                   
               
               
                   
                   
                 CATGTACGTTGCATGCTGTCCCTGTCCCGCGCTTCCAATATTTTATTCC 
                   
               
               
                   
                   
                 CGGGCGAGAAAGTGATGGAAGAAGCGAAGGCGTTTACGACCAACTAT 
                   
               
               
                   
                   
                 CTTAAGAAAGTCCTGGCGGGTCGTGAAGCAACTCATGTCGACGAGAGT 
                   
               
               
                   
                   
                 CTCCTTGGAGAGGTCAAGTATGCACTAGAATTTCCGTGGCATTGTTCC 
                   
               
               
                   
                   
                 GTGCAGCGCTGGGAGGCACGTTCTTTTATCGAAATTTTCGGTCAGATT 
                   
               
               
                   
                   
                 GATAGTGAACTGAAAAGCAACCTCTCTAAAAAAATGCTCGAACTCGC 
                   
               
               
                   
                   
                 AAAACTTGATTTTAACATACTCCAGTGTACGCATCAAAAAGAGCTCCA 
                   
               
               
                   
                   
                 GATCATTAGTCGATGGTTCGCCGATTCAAGTATCGCAAGTCTGAACTT 
                   
               
               
                   
                   
                 TTACCGTAAATGCTATGTGGAATTTTACTTCTGGATGGCCGCGGCAATT 
                   
               
               
                   
                   
                 TCAGAACCAGAATTTAGTGGCTCTCGCGTGGCATTCACTAAAATTGCG 
                   
               
               
                   
                   
                 ATCTTGATGACAATGTTAGATGACTTATACGACACGCATGGGACGCTG 
                   
               
               
                   
                   
                 GATCAATTGAAAATATTTACCGAAGGTGTGCGCAGGTGGGACGTGTCG 
                   
               
               
                   
                   
                 CTGGTGGAGGGCCTGCCGGATTTCATGAAAATTGCCTTTGAGTTCTGG 
                   
               
               
                   
                   
                 TTAAAGACCTCCAACGAACTGATTGCGGAGGCGGTTAAGGCCCAAGG 
                   
               
               
                   
                   
                 CCAGGATATGGCGGCCTATATCCGCAAAAACGCTTGGGAACGCTATCT 
                   
               
               
                   
                   
                 GGAAGCGTATTTGCAGGATGCCGAATGGATCGCCACCGGTCACGTTCC 
                   
               
               
                   
                   
                 GACATTCGATGAATATCTGAACAATGGCACCCCCAACACCGGTATGTG 
                   
               
               
                   
                   
                 TGTACTTAATCTGATCCCGTTGCTGCTTATGGGCGAACACTTGCCGATC 
                   
               
               
                   
                   
                 GATATTCTTGAACAGATCTTTCTGCCGAGCCGGTTCCACCATCTGATTG 
                   
               
               
                   
                   
                 AACTGGCTAGCCGACTGGTCGATGATGCGAGAGATTTTCAAGCCGAAA 
                   
               
               
                   
                   
                 AAGATCATGGTGATTTATCCTGCATCGAATGCTACCTGAAAGACCATC 
                   
               
               
                   
                   
                 CGGAATCAACAGTTGAAGACGCCCTGAATCACGTCAACGGCCTGCTGG 
                   
               
               
                   
                   
                 GGAATTGTTTGCTGGAAATGAATTGGAAATTTCTGAAAAAACAGGACT 
                   
               
               
                   
                   
                 CGGTACCTCTGTCGTGTAAAAAATACTCATTCCACGTCCTGGCGCGGT 
                   
               
               
                   
                   
                 CGATTCAGTTTATGTATAACCAGGGGGACGGGTTTTCGATTTCGAACA 
                   
               
               
                   
                   
                 AAGTTATTAAAGACCAGGTCCAGAAAGTTCTAATCGTTCCGGTTCCTA 
                   
               
               
                   
                   
                 TATAA 
                   
               
               
                   
               
               
                 ABS 
                 
                   Abies 
                 
                 TGAAACGAGAATTTCCTCCAGGATTTTGGAAGGATGATCTTATCGATT 
                 SEQ 
               
               
                   
                 
                   grandis 
                 
                 CTCTAACGTCATCTCACAAGGTTGCAGCATCAGACGAGAAGCGTATCG 
                 ID 
               
               
                   
                   
                 AGACATTAATATCCGAGATTAAGAATATGTTTAGATGTATGGGCTATG 
                 No. 89 
               
               
                   
                   
                 GCGAAACGAATCCCTCTGCATATGACACTGCTTGGGTAGCAAGGATTC 
                   
               
               
                   
                   
                 CAGCAGTTGATGGCTCTGACAACCCTCACTTTCCTGAGACGGTTGAAT 
                   
               
               
                   
                   
                 GGATTCTTCAAAATCAGTTGAAAGATGGGTCTTGGGGTGAAGGATTCT 
                   
               
               
                   
                   
                 ACTTCTTGGCATATGACAGAATACTGGCTACACTTGCATGTATTATTAC 
                   
               
               
                   
                   
                 CCTTACCCTCTGGCGTACTGGGGAGACACAAGTACAGAAAGGTATTGA 
                   
               
               
                   
                   
                 ATTCTTCAGGACACAAGCTGGAAAGATGGAAGATGAAGCTGATAGTC 
                   
               
               
                   
                   
                 ATAGGCCAAGTGGATTTGAAATAGTATTTCCTGCAATGCTAAAGGAAG 
                   
               
               
                   
                   
                 CTAAAATCTTAGGCTTGGATCTGCCTTACGATTTGCCATTCCTGAAACA 
                   
               
               
                   
                   
                 AATCATCGAAAAGCGGGAGGCTAAGCTTAAAAGGATTCCC 
                   
               
               
                   
                   
                 ACTGATGTTCTCTATGCCCTTCCAACAACGTTATTGTATTCTTTGGAAG 
                   
               
               
                   
                   
                 GTTTACAAGAAATAGTAGACTGGCAGAAAATAATGAAACTTCAATCC 
                   
               
               
                   
                   
                 AAGGATGGATCATTTCTCAGCTCTCCGGCATCTACAGCGGCTGTATTC 
                   
               
               
                   
                   
                 ATGCGTACAGGGAACAAAAAGTGCTTGGATTTCTTGAACTTTGTCTTG 
                   
               
               
                   
                   
                 AAGAAATTCGGAAACCATGTGCCTTGTCACTATCCGCTTGATCTATTTG 
                   
               
               
                   
                   
                 AACGTTTGTGGGCGGTTGATACAGTTGAGCGGCTAGGTATCGATCGTC 
                   
               
               
                   
                   
                 ATTTCAAAGAGGAGATCAAGGAAGCATTGGATTATGTTTACAGCCATT 
                   
               
               
                   
                   
                 GGGACGAAAGAGGCATTGGATGGGCGAGAGAGAATCCTGTTCCTGAT 
                   
               
               
                   
                   
                 ATTGATGATACAGCCATGGGCCTTCGAATCTTGAGATTACATGGATAC 
                   
               
               
                   
                   
                 AATGTATCCTCAGATGTTTTAAAAACATTTAGAGATGAGAATGGGGAG 
                   
               
               
                   
                   
                 TTCTTTTGCTTCTTGGGTCAAACACAGAGAGGAGTTACAGACATGTTA 
                   
               
               
                   
                   
                 AACGTCAATCGTTGTTCACATGTTTCATTTCCGGGAGAAACGATCATG 
                   
               
               
                   
                   
                 GAAGAAGCAAAACTCTGTACCGAAAGGTATCTGAGGAATGCTCTGGA 
                   
               
               
                   
                   
                 AAATGTGGATGCCTTTGACAAATGGGCTTTTAAAAAGAATATTCGGGG 
                   
               
               
                   
                   
                 AGAGGTAGAGTATGCACTCAAATATCCCTGGCATAAGAGTATGCCAA 
                   
               
               
                   
                   
                 GGTTGGAGGCTAGAAGCTATATTGAAAACTATGGGCCAGATGATGTGT 
                   
               
               
                   
                   
                 GGCTTGGAAAAACTGTATATATGATGCCATACATTTCGAATGAAAAGT 
                   
               
               
                   
                   
                 ATTTAGAACTAGCGAAACTGGACTTCAATAAGGTGCAGTCTATACACC 
                   
               
               
                   
                   
                 AAACAGAGCTTCAAGATCTTCGAAGGTGGTGGAAATCATCCGGTTTCA 
                   
               
               
                   
                   
                 CGGATCTGAATTTCACTCGTGAGCGTGTGACGGAAATATATTTCTCAC 
                   
               
               
                   
                   
                 CGGCATCCTTTATCTTTGAGCCCGAGTTTTCTAAGTGCAGAGAGGTTTA 
                   
               
               
                   
                   
                 TACAAAAACTTCCAATTTCACTGTTATTTTAGATGATCTTTATGACGCC 
                   
               
               
                   
                   
                 CATGGATCTTTAGACGATCTTAAGTTGTTCACAGAATCAGTCAAAAGA 
                   
               
               
                   
                   
                 TGGGATCTATCACTAGTGGACCAAATGCCACAACAAATGAAAATATGT 
                   
               
               
                   
                   
                 TTTGTGGGTTTCTACAATACTTTTAATGATATAGCAAAAGAAGGACGT 
                   
               
               
                   
                   
                 GAGAGGCAAGGGCGCGATGTGCTAGGCTACATTCAAAATGTTTGGAA 
                   
               
               
                   
                   
                 AGTCCAACTTGAAGCTTACACGAAAGAAGCAGAATGGTCTGAAGCTA 
                   
               
               
                   
                   
                 AATATGTGCCATCCTTCAATGAATACATAGAGAATGCGAGTGTGTCAA 
                   
               
               
                   
                   
                 TAGCATTGGGAACAGTCGTTCTCATTAGTGCTCTTTTCACTGGGGAGGT 
                   
               
               
                   
                   
                 TCTTACAGATGAAGTACTCTCCAAAATTGATCGCGAATCTAGATTTCTT 
                   
               
               
                   
                   
                 CAACTCATGGGCTTAACAGGGCGTTTGGTGAATGACACCAAAACTTAT 
                   
               
               
                   
                   
                 CAGGCAGAGAGAGGTCAAGGTGAGGTGGCTTCTGCCATACAATGTTAT 
                   
               
               
                   
                   
                 ATGAAGGACCATCCTAAAATCTCTGAAGAAGAAGCTCTACAACATGTC 
                   
               
               
                   
                   
                 TATAGTGTCATGGAAAATGCCCTCGAAGAGTTGAATAGGGAGTTTGTG 
                   
               
               
                   
                   
                 AATAACAAAATACCGGATATTTACAAAAGACTGGTTTTTGAAACTGCA 
                   
               
               
                   
                   
                 AGAATAATGCAACTCTTTTATATGCAAGGGGATGGTTTGACACTATCA 
                   
               
               
                   
                   
                 CATGATATGGAAATTAAAGAGCATGTCAAAAATTGCCTCTTCCAACCA 
                   
               
               
                   
                   
                 GTTGCC 
                   
               
               
                   
               
               
                 TXS 
                 
                   Taxus 
                 
                 ATGAGCAGCAGCACTGGCACTAGCAAGGTGGTTTCCGAGACTTCCAGT 
                 SEQ 
               
               
                   
                 
                   brevifola 
                 
                 ACCATTGTGGATGATATCCCTCGACTCTCCGCCAATTATCATGGCGATC 
                 ID 
               
               
                   
                   
                 TGTGGCACCACAATGTTATACAAACTCTGGAGACACCGTTTCGTGAGA 
                 No. 90 
               
               
                   
                   
                 GTTCTACTTACCAAGAACGGGCAGATGAGCTGGTTGTGAAAATTAAAG 
                   
               
               
                   
                   
                 ATATGTTCAATGCGCTCGGAGACGGAGATATCAGTCCGTCTGCATACG 
                   
               
               
                   
                   
                 ACACTGCGTGGGTGGCGAGGCTGGCGACCATTTCCTCTGATGGATCTG 
                   
               
               
                   
                   
                 AGAAGCCACGGTTTCCTCAGGCCCTCAACTGGGTTTTCAACAACCAGC 
                   
               
               
                   
                   
                 TCCAGGATGGATCGTGGGGTATCGAATCGCACTTTAGTTTATGCGATC 
                   
               
               
                   
                   
                 GATTGCTTAACACGACCAATTCTGTTATCGCCCTCTCGGTTTGGAAAAC 
                   
               
               
                   
                   
                 AGGGCACAGCCAAGTACAACAAGGTGCTGAGTTTATTGCAGAGAATC 
                   
               
               
                   
                   
                 TAAGATTACTCAATGAGGAAGATGAGTTGTCCCCGGATTTCCAAATAA 
                   
               
               
                   
                   
                 TCTTTCCTGCTCTGCTGCAAAAGGCAAAAGCGTTGGGGATCAATCTTC 
                   
               
               
                   
                   
                 CTTACGATCTTCCATTTATCAAATATTTGTCGACAACACGGGAAGCCA 
                   
               
               
                   
                   
                 GGCTTACAGATGTTTCTGCGGCAGCAGACAATATTCCAGCCAACATGT 
                   
               
               
                   
                   
                 TGAATGCGTTGGAAGGACTCGAGGAAGTTATTGACTGGAACAAGATT 
                   
               
               
                   
                   
                 ATGAGGTTTCAAAGTAAAGATGGATCTTTCCTGAGCTCCCCTGCCTCC 
                   
               
               
                   
                   
                 ACTGCCTGTGTACTGATGAATACAGGGGACGAAAAATGTTTCACTTTT 
                   
               
               
                   
                   
                 CTCAACAATCTGCTCGACAAATTCGGCGGCTGCGTGCCCTGTATGTAT 
                   
               
               
                   
                   
                 TCCATCGATCTGCTGGAACGCCTTTCGCTGGTTGATAACATTGAGCATC 
                   
               
               
                   
                   
                 TCGGAATCGGTCGCCATTTCAAACAAGAAATCAAAGGAGCTCTTGATT 
                   
               
               
                   
                   
                 ATGTCTACAGACATTGGAGTGAAAGGGGCATCGGTTGGGGCAGAGAC 
                   
               
               
                   
                   
                 AGCCTTGTTCCAGATCTCAACACCACAGCCCTCGGCCTGCGAACTCTT 
                   
               
               
                   
                   
                 CGCATGCACGGATACAATGTTTCTTCAGACGTTTTGAATAATTTCAAA 
                   
               
               
                   
                   
                 GATGAAAACGGGCGGTTCTTCTCCTCTGCGGGCCAAACCCATGTCGAA 
                   
               
               
                   
                   
                 TTGAGAAGCGTGGTGAATCTTTTCAGAGCTTCCGACCTTGCATTTCCTG 
                   
               
               
                   
                   
                 ACGAAAGAGCTATGGACGATGCTAGAAAATTTGCAGAACCATATCTTA 
                   
               
               
                   
                   
                 GAGAGGCACTTGCAACGAAAATCTCAACCAATACAAAACTATTCAAA 
                   
               
               
                   
                   
                 GAGATTGAGTACGTGGTGGAGTACCCTTGGCACATGAGTATCCCACGC 
                   
               
               
                   
                   
                 TTAGAAGCCAGAAGTTATATTGATTCATATGACGACAATTATGTATGG 
                   
               
               
                   
                   
                 CAGAGGAAGACTCTATATAGAATGCCATCTTTGAGTAATTCAAAATGT 
                   
               
               
                   
                   
                 TTAGAATTGGCAAAATTGGACTTCAATATCGTACAATCTTTGCATCAA 
                   
               
               
                   
                   
                 GAGGAGTTGAAGCTTCTAACAAGATGGTGGAAGGAATCCGGCATGGC 
                   
               
               
                   
                   
                 AGATATAAATTTCACTCGACACCGAGTGGCGGAGGTTTATTTTTCATC 
                   
               
               
                   
                   
                 AGCTACATTTGAACCCGAATATTCTGCCACTAGAATTGCCTTCACAAA 
                   
               
               
                   
                   
                 AATTGGTTGTTTACAAGTCCTTTTTGATGATATGGCTGACATCTTTGCA 
                   
               
               
                   
                   
                 ACACTAGATGAATTGAAAAGTTTCACTGAGGGAGTAAAGAGATGGGA 
                   
               
               
                   
                   
                 TACATCTTTGCTACATGAGATTCCAGAGTGTATGCAAACTTGCTTTAAA 
                   
               
               
                   
                   
                 GTTTGGTTCAAATTAATGGAAGAAGTAAATAATGATGTGGTTAAGGTA 
                   
               
               
                   
                   
                 CAAGGACGTGACATGCTCGCTCACATAAGAAAACCCTGGGAGTTGTAC 
                   
               
               
                   
                   
                 TTCAATTGTTATGTACAAGAAAGGGAGTGGCTTGAAGCCGGGTATATA 
                   
               
               
                   
                   
                 CCAACTTTTGAAGAGTACTTAAAGACTTATGCTATATCAGTAGGCCTT 
                   
               
               
                   
                   
                 GGACCGTGTACCCTACAACCAATACTACTAATGGGTGAGCTTGTGAAA 
                   
               
               
                   
                   
                 GATGATGTTGTTGAGAAAGTGCACTATCCCTCAAATATGTTTGAGCTT 
                   
               
               
                   
                   
                 GTATCCTTGAGCTGGCGACTAACAAACGACACCAAAACATATCAGGCT 
                   
               
               
                   
                   
                 GAAAAGGCTCGAGGACAACAAGCCTCAGGCATAGCATGCTATATGAA 
                   
               
               
                   
                   
                 GGATAATCCAGGAGCAACTGAGGAAGATGCCATTAAGCACATATGTC 
                   
               
               
                   
                   
                 GTGTTGTTGATCGGGCCTTGAAAGAAGCAAGCTTTGAATATTTCAAAC 
                   
               
               
                   
                   
                 CATCCAATGATATCCCAATGGGTTGCAAGTCCTTTATTTTTAACCTTAG 
                   
               
               
                   
                   
                 ATTGTGTGTCCAAATCTTTTACAAGTTTATAGATGGGTACGGAATCGC 
                   
               
               
                   
                   
                 CAATGAGGAGATTAA 
                   
               
               
                   
               
               
                   
                   
                 GGACTATATAAGAAAAGTTTATATTGATCCAATTCAAGTATGA 
                   
               
               
                 GGPPS 
                 
                   Taxus 
                 
                 ATGTTTGATTTCAATGAATATATGAAAAGTAAGGCTGTTGCGGTAGAC 
                 SEQ 
               
               
                   
                 
                   Canadensis 
                 
                 GCGGCTCTGGATAAAGCGATTCCGCTGGAATATCCCGAGAAGATTCAC 
                 ID 
               
               
                   
                   
                 GAATCGATGCGCTACTCCCTGTTAGCAGGAGGGAAACGCGTTCGTCCG 
                 No. 91 
               
               
                   
                   
                 GCATTATGCATCGCGGCCTGTGAACTCGTCGGCGGTTCACAGGACTTA 
                   
               
               
                   
                   
                 GCAATGCCAACTGCTTGCGCAATGGAAATGATTCACACAATGAGCCTG 
                   
               
               
                   
                   
                 ATTCATGATGATTTGCCTTGCATGGACAACGATGACTTTCGGCGCGGT 
                   
               
               
                   
                   
                 AAACCTACTAATCATAAGGTTTTTGGCGAAGATACTGCAGTGCTGGCG 
                   
               
               
                   
                   
                 GGCGATGCGCTGCTGTCGTTTGCCTTCGAACATATCGCCGTCGCGACC 
                   
               
               
                   
                   
                 TCGAAAACCGTCCCGTCGGACCGTACGCTTCGCGTGATTTCCGAGCTG 
                   
               
               
                   
                   
                 GGAAAGACCATCGGCTCTCAAGGACTCGTGGGTGGTCAGGTAGTTGAT 
                   
               
               
                   
                   
                 ATCACGTCTGAGGGTGACGCGAACGTGGACCTGAAAACCCTGGAGTG 
                   
               
               
                   
                   
                 GATCCATATTCACAAAACGGCCGTGCTGCTGGAATGTAGCGTGGTGTC 
                   
               
               
                   
                   
                 AGGGGGGATCTTGGGGGGCGCCACGGAGGATGAAATCGCGCGTATTC 
                   
               
               
                   
                   
                 GTCGTTATGCCCGCTGTGTTGGACTGTTATTTCAGGTGGTGGATGACAT 
                   
               
               
                   
                   
                 CCTGGATGTCACAAAATCCAGCGAAGAGCTTGGCAAGACCGCGGGCA 
                   
               
               
                   
                   
                 AAGACCTTCTGACGGATAAGGCTACATACCCGAAATTGATGGGCTTGG 
                   
               
               
                   
                   
                 AGAAAGCCAAGGAGTTCGCAGCTGAACTTGCCACGCGGGCGAAGGAA 
                   
               
               
                   
                   
                 GAACTCTCTTCTTTCGATCAAATCAAAGCCGCGCCACTGCTGGGCCTC 
                   
               
               
                   
                   
                 GCCGATTACATTGCGTTTCGTCAGAACTGA 
                   
               
               
                   
               
               
                 P450 BM3   
                 
                   Bacillus 
                 
                 ATGACAATTAAAGAAATGCCTCAGCCAAAAACGTTTGGAGAGCTTAA 
                 SEQ 
               
               
                   
                 
                   megaterium 
                 
                 AAATTTACCGTTATTAAACACAGATAAACCGGTTCAAGCTTTGATGAA 
                 ID 
               
               
                   
                   
                 AATTGCGGATGAATTAGGAGAAATCTTTAAATTCGAGGCGCCTGGTCG 
                 No. 92 
               
               
                   
                   
                 TGTAACGCGCTACTTATCAAGTCAGCGTCTAATTAAAGAAGCATGCGA 
                   
               
               
                   
                   
                 TGAATCACGCTTTGATAAAAACTTAAGTCAAGCGCTTAAATTTGTACG 
                   
               
               
                   
                   
                 TGATTTTGCAGGAGACGGGTTATTTACAAGCTGGACGCATGAAAAAAA 
                   
               
               
                   
                   
                 TTGGAAAAAAGCGCATAATATCTTACTTCCAAGCTTCAGTCAGCAGGC 
                   
               
               
                   
                   
                 AATGAAAGGCTATCATGCGATGATGGTCGATATCGCCGTGCAGCTTGT 
                   
               
               
                   
                   
                 TCAAAAGTGGGAGCGTCTAAATGCAGATGAGCATATTGAAGTACCGG 
                   
               
               
                   
                   
                 AAGACATGACACGTTTAACGCTTGATACAATTGGTCTTTGCGGCTTTA 
                   
               
               
                   
                   
                 ACTATCGCTTTAACAGCTTTTACCGAGATCAGCCTCATCCATTTATTAC 
                   
               
               
                   
                   
                 AAGTATGGTCCGTGCACTGGATGAAGCAATGAACAAGCTGCAGCGAG 
                   
               
               
                   
                   
                 CAAATCCAGACGACCCAGCTTATGATGAAAACAAGCGCCAGTTTCAA 
                   
               
               
                   
                   
                 GAAGATATCAAGGTGATGAACGACCTAGTAGATAAAATTATTGCAGA 
                   
               
               
                   
                   
                 TCGCAAAGCAAGCGGTGAACAAAGCGATGATTTATTAACGCATATGCT 
                   
               
               
                   
                   
                 AAACGGAAAAGATCCAGAAACGGGTGAGCCGCTTGATGACGAGAACA 
                   
               
               
                   
                   
                 TTCGCTATCAAATTATTACATTCTTAATTGCGGGACACGAAACAACAA 
                   
               
               
                   
                   
                 GTGGTCTTTTATCATTTGCGCTGTATTTCTTAGTGAAAAATCCACATGT 
                   
               
               
                   
                   
                 ATTACAAAAAGCAGCAGAAGAAGCAGCACGAGTTCTAGTAGATCCTG 
                   
               
               
                   
                   
                 TTCCAAGCTACAAACAAGTCAAACAGCTTAAATATGTCGGCATGGTCT 
                   
               
               
                   
                   
                 TAAACGAAGCGCTGCGCTTATGGCCAACTGCTCCTGCGTTTTCCCTATA 
                   
               
               
                   
                   
                 TGCAAAAGAAGATACGGTGCTTGGAGGAGAATATCCTTTAGAAAAAG 
                   
               
               
                   
                   
                 GCGACGAACTAATGGTTCTGATTCCTCAGCTTCACCGTGATAAAACAA 
                   
               
               
                   
                   
                 TTTGGGGAGACGATGTGGAAGAGTTCCGTCCAGAGCGTTTTGAAAATC 
                   
               
               
                   
                   
                 CAAGTGCGATTCCGCAGCATGCGTTTAAACCGTTTGGAAACGGTCAGC 
                   
               
               
                   
                   
                 GTGCGTGTATCGGTCAGCAGTTCGCTCTTCATGAAGCAACGCTGGTAC 
                   
               
               
                   
                   
                 TTGGTATGATGCTAAAACACTTTGACTTTGAAGATCATACAAACTACG 
                   
               
               
                   
                   
                 AGCTGGATATTAAAGAAACTTTAACGTTAAAACCTGAAGGCTTTGTGG 
                   
               
               
                   
                   
                 TAAAAGCAAAATCGAAAAAAATTCCGCTTGGCGGTATTCCTTCACCTA 
                   
               
               
                   
                   
                 GCACTGAACAGTCTGCTAAAAAAGTACGCAAAAAGGCAGAAAACGCT 
                   
               
               
                   
                   
                 CATAATACGCCGCTGCTTGTGCTATACGGTTCAAATATGGGAACAGCT 
                   
               
               
                   
                   
                 GAAGGAACGGCGCGTGATTTAGCAGATATTGCAATGAGCAAAGGATT 
                   
               
               
                   
                   
                 TGCACCGCAGGTCGCAACGCTTGATTCACACGCCGGAAATCTTCCGCG 
                   
               
               
                   
                   
                 CGAAGGAGCTGTATTAATTGTAACGGCGTCTTATAACGGTCATCCGCC 
                   
               
               
                   
                   
                 TGATAACGCAAAGCAATTTGTCGACTGGTTAGACCAAGCGTCTGCTGA 
                   
               
               
                   
                   
                 TGAAGTAAAAGGCGTTCGCTACTCCGTATTTGGATGCGGCGATAAAAA 
                   
               
               
                   
                   
                 CTGGGCTACTACGTATCAAAAAGTGCCTGCTTTTATCGATGAAACGCT 
                   
               
               
                   
                   
                 TGCCGCTAAAGGGGCAGAAAACATCGCTGACCGCGGTGAAGCAGATG 
                   
               
               
                   
                   
                 CAAGCGACGACTTTGAAGGCACATATGAAGAATGGCGTGAACATATG 
                   
               
               
                   
                   
                 TGGAGTGACGTAGCAGCCTACTTTAACCTCGACATTGAAAACAGTGAA 
                   
               
               
                   
                   
                 GATAATAAATCTACTCTTTCACTTCAATTTGTCGACAGCGCCGCGGAT 
                   
               
               
                   
                   
                 ATGCCGCTTGCGAAAATGCACGGTGCGTTTTCAACGAACGTCGTAGCA 
                   
               
               
                   
                   
                 AGCAAAGAACTTCAACAGCCAGGCAGTGCACGAAGCACGCGACATCT 
                   
               
               
                   
                   
                 TGAAATTGAACTTCCAAAAGAAGCTTCTTATCAAGAAGGAGATCATTT 
                   
               
               
                   
                   
                 AGGTGTTATTCCTCGCAACTATGAAGGAATAGTAAACCGTGTAACAGC 
                   
               
               
                   
                   
                 AAGGTTCGGCCTAGATGCATCACAGCAAATCCGTCTGGAAGCAGAAG 
                   
               
               
                   
                   
                 AAGAAAAATTAGCTCATTTGCCACTCGCTAAAACAGTATCCGTAGAAG 
                   
               
               
                   
                   
                 AGCTTCTGCAATACGTGGAGCTTCAAGATCCTGTTACGCGCACGCAGC 
                   
               
               
                   
                   
                 TTCGCGCAATGGCTGCTAAAACGGTCTGCCCGCCGCATAAAGTAGAGC 
                   
               
               
                   
                   
                 TTGAAGCCTTGCTTGAAAAGCAAGCCTACAAAGAACAAGTGCTGGCA 
                   
               
               
                   
                   
                 AAACGTTTAACAATGCTTGAACTGCTTGAAAAATACCCGGCGTGTGAA 
                   
               
               
                   
                   
                 ATGAAATTCAGCGAATTTATCGCCCTTCTGCCAAGCATACGCCCGCGC 
                   
               
               
                   
                   
                 TATTACTCGATTTCTTCATCACCTCGTGTCGATGAAAAACAAGCAAGC 
                   
               
               
                   
                   
                 ATCACGGTCAGCGTTGTCTCAGGAGAAGCGTGGAGCGGATATGGAGA 
                   
               
               
                   
                   
                 ATATAAAGGAATTGCGTCGAACTATCTTGCCGAGCTGCAAGAAGGAG 
                   
               
               
                   
                   
                 ATACGATTACGTGCTTTATTTCCACACCGCAGTCAGAATTTACGCTGCC 
                   
               
               
                   
                   
                 AAAAGACCCTGAAACGCCGCTTATCATGGTCGGACCGGGAACAGGCG 
                   
               
               
                   
                   
                 TCGCGCCGTTTAGAGGCTTTGTGCAGGCGCGCAAACAGCTAAAAGAAC 
                   
               
               
                   
                   
                 AAGGACAGTCACTTGGAGAAGCACATTTATACTTCGGCTGCCGTTCAC 
                   
               
               
                   
                   
                 CTCATGAAGACTATCTGTATCAAGAAGAGCTTGAAAACGCCCAAAGC 
                   
               
               
                   
                   
                 GAAGGCATCATTACGCTTCATACCGCTTTTTCTCGCATGCCAAATCAGC 
                   
               
               
                   
                   
                 CGAAAACATACGTTCAGCACGTAATGGAACAAGACGGCAAGAAATTG 
                   
               
               
                   
                   
                 ATTGAACTTCTTGATCAAGGAGCGCACTTCTATATTTGCGGAGACGGA 
                   
               
               
                   
                   
                 AGCCAAATGGCACCTGCCGTTGAAGCAACGCTTATGAAAAGCTATGCT 
                   
               
               
                   
                   
                 GACGTTCACCAAGTGAGTGAAGCAGACGCTCGCTTATGGCTGCAGCAG 
                   
               
               
                   
                   
                 CTAGAAGAAAAAGGCCGATACGCAAAAGACGTGTGGGCTGGGTAA 
                   
               
               
                   
               
               
                 SpecR 
                 Bacterial 
                 ATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGT 
                 SEQ 
               
               
                   
                   
                 AGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACA 
                 ID 
               
               
                   
                   
                 TTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGTGATAT 
                 No. 93 
               
               
                   
                   
                 TGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCG 
                   
               
               
                   
                   
                 AGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAG 
                   
               
               
                   
                   
                 CGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACAT 
                   
               
               
                   
                   
                 CATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATG 
                   
               
               
                   
                   
                 GCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGA 
                   
               
               
                   
                   
                 CATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGC 
                   
               
               
                   
                   
                 CTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACA 
                   
               
               
                   
                   
                 GGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCC 
                   
               
               
                   
                   
                 GCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCG 
                   
               
               
                   
                   
                 CATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCG 
                   
               
               
                   
                   
                 CTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCA 
                   
               
               
                   
                   
                 TACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGG 
                   
               
               
                   
                   
                 CCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCACTACGTGAAAGGCG 
                   
               
               
                   
                   
                 AGATCACCAAGGTAGTCGGCAAA 
                   
               
               
                   
               
               
                 LOV2 
                 
                   Avena 
                 
                 TTGGCTACTACACTTGAACGTATTGAGAAGAACTTTGTCATTACTGAC 
                 SEQ 
               
               
                   
                 
                   sativa 
                 
                 CCAAGGTTGCCAGATAATCCCATTATATTCGCGTCCGATAGTTTCTTGC 
                 ID 
               
               
                   
                   
                 AGTTGACAGAATATAGCCGTGAAGAAATTTTGGGAAGAAACTGCAGG 
                 No. 94 
               
               
                   
                   
                 TTTCTACAAGGTCCTGAAACTGATCGCGCGACAGTGAGAAAAATTAGA 
                   
               
               
                   
                   
                 GATGCCATAGATAACCAAACAGAGGTCACTGTTCAGCTGATTAATTAT 
                   
               
               
                   
                   
                 ACAAAGAGTGGTAAAAAGTTCTGGAACCTCTTTCACTTGCAGCCTATG 
                   
               
               
                   
                   
                 CGAGATCAGAAGGGAGATGTCCAGTACTTTATTGGGGTTCAGTTGGAT 
                   
               
               
                   
                   
                 GGAACTGAGCATGTCCGAGATGCTGCCGAGAGAGAGGGAGTCATGCT 
                   
               
               
                   
                   
                 GATTAAGAAAACTGCAGAAAATATTGATGAGGCGGCAAAAGAACTTC 
                   
               
               
                   
                   
                 CA 
                   
               
               
                   
               
               
                 BphP1 
                   Rhodo - 
                 ATGGCTAGCGTGGCAGGTCATGCCTCTGGCAGCCCCGCATTCGGGACC 
                 SEQ 
               
               
                   
                 
                   pseudomonas 
                 
                 GCCGATCTTTCGAATTGCGAACGTGAAGAGATCCACCTCGCCGGCTCG 
                 ID 
               
               
                   
                 
                   palustris 
                 
                 ATCCAGCCGCATGGCGCGCTTCTGGTCGTCAGCGAGCCGGATCATCGC 
                 No. 95 
               
               
                   
                   
                 ATCATCCAGGCCAGCGCCAACGCCGCGGAATTTCTGAATCTCGGAAGC 
                   
               
               
                   
                   
                 GTGCTCGGCGTTCCGCTCGCCGAGATCGACGGCGATCTGTTGATCAAG 
                   
               
               
                   
                   
                 ATCCTGCCGCATCTCGATCCCACCGCCGAAGGCATGCCGGTCGCGGTG 
                   
               
               
                   
                   
                 CGCTGCCGGATCGGCAATCCCTCCACGGAGTACGACGGTCTGATGCAT 
                   
               
               
                   
                   
                 CGGCCTCCGGAAGGCGGGCTGATCATCGAGCTCGAACGTGCCGGCCC 
                   
               
               
                   
                   
                 GCCGATCGATCTGTCCGGCACGCTGGCGCCGGCGCTGGAGCGGATCCG 
                   
               
               
                   
                   
                 CACGGCGGGCTCGCTGCGCGCGCTGTGCGATGACACCGCGCTGCTGTT 
                   
               
               
                   
                   
                 TCAGCAGTGCACCGGCTACGACCGGGTGATGGTGTATCGCTTCGACGA 
                   
               
               
                   
                   
                 GCAGGGCCACGGCGAAGTGTTCTCCGAGCGCCACGTGCCCGGGCTCG 
                   
               
               
                   
                   
                 AATCCTATTTCGGCAACCGCTATCCGTCGTCGGACATTCCGCAGATGG 
                   
               
               
                   
                   
                 CGCGGCGGCTGTACGAGCGGCAGCGCGTCCGCGTGCTGGTCGACGTCA 
                   
               
               
                   
                   
                 GCTATCAGCCGGTGCCGCTGGAGCCGCGGCTGTCGCCGCTGACCGGGC 
                   
               
               
                   
                   
                 GCGATCTCGACATGTCGGGCTGCTTCCTGCGCTCGATGTCGCCGATCC 
                   
               
               
                   
                   
                 ATCTGCAGTACCTGAAGAACATGGGCGTGCGCGCCACCCTGGTGGTGT 
                   
               
               
                   
                   
                 CGCTGGTGGTCGGCGGCAAGCTGTGGGGCCTGGTTGCCTGTCATCATT 
                   
               
               
                   
                   
                 ATCTGCCGCGCTTCATGCATTTCGAGCTGCGGGCGATCTGCGAACTGC 
                   
               
               
                   
                   
                 TCGCCGAAGCGATCGCGACGCGGATCACCGCGCTTGAGAGCTTCGCGC 
                   
               
               
                   
                   
                 AGAGCCAGTCGGAGCTGTTCGTGCAGCGGCTCGAACAGCGCATGATC 
                   
               
               
                   
                   
                 GAAGCGATTACCCGTGAAGGCGATTGGCGCGCAGCGATTTTCGACACC 
                   
               
               
                   
                   
                 AGCCAATCGATCCTGCAGCCGCTGCACGCCGCCGGTTGCGCGCTGGTG 
                   
               
               
                   
                   
                 TACGAAGACCAGATCAGGACCATCGGCGACGTGCCTTCCACGCAGGA 
                   
               
               
                   
                   
                 TGTGCGCGAGATCGCCGGGTGGCTCGATCGCCAGCCGCGCGCGGCGGT 
                   
               
               
                   
                   
                 GACCTCGACCGCGTCGCTCGGTCTCGACGTGCCGGAGCTCGCGCATCT 
                   
               
               
                   
                   
                 GACGCGGATGGCGAGCGGCGTGGTCGCGGCGCCGATTTCGGATCATC 
                   
               
               
                   
                   
                 GCGGCGAGTTTCTGATGTGGTTCCGCCCCGAGCGCGTCCACACCGTTA 
                   
               
               
                   
                   
                 CCTGGGGCGGCGATCCGAAGAAGCCGTTCACGATGGGCGATACACCG 
                   
               
               
                   
                   
                 GCGGATCTGTCGCCGCGGCGCTCCTTCGCCAAATGGCATCAGGTTGTC 
                   
               
               
                   
                   
                 GAAGGCACGTCCGATCCGTGGACGGCCGCCGATCTCGCCGCGGCTCGC 
                   
               
               
                   
                   
                 ACCATCGGTCAGACCGTCGCCGACATCGTGCTGCAATTCCGCGCGGTG 
                   
               
               
                   
                   
                 CGGACACTGATCGCCCGCGAACAGTACGAACAGTTTTCGTCCCAGGTG 
                   
               
               
                   
                   
                 CACGCTTCGATGCAGCCGGTGCTGATCACCGACGCCGAAGGCCGCATC 
                   
               
               
                   
                   
                 CTGCTGATGAACGACTCGTTCCGCGACATGTTGCCGGCGGGTTCGCCA 
                   
               
               
                   
                   
                 TCCGCCGTCCATCTCGACGATCTCGCCGGGTTCTTCGTCGAATCGAAC 
                   
               
               
                   
                   
                 GATTTCCTGCGCAACGTCGCCGAACTGATCGATCACGGCCGCGGGTGG 
                   
               
               
                   
                   
                 CGCGGCGAAGTTCTGCTGCGCGGCGCAGGCAACCGCCCGTTGCCGCTG 
                   
               
               
                   
                   
                 GCAGTGCGCGCCGATCCGGTGACGCGCACGGAGGACCAGTCGCTCGG 
                   
               
               
                   
                   
                 CTTCGTGCTGATCTTCAGCGACGCTACCGATCGTCGCACCGCAGATGC 
                   
               
               
                   
                   
                 CGCACGCACGCGTTTCCAGGAAGGCATTCTTGCCAGCGCACGTCCCGG 
                   
               
               
                   
                   
                 CGTGCGGCTCGACTCCAAGTCCGACCTGTTGCACGAGAAGCTGCTGTC 
                   
               
               
                   
                   
                 CGCGCTGGTCGAGAACGCGCAGCTTGCCGCATTGGAAATCACTTACGG 
                   
               
               
                   
                   
                 CGTCGAGACCGGACGCATCGCCGAGCTGCTCGAAGGCGTCCGCCAGTC 
                   
               
               
                   
                   
                 GATGCTGCGCACCGCCGAAGTGCTCGGCCATCTGGTGCAGCACGCGGC 
                   
               
               
                   
                   
                 GCGCACGGCCGGCAGCGACAGCTCGAGCAATGGCTCGCAGAACAAGA 
                   
               
               
                   
                   
                 AGGAATTCGATAGTGCTGGTAGTGCTGGTAGTGCTGGTACTAGT 
                   
               
               
                   
               
               
                 PTP1B 1-435   
                 
                   H. 
                 
                 ATGGAGATGGAAAAGGAGTTCGAGCAGATCGACAAGTCCGGGAGCTG 
                 SEQ 
               
               
                   
                 
                   Sapiens 
                 
                 GGCGGCCATTTACCAGGATATCCGACATGAAGCCAGTGACTTCCCATG 
                 ID 
               
               
                   
                   
                 TAGAGTGGCCAAGCTTCCTAAGAACAAAAACCGAAATAGGTACAGAG 
                 No. 96 
               
               
                   
                   
                 ACGTCAGTCCCTTTGACCATAGTCGGATTAAACTACATCAAGAAGATA 
                   
               
               
                   
                   
                 ATGACTATATCAACGCTAGTTTGATAAAAATGGAAGAAGCCCAAAGG 
                   
               
               
                   
                   
                 AGTTACATTCTTACCCAGGGCCCTTTGCCTAACACATGCGGTCACTTTT 
                   
               
               
                   
                   
                 GGGAGATGGTGTGGGAGCAGAAAAGCAGGGGTGTCGTCATGCTCAAC 
                   
               
               
                   
                   
                 AGAGTGATGGAGAAAGGTTCGTTAAAATGCGCACAATACTGGCCACA 
                   
               
               
                   
                   
                 AAAAGAAGAAAAAGAGATGATCTTTGAAGACACAAATTTGAAATTAA 
                   
               
               
                   
                   
                 CATTGATCTCTGAAGATATCAAGTCATATTATACAGTGCGACAGCTAG 
                   
               
               
                   
                   
                 AATTGGAAAACCTTACAACCCAAGAAACTCGAGAGATCTTACATTTCC 
                   
               
               
                   
                   
                 ACTATACCACATGGCCTGACTTTGGAGTCCCTGAATCACCAGCCTCAT 
                   
               
               
                   
                   
                 TCTTGAACTTTCTTTTCAAAGTCCGAGAGTCAGGGTCACTCAGCCCGG 
                   
               
               
                   
                   
                 AGCACGGGCCCGTTGTGGTGCACTGCAGTGCAGGCATCGGCAGGTCTG 
                   
               
               
                   
                   
                 GAACCTTCTGTCTGGCTGATACCTGCCTCTTGCTGATGGACAAGAGGA 
                   
               
               
                   
                   
                 AAGACCCTTCTTCCGTTGATATCAAGAAAGTGCTGTTAGAAATGAGGA 
                   
               
               
                   
                   
                 AGTTTCGGATGGGGCTGATCCAGACAGCCGACCAGCTGCGCTTCTCCT 
                   
               
               
                   
                   
                 ACCTGGCTGTGATCGAAGGTGCCAAATTCATCATGGGGGACTCTTCCG 
                   
               
               
                   
                   
                 TGCAGGATCAGTGGAAGGAGCTTTCCCACGAGGACCTGGAGCCCCCA 
                   
               
               
                   
                   
                 CCCGAGCATATCCCCCCACCTCCCCGGCCACCCAAACGAATCCTGGAG 
                   
               
               
                   
                   
                 CCACACAATGGGAAATGCAGGGAGTTCTTCCCAAATCACCAGTGGGTG 
                   
               
               
                   
                   
                 AAGGAAGAGACCCAGGAGGATAAAGACTGCCCCATCAAGGAAGAAA 
                   
               
               
                   
                   
                 AAGGAAGCCCCTTAAATGCCGCACCCTACGGCATCGAAAGCATGAGT 
                   
               
               
                   
                   
                 CAAGACACTGAAGTTAGAAGTCGGGTCGTGGGGGGAAGTCTTCGAGG 
                   
               
               
                   
                   
                 TGCCCAGGCTGCCTCCCCAGCCAAAGGGGAGCCGTCACTGCCCGAGA 
                   
               
               
                   
                   
                 AGGACGAGGACCATGCACTGAGTTACTGGAAGCCCTTCCTGGTCAACA 
                   
               
               
                   
                   
                 TGTGCGTGGCTACGGTCCTCACGGCCGGCGCTTACCTCTGCTACAGGT 
                   
               
               
                   
                   
                 TCCTGTTCAACAGCAACACATAG 
                   
               
               
                   
               
               
                 TC- 
                 
                   H. 
                 
                 ATGCCCACCACCATCGAGCGGGAGTTCGAAGAGTTGGATACTCAGCGT 
                 SEQ 
               
               
                 PTP 
                 
                   Sapiens 
                 
                 CGCTGGCAGCCGCTGTACTTGGAAATTCGAAATGAGTCCCATGACTAT 
                 ID 
               
               
                 (full) 
                   
                 CCTCATAGAGTGGCCAAGTTTCCAGAAAACAGAAATCGAAACAGATA 
                 No. 97 
               
               
                   
                   
                 CAGAGATGTAAGCCCATATGATCACAGTCGTGTTAAACTGCAAAATGC 
                   
               
               
                   
                   
                 TGAGAATGATTATATTAATGCCAGTTTAGTTGACATAGAAGAGGCACA 
                   
               
               
                   
                   
                 AAGGAGTTACATCTTAACACAGGGTCCACTTCCTAACACATGCTGCCA 
                   
               
               
                   
                   
                 TTTCTGGCTTATGGTTTGGCAGCAGAAGACCAAAGCAGTTGTCATGCT 
                   
               
               
                   
                   
                 GAACCGCATTGTGGAGAAAGAATCGGTTAAATGTGCACAGTACTGGC 
                   
               
               
                   
                   
                 CAACAGATGACCAAGAGATGCTGTTTAAAGAAACAGGATTCAGTGTG 
                   
               
               
                   
                   
                 AAGCTCTTGTCAGAAGATGTGAAGTCGTATTATACAGTACATCTACTA 
                   
               
               
                   
                   
                 CAATTAGAAAATATCAATAGTGGTGAAACCAGAACAATATCTCACTTT 
                   
               
               
                   
                   
                 CATTATACTACCTGGCCAGATTTTGGAGTCCCTGAATCACCAGCTTCAT 
                   
               
               
                   
                   
                 TTCTCAATTTCTTGTTTAAAGTGAGAGAATCTGGCTCCTTGAACCCTGA 
                   
               
               
                   
                   
                 CCATGGGCCTGCGGTGATCCACTGTAGTGCAGGCATTGGGCGCTCTGG 
                   
               
               
                   
                   
                 CACCTTCTCTCTGGTAGACACTTGTCTTGTTTTGATGGAAAAAGGAGAT 
                   
               
               
                   
                   
                 GATATTAACATAAAACAAGTGTTACTGAACATGAGAAAATACCGAAT 
                   
               
               
                   
                   
                 GGGTCTTATTCAGACCCCAGATCAACTGAGATTCTCATACATGGCTAT 
                   
               
               
                   
                   
                 AATAGAAGGAGCAAAATGTATAAAGGGAGATTCTAGTATACAGAAAC 
                   
               
               
                   
                   
                 GATGGAAAGAACTTTCTAAGGAAGACTTATCTCCTGCCTTTGATCATT 
                   
               
               
                   
                   
                 CACCAAACAAAATAATGACTGAAAAATACAATGGGAACAGA 
                   
               
               
                   
               
               
                 PTPN5 
                 
                   H. sapiens 
                 
                 ATGTCTTCTGGTGTAGATCTGGGTACCGAGAACCTGTACTTCCAATCC 
                 SEQ 
               
               
                   
                   
                 ATGTCCCGTGTCCTCCAAGCAGAAGAGCTTCATGAAAAGGCCCTGGAC 
                 ID 
               
               
                   
                   
                 CCTTTCCTGCTGCAGGCGGAATTCTTTGAAATCCCCATGAACTTTGTGG 
                 No. 98 
               
               
                   
                   
                 ATCCGAAAGAGTACGACATCCCTGGGCTGGTGCGGAAGAACCGGTAC 
                   
               
               
                   
                   
                 AAAACCATACTTCCCAACCCTCACAGCAGAGTGTGTCTGACCTCACCA 
                   
               
               
                   
                   
                 GACCCTGACGACCCTCTGAGTTCCTACATCAATGCCAACTACATCCGG 
                   
               
               
                   
                   
                 GGCTATGGTGGGGAGGAGAAGGTGTACATCGCCACTCAGGGACCCAT 
                   
               
               
                   
                   
                 CGTCAGCACGGTCGCCGACTTCTGGCGCATGGTGTGGCAGGAGCACAC 
                   
               
               
                   
                   
                 GCCCATCATTGTCATGATCACCAACATCGAGGAGATGAACGAGAAAT 
                   
               
               
                   
                   
                 GCACCGAGTATTGGCCGGAGGAGCAGGTGGCGTACGACGGTGTTGAG 
                   
               
               
                   
                   
                 ATCACTGTGCAGAAAGTCATTCACACGGAGGATTACCGGCTGCGACTC 
                   
               
               
                   
                   
                 ATCTCCCTCAAGAGTGGGACTGAGGAGCGAGGCCTGAAGCATTACTG 
                   
               
               
                   
                   
                 GTTCACATCCTGGCCCGACCAGAAGACCCCAGACCGGGCCCCCCCACT 
                   
               
               
                   
                   
                 CCTGCACCTGGTGCGGGAGGTGGAGGAGGCAGCCCAGCAGGAGGGGC 
                   
               
               
                   
                   
                 CCCACTGTGCCCCCATCATCGTCCACTGCAGTGCAGGGATTGGGAGGA 
                   
               
               
                   
                   
                 CCGGCTGCTTCATTGCCACCAGCATCTGCTGCCAGCAGCTGCGGCAGG 
                   
               
               
                   
                   
                 AGGGTGTAGTGGACATCCTGAAGACCACGTGCCAGCTCCGTCAGGAC 
                   
               
               
                   
                   
                 AGGGGCGGCATGATCCAGACATGCGAGCAGTACCAGTTTGTGCACCA 
                   
               
               
                   
                   
                 CGTCATGAGCCTCTACGAAAAGCAGCTGTCCCACCAGTCCTGA 
                   
               
               
                   
               
               
                 PTPN6 
                 
                   H. sapiens 
                 
                 ATGGTGAGGTGGTTTCACCGAGACCTCAGTGGGCTGGATGCAGAGACC 
                 SEQ 
               
               
                   
                   
                 CTGCTCAAGGGCCGAGGTGTCCACGGTAGCTTCCTGGCTCGGCCCAGT 
                 ID 
               
               
                   
                   
                 CGCAAGAACCAGGGTGACTTCTCGCTCTCCGTCAGGGTGGGGGATCAG 
                 No. 99 
               
               
                   
                   
                 GTGACCCATATTCGGATCCAGAACTCAGGGGATTTCTATGACCTGTAT 
                   
               
               
                   
                   
                 GGAGGGGAGAAGTTTGCGACTCTGACAGAGCTGGTGGAGTACTACAC 
                   
               
               
                   
                   
                 TCAGCAGCAGGGTGTGGTGCAGGACCGCGACGGCACCATCATCCACCT 
                   
               
               
                   
                   
                 CAAGTACCCGCTGAACTGCTCCGATCCCACTAGTGAGAGGTGGTACCA 
                   
               
               
                   
                   
                 TGGCCACATGTCTGGCGGGCAGGCAGAGACGCTGCTGCAGGCCAAGG 
                   
               
               
                   
                   
                 GCGAGCCCTGGACGTTTCTTGTGCGTGAGAGCCTCAGCCAGCCTGGAG 
                   
               
               
                   
                   
                 ACTTCGTGCTTTCTGTGCTCAGTGACCAGCCCAAGGCTGGCCCAGGCT 
                   
               
               
                   
                   
                 CCCCGCTCAGGGTCACCCACATCAAGGTCATGTGCGAGGGTGGACGCT 
                   
               
               
                   
                   
                 ACACAGTGGGTGGTTTGGAGACCTTCGACAGCCTCACGGACCTGGTGG 
                   
               
               
                   
                   
                 AGCATTTCAAGAAGACGGGGATTGAGGAGGCCTCAGGCGCCTTTGTCT 
                   
               
               
                   
                   
                 ACCTGCGGCAGCCGTACTATGCCACGAGGGTGAATGCGGCTGACATTG 
                   
               
               
                   
                   
                 AGAACCGAGTGTTGGAACTGAACAAGAAGCAGGAGTCCGAGGATACA 
                   
               
               
                   
                   
                 GCCAAGGCTGGCTTCTGGGAGGAGTTTGAGAGTTTGCAGAAGCAGGA 
                   
               
               
                   
                   
                 GGTGAAGAACTTGCACCAGCGTCTGGAAGGGCAACGGCCAGAGAACA 
                   
               
               
                   
                   
                 AGGGCAAGAACCGCTACAAGAACATTCTCCCCTTTGACCACAGCCGAG 
                   
               
               
                   
                   
                 TGATCCTGCAGGGACGGGACAGTAACATCCCCGGGTCCGACTACATCA 
                   
               
               
                   
                   
                 ATGCCAACTACATCAAGAACCAGCTGCTAGGCCCTGATGAGAACGCTA 
                   
               
               
                   
                   
                 AGACCTACATCGCCAGCCAGGGCTGTCTGGAGGCCACGGTCAATGACT 
                   
               
               
                   
                   
                 TCTGGCAGATGGCGTGGCAGGAGAACAGCCGTGTCATCGTCATGACCA 
                   
               
               
                   
                   
                 CCCGAGAGGTGGAGAAAGGCCGGAACAAATGCGTCCCATACTGGCCC 
                   
               
               
                   
                   
                 GAGGTGGGCATGCAGCGTGCTTATGGGCCCTACTCTGTGACCAACTGC 
                   
               
               
                   
                   
                 GGGGAGCATGACACAACCGAATACAAACTCCGTACCTTACAGGTCTCC 
                   
               
               
                   
                   
                 CCGCTGGACAATGGAGACCTGATTCGGGAGATCTGGCATTACCAGTAC 
                   
               
               
                   
                   
                 CTGAGCTGGCCCGACCATGGGGTCCCCAGTGAGCCTGGGGGTGTCCTC 
                   
               
               
                   
                   
                 AGCTTCCTGGACCAGATCAACCAGCGGCAGGAAAGTCTGCCTCACGCA 
                   
               
               
                   
                   
                 GGGCCCATCATCGTGCACTGCAGCGCCGGCATCGGCCGCACAGGCACC 
                   
               
               
                   
                   
                 ATCATTGTCATCGACATGCTCATGGAGAACATCTCCACCAAGGGCCTG 
                   
               
               
                   
                   
                 GACTGTGACATTGACATCCAGAAGACCATCCAGATGGTGCGGGCGCA 
                   
               
               
                   
                   
                 GCGCTCGGGCATGGTGCAGACGGAGGCGCAGTACAAGTTCATCTACGT 
                   
               
               
                   
                   
                 GGCCATCGCCCAGTTCATTGAAACCACTAAGAAGAAGCTGGAGGTCCT 
                   
               
               
                   
                   
                 GCAGTCGCAGAAGGGCCAGGAGTCGGAGTACGGGAACATCACCTATC 
                   
               
               
                   
                   
                 CCCCAGCCATGAAGAATGCCCATGCCAAGGCCTCCCGCACCTCGTCCA 
                   
               
               
                   
                   
                 AACACAAGGAGGATGTGTATGAGAACCTGCACACTAAGAACAAGAGG 
                   
               
               
                   
                   
                 GAGGAGAAAGTGAAGAAGCAGCGGTCAGCAGACAAGGAGAAGAGCA 
                   
               
               
                   
                   
                 AGGGTTCCCTCAAGAGGAAGTGA 
                   
               
               
                   
               
               
                 PTPN11 
                 
                   H. sapiens 
                 
                 ATGACATCGCGGAGATGGTTTCACCCAAATATCACTGGTGTGGAGGCA 
                 SEQ 
               
               
                   
                   
                 GAAAACCTACTGTTGACAAGAGGAGTTGATGGCAGTTTTTTGGCAAGG 
                 ID 
               
               
                   
                   
                 CCTAGTAAAAGTAACCCTGGAGACTTCACACTTTCCGTTAGAAGAAAT 
                 No. 
               
               
                   
                   
                 GGAGCTGTCACCCACATCAAGATTCAGAACACTGGTGATTACTATGAC 
                 100 
               
               
                   
                   
                 CTGTATGGAGGGGAGAAATTTGCCACTTTGGCTGAGTTGGTCCAGTAT 
                   
               
               
                   
                   
                 TACATGGAACATCACGGGCAATTAAAAGAGAAGAATGGAGATGTCAT 
                   
               
               
                   
                   
                 TGAGCTTAAATATCCTCTGAACTGTGCAGATCCTACCTCTGAAAGGTG 
                   
               
               
                   
                   
                 GTTTCATGGACATCTCTCTGGGAAAGAAGCAGAGAAATTATTAACTGA 
                   
               
               
                   
                   
                 AAAAGGAAAACATGGTAGTTTTCTTGTACGAGAGAGCCAGAGCCACC 
                   
               
               
                   
                   
                 CTGGAGATTTTGTTCTTTCTGTGCGCACTGGTGATGACAAAGGGGAGA 
                   
               
               
                   
                   
                 GCAATGACGGCAAGTCTAAAGTGACCCATGTTATGATTCGCTGTCAGG 
                   
               
               
                   
                   
                 AACTGAAATACGACGTTGGTGGAGGAGAACGGTTTGATTCTTTGACAG 
                   
               
               
                   
                   
                 ATCTTGTGGAACATTATAAGAAGAATCCTATGGTGGAAACATTGGGTA 
                   
               
               
                   
                   
                 CAGTACTACAACTCAAGCAGCCCCTTAACACGACTCGTATAAATGCTG 
                   
               
               
                   
                   
                 CTGAAATAGAAAGCAGAGTTCGAGAACTAAGCAAATTAGCTGAGACC 
                   
               
               
                   
                   
                 ACAGATAAAGTCAAACAAGGCTTTTGGGAAGAATTTGAGACACTACA 
                   
               
               
                   
                   
                 ACAACAGGAGTGCAAACTTCTCTACAGCCGAAAAGAGGGTCAAAGGC 
                   
               
               
                   
                   
                 AAGAAAACAAAAACAAAAATAGATATAAAAACATCCTGCCCTTTGAT 
                   
               
               
                   
                   
                 CATACCAGGGTTGTCCTACACGATGGTGATCCCAATGAGCCTGTTTCA 
                   
               
               
                   
                   
                 GATTACATCAATGCAAATATCATCATGCCTGAATTTGAAACCAAGTGC 
                   
               
               
                   
                   
                 AACAATTCAAAGCCCAAAAAGAGTTACATTGCCACACAAGGCTGCCT 
                   
               
               
                   
                   
                 GCAAAACACGGTGAATGACTTTTGGCGGATGGTGTTCCAAGAAAACTC 
                   
               
               
                   
                   
                 CCGAGTGATTGTCATGACAACGAAAGAAGTGGAGAGAGGAAAGAGTA 
                   
               
               
                   
                   
                 AATGTGTCAAATACTGGCCTGATGAGTATGCTCTAAAAGAATATGGCG 
                   
               
               
                   
                   
                 TCATGCGTGTTAGGAACGTCAAAGAAAGCGCCGCTCATGACTATACGC 
                   
               
               
                   
                   
                 TAAGAGAACTTAAACTTTCAAAGGTTGGACAAGGGAATACGGAGAGA 
                   
               
               
                   
                   
                 ACGGTCTGGCAATACCACTTTCGGACCTGGCCGGACCACGGCGTGCCC 
                   
               
               
                   
                   
                 AGCGACCCTGGGGGCGTGCTGGACTTCCTGGAGGAGGTGCACCATAA 
                   
               
               
                   
                   
                 GCAGGAGAGCATCATGGATGCAGGGCCGGTCGTGGTGCACTGCAGTG 
                   
               
               
                   
                   
                 CTGGAATTGGCCGGACAGGGACGTTCATTGTGATTGATATTCTTATTG 
                   
               
               
                   
                   
                 ACATCATCAGAGAGAAAGGTGTTGACTGCGATATTGACGTTCCCAAAA 
                   
               
               
                   
                   
                 CCATCCAGATGGTGCGGTCTCAGAGGTCAGGGATGGTCCAGACAGAA 
                   
               
               
                   
                   
                 GCACAGTACCGATTTATCTATATGGCGGTCCAGCATTATATTGAAACA 
                   
               
               
                   
                   
                 CTACAGCGCAGGATTGAAGAAGAGCAGAAAAGCAAGAGGAAAGGGC 
                   
               
               
                   
                   
                 ACGAATATACAAATATTAAGTATTCTCTAGCGGACCAGACGAGTGGAG 
                   
               
               
                   
                   
                 ATCAGAGCCCTCTCCCGCCTTGTACTCCAACGCCACCCTGTGCAGAAA 
                   
               
               
                   
                   
                 TGAGAGAAGACAGTGCTAGAGTCTATGAAAACGTGGGCCTGATGCAA 
                   
               
               
                   
                   
                 CAGCAGAAAAGTTTCAGATGA 
                   
               
               
                   
               
               
                 PTPN12 
                 
                   H. sapiens 
                 
                 ATGGAGCAAGTGGAGATCCTGAGGAAATTCATCCAGAGGGTCCAGGC 
                 SEQ 
               
               
                   
                   
                 CATGAAGAGTCCTGACCACAATGGGGAGGACAACTTCGCCCGGGACT 
                 ID 
               
               
                   
                   
                 TCATGCGGTTAAGAAGATTGTCTACCAAATATAGAACAGAAAAGATAT 
                 No. 
               
               
                   
                   
                 ATCCCACAGCCACTGGAGAAAAAGAAGAAAATGTTAAAAAGAACAGA 
                 101 
               
               
                   
                   
                 TACAAGGACATACTGCCATTTGATCACAGCCGAGTTAAATTGACATTA 
                   
               
               
                   
                   
                 AAGACTCCTTCACAAGATTCAGACTATATCAATGCAAATTTTATAAAG 
                   
               
               
                   
                   
                 GGCGTCTATGGGCCAAAAGCATATGTAGCAACTCAAGGACCTTTAGCA 
                   
               
               
                   
                   
                 AATACAGTAATAGATTTTTGGAGGATGGTATGGGAGTATAATGTTGTG 
                   
               
               
                   
                   
                 ATCATTGTAATGGCCTGCCGAGAATTTGAGATGGGAAGGAAAAAATG 
                   
               
               
                   
                   
                 TGAGCGCTATTGGCCTTTGTATGGAGAAGACCCCATAACGTTTGCACC 
                   
               
               
                   
                   
                 ATTTAAAATTTCTTGTGAGGATGAACAAGCAAGAACAGACTACTTCAT 
                   
               
               
                   
                   
                 CAGGACACTCTTACTTGAATTTCAAAATGAATCTCGTAGGCTGTATCA 
                   
               
               
                   
                   
                 GTTTCATTATGTGAACTGGCCAGACCATGATGTTCCTTCATCATTTGAT 
                   
               
               
                   
                   
                 TCTATTCTGGACATGATAAGCTTAATGAGGAAATATCAAGAACATGAA 
                   
               
               
                   
                   
                 GATGTTCCTATTTGTATTCATTGCAGTGCAGGCTGTGGAAGAACAGGT 
                   
               
               
                   
                   
                 GCCATTTGTGCCATAGATTATACGTGGAATTTACTAAAAGCTGGGAAA 
                   
               
               
                   
                   
                 ATACCAGAGGAATTTAATGTATTTAATTTAATACAAGAAATGAGAACA 
                   
               
               
                   
                   
                 CAAAGGCATTCTGCAGTACAAACAAAGGAGCAATATGAACTTGTTCAT 
                   
               
               
                   
                   
                 AGAGCTATTGCCCAACTGTTTGAAAAACAGCTACAACTATATGAAATT 
                   
               
               
                   
                   
                 CATGGAGCTCAGAAAATTGCTGATGGAGTGAATGAAATTAACACTGA 
                   
               
               
                   
                   
                 AAACATGGTCAGCTCCATAGAGCCTGAAAAACAAGATTCTCCTCCTCC 
                   
               
               
                   
                   
                 AAAACCACCAAGGACCCGCAGTTGCCTTGTTGAAGGGGATGCTAAAG 
                   
               
               
                   
                   
                 AAGAAATACTGCAGCCACCGGAACCTCATCCAGTGCCACCCATCTTGA 
                   
               
               
                   
                   
                 CACCTTCTCCCCCTTCAGCTTTTCCAACAGTCACTACTGTGTGGCAGGA 
                   
               
               
                   
                   
                 CAATGATAGATACCATCCAAAGCCAGTGTTGCAATGGTTTCATCAGAA 
                   
               
               
                   
                   
                 CAACATTCAGCAGACCTCAACAGAAACTATAGTAAATCAACAGAACTT 
                   
               
               
                   
                   
                 CCAGGGAAAAATGAATCAACAATTGAACAGA 
                   
               
               
                   
               
               
                 PTPN22 
                 
                   H. sapiens 
                 
                 ATGGACCAAAGAGAAATTCTGCAGAAGTTCCTGGATGAGGCCCAAAG 
                 SEQ 
               
               
                   
                   
                 CAAGAAAATTACTAAAGAGGAGTTTGCCAATGAATTTCTGAAGCTGAA 
                 ID 
               
               
                   
                   
                 AAGGCAATCTACCAAGTACAAGGCAGACAAAACCTATCCTACAACTG 
                 No. 
               
               
                   
                   
                 TGGCTGAGAAGCCCAAGAATATCAAGAAAAACAGATATAAGGATATT 
                 102 
               
               
                   
                   
                 TTGCCCTATGATTATAGCCGGGTAGAACTATCCCTGATAACCTCTGAT 
                   
               
               
                   
                   
                 GAGGATTCCAGCTACATCAATGCCAACTTCATTAAGGGAGTTTATGGA 
                   
               
               
                   
                   
                 CCCAAGGCTTATATTGCCACCCAGGGTCCTTTATCTACAACCCTCCTGG 
                   
               
               
                   
                   
                 ACTTCTGGAGGATGATTTGGGAATATAGTGTCCTTATCATTGTTATGGC 
                   
               
               
                   
                   
                 ATGCATGGAGTATGAAATGGGAAAGAAAAAGTGTGAGCGCTACTGGG 
                   
               
               
                   
                   
                 CTGAGCCAGGAGAGATGCAGCTGGAATTTGGCCCTTTCTCTGTATCCT 
                   
               
               
                   
                   
                 GTGAAGCTGAAAAAAGGAAATCTGATTATATAATCAGGACTCTAAAA 
                   
               
               
                   
                   
                 GTTAAGTTCAATAGTGAAACTCGAACTATCTACCAGTTTCATTACAAG 
                   
               
               
                   
                   
                 AATTGGCCAGACCATGATGTACCTTCATCTATAGACCCTATTCTTGAGC 
                   
               
               
                   
                   
                 TCATCTGGGATGTACGTTGTTACCAAGAGGATGACAGTGTTCCCATAT 
                   
               
               
                   
                   
                 GCATTCACTGCAGTGCTGGCTGTGGAAGGACTGGTGTTATTTGTGCTA 
                   
               
               
                   
                   
                 TTGATTATACATGGATGTTGCTAAAAGATGGGATAATTCCTGAGAACT 
                   
               
               
                   
                   
                 TCAGTGTTTTCAGTTTGATCCGGGAAATGCGGACACAGAGGCCTTCAT 
                   
               
               
                   
                   
                 TAGTTCAAACGCAGGAACAATATGAACTGGTCTACAATGCTGTATTAG 
                   
               
               
                   
                   
                 AACTATTTAAGAGACAGATGGATGTTATCAGAGATAA 
                   
               
               
                   
               
               
                 GalK 
                 
                   Escherichia 
                 
                 ATGAGTCTGAAAGAAAAAACACAATCTCTGTTTGCCAACGCATTTGGC 
                 SEQ 
               
               
                   
                 
                   coli 
                 
                 TACCCTGCCACTCACACCATTCAGGCGCCTGGCCGCGTGAATTTGATT 
                 ID 
               
               
                   
                   
                 GGTGAACACACCGACTACAACGACGGTTTCGTTCTGCCCTGCGCGATT 
                 No. 
               
               
                   
                   
                 GATTATCAAACCGTGATCAGTTGTGCACCACGCGATGACCGTAAAGTT 
                 103 
               
               
                   
                   
                 CGCGTGATGGCAGCCGATTATGAAAATCAGCTCGACGAGTTTTCCCTC 
                   
               
               
                   
                   
                 GATGCGCCCATTGTCGCACATGAAAACTATCAATGGGCTAACTACGTT 
                   
               
               
                   
                   
                 CGTGGCGTGGTGAAACATCTGCAACTGCGTAACAACAGCTTCGGCGGC 
                   
               
               
                   
                   
                 GTGGACATGGTGATCAGCGGCAATGTGCCGCAGGGTGCCGGGTTAAG 
                   
               
               
                   
                   
                 TTCTTCCGCTTCACTGGAAGTCGCGGTCGGAACCGTATTGCAGCAGCT 
                   
               
               
                   
                   
                 TTATCATCTGCCGCTGGACGGCGCACAAATCGCGCTTAACGGTCAGGA 
                   
               
               
                   
                   
                 AGCAGAAAACCAGTTTGTAGGCTGTAACTGCGGGATCATGGATCAGCT 
                   
               
               
                   
                   
                 AATTTCCGCGCTCGGCAAGAAAGATCATGCCTTGCTGATCGATTGCCG 
                   
               
               
                   
                   
                 CTCACTGGGGACCAAAGCAGTTTCCATGCCCAAAGGTGTGGCTGTCGT 
                   
               
               
                   
                   
                 CATCATCAACAGTAACTTCAAACGTACCCTGGTTGGCAGCGAATACAA 
                   
               
               
                   
                   
                 CACCCGTCGTGAACAGTGCGAAACCGGTGCGCGTTTCTTCCAGCAGCC 
                   
               
               
                   
                   
                 AGCCCTGCGTGATGTCACCATTGAAGAGTTCAACGCTGTTGCGCATGA 
                   
               
               
                   
                   
                 ACTGGACCCGATCGTGGCAAAACGCGTGCGTCATATACTGACTGAAAA 
                   
               
               
                   
                   
                 CGCCCGCACCGTTGAAGCTGCCAGCGCGCTGGAGCAAGGCGACCTGA 
                   
               
               
                   
                   
                 AACGTATGGGCGAGTTGATGGCGGAGTCTCATGCCTCTATGCGCGATG 
                   
               
               
                   
                   
                 ATTTCGAAATCACCGTGCCGCAAATTGACACTCTGGTAGAAATCGTCA 
                   
               
               
                   
                   
                 AAGCTGTGATTGGCGACAAAGGTGGCGTACGCATGACCGGCGGCGGA 
                   
               
               
                   
                   
                 TTTGGCGGCTGTATCGTCGCGCTGATCCCGGAAGAGCTGGTGCCTGCC 
                   
               
               
                   
                   
                 GTACAGCAAGCTGTCGCTGAACAATATGAAGCAAAAACAGGTATTAA 
                   
               
               
                   
                   
                 AGAGACTTTTTACGTTTGTAAACCATCACAAGGAGCAGGACAGTGCTG 
                   
               
               
                   
                   
                 A 
                   
               
               
                   
               
               
                 SacB 
                 
                   Bacillus 
                 
                 ATGAACATCAAAAAGTTTGCAAAACAAGCAACAGTATTAACCTTTACT 
                 SEQ 
               
               
                   
                 
                   subtilis 
                 
                 ACCGCACTGCTGGCAGGAGGCGCAACTCAAGCGTTTGCGAAAGAAAC 
                 ID 
               
               
                   
                   
                 GAACCAAAAGCCATATAAGGAAACATACGGCATTTCCCATATTACACG 
                 No. 
               
               
                   
                   
                 CCATGATATGCTGCAAATCCCTGAACAGCAAAAAAATGAAAAATATC 
                 104 
               
               
                   
                   
                 AAGTTCCTGAATTCGATTCGTCCACAATTAAAAATATCTCTTCTGCAAA 
                   
               
               
                   
                   
                 AGGCCTGGACGTTTGGGACAGCTGGCCATTACAAAACGCTGACGGCA 
                   
               
               
                   
                   
                 CTGTCGCAAACTATCACGGCTACCACATCGTCTTTGCATTAGCCGGAG 
                   
               
               
                   
                   
                 ATCCTAAAAATGCGGATGACACATCGATTTACATGTTCTATCAAAAAG 
                   
               
               
                   
                   
                 TCGGCGAAACTTCTATTGACAGCTGGAAAAACGCTGGCCGCGTCTTTA 
                   
               
               
                   
                   
                 AAGACAGCGACAAATTCGATGCAAATGATTCTATCCTAAAAGACCAA 
                   
               
               
                   
                   
                 ACACAAGAATGGTCAGGTTCAGCCACATTTACATCTGACGGAAAAATC 
                   
               
               
                   
                   
                 CGTTTATTCTACACTGATTTCTCCGGTAAACATTACGGCAAACAAACA 
                   
               
               
                   
                   
                 CTGACAACTGCACAAGTTAACGTATCAGCATCAGACAGCTCTTTGAAC 
                   
               
               
                   
                   
                 ATCAACGGTGTAGAGGATTATAAATCAATCTTTGACGGTGACGGAAAA 
                   
               
               
                   
                   
                 ACGTATCAAAATGTACAGCAGTTCATCGATGAAGGCAACTACAGCTCA 
                   
               
               
                   
                   
                 GGCGACAACCATACGCTGAGAGATCCTCACTACGTAGAAGATAAAGG 
                   
               
               
                   
                   
                 CCACAAATACTTAGTATTTGAAGCAAACACTGGAACTGAAGATGGCTA 
                   
               
               
                   
                   
                 CCAAGGCGAAGAATCTTTATTTAACAAAGCATACTATGGCAAAAGCAC 
                   
               
               
                   
                   
                 ATCATTCTTCCGTCAAGAAAGTCAAAAACTTCTGCAAAGCGATAAAAA 
                   
               
               
                   
                   
                 ACGCACGGCTGAGTTAGCAAACGGCGCTCTCGGTATGATTGAGCTAAA 
                   
               
               
                   
                   
                 CGATGATTACACACTGAAAAAAGTGATGAAACCGCTGATTGCATCTAA 
                   
               
               
                   
                   
                 CACAGTAACAGATGAAATTGAACGCGCGAACGTCTTTAAAATGAACG 
                   
               
               
                   
                   
                 GCAAATGGTACCTGTTCACTGACTCCCGCGGATCAAAAATGACGATTG 
                   
               
               
                   
                   
                 ACGGCATTACGTCTAACGATATTTACATGCTTGGTTATGTTTCTAATTC 
                   
               
               
                   
                   
                 TTTAACTGGCCCATACAAGCCGCTGAACAAAACTGGCCTTGTGTTAAA 
                   
               
               
                   
                   
                 AATGGATCTTGATCCTAACGATGTAACCTTTACTTACTCACACTTCGCT 
                   
               
               
                   
                   
                 GTACCTCAAGCGAAAGGAAACAATGTCGTGATTACAAGCTATATGAC 
                   
               
               
                   
                   
                 AAACAGAGGATTCTACGCAGACAAACAATCAACGTTTGCGCCAAGCTT 
                   
               
               
                   
                   
                 CCTGCTGAACATCAAAGGCAAGAAAACATCTGTTGTCAAAGACAGCA 
                   
               
               
                   
                   
                 TCCTTGAACAAGGACAATTAACAGTTAACAAATAA 
               
               
                   
               
            
           
         
       
     
     Abbreviations 
     PTP IB, protein tyrosine phosphatase IB; TC-PTP, T-cell protein tyrosine phosphatase; SHP2, protein tyrosine phosphatase non-receptor type 11; BBR, 3-(3,5-Dibromo-4-hydroxy-benzoyl)-2-ethyl-benzofuran-6-sulfonicacid-(4-(thiazol-2-ylsulfamyl)-phenyl)-amide; TCS401, 2-[(Carbox-ycarbonyl)amino]-4,5,6,7-tetrahydro-thieno[2,3-c]pyridine-3-carboxylic acid hydrochloride; AA, abietic acid; SCA, statistical coupling analysis. PTP1B 1-435 , protein tyrosine phosphatase 1B (full-length); SacB, levansucrase; GHS, γ-humulene synthase; ADS, amorphadiene synthase; ABS (or AgAs), abietadiene synthase; TXS, taxadiene synthase, PTPNS, protein tyrosine phosphatase non-receptor type 5; PTPN6, protein tyrosine phosphatase non-receptor type 6; PTPN11, protein tyrosine phosphatase non-receptor type 11; PTPN12, protein tyrosine phosphatase non-receptor type 12; PPTN22, protein tyrosine phosphatase non-receptor type 22; RpoZ, omega subunit of RNA polymerase; cI (or cI434), cI repressor protein from lambda phage; Kras (or p130cas), p130cas phosphotyrosine substrate; MidT, phosphotyrosine substrate from hamster polyoma virus; EGFR substrate, phosphotyrosine substrate from epidermal growth factor receptor; Src, Src kinase; CDC37, Hsp90 co-chaperone Cdc37; MBP, maltose-binding protein; LuxAB, bacterial luciferase modules A and B; SpecR, spectinomycin resistance gene; GGPPS, geranylgeranyl diphosphate synthase; P450 (or P450 BM3 ) Cytochrome P450; LOV2, light-oxygen-voltage domain 2 from phototropin 1; BphP1, bacterial phytochrome; Galk, galatokinase. 
     Examples 
     The following examples are offered to illustrate various embodiments of the invention, but should not be viewed as limiting the scope of the invention. 
     Statistical Analysis of Kinetic Models. We evaluated four kinetic models of inhibition as described previously (19). In brief, we used an F-test to compare a two-parameter mixed model to several single-parameter models, and we used Akaike&#39;s Information Criterion (AIC, or Ai) to compare the single-parameter models to one another. Mixed models with p&lt;0.05 are superior to all single-parameter models, and single-parameter models with Aj &gt;10 are inferior to the reference (i.e., “best fit”) model. 
     Exemplary Estimation of IC50. We estimated the half maximal inhibitory concentration (IC50) of BBR by using kinetic models to estimate the concentration of inhibitor required to reduce initial rates of PTP-catalyzed hydrolysis of 20 mM of pNPP by 50%, and we used the MATLAB function “nlparci” to determine the confidence intervals on those estimates (19). 
     All publications and patents mentioned in the above specification are herein incorporated by reference. Various modifications and variations of the described methods and system of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention that are obvious to those skilled in medicine, molecular biology, cell biology, genetics, statistics or related fields are intended to be within the scope of the following claims.