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[[sbb13-OligoWishList]]
<pre>
EIPCR primers for making a 6xHis_tADH1 "Part 4" part plasmid
sbb13-1F: GCATCGTCTCACATCATCATCATCATCACtaactcgaggcgaatttc
sbb13-2R: ATGCCGTCTCAGATGggatggagaccgactacc
template: pGG062
PCR product should be 1947bp.  Cut with BsmBI, ligate, plate on LB+Cam (ColE1 origin).
Then when you assemble an expression plasmid, you can either use pGG062 to add the stop codon+terminator, or this new plasmid to add a 6xHis+stop+terminator.
</pre>
===[[User:JCAnderson|JCAnderson]] 13:43, 5 February 2013 (EST) Targets for further analysis:===
===[[User:JCAnderson|JCAnderson]] 13:43, 5 February 2013 (EST) Targets for further analysis:===
* dodecanol
* butane
* vanillin
* methyl caffeate
* 4-Anisaldehyde
* styrene
* tyramine
* Menadione
* mandelate
* resorcinol
* ethyl cinnamate
* phthalic acid diethyl ester
* N-acetyl-5-methoxytryptamine
* piceatannol
* aspartame
* aureusidin
* Tyr-Arg
* cetylpalmitate
* trans-1,3-dichloropropene
* nitrocyclohexane
* phenylhydrazine
* N-methyltyramine
* ethylacrylate
* 2-nitropropane
* methacrylamide
* methyl tert-butyl ether
* fluorocitrate
* p-tyrosol
* terephthalate
* L-djenkolate
* diethylamine
* acrylamide
* Anserine
* 2-tert-butyl-4-methoxyphenol
*      propyl paraben
*      cAMP
*      Menadione
*      Limonene
*      Spermine
*      Ethyl cinnamate
*      Daidzein
*      Indigo
*      berberine
*      cortisol
*      Prednisone
*      Histamine
*      Octopamine
*      Resorcinol
*      Synephrine
*      Carnosine
*      Terephthalic acid:
* Vanillate
* Salicylate
* Guaiacol
* Isoniazid
* Adiponitrile
* Nerol
*      ATP
*      Acetone
*      ascorbate
*      salicylamide
*      biotin
==Notes==
1. nothing
==Examples==
N-feruloyl-N-methyltyramine
1)
uuid: 1356
ec5: 1.1.1.2
rxnName:  {Thermoanaerobacter ethanolicus} acetyl-CoA + NADPH -?> acetaldehyde + CoA + NADP+ <34>
substrates: [7595, 7045]
products: [8958, 7204, 6997],
2)
uuid: 5523
ec5: 1.14.13.11
rxnName:  {Arabidopsis thaliana} (2E)-3-(3-hydroxyphenyl)prop-2-enoic acid + NADPH + H+ + O2 -?> (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoic acid + NADP+ + H2O <34>
substrates: [17306, 7045, 17657, 17644]
products: [17322, 6997, 32503],
3)
uuid: 11734
ec5: 2.1.1.27
rxnName:  {Hordeum vulgare} S-adenosyl-L-methionine + tyramine -?> N-methyltyramine + S-adenosyl-L-homocysteine <1>
substrates: [4207, 15233]
products: [16740, 3593],
4)
uuid: 11943
ec5: 2.1.1.68
rxnName:  {Medicago sativa} S-adenosyl-L-methionine + caffeic acid -?> S-adenosyl-L-homocysteine + 4-hydroxy-3-methoxy-trans-cinnamic acid <21>
substrates: [4207, 17322] (from step 2 and 4207 is marked as cofactor)
products: [3593, 143],
5)
uuid: 41435
ec5: 6.2.1.34
rxnName:  {Pseudomonas fluorescens} ferulic acid + CoASH + ATP -?> trans-feruloyl-CoA + products of ATP breakdown <1>
substrates: [143, 7204, 944] (from step 4 and step 1)
products: [9258, 18030],
6)
uuid: 12323
ec5: 2.3.1.110
rxnName:  {Nicotiana tabacum} feruloyl-CoA + N-methyltyramine -?> CoA + N-feruloyl-N-methyltyramine <1>
substrates: [9258, 16740] (from step 5 and 3)
products: [7204, 21675]
4-bromo-threonin
1)
uuid: 38633
ec5: 4.1.2.5
rxnName:  {Pseudomonas putida} glycine + bromoacetaldehyde -?> 4-bromo-threonine <24>
substrates: [8990, 8927]
products: [29193]
nitrocatechol sulfate
1)
uuid: 5760
ec5: 1.14.13.29
rxnName:  {Rattus norvegicus} 4-nitrophenol + NAD(P)H + O2 -?> 4-nitrocatechol + NAD(P)+ + H2O <8>
substrates: [13574, 7045, 17644]
products: [13577, 6997, 32503],
2)
uuid: 21191
ec5: 2.8.2.2
rxnName:  {Mus musculus} 3'-phosphoadenylylsulfate + p-nitrocatechol <-> adenosine 3',5'-bisphosphate + p-nitrocatechol sulfate <23>
substrates: [823, 13577]
products: [809, 13582]
D-4-nitrophenylserine
1)
uuid: 38606
ec5: 4.1.2.42
rxnName:  {Alcaligenes xylosoxidans} 4-nitrobenzaldehyde + glycine -?> D-4-nitrophenylserine <8>
substrates: [14627, 8990]
products: [16275]
naringenin 3-O-glucoside
1)
uuid: 21547
ec5: 2.8.3.3
rxnName:  {Pseudomonas ovalis} butyryl-CoA + malonate -?> malonyl-CoA + butanoate <1>
substrates: [8019, 10006]
products: [7749, 11180],
2)
uuid: 20784
ec5: 2.7.7.64
rxnName:  {Pisum sativum, Glycine max, Thermus caldophilus} UTP + D-glucose 1-phosphate <-> diphosphate + UDP-glucose <2, 3, 4>
substrates: [16843, 13174]
products: [17603, 4291],
3)
uuid: 12674
ec5: 2.3.1.159
rxnName:  {Ruta graveolens} malonyl-CoA + 4-coumaroyl-CoA -?> CoA + naringenin chalcone <6, 7>
substrates: [7749, 9107] (from step 1)
products: [7204, 3935],
4)
uuid: 40914
ec5: 5.5.1.6
rxnName:  {Eubacterium ramulus} naringenin chalcone -?> naringenin <33>
substrates: [3935]
products: [3942],
5)
uuid: 16206
ec5: 2.4.1.91
rxnName:  {Hippeastrum sp.} UDPglucose + naringenin -?> UDP + naringenin 3-O-glucoside <8>
substrates: [4291, 3942] (from step 2 and step 4)
products: [16776, 22581]
4-hydroxyphenylethanal
labeled as native
L-3,4-methylenedioxyphenylserine
1)
uuid: 21458
ec5: 2.8.3.1
rxnName:  {Clostridium propionicum, Clostridium propionicum Q9L3F7 UniProt} acetyl-CoA + propanoate <-> acetate + propanoyl-CoA <1, 6>
substrates: [7595, 10107]
products: [8960, 7794],
2)
uuid: 37991
ec5: 4.1.1.83
rxnName:  {Clostridium difficile, Clostridium scatologenes} (3,4-dihydroxyphenyl)acetate + H+ -?> 4-methylcatechol + CO2 <2, 4>
substrates: [16080, 17657]
products: [14894, 17533],
3)
uuid: 9277
ec5: 1.3.99.2
rxnName:  {Bos taurus, Clostridium acetobutylicum} propionyl-CoA + 2,6-dichlorophenolindophenol -?> 2-propenoyl-CoA + reduced acceptor <44, 51>
substrates: [7794, 2893] (from step 1)
products: [7748, 32490],
4)
uuid: 4202
ec5: 1.1.99.6
rxnName:  {Proteus vulgaris} phenylpyruvate + reduced acceptor <-> phenyl-(R)-lactate + acceptor <3>
substrates: [17302, 32490] (from step 3)
products: [16380, 32477],
5)
uuid: 6993
ec5: 1.17.99.1
rxnName:  {Pseudomonas putida, denitrifying bacterium} 4-methylcatechol + acceptor + H2O -?> 3,4-dihydroxybenzaldehyde + reduced acceptor <1, 12>
substrates: [14894, 32477, 32503] (from step 2 and step 4)
products: [14703, 32490],
6)
uuid: 38645
ec5: 4.1.2.5
rxnName:  {Pseudomonas putida} glycine + L-3,4-dihydroxybenzaldehyde -?> L-3,4-methylenedioxyphenylserine <25>
substrates: [8990, 14703]
products: [17809]
trans-1-chloro-2-(4-hydroxyphenyl)ethylene
1)
uuid: 4350
ec5: 1.11.1.10
rxnName:  {Caldariomyces fumago} trans-4-hydroxycinnamic acid + Cl- + H+ + H2O2 -?> trans-1-chloro-2-(4-hydroxyphenyl)ethylene + H2O <16>
substrates: [17309, 17542, 17657, 17567] (the acid is marked as native)
products: [31858, 32503]

Latest revision as of 12:30, 5 March 2013

sbb13-OligoWishList 

EIPCR primers for making a 6xHis_tADH1 "Part 4" part plasmid

sbb13-1F: GCATCGTCTCACATCATCATCATCATCACtaactcgaggcgaatttc
sbb13-2R: ATGCCGTCTCAGATGggatggagaccgactacc
template: pGG062

PCR product should be 1947bp.  Cut with BsmBI, ligate, plate on LB+Cam (ColE1 origin).
Then when you assemble an expression plasmid, you can either use pGG062 to add the stop codon+terminator, or this new plasmid to add a 6xHis+stop+terminator.

JCAnderson 13:43, 5 February 2013 (EST) Targets for further analysis:

  • dodecanol
  • butane
  • vanillin
  • methyl caffeate
  • 4-Anisaldehyde
  • styrene
  • tyramine
  • Menadione
  • mandelate
  • resorcinol
  • ethyl cinnamate
  • phthalic acid diethyl ester
  • N-acetyl-5-methoxytryptamine
  • piceatannol
  • aspartame
  • aureusidin
  • Tyr-Arg
  • cetylpalmitate
  • trans-1,3-dichloropropene
  • nitrocyclohexane
  • phenylhydrazine
  • N-methyltyramine
  • ethylacrylate
  • 2-nitropropane
  • methacrylamide
  • methyl tert-butyl ether
  • fluorocitrate
  • p-tyrosol
  • terephthalate
  • L-djenkolate
  • diethylamine
  • acrylamide
  • Anserine
  • 2-tert-butyl-4-methoxyphenol
  • propyl paraben
  • cAMP
  • Menadione
  • Limonene
  • Spermine
  • Ethyl cinnamate
  • Daidzein
  • Indigo
  • berberine
  • cortisol
  • Prednisone
  • Histamine
  • Octopamine
  • Resorcinol
  • Synephrine
  • Carnosine
  • Terephthalic acid:
  • Vanillate
  • Salicylate
  • Guaiacol
  • Isoniazid
  • Adiponitrile
  • Nerol
  • ATP
  • Acetone
  • ascorbate
  • salicylamide
  • biotin

Notes

1. nothing

Examples

N-feruloyl-N-methyltyramine 1) 

uuid: 1356
ec5: 1.1.1.2 
rxnName:  {Thermoanaerobacter ethanolicus} acetyl-CoA + NADPH -?> acetaldehyde + CoA + NADP+ <34> 
substrates: [7595, 7045] 
products: [8958, 7204, 6997],

2) 

uuid: 5523
ec5: 1.14.13.11 
rxnName:  {Arabidopsis thaliana} (2E)-3-(3-hydroxyphenyl)prop-2-enoic acid + NADPH + H+ + O2 -?> (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoic acid + NADP+ + H2O <34> 
substrates: [17306, 7045, 17657, 17644] 
products: [17322, 6997, 32503],

3) 

uuid: 11734
ec5: 2.1.1.27 
rxnName:  {Hordeum vulgare} S-adenosyl-L-methionine + tyramine -?> N-methyltyramine + S-adenosyl-L-homocysteine <1> 
substrates: [4207, 15233]
products: [16740, 3593],

4) 

uuid: 11943
ec5: 2.1.1.68 
rxnName:  {Medicago sativa} S-adenosyl-L-methionine + caffeic acid -?> S-adenosyl-L-homocysteine + 4-hydroxy-3-methoxy-trans-cinnamic acid <21> 
substrates: [4207, 17322] (from step 2 and 4207 is marked as cofactor)
products: [3593, 143],

5) 

uuid: 41435
ec5: 6.2.1.34 
rxnName:  {Pseudomonas fluorescens} ferulic acid + CoASH + ATP -?> trans-feruloyl-CoA + products of ATP breakdown <1> 
substrates: [143, 7204, 944] (from step 4 and step 1)
products: [9258, 18030],

6) 

uuid: 12323
ec5: 2.3.1.110 
rxnName:  {Nicotiana tabacum} feruloyl-CoA + N-methyltyramine -?> CoA + N-feruloyl-N-methyltyramine <1> 
substrates: [9258, 16740] (from step 5 and 3)
products: [7204, 21675]

4-bromo-threonin 1) 

uuid: 38633
ec5: 4.1.2.5 
rxnName:  {Pseudomonas putida} glycine + bromoacetaldehyde -?> 4-bromo-threonine <24> 
substrates: [8990, 8927] 
products: [29193]


nitrocatechol sulfate 1) 

uuid: 5760
ec5: 1.14.13.29 
rxnName:  {Rattus norvegicus} 4-nitrophenol + NAD(P)H + O2 -?> 4-nitrocatechol + NAD(P)+ + H2O <8> 
substrates: [13574, 7045, 17644] 
products: [13577, 6997, 32503],

2) 

uuid: 21191
ec5: 2.8.2.2 
rxnName:  {Mus musculus} 3'-phosphoadenylylsulfate + p-nitrocatechol <-> adenosine 3',5'-bisphosphate + p-nitrocatechol sulfate <23> 
substrates: [823, 13577] 
products: [809, 13582]


D-4-nitrophenylserine 1) 

uuid: 38606
ec5: 4.1.2.42 
rxnName:  {Alcaligenes xylosoxidans} 4-nitrobenzaldehyde + glycine -?> D-4-nitrophenylserine <8> 
substrates: [14627, 8990] 
products: [16275]


naringenin 3-O-glucoside 1) 

uuid: 21547
ec5: 2.8.3.3 
rxnName:  {Pseudomonas ovalis} butyryl-CoA + malonate -?> malonyl-CoA + butanoate <1> 
substrates: [8019, 10006] 
products: [7749, 11180],

2) 

uuid: 20784
ec5: 2.7.7.64 
rxnName:  {Pisum sativum, Glycine max, Thermus caldophilus} UTP + D-glucose 1-phosphate <-> diphosphate + UDP-glucose <2, 3, 4> 
substrates: [16843, 13174] 
products: [17603, 4291],

3) 

uuid: 12674
ec5: 2.3.1.159 
rxnName:  {Ruta graveolens} malonyl-CoA + 4-coumaroyl-CoA -?> CoA + naringenin chalcone <6, 7> 
substrates: [7749, 9107] (from step 1)
products: [7204, 3935],

4) 

uuid: 40914
ec5: 5.5.1.6 
rxnName:  {Eubacterium ramulus} naringenin chalcone -?> naringenin <33> 
substrates: [3935] 
products: [3942],

5) 

uuid: 16206
ec5: 2.4.1.91 
rxnName:  {Hippeastrum sp.} UDPglucose + naringenin -?> UDP + naringenin 3-O-glucoside <8> 
substrates: [4291, 3942] (from step 2 and step 4)
products: [16776, 22581]


4-hydroxyphenylethanal labeled as native


L-3,4-methylenedioxyphenylserine 1) 

uuid: 21458
ec5: 2.8.3.1 
rxnName:  {Clostridium propionicum, Clostridium propionicum Q9L3F7 UniProt} acetyl-CoA + propanoate <-> acetate + propanoyl-CoA <1, 6> 
substrates: [7595, 10107] 
products: [8960, 7794],

2) 

uuid: 37991
ec5: 4.1.1.83 
rxnName:  {Clostridium difficile, Clostridium scatologenes} (3,4-dihydroxyphenyl)acetate + H+ -?> 4-methylcatechol + CO2 <2, 4> 
substrates: [16080, 17657] 
products: [14894, 17533],

3) 

uuid: 9277
ec5: 1.3.99.2 
rxnName:  {Bos taurus, Clostridium acetobutylicum} propionyl-CoA + 2,6-dichlorophenolindophenol -?> 2-propenoyl-CoA + reduced acceptor <44, 51> 
substrates: [7794, 2893] (from step 1)
products: [7748, 32490],

4) 

uuid: 4202
ec5: 1.1.99.6 
rxnName:  {Proteus vulgaris} phenylpyruvate + reduced acceptor <-> phenyl-(R)-lactate + acceptor <3> 
substrates: [17302, 32490] (from step 3)
products: [16380, 32477],

5) 

uuid: 6993
ec5: 1.17.99.1 
rxnName:  {Pseudomonas putida, denitrifying bacterium} 4-methylcatechol + acceptor + H2O -?> 3,4-dihydroxybenzaldehyde + reduced acceptor <1, 12> 
substrates: [14894, 32477, 32503] (from step 2 and step 4)
products: [14703, 32490],

6) 

uuid: 38645
ec5: 4.1.2.5 
rxnName:  {Pseudomonas putida} glycine + L-3,4-dihydroxybenzaldehyde -?> L-3,4-methylenedioxyphenylserine <25> 
substrates: [8990, 14703] 
products: [17809]

trans-1-chloro-2-(4-hydroxyphenyl)ethylene 1) 

uuid: 4350
ec5: 1.11.1.10 
rxnName:  {Caldariomyces fumago} trans-4-hydroxycinnamic acid + Cl- + H+ + H2O2 -?> trans-1-chloro-2-(4-hydroxyphenyl)ethylene + H2O <16> 
substrates: [17309, 17542, 17657, 17567] (the acid is marked as native)
products: [31858, 32503]
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