Difference between revisions of "Part:BBa K1159001:Design"

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<html><table border="1" cellspacing="0" width="100%" !important><tr><td colspan="200" width="20%"><strong>BioBrick: <partinfo>BBa_</partinfo></strong></td><td colspan="800" width="80%"><strong>Automatically determined parameters using the <a href="http://2013.igem.org/Team:TU-Munich/Results/Software">BioBrick-AutoAnnotator</a> version 1.0</strong></td></tr><tr><td colspan="100" width="10%"><strong>RFC standard:</strong></td><td colspan="600" width="60%">RFC 25 BioBrick, so ATGGCCGGC and ACCGGT were added to the 5' and 3' ends.</td><td colspan="300" width="30%">ORF from -8 to 516 (excluding stop-codon)</td></tr><tr><td colspan="1000"><strong>Nucleotide sequence:</strong> (underlined part encodes the protein, italic parts were added)<br><span style="font-family:'Courier New', Arial;">&nbsp;<u><i>ATGGCCGGC</i>GTGTTCACC&nbsp;...&nbsp;ATCCTTGCT<i>ACCGGT</i></u></span></td></tr><tr><td colspan="1000"><strong>Amino acid sequence:</strong><br><span style="font-family:'Courier New', Arial;">&nbsp;&nbsp;1&nbsp;MAGVFTLEDFVGDWRQTAGYNLDQVLEQGGVSSLFQNLGVSVTPIQRIVLSGENGLKIDIHVIIPYEGLSGDQMGQIEKIFKVVYPVDDHHFKVILHYGT<br>101&nbsp;LVIDGVTPNMIDYFGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLINPDGSLLFRVTINGVTGWRLCERILATG<br></span></td></tr><tr><td colspan="1000"><strong>Amino acid composition:</strong></td></tr><tr><td colspan="100" width="10.0%">A (Ala)</td><td colspan=" 99" width=" 9.9%">4 (2.3%)</td><td colspan=" 1" width=" 0.1%"></td><td colspan="100" width="10.0%">C (Cys)</td><td colspan=" 99" width=" 9.9%">1 (0.6%)</td><td colspan=" 1" width=" 0.1%"></td><td colspan="100" width="10.0%">H (His)</td><td colspan=" 99" width=" 9.9%">4 (2.3%)</td><td colspan=" 1" width=" 0.1%"></td><td colspan="100" width="10.0%">M (Met)</td><td colspan=" 99" width=" 9.9%">3 (1.7%)</td><td colspan=" 1" width=" 0.1%"></td><td colspan="100" width="10.0%">T (Thr)</td><td colspan="100" width="10.0%">11 (6.3%)</td></tr><tr><td colspan="100" width="10.0%">R (Arg)</td><td colspan=" 99" width=" 9.9%">7 (4.0%)</td><td colspan=" 1" width=" 0.1%"></td><td colspan="100" width="10.0%">Q (Gln)</td><td colspan=" 99" width=" 9.9%">7 (4.0%)</td><td colspan=" 1" width=" 0.1%"></td><td colspan="100" width="10.0%">I (Ile)</td><td colspan=" 99" width=" 9.9%">18 (10.3%)</td><td colspan=" 1" width=" 0.1%"></td><td colspan="100" width="10.0%">F (Phe)</td><td colspan=" 99" width=" 9.9%">8 (4.6%)</td><td colspan=" 1" width=" 0.1%"></td><td colspan="100" width="10.0%">W (Trp)</td><td colspan="100" width="10.0%">3 (1.7%)</td></tr><tr><td colspan="100" width="10.0%">N (Asn)</td><td colspan=" 99" width=" 9.9%">8 (4.6%)</td><td colspan=" 1" width=" 0.1%"></td><td colspan="100" width="10.0%">E (Glu)</td><td colspan=" 99" width=" 9.9%">8 (4.6%)</td><td colspan=" 1" width=" 0.1%"></td><td colspan="100" width="10.0%">L (Leu)</td><td colspan=" 99" width=" 9.9%">16 (9.1%)</td><td colspan=" 1" width=" 0.1%"></td><td colspan="100" width="10.0%">P (Pro)</td><td colspan=" 99" width=" 9.9%">6 (3.4%)</td><td colspan=" 1" width=" 0.1%"></td><td colspan="100" width="10.0%">Y (Tyr)</td><td colspan="100" width="10.0%">6 (3.4%)</td></tr><tr><td colspan="100" width="10.0%">D (Asp)</td><td colspan=" 99" width=" 9.9%">12 (6.9%)</td><td colspan=" 1" width=" 0.1%"></td><td colspan="100" width="10.0%">G (Gly)</td><td colspan=" 99" width=" 9.9%">22 (12.6%)</td><td colspan=" 1" width=" 0.1%"></td><td colspan="100" width="10.0%">K (Lys)</td><td colspan=" 99" width=" 9.9%">7 (4.0%)</td><td colspan=" 1" width=" 0.1%"></td><td colspan="100" width="10.0%">S (Ser)</td><td colspan=" 99" width=" 9.9%">6 (3.4%)</td><td colspan=" 1" width=" 0.1%"></td><td colspan="100" width="10.0%">V (Val)</td><td colspan="100" width="10.0%">18 (10.3%)</td></tr><tr><td colspan="100" width="10.0%"><strong>Amino acid counting:</strong></td><td colspan="200" width="20.0%">Total number of amino acids (aa):</td><td colspan="100" width="10.0%">175</td><td colspan="200" width="20.0%">Positively charged aa (Arg + Lys):</td><td colspan="100" width="10.0%">14</td><td colspan="200" width="20.0%">Negatively charged aa (Asp + Glu):</td><td colspan="100" width="10.0%">20</td></tr><tr><td colspan="100" width="10.0%"><strong>Biochemical parameters:</strong></td><td colspan="200" width="20.0%">Molecular weight [Da]:</td><td colspan="100" width="10.0%">19381.3</td><td colspan="200" width="20.0%">Theoretical pI:</td><td colspan="100" width="10.0%">5.1</td><td colspan="200" width="20.0%">Extinction coefficient at 280 nm [M<sup>-1</sup> cm<sup>-1</sup>]:</td><td colspan="100" width="10.0%">25502.5 (all Cys as cystine)<br>25440 (all Cys reduced)</td></tr><tr><td colspan="100" width="10.0%"><strong>Estimated half-life [h]:</strong></td><td colspan="200" width="20.0%"><i>E. coli</i>:</td><td colspan="100" width="10.0%">>10</td><td colspan="200" width="20.0%"><i>S. cervisiae:</i></td><td colspan="100" width="10.0%">>20</td><td colspan="200" width="20.0%">Mammals:</td><td colspan="100" width="10.0%">30</td></tr><tr><td colspan="100" width="10.0%"><strong>Codon usage (CAI):</strong></td><td colspan="200" width="20.0%"><i>E. coli</i>:</td><td colspan="100" width="10.0%">0.66</td><td colspan="200" width="20.0%"><i>S. cervisiae:</i></td><td colspan="100" width="10.0%">0.62</td><td colspan="200" width="20.0%">Mammals:</td><td colspan="100" width="10.0%">0.82</td></tr><tr><td colspan="1000" width="100.0%"> The BioBrick-AutoAnnotator was created by <a href="http://2013.igem.org/Team:TU-Munich">TU-Munich 2013</a> iGEM team. For information please read the <a href="http://2013.igem.org/Team:TU-Munich/Results/Software">description</a>.</td></tr></table><br></html>
+
<html><table border="1" cellspacing="0" width="100%" !important><tr><td width="100%" colspan="2"><strong>==Parameters for BioBrick <a href="https://parts.igem.org/wiki/index.php?title=Part:BBa_K1159001">BBa_K1159001</a> automatically created by the <a href="http://2013.igem.org/Team:TU-Munich/Results/AutoAnnotator">BioBrick-AutoAnnotator</a> version 1.0==</strong></td></tr><tr><td width="100%" colspan="2"><strong>Nucleotide sequence</strong> in <strong>RFC 10</strong>: (underlined part encodes the protein)<br><span style="font-family:'Courier New', Arial;">&nbsp;<u>ATGGCCGGC&nbsp;...&nbsp;GCTACCGGT</u>TAA</span><br>&nbsp;<strong>ORF</strong> from 1 to 525 (excluding stop-codon)</td></tr><tr><td width="100%" colspan="2"><strong>Amino acid sequence:</strong><br><span style="font-family:'Courier New', Arial;">&nbsp;&nbsp;1&nbsp;MAGVFTLEDFVGDWRQTAGYNLDQVLEQGGVSSLFQNLGVSVTPIQRIVLSGENGLKIDIHVIIPYEGLSGDQMGQIEKIFKVVYPVDDHHFKVILHYGT<br>101&nbsp;LVIDGVTPNMIDYFGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLINPDGSLLFRVTINGVTGWRLCERILATG<br></span></td></tr><tr><td width="100%" colspan="2"><strong>Amino acid composition:</strong><table border="0" cellspacing="0" width="100%"><tr><td width="20%"><table border="1" cellspacing="0" width="100%"><tr><td width="50%">A (Ala)</td><td width="50%">4 (2.3%)</td></tr><tr><td width="50%">R (Arg)</td><td width="50%">7 (4.0%)</td></tr><tr><td width="50%">N (Asn)</td><td width="50%">8 (4.6%)</td></tr><tr><td width="50%">D (Asp)</td><td width="50%">12 (6.9%)</td></tr></table></td><td width="20%"><table border="1" cellspacing="0" width="100%"><tr><td width="50%">C (Cys)</td><td width="50%">1 (0.6%)</td></tr><tr><td width="50%">Q (Gln)</td><td width="50%">7 (4.0%)</td></tr><tr><td width="50%">E (Glu)</td><td width="50%">8 (4.6%)</td></tr><tr><td width="50%">G (Gly)</td><td width="50%">22 (12.6%)</td></tr></table></td><td width="20%"><table border="1" cellspacing="0" width="100%"><tr><td width="50%">H (His)</td><td width="50%">4 (2.3%)</td></tr><tr><td width="50%">I (Ile)</td><td width="50%">18 (10.3%)</td></tr><tr><td width="50%">L (Leu)</td><td width="50%">16 (9.1%)</td></tr><tr><td width="50%">K (Lys)</td><td width="50%">7 (4.0%)</td></tr></table></td><td width="20%"><table border="1" cellspacing="0" width="100%"><tr><td width="50%">M (Met)</td><td width="50%">3 (1.7%)</td></tr><tr><td width="50%">F (Phe)</td><td width="50%">8 (4.6%)</td></tr><tr><td width="50%">P (Pro)</td><td width="50%">6 (3.4%)</td></tr><tr><td width="50%">S (Ser)</td><td width="50%">6 (3.4%)</td></tr></table></td><td width="20%"><table border="1" cellspacing="0" width="100%"><tr><td width="50%">T (Thr)</td><td width="50%">11 (6.3%)</td></tr><tr><td width="50%">W (Trp)</td><td width="50%">3 (1.7%)</td></tr><tr><td width="50%">Y (Tyr)</td><td width="50%">6 (3.4%)</td></tr><tr><td width="50%">V (Val)</td><td width="50%">18 (10.3%)</td></tr></table></td></tr></table></td></tr><tr><td width="40%"><strong>Amino acid counting:</strong>&nbsp;&nbsp;<table border="0" cellspacing="0" width="100%"><tr><td width=" 5%"></td><td width="55%">Total number:</td><td width="40%">175</td></tr><tr><td width=" 5%"></td><td width="55%">Positively charged (Arg+Lys):</td><td width="40%">14 (8.0%)</td></tr><tr><td width=" 5%"></td><td width="55%">Negatively charged (Asp+Glu):</td><td width="40%">20 (11.4%)</td></tr></table></td><td width="60%"><strong>Biochemical parameters:</strong><table border="0" cellspacing="0" width="100%"><tr><td width=" 5%"></td><td width="55%">Molecular mass [Da]:</td><td width="40%">19381.3</td></tr><tr><td width=" 5%"></td><td width="55%">Theoretical pI:</td><td width="40%">5.10</td></tr><tr><td width=" 5%"></td><td width="55%">Extinction coefficient at 280 nm [M<sup>-1</sup> cm<sup>-1</sup>]:</td><td width="40%">25440 / 25503 (all Cys red/ox)</td></tr></table></td></tr><tr><td colspan="2" width="100%"><strong>Organism specific parameters</strong><table border="1" cellspacing="0" width="100%"><tr><td width="40%"><table border="0" cellspacing="0" width="100%"><tr><td><strong>Organism</strong></td></tr><tr><td><i>E. coli</i></td></tr><tr><td><i>B. subtilis</i></td></tr><tr><td><i>S. cervisiae</i></td></tr><tr><td><i>A. thaliana</i></td></tr><tr><td>Mammals</td></tr></table></td><td width="30%"><table border="0" cellspacing="0" width="100%"><tr><td><strong>Estimated half-life [h]</strong></td></tr><tr><td>>10</td></tr><tr><td>Platzhalter </td></tr><tr><td>>20</td></tr><tr><td>Platzhalter</td></tr><tr><td>30</td></tr></table></td><td width="30%"><table border="0" cellspacing="0" width="100%"><tr><td><strong>Codon usage (CAI)</strong></td></tr><tr><td>good (0.66)</td></tr><tr><td><i>B. subtilis</i></td></tr><tr><td>good (0.62)</td></tr><tr><td><i>A. thaliana</i></td></tr><tr><td>excellent (0.82)</td></tr></table></td></tr></table></td></tr><tr><td colspan="2" width="100%"><strong>Organism specific parameters</strong><table border="1" cellspacing="0" width="100%"><tr><td><strong>Organism:</strong></td><td><i>E. coli</i></td><td><i>B. subtilis</i></td><td><i>S. cervisiae</i></td><td><i>A. thaliana</i></td><td>Mammals</td></tr><tr><td><strong>Estimated half-life [h]</strong></td><td>>10</td><td>Platzhalter</td><td>>20</td><td>Platzhalter</td><td>30</td></tr><tr><td><strong>Codon usage (CAI)</strong></td><td>good (0.66)</td><td><i>B. subtilis</i></td><td>good (0.62)</td><td><i>A. thaliana</i></td><td>excellent (0.82)</td></tr></table></td></tr><tr><td colspan="2" width="100%"><strong>Sequence features:</strong></td></tr><tr><td colspan="2" width="100%"> The BioBrick-AutoAnnotator was created by <a href="http://2013.igem.org/Team:TU-Munich">TU-Munich 2013</a> iGEM team. For more information please see the <a href="http://2013.igem.org/Team:TU-Munich/Results/Software">documentation</a>.<br>If you have any questions, comments or suggestions, please email us at <a href="mailto:igem@wzw.tum.de?Subject=AutoAnnotator" target="_top">igem@wzw.tum.de</a>.</td></tr></table><br></html>
  
 
===Source===
 
===Source===

Revision as of 14:50, 2 August 2013

NanoLuc Luciferase in RFC[25]


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal XhoI site found at 10
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Keywords:


Abbreviations:

Design Notes

Related BioBrick:

Quality control measures:

Backbone:

Protein coding:

Enzymatic activity:

Cytotoxicity:

Safety notes:

Intellectual property:

Corresponding part author/authors:



==Parameters for BioBrick BBa_K1159001 automatically created by the BioBrick-AutoAnnotator version 1.0==
Nucleotide sequence in RFC 10: (underlined part encodes the protein)
 ATGGCCGGC ... GCTACCGGTTAA
 ORF from 1 to 525 (excluding stop-codon)
Amino acid sequence:
  1 MAGVFTLEDFVGDWRQTAGYNLDQVLEQGGVSSLFQNLGVSVTPIQRIVLSGENGLKIDIHVIIPYEGLSGDQMGQIEKIFKVVYPVDDHHFKVILHYGT
101 LVIDGVTPNMIDYFGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLINPDGSLLFRVTINGVTGWRLCERILATG
Amino acid composition:
A (Ala)4 (2.3%)
R (Arg)7 (4.0%)
N (Asn)8 (4.6%)
D (Asp)12 (6.9%)
C (Cys)1 (0.6%)
Q (Gln)7 (4.0%)
E (Glu)8 (4.6%)
G (Gly)22 (12.6%)
H (His)4 (2.3%)
I (Ile)18 (10.3%)
L (Leu)16 (9.1%)
K (Lys)7 (4.0%)
M (Met)3 (1.7%)
F (Phe)8 (4.6%)
P (Pro)6 (3.4%)
S (Ser)6 (3.4%)
T (Thr)11 (6.3%)
W (Trp)3 (1.7%)
Y (Tyr)6 (3.4%)
V (Val)18 (10.3%)
Amino acid counting:  
Total number:175
Positively charged (Arg+Lys):14 (8.0%)
Negatively charged (Asp+Glu):20 (11.4%)
Biochemical parameters:
Molecular mass [Da]:19381.3
Theoretical pI:5.10
Extinction coefficient at 280 nm [M-1 cm-1]:25440 / 25503 (all Cys red/ox)
Organism specific parameters
Organism
E. coli
B. subtilis
S. cervisiae
A. thaliana
Mammals
Estimated half-life [h]
>10
Platzhalter
>20
Platzhalter
30
Codon usage (CAI)
good (0.66)
B. subtilis
good (0.62)
A. thaliana
excellent (0.82)
Organism specific parameters
Organism:E. coliB. subtilisS. cervisiaeA. thalianaMammals
Estimated half-life [h]>10Platzhalter>20Platzhalter30
Codon usage (CAI)good (0.66)B. subtilisgood (0.62)A. thalianaexcellent (0.82)
Sequence features:
The BioBrick-AutoAnnotator was created by TU-Munich 2013 iGEM team. For more information please see the documentation.
If you have any questions, comments or suggestions, please email us at igem@wzw.tum.de.

Source

Source:


Organism:


References

Literature references:

Database references: