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

Latest revision as of 10:10, 18 September 2015

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: Other versions:BBa_K1734004: Nanoluc (Codon optimized for Sf9 cells)

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. 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)

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:

@@ Line 1: / Line 1: @@
 __NOTOC__
 <partinfo>BBa_K1159001 short</partinfo>
@@ Line 5: / Line 4: @@
 <partinfo>BBa_K1159001 SequenceAndFeatures</partinfo>
+<br>'''Keywords:'''
+<!--These keywords are necessary to find your part using a fulltext sarch.-->
+<!--keyword_1, keyword_2, keyword_3, keyword_4, keyword_5-->
+<br>'''Abbreviations:'''
+<!--*used_abbreviation_1 = full_name_of_used_abbreviations_1-->
+<!--*used_abbreviation_2 = full_name_of_used_abbreviations_2-->
 ===Design Notes===
-x
+'''Related BioBrick:'''
+Other versions:[https://parts.igem.org/wiki/index.php?title=Part:BBa_K1734004 BBa_K1734004: Nanoluc (Codon optimized for Sf9 cells)]
+<!--*Related BioBricks:[https://parts.igem.org/wiki/index.php?title=Part:BBa_?????? BBa_??????: Name_of_part]
+'''Cloning details:'''<br>
+<!--*Designed in RFC10/RFC23/RFC25-->
+<!--*Mutation C889G to delete XbaI restriction site-->
+<!--*Truncation upstream/downstream compared to template, ?explanation?-->
+'''Quality control measures:'''<br>
+<!--*Test digestion using ?enzyme1? & ?enzyme2?/Not yet performed-->
+<!--*Sequencing using primer ?primer_name?/Not yet sequenced-->
+<!--*Part was partly sequenced/Part was totally sequenced-->
+'''Backbone:'''<br>
+<!--*Backbone name: pSB1C3'/?backbone_name?-->
+<!--*Resistance: Amp/Cp/Kan/-->
+<!--*Copynumber: low/medium/high-->
+'''Protein coding:'''<br>
+<!--*Protein: ?Name_of_gene_product? [Nucleotide 1 to ???]-->
+<!--*The protein has the amino acid replacements ???99??? to ???99???.-->
+<!--*The protein encoded is posttranslationally modified by ???.-->
+<!--*Tag: n-terminally fused/c-terminally fused His5/His6/Strep/Flag/other-->
+'''Enzymatic activity:'''
+<!--none/EC-number ?.?.?.?-->
+'''Cytotoxicity:'''<br>
+<!--none/not known/cytotoxic for ''organism name''-->
+'''Safety notes:'''<br>
+<!--Known and anticipated sefety issues: none/health_risk/environmental_risk/other_risk-->
+<!--Known and anticipated security issues: none/other.-->
+'''Intellectual property:'''
+<!--Information on patent situation.-->
+<!--Intellectual property claims made by the authors.-->
+'''Corresponding part author/authors:'''
+<!--https://igem.org/User_Information.cgi?user_id=????/email-->
+<html><table border="1" cellspacing="0" width="100%" !important><tr><td width="100%" colspan="2"><strong><H3>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</H3></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===
-x
+'''Source:'''<br>
+<!--*Commercial system: plasmid name, system name, company name-->
+<!--*Plasmid: p???, provided by ?name_of_person?, ?institute/university?, ?country?-->
+<!--*Preexisting BioBrick ?Bba_number?-->
+<!--*cDNA Clone: ?clone_name?, ?company_name?-->
+<!--*Synthesized by ?company_name?.-->
+<!--'''Forward Primer:'''<br><code>5'- ??? - 3'</code><br>-->
+<!--'''Reverse Primer:'''<br><code>5'- ??? - 3'</code><br>-->
+'''Organism:'''<br>
+<!--*Genesequence derived from ''?organism_name?''-->
+<!--*Codonoptimized for ''?organism_name?''-->
+<!--*Designed for the following Chassis: ''?organism-name?''-->
+<!--*Statement about functionality in other chassis.-->
+<!--Thank you very much for using BBF RFC 82 to describe the present BioBrick. If you have any remarks or recommendations concerning this RFC we would highly appreciate to get your feedback on: []-->
 ===References===
+<!-- Here you find templates to insert references to literature and different databases-->
+'''Literature references:'''<br>
+<!--*[http://www.ncbi.nlm.nih.gov/pubmed/?PMID? '''Pubmed:''' ?Author(s)?, ?year?: ?title?]-->
+'''Database references:'''<br>
+<!--*[http://www.ncbi.nlm.nih.gov/nuccore/?accessNr? '''GenBank''': ?title?]-->
+<!--*[http://www.ebi.ac.uk/interpro/IEntry?ac=?accessNr? '''Interpro''': ?title?]-->
+<!--*[http://www.uniprot.org/uniprot/?accessNr? '''Uniprot''': ?title?]-->
+<!--*[http://pfam.sanger.ac.uk/family/?accessNr? '''Pfam:''' ?title?]-->
+<!--*[http://www.rcsb.org/pdb/explore/explore.do?structureId=?accessNR? '''PDB:''' ?tile?]-->
+<!--*[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=?accessNr? '''Branda:''' ?title?]-->