Difference between revisions of "Part:BBa K801060:Design"
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<partinfo>BBa_K801060 SequenceAndFeatures</partinfo> | <partinfo>BBa_K801060 SequenceAndFeatures</partinfo> | ||
− | + | <html><!--- Please copy this table containing parameters for BBa_K801060 at the end of the parametrs section ahead of the references. ---><style type="text/css">table#AutoAnnotator {border:1px solid black; width:100%; border-collapse:collapse;} th#AutoAnnotatorHeader { border:1px solid black; width:100%; background-color: rgb(221, 221, 221);} td.AutoAnnotator1col { width:100%; border:1px solid black; } span.AutoAnnotatorSequence { font-family:'Courier New', Arial; } td.AutoAnnotatorSeqNum { text-align:right; width:2%; } td.AutoAnnotatorSeqSeq { width:98% } td.AutoAnnotatorSeqFeat1 { width:3% } td.AutoAnnotatorSeqFeat2a { width:27% } td.AutoAnnotatorSeqFeat2b { width:97% } td.AutoAnnotatorSeqFeat3 { width:70% } table.AutoAnnotatorNoBorder { border:0px; width:100%; border-collapse:collapse; } table.AutoAnnotatorWithBorder { border:1px solid black; width:100%; border-collapse:collapse; } td.AutoAnnotatorOuterAmino { border:0px solid black; width:20% } td.AutoAnnotatorInnerAmino { border:1px solid black; width:50% } td.AutoAnnotatorAminoCountingOuter { border:1px solid black; width:40%; } td.AutoAnnotatorBiochemParOuter { border:1px solid black; width:60%; } td.AutoAnnotatorAminoCountingInner1 { width: 7.5% } td.AutoAnnotatorAminoCountingInner2 { width:62.5% } td.AutoAnnotatorAminoCountingInner3 { width:30% } td.AutoAnnotatorBiochemParInner1 { width: 5% } td.AutoAnnotatorBiochemParInner2 { width:55% } td.AutoAnnotatorBiochemParInner3 { width:40% } td.AutoAnnotatorCodonUsage1 { width: 3% } td.AutoAnnotatorCodonUsage2 { width:14.2% } td.AutoAnnotatorCodonUsage3 { width:13.8% } </style><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1378591073204 --><th id="AutoAnnotatorHeader" colspan="2">Protein data table for BioBrick <a href="https://parts.igem.org/wiki/index.php?title=Part:BBa_K801060">BBa_K801060</a> automatically created by the <a href="http://2013.igem.org/Team:TU-Munich/Results/AutoAnnotator">BioBrick-AutoAnnotator</a> version 1.0</th></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Nucleotide sequence</strong> in <strong>RFC 10</strong>: (underlined part encodes the protein)<br><span class="AutoAnnotatorSequence"> GTACACA<u>ATGCGTCGT ... TTCGAAAAA</u>TAA</span><br> <strong>ORF</strong> from nucleotide position 8 to 1705 (excluding stop-codon)</td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Amino acid sequence:</strong> (RFC25 scars in shown in bold, other sequence features underlined; both given below)<br><span class="AutoAnnotatorSequence"><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorSeqNum">1 <br>101 <br>201 <br>301 <br>401 <br>501 </td><td class="AutoAnnotatorSeqSeq">MRRSANYQPSIWDHDFLQSLNSNYTDEAYKRRAEELRGKVKIAIKDVIEPLDQLDLIDNLQRLGLAHRFETEIRNILNNIYNNNKDYNWRKENLYATSLE<br>FRLLRQHGYPVSQEVFNGFKDDQGGFICDDFKGILSLHEASYYSLEGESIMEEAWQFTSKHLKEVMISKNMEEDVFVAEQAKRALELPLHWKVPMLEARW<br>FIHIYERREDKNHLLLELAKMEFNTLQAIYQEELKEISGWWKDTGLGEKLSFARNRLVASFLWSMGIAFEPQFAYCRRVLTISIALITVIDDIYDVYGTL<br>DELEIFTDAVERWDINYALKHLPGYMKMCFLALYNFVNEFAYYVLKQQDFDLLLSIKNAWLGLIQAYLVEAKWYHSKYTPKLEEYLENGLVSITGPLIIT<br>ISYLSGTNPIIKKELEFLESNPDIVHWSSKIFRLQDDLGTSSDEIQRGDVPKSIQCYMHETGASEEVARQHIKDMMRQMWKKVNAYTADKDSPLTGTTTE<br>FLLNLVRMSHFMYLHGDGHGVQNQETIDVGFTLLFQPIPLEDKHMAFTASPGTKG<b>TG</b>A<u>WSHPQFEK</u>*</td></tr></table></span></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Sequence features:</strong> (with their position in the amino acid sequence, see the <a href="http://2013.igem.org/Team:TU-Munich/Results/Software/FeatureList">list of supported features</a>)<table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorSeqFeat1"></td><td class="AutoAnnotatorSeqFeat2a">RFC25 scar (shown in bold): </td><td class="AutoAnnotatorSeqFeat3">556 to 557</td></tr><tr><td class="AutoAnnotatorSeqFeat1"></td><td class="AutoAnnotatorSeqFeat2a"><i>Strep</i>-tag II: </td><td class="AutoAnnotatorSeqFeat3">559 to 566</td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Amino acid composition:</strong><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Ala (A)</td><td class="AutoAnnotatorInnerAmino">33 (5.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Arg (R)</td><td class="AutoAnnotatorInnerAmino">25 (4.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asn (N)</td><td class="AutoAnnotatorInnerAmino">27 (4.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asp (D)</td><td class="AutoAnnotatorInnerAmino">34 (6.0%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Cys (C)</td><td class="AutoAnnotatorInnerAmino">4 (0.7%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gln (Q)</td><td class="AutoAnnotatorInnerAmino">24 (4.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Glu (E)</td><td class="AutoAnnotatorInnerAmino">48 (8.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gly (G)</td><td class="AutoAnnotatorInnerAmino">29 (5.1%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">His (H)</td><td class="AutoAnnotatorInnerAmino">18 (3.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ile (I)</td><td class="AutoAnnotatorInnerAmino">39 (6.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Leu (L)</td><td class="AutoAnnotatorInnerAmino">64 (11.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Lys (K)</td><td class="AutoAnnotatorInnerAmino">36 (6.4%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Met (M)</td><td class="AutoAnnotatorInnerAmino">16 (2.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Phe (F)</td><td class="AutoAnnotatorInnerAmino">28 (4.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Pro (P)</td><td class="AutoAnnotatorInnerAmino">17 (3.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ser (S)</td><td class="AutoAnnotatorInnerAmino">33 (5.8%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Thr (T)</td><td class="AutoAnnotatorInnerAmino">26 (4.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Trp (W)</td><td class="AutoAnnotatorInnerAmino">14 (2.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Tyr (Y)</td><td class="AutoAnnotatorInnerAmino">27 (4.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Val (V)</td><td class="AutoAnnotatorInnerAmino">24 (4.2%)</td></tr></table></td></tr></table></td></tr><tr><td class="AutoAnnotatorAminoCountingOuter"><strong>Amino acid counting</strong><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Total number:</td><td class="AutoAnnotatorAminoCountingInner3">566</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Positively charged (Arg+Lys):</td><td class="AutoAnnotatorAminoCountingInner3">61 (10.8%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Negatively charged (Asp+Glu):</td><td class="AutoAnnotatorAminoCountingInner3">82 (14.5%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Aromatic (Phe+His+Try+Tyr):</td><td class="AutoAnnotatorAminoCountingInner3">87 (15.4%)</td></tr></table></td><td class="AutoAnnotatorBiochemParOuter"><strong>Biochemical parameters</strong><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Atomic composition:</td><td class="AutoAnnotatorBiochemParInner3">C<sub>3002</sub>H<sub>4586</sub>N<sub>778</sub>O<sub>868</sub>S<sub>20</sub></td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Molecular mass [Da]:</td><td class="AutoAnnotatorBiochemParInner3">66105.3</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Theoretical pI:</td><td class="AutoAnnotatorBiochemParInner3">5.38</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Extinction coefficient at 280 nm [M<sup>-1</sup> cm<sup>-1</sup>]:</td><td class="AutoAnnotatorBiochemParInner3">117230 / 117480 (all Cys red/ox)</td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Hydrophobicity and charge plot</strong><span id="hydrophobicity_charge_explanation"></span> <input type='button' id='hydrophobicity_charge_button' onclick='show_or_hide_plot()' value='Show'><br><div id="hydrophobicity_charge_container" style='display:none'><div id="hydrophobicity_charge_placeholder0" style="width:100%;height:150px"></div><br><div id="hydrophobicity_charge_placeholder1" style="width:100%;height:150px"></div><br><div id="hydrophobicity_charge_placeholder2" style="width:100%;height:150px"></div></div></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Codon usage</strong><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorCodonUsage1"></td><td class="AutoAnnotatorCodonUsage2">Organism:</td><td class="AutoAnnotatorCodonUsage3"><i>E. coli</i></td><td class="AutoAnnotatorCodonUsage3"><i>B. subtilis</i></td><td class="AutoAnnotatorCodonUsage3"><i>S. cerevisiae</i></td><td class="AutoAnnotatorCodonUsage3"><i>A. thaliana</i></td><td class="AutoAnnotatorCodonUsage3"><i>P. patens</i></td><td class="AutoAnnotatorCodonUsage3">Mammals</td></tr><tr><td class="AutoAnnotatorCodonUsage1"></td><td class="AutoAnnotatorCodonUsage2">Codon quality (<a href="http://en.wikipedia.org/wiki/Codon_Adaptation_Index">CAI</a>):</td><td class="AutoAnnotatorCodonUsage3">good (0.71)</td><td class="AutoAnnotatorCodonUsage3">good (0.75)</td><td class="AutoAnnotatorCodonUsage3">good (0.69)</td><td class="AutoAnnotatorCodonUsage3">good (0.78)</td><td class="AutoAnnotatorCodonUsage3">excellent (0.80)</td><td class="AutoAnnotatorCodonUsage3">good (0.68)</td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"> 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 leave us a <a href="http://2013.igem.org/Team:TU-Munich/Results/AutoAnnotator">comment</a>.</td></tr></table><br><!-- IMPORTANT: DON'T REMOVE THIS LINE, OTHERWISE NOT SUPPORTED FOR IE BEFORE 9 --><!--[if lte IE 8]><script language="javascript" type="text/javascript" src="excanvas.min.js"></script><![endif]--><script type='text/javascript' src='http://code.jquery.com/jquery-1.10.0.min.js'></script><script type='text/javascript' src='http://2013.igem.org/Team:TU-Munich/Flot.js?action=raw&ctype=text/js'></script><script> | |
+ | alert("Start"); | ||
+ | var hydrophobicity_datapoints = 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charge_datapoints = 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flot_plot_options = []; flot_plot_options[0] = { grid: { borderWidth: { top: 0, right: 0, bottom: 0, left: 0 } }, legend: {show: false}, xaxes: [{ min: 0, max: 200, ticks: [[0.5, '1'], [24.5, '25'], [49.5, '50'], [74.5, '75'], [99.5, '100'], [124.5, '125'], [149.5, '150'], [174.5, '175'], [199.5, '200']], tickLength: -5 }], yaxes: [{ ticks: [[0, '0'], [4.5,'hydro-<br>phobic '], [-4.5,'hydro-<br>philic ']], min: -4.5, max: +4.5, font: { size: 12, lineHeight: 14, style: 'italic', weight: 'bold', family: 'sans-serif', variant: 'small-caps', color: 'rgba(100,149,237,1)' } }, { ticks: [[0, ''], [1,'positive<br> charge'], [-1,'negative<br> charge']], position: 'right', min: -1, max: 1, font: { size: 12, lineHeight: 14, style: 'italic', weight: 'bold', family: 'sans-serif', variant: 'small-caps', color: 'rgba(255,99,71,1)' } }]};var number_of_plots = Math.ceil(amino_sequence.length/200);for ( plot_num = 1 ; plot_num < number_of_plots ; plot_num ++){flot_plot_options[plot_num] = $.extend(true, {} ,flot_plot_options[0]);flot_plot_options[plot_num].xaxes = [{ min: plot_num*200, max: (plot_num + 1)*200, ticks: [ [plot_num*200 + 0.5, (plot_num*200 + 1).toString()], [plot_num*200 + 24.5, (plot_num*200 + 25).toString()], [plot_num*200 + 49.5, (plot_num*200 + 50).toString()], [plot_num*200 + 74.5, (plot_num*200 + 75).toString()], [plot_num*200 + 99.5, (plot_num*200 + 100).toString()], [plot_num*200 + 124.5, (plot_num*200 + 125).toString()], [plot_num*200 + 149.5, (plot_num*200 + 150).toString()], [plot_num*200 + 174.5, (plot_num*200 + 175).toString()], [plot_num*200 + 199.5, (plot_num*200 + 200).toString()] ], tickLength: -5 }];}; | ||
alert("Here"); | alert("Here"); | ||
function show_or_hide_plot(){ try { if( $('#hydrophobicity_charge_button').val() =='Show' ){ $('#hydrophobicity_charge_container').css('display','block'); for (plot_num = 0 ; plot_num < number_of_plots ; plot_num ++){ $.plot('#hydrophobicity_charge_placeholder'+ plot_num.toString(), [{ color: 'rgba(100,149,237,1)', data: hydrophobicity_datapoints, label: 'Hydrophobicity', lines: { show: true, fill: true, fillColor: 'rgba(100,149,237,0.1)' }, yaxis: 1 }, { color: 'rgba(255,99,71,1)', data: charge_datapoints, label: 'Charge', lines: { show: true, fill: true, fillColor: 'rgba(255,99,71,0.1)' }, yaxis: 2 }], flot_plot_options[plot_num] ); } $('#hydrophobicity_charge_button').val('Hide'); $('#hydrophobicity_charge_explanation').text(': Moving average over 5 amino acids for hydrophobicity (blue) and charge (red)'); } else{ $('#hydrophobicity_charge_container').css('display','none'); $('#hydrophobicity_charge_button').val('Show'); $('#hydrophobicity_charge_explanation').text(''); } } catch(err){ txt='There was an error with the button controlling the visibility of the plot. | function show_or_hide_plot(){ try { if( $('#hydrophobicity_charge_button').val() =='Show' ){ $('#hydrophobicity_charge_container').css('display','block'); for (plot_num = 0 ; plot_num < number_of_plots ; plot_num ++){ $.plot('#hydrophobicity_charge_placeholder'+ plot_num.toString(), [{ color: 'rgba(100,149,237,1)', data: hydrophobicity_datapoints, label: 'Hydrophobicity', lines: { show: true, fill: true, fillColor: 'rgba(100,149,237,0.1)' }, yaxis: 1 }, { color: 'rgba(255,99,71,1)', data: charge_datapoints, label: 'Charge', lines: { show: true, fill: true, fillColor: 'rgba(255,99,71,0.1)' }, yaxis: 2 }], flot_plot_options[plot_num] ); } $('#hydrophobicity_charge_button').val('Hide'); $('#hydrophobicity_charge_explanation').text(': Moving average over 5 amino acids for hydrophobicity (blue) and charge (red)'); } else{ $('#hydrophobicity_charge_container').css('display','none'); $('#hydrophobicity_charge_button').val('Show'); $('#hydrophobicity_charge_explanation').text(''); } } catch(err){ txt='There was an error with the button controlling the visibility of the plot. |
Revision as of 22:03, 7 September 2013
(+)-Limonene synthase 1 with Strep-tag and yeast consensus sequence.
Assembly Compatibility:
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000INCOMPATIBLE WITH RFC[1000]Illegal BsaI site found at 1683
Illegal SapI.rc site found at 107
Protein data table for BioBrick BBa_K801060 automatically created by the BioBrick-AutoAnnotator version 1.0 | ||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Nucleotide sequence in RFC 10: (underlined part encodes the protein) GTACACAATGCGTCGT ... TTCGAAAAATAA ORF from nucleotide position 8 to 1705 (excluding stop-codon) | ||||||||||||||||||||||||||||||||||||||||||||||
Amino acid sequence: (RFC25 scars in shown in bold, other sequence features underlined; both given below)
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Sequence features: (with their position in the amino acid sequence, see the list of supported features)
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Amino acid composition:
| ||||||||||||||||||||||||||||||||||||||||||||||
Amino acid counting
| Biochemical parameters
| |||||||||||||||||||||||||||||||||||||||||||||
Hydrophobicity and charge plot | ||||||||||||||||||||||||||||||||||||||||||||||
Codon usage
| ||||||||||||||||||||||||||||||||||||||||||||||
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 leave us a comment. |
Keywords:
limonene synthase, limonene
Abbreviations:
Design Notes
Related BioBrick:
- BBa_K801061: (+)-Limonene synthase 1 coding region
- BBa_K801062: (+)-limonene synthase 1 expression cassette for yeast
- BBa_K801063: (+)-limonene synthase 1 expression cassette for yeast
- BBa_K801064: (+)-limonene synthase 1 expression cassette for yeast
- BBa_K801065: (+)-limonene synthase 1 with Strep-Tag
- BBa_K801066: (+)-limonene synthase 1 with Yeast Consensus Sequence for improved expression
Quality control measures:
- Biobrick was sequenced
Backbone:
- Backbone name: pSB1C3
- Resistance: Cp
- Copynumber: high
Protein coding:
- BioBrick encodes (+)-limonene synthase
- UniProt entry: [http://www.uniprot.org/uniprot/Q8L5K3 Q8L5K3]
Enzymatic activity:
- E.C. Number: [http://enzyme.expasy.org/EC/4.2.3.20 4.2.3.20]
Cytotoxicity:
- see toxicity assay
Safety notes:
Intellectual property:
Corresponding part author/authors:
Source
Source:
- BioBrick: BBa_I742111
- Forward Primer: TUM12-LIMS1-fw-cons: 5'- GGATCCTCTAGAGTACACAATGCGTCGTTCAGCAAAC - 3'
- Reverse Primer: TUM12-LIMS1-rv: 5'- GGATCCACCGGTGCCTTTGGTGCCAGGAGA - 3'
Organism:
- Gene sequence derived from Citrus limon
References
Literature references:
- [http://www.ncbi.nlm.nih.gov/pubmed/12084056Pubmed: Lücker, J., El Tamer, M. K., Schwab, W., Verstappen, F. W. A., van der Plas, L. H. W., Bouwmeester, H. J., and Verhoeven, H. A., 2002: Monoterpene biosynthesis in lemon (Citrus limon). cDNA isolation and functional analysis of four monoterpene synthases. Eur J Biochem, 269(13):3160–71.]
Database references:
- [http://www.ncbi.nlm.nih.gov/nuccore/21435702 GenBank: source of the sequence]
- [http://www.uniprot.org/uniprot/Q8L5K3 Uniprot: (R)-limonene synthase 1]