Difference between revisions of "Part:BBa K801060:Design"

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<partinfo>BBa_K801060 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K801060 SequenceAndFeatures</partinfo>
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<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% } td.AutoAnnotatorAlignment1 { width: 3% } td.AutoAnnotatorAlignment2 { width: 10% } td.AutoAnnotatorAlignment3 { width: 87% } td.AutoAnnotatorLocalizationOuter {border:1px solid black; width:40%} td.AutoAnnotatorGOOuter {border:1px solid black; width:60%} td.AutoAnnotatorLocalization1 { width: 7.5% } td.AutoAnnotatorLocalization2 { width: 22.5% } td.AutoAnnotatorLocalization3 { width: 70% } td.AutoAnnotatorGO1 { width: 5% } td.AutoAnnotatorGO2 { width: 35% } td.AutoAnnotatorGO3 { width: 60% } td.AutoAnnotatorPredFeat1 { width:3% } td.AutoAnnotatorPredFeat2a { width:27% } td.AutoAnnotatorPredFeat3 { width:70% } div.AutoAnnotator_trans { position:absolute; background:rgb(11,140,143); background-color:rgba(11,140,143, 0.8); height:5px; top:100px; } div.AutoAnnotator_sec_helix { position:absolute; background:rgb(102,0,102); background-color:rgba(102,0,102, 0.8); height:5px; top:110px; } div.AutoAnnotator_sec_strand { position:absolute; background:rgb(245,170,26); background-color:rgba(245,170,26, 1); height:5px; top:110px; } div.AutoAnnotator_acc_buried { position:absolute; background:rgb(89,168,15); background-color:rgba(89,168,15, 0.8); height:5px; top:120px; } div.AutoAnnotator_acc_exposed { position:absolute; background:rgb(0, 0, 255); background-color:rgba(0, 0, 255, 0.8); height:5px; top:120px; } div.AutoAnnotator_dis { position:absolute; text-align:center; font-family:Arial,Helvetica,sans-serif; background:rgb(255, 200, 0); background-color:rgba(255, 200, 0, 1); height:16px; width:16px; top:80px; border-radius:50%; } </style><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1379608715361 --><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">&nbsp;GTACACA<u>ATGCGTCGT&nbsp;...&nbsp;TTCGAAAAA</u>TAA</span><br>&nbsp;<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> (RFC 25 scars in shown in bold, other sequence features underlined; both given below)<br><span class="AutoAnnotatorSequence"><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorSeqNum">1&nbsp;<br>101&nbsp;<br>201&nbsp;<br>301&nbsp;<br>401&nbsp;<br>501&nbsp;</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):&nbsp;</td><td class="AutoAnnotatorSeqFeat3">556 to 557</td></tr><tr><td class="AutoAnnotatorSeqFeat1"></td><td class="AutoAnnotatorSeqFeat2a"><i>Strep</i>-tag II:&nbsp;</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>Plot for hydrophobicity, charge, predicted secondary structure, solvent accessability, transmembrane helices and disulfid bridges</strong>&nbsp;<input type='button' id='hydrophobicity_charge_button' onclick='show_or_hide_plot()' value='Show'><span id="hydrophobicity_charge_explanation"></span><div id="hydrophobicity_charge_container" style='display:none'><div id="hydrophobicity_charge_placeholder0" style="width:100%;height:150px"></div><div id="hydrophobicity_charge_placeholder1" style="width:100%;height:150px"></div><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"><strong>Alignments</strong> (obtained from <a href='http://predictprotein.org'>PredictProtein.org</a>)<table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorAlignment1"></td><td class="AutoAnnotatorAlignment2">SwissProt:</td><td class="AutoAnnotatorAlignment3"><a href='http://www.uniprot.org/uniprot/Q8L5K3'>Q8L5K3</a> (99% identity on 554 AAs), <a href='http://www.uniprot.org/uniprot/Q93X23'>Q93X23</a> (54% identity on 536 AAs)</td></tr><tr><td class="AutoAnnotatorAlignment1"></td><td class="AutoAnnotatorAlignment2">TrEML:</td><td class="AutoAnnotatorAlignment3"><a href='http://www.uniprot.org/uniprot/A7BG59'>A7BG59</a> (99% identity on 554 AAs), <a href='http://www.uniprot.org/uniprot/Q8L5K1'>Q8L5K1</a> (96% identity on 554 AAs)</td></tr><tr><td class="AutoAnnotatorAlignment1"></td><td class="AutoAnnotatorAlignment2">PDB:</td><td class="AutoAnnotatorAlignment3"><a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1n1z'>1n1z</a> (44% identity on 530 AAs), <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1n20'>1n20</a> (44% identity on 525 AAs)</td></tr></table></td></tr><tr><th id='AutoAnnotatorHeader' colspan="2"><strong>Predictions</strong> (obtained from <a href='http://predictprotein.org'>PredictProtein.org</a>)</th></tr><tr><td class="AutoAnnotatorLocalizationOuter"><strong>Subcellular Localization</strong> (reliability in brackets)<table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorLocalization1"></td><td class="AutoAnnotatorLocalization2">Archaea:</td><td class="AutoAnnotatorLocalization3">cytosol (100%)</td></tr><tr><td class="AutoAnnotatorLocalization1"></td><td class="AutoAnnotatorLocalization2">Bacteria:</td><td class="AutoAnnotatorLocalization3">cytosol (95%)</td></tr><tr><td class="AutoAnnotatorLocalization1"></td><td class="AutoAnnotatorLocalization2">Eukarya:</td><td class="AutoAnnotatorLocalization3">nucleus (15%)</td></tr></table></td><td class="AutoAnnotatorGOOuter"><strong>Gene Ontology</strong> (reliability in brackets)<br><table class="AutoAnnotatorNoBorder"><tr><td class='AutoAnnotatorGO1'></td><td class='AutoAnnotatorGO2'>Molecular Function Ontology:</td><td class='AutoAnnotatorGO3'><a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0050551'>GO:0050551</a> (24%), <a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0034768'>GO:0034768</a> (24%)</td></tr><tr><td class='AutoAnnotatorGO1'></td><td class='AutoAnnotatorGO2'>Biological Process Ontology:</td><td class='AutoAnnotatorGO3'><a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0071485'>GO:0071485</a> (19%), <a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0009611'>GO:0009611</a> (18%)</td></tr><tr><td class='AutoAnnotatorGO1'> </td><td class='AutoAnnotatorGO2'> </td><td class='AutoAnnotatorGO3'>&nbsp;</td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Predicted features:</strong><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorPredFeat1"></td><td class="AutoAnnotatorPredFeat2a">Disulfid bridges:</td><td class="AutoAnnotatorPredFeat3">&nbsp;- </td></tr><tr><td class="AutoAnnotatorPredFeat1"></td><td class="AutoAnnotatorPredFeat2a">Transmembrane helices:</td><td class="AutoAnnotatorPredFeat3">&nbsp;- </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>var hydrophobicity_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: [{show: true,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: [{show: true,ticks: [[0, '0'], [4.5,'hydro-<br>phobic&nbsp;&nbsp;'], [-4.5,'hydro-<br>philic&nbsp;&nbsp;']],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)'}},{show: true,ticks: [[0, ''], [1,'positive<br>&nbsp;charge'], [-1,'negative<br>&nbsp;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 = 3;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}];};function show_or_hide_plot(){try {if( $('#hydrophobicity_charge_button').val() =='Show' ){$('#hydrophobicity_charge_container').css('display','block');$('#hydrophobicity_charge_button').val('Hide');var description_html = '<div id='AutoAnnotator_plot_selectors'';description_html = description_html + '<br>&nbsp;<input type='checkbox' id='hydrophobicity_checkbox' checked='checked'>&nbsp;Moving average over 5 amino acids for hydrophobicity (<img src='https://static.igem.org/mediawiki/2013/e/e9/TUM13_hydrophobicity_icon.png' alt='blue graph' height='10'></img>)';description_html = description_html + '<br>&nbsp;<input type='checkbox' id='charge_checkbox' checked='checked'>&nbsp;Moving average over 5 amino acids for charge (<img src='https://static.igem.org/mediawiki/2013/3/3e/TUM13_charge_icon.png' alt='red graph' height='10'></img>)';description_html = description_html + '<br>&nbsp;<input type='checkbox' id='dis_checkbox' checked='checked'>&nbsp;Predicted disulfid bridges (<img src='https://static.igem.org/mediawiki/2013/2/28/TUM13_dis_icon.png' alt='yellow circle' height='10'></img>) with the number of the bridge in the center';description_html = description_html + '<br>&nbsp;<input type='checkbox' id='trans_checkbox' checked='checked'>&nbsp;Predicted transmembrane helices (<img src='https://static.igem.org/mediawiki/2013/7/78/TUM13_trans_icon.png' alt='turquois bars' height='10'></img>)';description_html = description_html + '<br>&nbsp;<input type='checkbox' id='sec_checkbox' checked='checked'>&nbsp;Predicted secondary structure: Helices (<img src='https://static.igem.org/mediawiki/2013/b/bf/TUM13_helix_icon.png' alt='violet bars' height='10'></img>) and beta-strands (<img src='https://static.igem.org/mediawiki/2013/b/bf/TUM13_strand_icon.png' alt='yellow bars' height='10'></img>)';description_html = description_html + '<br>&nbsp;<input type='checkbox' id='acc_checkbox' checked='checked'>&nbsp;Predicted solvent accessability: Exposed (<img src='https://static.igem.org/mediawiki/2013/1/16/TUM13_exposed_icon.png' alt='blue bars' height='10'></img>) and buried (<img src='https://static.igem.org/mediawiki/2013/0/0b/TUM13_buried_icon.png' alt='green bars' height='10'></img>) residues';description_html = description_html + '<br></div>';$('#hydrophobicity_charge_explanation').html(description_html);plot_according_to_selectors();$('#AutoAnnotator_plot_selectors').find('input').click(plot_according_to_selectors);}else{$('#hydrophobicity_charge_container').css('display','none');$('#hydrophobicity_charge_button').val('Show');$('#hydrophobicity_charge_explanation').html('');}}catch(err){txt='There was an error with the button controlling the visibility of the plot.\n';txt=txt+'The originating error is:\n' + err + '\n\n';alert(txt);}};function plot_according_to_selectors(){try{var plot_datasets = [[],[]];if($('#hydrophobicity_checkbox').prop('checked') == true){plot_datasets[0] = { color: 'rgba(100,149,237,1)',data: hydrophobicity_datapoints,label: 'Hydrophobicity',lines: { show: true, fill: true, fillColor: 'rgba(100,149,237,0.1)' },yaxis: 1};}if($('#charge_checkbox').prop('checked') == true){plot_datasets[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};}for (plot_num = 0 ; plot_num < number_of_plots ; plot_num ++){$.plot('#hydrophobicity_charge_placeholder'+ plot_num.toString(), plot_datasets, flot_plot_options[plot_num] );}var screen_width = $('canvas.flot-base').width(); var pos_of_first_tick = 46;var pos_of_last_tick = screen_width - 51;var tick_diff = (screen_width - 97)/199;if($('#dis_checkbox').prop('checked') == true){for ( j = 0 ; j < dis_datapoints.length ; j++ ){$('#hydrophobicity_charge_placeholder' + Math.floor((dis_datapoints[j][0] - 1)/200) ).append('<div class='AutoAnnotator_dis' style='left:' + ((pos_of_first_tick - 8 + (dis_datapoints[j][0] - 1)*tick_diff - Math.floor((dis_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px;'><b>' + (j+1) + '</b></div>');$('#hydrophobicity_charge_placeholder' + Math.floor((dis_datapoints[j][1] - 1)/200) ).append('<div class='AutoAnnotator_dis' style='left:' + ((pos_of_first_tick - 8 + (dis_datapoints[j][1] - 1)*tick_diff - Math.floor((dis_datapoints[j][1] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px;'><b>' + (j+1) + '</b></div>');}}if($('#trans_checkbox').prop('checked') == true){for ( j = 0 ; j < trans_datapoints.length ; j++ ){$('#hydrophobicity_charge_placeholder' + Math.floor((trans_datapoints[j][0] - 1)/200) ).append('<div class='AutoAnnotator_trans' style='width:' + (((trans_datapoints[j][1] - trans_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px ;left:' + ((pos_of_first_tick + (trans_datapoints[j][0] - 1.5)*tick_diff - Math.floor((trans_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px'></div>');}}if($('#sec_checkbox').prop('checked') == true){for ( j = 0 ; j < sec_helix_datapoints.length ; j++ ){$('#hydrophobicity_charge_placeholder' + Math.floor((sec_helix_datapoints[j][0] - 1)/200) ).append('<div class='AutoAnnotator_sec_helix' style='width:' + (((sec_helix_datapoints[j][1] - sec_helix_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px; left:' + ((pos_of_first_tick + (sec_helix_datapoints[j][0] - 1.5)*tick_diff - Math.floor((sec_helix_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px'></div>');}for ( j = 0 ; j < sec_strand_datapoints.length ; j++ ){$('#hydrophobicity_charge_placeholder' + Math.floor((sec_strand_datapoints[j][0] - 1)/200) ).append('<div class='AutoAnnotator_sec_strand' style='width:' + (((sec_strand_datapoints[j][1] - sec_strand_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px; left:' + ((pos_of_first_tick + (sec_strand_datapoints[j][0] - 1.5)*tick_diff - Math.floor((sec_strand_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px'></div>');}}if($('#acc_checkbox').prop('checked') == true){for ( j = 0 ; j < acc_buried_datapoints.length ; j++ ){$('#hydrophobicity_charge_placeholder' + Math.floor((acc_buried_datapoints[j][0] - 1)/200) ).append('<div class='AutoAnnotator_acc_buried' style='width:' + (((acc_buried_datapoints[j][1] - 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 +
  
 
<br>'''Keywords:'''
 
<br>'''Keywords:'''
 +
limonene synthase, limonene
 
<!--These keywords are necessary to find your part using a fulltext sarch.-->
 
<!--These keywords are necessary to find your part using a fulltext sarch.-->
 
<!--keyword_1, keyword_2, keyword_3, keyword_4, keyword_5-->
 
<!--keyword_1, keyword_2, keyword_3, keyword_4, keyword_5-->
Line 15: Line 19:
  
 
'''Related BioBrick:'''
 
'''Related BioBrick:'''
 +
* [https://parts.igem.org/Part:BBa_K801061 BBa_K801061: (+)-Limonene synthase 1 coding region]
 +
* [https://parts.igem.org/Part:BBa_K801062 BBa_K801062: (+)-limonene synthase 1 expression cassette for yeast]
 +
* [https://parts.igem.org/Part:BBa_K801063 BBa_K801063: (+)-limonene synthase 1 expression cassette for yeast]
 +
* [https://parts.igem.org/Part:BBa_K801064 BBa_K801064: (+)-limonene synthase 1 expression cassette for yeast]
 +
* [https://parts.igem.org/Part:BBa_K801065 BBa_K801065: (+)-limonene synthase 1 with Strep-Tag]
 +
* [https://parts.igem.org/Part:BBa_K801066 BBa_K801066: (+)-limonene synthase 1 with Yeast Consensus Sequence for improved expression]
 
<!--*Other versions:[https://parts.igem.org/wiki/index.php?title=Part:BBa_?????? BBa_??????: Name_of_part] -->
 
<!--*Other versions:[https://parts.igem.org/wiki/index.php?title=Part:BBa_?????? BBa_??????: Name_of_part] -->
 
<!--*Related BioBricks:[https://parts.igem.org/wiki/index.php?title=Part:BBa_?????? BBa_??????: Name_of_part]
 
<!--*Related BioBricks:[https://parts.igem.org/wiki/index.php?title=Part:BBa_?????? BBa_??????: Name_of_part]
Line 24: Line 34:
  
 
'''Quality control measures:'''<br>
 
'''Quality control measures:'''<br>
 +
* Biobrick was sequenced
 
<!--*Test digestion using ?enzyme1? & ?enzyme2?/Not yet performed-->
 
<!--*Test digestion using ?enzyme1? & ?enzyme2?/Not yet performed-->
 
<!--*Sequencing using primer ?primer_name?/Not yet sequenced-->
 
<!--*Sequencing using primer ?primer_name?/Not yet sequenced-->
Line 29: Line 40:
  
 
'''Backbone:'''<br>
 
'''Backbone:'''<br>
−
<!--*Backbone name: pSB1C3'/?backbone_name?-->
+
* Backbone name: pSB1C3
−
<!--*Resistance: Amp/Cp/Kan/Tet-->
+
* Resistance: Cp
−
<!--*Copynumber: low/medium/high-->
+
* Copynumber: high
  
 
'''Protein coding:'''<br>
 
'''Protein coding:'''<br>
−
<!--*Protein: ?Name_of_gene_product? [Nucleotide 1 to ???]-->
+
* BioBrick encodes (+)-limonene synthase
−
<!--*The protein has the amino acid replacements ???99??? to ???99???.-->
+
* UniProt entry: [http://www.uniprot.org/uniprot/Q8L5K3 Q8L5K3]
−
<!--*The protein encoded is posttranslationally modified by ???.-->
+
<!--none/not known/cytotoxic for ''organism name''-->
−
<!--*Tag: n-terminally fused/c-terminally fused His5/His6/Strep/Flag/other-->
+
  
 
'''Enzymatic activity:'''
 
'''Enzymatic activity:'''
−
<!--none/EC-number ?.?.?.?-->
+
* E.C. Number: [http://enzyme.expasy.org/EC/4.2.3.20 4.2.3.20]
  
 
'''Cytotoxicity:'''<br>
 
'''Cytotoxicity:'''<br>
−
This Biobrick leads to the production of limonene. We investigated the toxicity of limonene and found out, that the growth of yeast strains was inhibited at concentrations of 1 mM. Limonene with a concentration of 100 mM even showed a lethal effect. Lower concentrations of limonene (range of mikro molar) did not show any growth inhibition or effect.
+
* see toxicity assay
 
<!--none/not known/cytotoxic for ''organism name''-->
 
<!--none/not known/cytotoxic for ''organism name''-->
  
Line 60: Line 70:
  
 
'''Source:'''<br>
 
'''Source:'''<br>
 +
*'''BioBrick:''' BBa_I742111
 
<!--*Commercial system: plasmid name, system name, company name-->
 
<!--*Commercial system: plasmid name, system name, company name-->
 
<!--*Plasmid: p???, provided by ?name_of_person?, ?institute/university?, ?country?-->
 
<!--*Plasmid: p???, provided by ?name_of_person?, ?institute/university?, ?country?-->
Line 66: Line 77:
 
<!--*Synthesized by ?company_name?.-->
 
<!--*Synthesized by ?company_name?.-->
  
 +
* '''Forward Primer:''' TUM12-LIMS1-fw-cons: 5'- GGATCCTCTAGAGTACACAATGCGTCGTTCAGCAAAC - 3'
 +
* '''Reverse Primer:''' TUM12-LIMS1-rv: 5'- GGATCCACCGGTGCCTTTGGTGCCAGGAGA - 3'
 
<!--'''Forward Primer:'''<br><code>5'- ??? - 3'</code><br>-->
 
<!--'''Forward Primer:'''<br><code>5'- ??? - 3'</code><br>-->
 
<!--'''Reverse Primer:'''<br><code>5'- ??? - 3'</code><br>-->
 
<!--'''Reverse Primer:'''<br><code>5'- ??? - 3'</code><br>-->
  
 
'''Organism:'''<br>
 
'''Organism:'''<br>
 +
* Gene sequence derived from ''Citrus limon''
 
<!--*Genesequence derived from ''?organism_name?''-->
 
<!--*Genesequence derived from ''?organism_name?''-->
 
<!--*Codonoptimized for ''?organism_name?''-->
 
<!--*Codonoptimized for ''?organism_name?''-->
 
<!--*Designed for the following Chassis: ''?organism-name?''-->
 
<!--*Designed for the following Chassis: ''?organism-name?''-->
 
<!--*Statement about functionality in other chassis.-->
 
<!--*Statement about functionality in other chassis.-->
−
 
  
 
===References===
 
===References===
Line 80: Line 93:
  
 
'''Literature references:'''<br>
 
'''Literature references:'''<br>
−
<!--*[http://www.ncbi.nlm.nih.gov/pubmed/?PMID? '''Pubmed:''' ?Author(s)?, ?year?: ?title?]-->
+
*[http://www.ncbi.nlm.nih.gov/pubmed/12084056'''Pubmed:''' 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:'''<br>
 
'''Database references:'''<br>
 
*[http://www.ncbi.nlm.nih.gov/nuccore/21435702 '''GenBank''': source of the sequence]
 
*[http://www.ncbi.nlm.nih.gov/nuccore/21435702 '''GenBank''': source of the sequence]
 
<!--*[http://www.ebi.ac.uk/interpro/IEntry?ac=?accessNr? '''Interpro''': ?title?]-->
 
<!--*[http://www.ebi.ac.uk/interpro/IEntry?ac=?accessNr? '''Interpro''': ?title?]-->
−
<!--*[http://www.uniprot.org/uniprot/?accessNr? '''Uniprot''': ?title?]-->
+
*[http://www.uniprot.org/uniprot/Q8L5K3 '''Uniprot''': (R)-limonene synthase 1]
 
<!--*[http://pfam.sanger.ac.uk/family/?accessNr? '''Pfam:''' ?title?]-->
 
<!--*[http://pfam.sanger.ac.uk/family/?accessNr? '''Pfam:''' ?title?]-->
 
<!--*[http://www.rcsb.org/pdb/explore/explore.do?structureId=?accessNR? '''PDB:''' ?tile?]-->
 
<!--*[http://www.rcsb.org/pdb/explore/explore.do?structureId=?accessNR? '''PDB:''' ?tile?]-->

Latest revision as of 16:38, 19 September 2013

(+)-Limonene synthase 1 with Strep-tag and yeast consensus sequence.


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE 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: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
1 
101 
201 
301 
401 
501 		MRRSANYQPSIWDHDFLQSLNSNYTDEAYKRRAEELRGKVKIAIKDVIEPLDQLDLIDNLQRLGLAHRFETEIRNILNNIYNNNKDYNWRKENLYATSLE
FRLLRQHGYPVSQEVFNGFKDDQGGFICDDFKGILSLHEASYYSLEGESIMEEAWQFTSKHLKEVMISKNMEEDVFVAEQAKRALELPLHWKVPMLEARW
FIHIYERREDKNHLLLELAKMEFNTLQAIYQEELKEISGWWKDTGLGEKLSFARNRLVASFLWSMGIAFEPQFAYCRRVLTISIALITVIDDIYDVYGTL
DELEIFTDAVERWDINYALKHLPGYMKMCFLALYNFVNEFAYYVLKQQDFDLLLSIKNAWLGLIQAYLVEAKWYHSKYTPKLEEYLENGLVSITGPLIIT
ISYLSGTNPIIKKELEFLESNPDIVHWSSKIFRLQDDLGTSSDEIQRGDVPKSIQCYMHETGASEEVARQHIKDMMRQMWKKVNAYTADKDSPLTGTTTE
FLLNLVRMSHFMYLHGDGHGVQNQETIDVGFTLLFQPIPLEDKHMAFTASPGTKGTGAWSHPQFEK*
Sequence features: (with their position in the amino acid sequence, see the list of supported features)
RFC25 scar (shown in bold): 556 to 557
Strep-tag II: 559 to 566
Amino acid composition:
Ala (A)33 (5.8%)
Arg (R)25 (4.4%)
Asn (N)27 (4.8%)
Asp (D)34 (6.0%)
Cys (C)4 (0.7%)
Gln (Q)24 (4.2%)
Glu (E)48 (8.5%)
Gly (G)29 (5.1%)
His (H)18 (3.2%)
Ile (I)39 (6.9%)
Leu (L)64 (11.3%)
Lys (K)36 (6.4%)
Met (M)16 (2.8%)
Phe (F)28 (4.9%)
Pro (P)17 (3.0%)
Ser (S)33 (5.8%)
Thr (T)26 (4.6%)
Trp (W)14 (2.5%)
Tyr (Y)27 (4.8%)
Val (V)24 (4.2%)
Amino acid counting
Total number:566
Positively charged (Arg+Lys):61 (10.8%)
Negatively charged (Asp+Glu):82 (14.5%)
Aromatic (Phe+His+Try+Tyr):87 (15.4%)
Biochemical parameters
Atomic composition:C3002H4586N778O868S20
Molecular mass [Da]:66105.3
Theoretical pI:5.38
Extinction coefficient at 280 nm [M-1 cm-1]:117230 / 117480 (all Cys red/ox)
Plot for hydrophobicity, charge, predicted secondary structure, solvent accessability, transmembrane helices and disulfid bridges 
Codon usage
Organism:E. coliB. subtilisS. cerevisiaeA. thalianaP. patensMammals
Codon quality (CAI):good (0.71)good (0.75)good (0.69)good (0.78)excellent (0.80)good (0.68)
Alignments (obtained from PredictProtein.org)
SwissProt:Q8L5K3 (99% identity on 554 AAs), Q93X23 (54% identity on 536 AAs)
TrEML:A7BG59 (99% identity on 554 AAs), Q8L5K1 (96% identity on 554 AAs)
PDB:1n1z (44% identity on 530 AAs), 1n20 (44% identity on 525 AAs)
Predictions (obtained from PredictProtein.org)
Subcellular Localization (reliability in brackets)
Archaea:cytosol (100%)
Bacteria:cytosol (95%)
Eukarya:nucleus (15%)
Gene Ontology (reliability in brackets)
Molecular Function Ontology:GO:0050551 (24%), GO:0034768 (24%)
Biological Process Ontology:GO:0071485 (19%), GO:0009611 (18%)
 
Predicted features:
Disulfid bridges: -
Transmembrane helices: -
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:

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]