Difference between revisions of "Part:BBa K1159000"
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===Usage and Biology=== | ===Usage and Biology=== | ||
| + | ===Protein Data Table for the erythromycin esterase (EreB) <partinfo>BBa_K1159000</partinfo>=== | ||
| + | <html><!--- Please copy this table containing parameters for BBa_ 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><div id='AutoAnnotator_container_1380912466041'><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1380912466041 --><th id="AutoAnnotatorHeader" colspan="2">Protein data table for BioBrick <a href="https://parts.igem.org/wiki/index.php?title=Part:BBa_BBa_K1159000">BBa_BBa_K1159000</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 25</strong>, so ATGGCCGGC and ACCGGT were added (in italics) to the 5' and 3' ends: (underlined part encodes the protein)<br><span class="AutoAnnotatorSequence"> <u><i>ATGGCCGGC</i>AGGTTCGAA ... GTTTATGAA<i>ACCGGT</i></u></span><br> <strong>ORF</strong> from nucleotide position -8 to 1260 (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 <br>101 <br>201 <br>301 <br>401 </td><td class="AutoAnnotatorSeqSeq">MAGRFEEWVKDKHIPFKLNHPDDNYDDFKPLRKIIGDTRVVALGENSHFIKEFFLLRHTLLRFFIEDLGFTTFAFEFGFAEGQIINNWIHGQGTDDEIGR<br>FLKHFYYPEELKTTFLWLREYNKAAKEKITFLGIDIPRNGGSYLPNMEIVHDFFRTADKEALHIIDDAFNIAKKIDYFSTSQAALNLHELTDSEKCRLTS<br>QLARVKVRLEAMAPIHIEKYGIDKYETILHYANGMIYLDYNIQAMSGFISGGGMQGDMGAKDKYMADSVLWHLKNPQSEQKVIVVAHNAHIQKTPILYDG<br>FLSCLPMGQRLKNAIGDDYMSLGITSYSGHTAALYPEVDTKYGFRVDNFQLQEPNEGSVEKAISGCGVTNSFVFFRNIPEDLQSIPNMIRFDSIYMKAEL<br>EKAFDGIFQIEKSSVSEVVYETG*</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="AutoAnnotatorSeqFeat2b">None of the supported features appeared in the sequence</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">27 (6.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Arg (R)</td><td class="AutoAnnotatorInnerAmino">16 (3.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asn (N)</td><td class="AutoAnnotatorInnerAmino">20 (4.7%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asp (D)</td><td class="AutoAnnotatorInnerAmino">29 (6.9%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Cys (C)</td><td class="AutoAnnotatorInnerAmino">3 (0.7%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gln (Q)</td><td class="AutoAnnotatorInnerAmino">14 (3.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Glu (E)</td><td class="AutoAnnotatorInnerAmino">30 (7.1%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gly (G)</td><td class="AutoAnnotatorInnerAmino">31 (7.3%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">His (H)</td><td class="AutoAnnotatorInnerAmino">15 (3.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ile (I)</td><td class="AutoAnnotatorInnerAmino">36 (8.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Leu (L)</td><td class="AutoAnnotatorInnerAmino">34 (8.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Lys (K)</td><td class="AutoAnnotatorInnerAmino">29 (6.9%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Met (M)</td><td class="AutoAnnotatorInnerAmino">12 (2.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Phe (F)</td><td class="AutoAnnotatorInnerAmino">31 (7.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Pro (P)</td><td class="AutoAnnotatorInnerAmino">14 (3.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ser (S)</td><td class="AutoAnnotatorInnerAmino">22 (5.2%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Thr (T)</td><td class="AutoAnnotatorInnerAmino">19 (4.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Trp (W)</td><td class="AutoAnnotatorInnerAmino">4 (0.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Tyr (Y)</td><td class="AutoAnnotatorInnerAmino">19 (4.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Val (V)</td><td class="AutoAnnotatorInnerAmino">18 (4.3%)</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">423</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Positively charged (Arg+Lys):</td><td class="AutoAnnotatorAminoCountingInner3">45 (10.6%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Negatively charged (Asp+Glu):</td><td class="AutoAnnotatorAminoCountingInner3">59 (13.9%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Aromatic (Phe+His+Try+Tyr):</td><td class="AutoAnnotatorAminoCountingInner3">69 (16.3%)</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>2204</sub>H<sub>3348</sub>N<sub>568</sub>O<sub>636</sub>S<sub>15</sub></td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Molecular mass [Da]:</td><td class="AutoAnnotatorBiochemParInner3">48459.2</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Theoretical pI:</td><td class="AutoAnnotatorBiochemParInner3">5.55</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">50310 / 50498 (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> <input type='button' id='hydrophobicity_charge_button' onclick='show_or_hide_plot_1380912466041()' 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 (0.74)</td><td class="AutoAnnotatorCodonUsage3">good (0.77)</td><td class="AutoAnnotatorCodonUsage3">good (0.75)</td><td class="AutoAnnotatorCodonUsage3">good (0.80)</td><td class="AutoAnnotatorCodonUsage3">good (0.76)</td><td class="AutoAnnotatorCodonUsage3">good (0.66)</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/P05789'>P05789</a> (100% identity on 418 AAs), <a href='http://www.uniprot.org/uniprot/P07684'>P07684</a> (24% identity on 381 AAs)</td></tr><tr><td class="AutoAnnotatorAlignment1"></td><td class="AutoAnnotatorAlignment2">TrEML:</td><td class="AutoAnnotatorAlignment3"><a href='http://www.uniprot.org/uniprot/Q2V0Y9'>Q2V0Y9</a> (100% identity on 418 AAs), <a href='http://www.uniprot.org/uniprot/D7J5T5'>D7J5T5</a> (44% identity on 402 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=2qgm'>2qgm</a> (20% identity on 373 AAs), <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=2rad'>2rad</a> (19% identity on 386 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 (100%)</td></tr><tr><td class="AutoAnnotatorLocalization1"></td><td class="AutoAnnotatorLocalization2">Eukarya:</td><td class="AutoAnnotatorLocalization3">cytosol (58%)</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'> - </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:0046677'>GO:0046677</a> (51%)</td></tr><tr><td class='AutoAnnotatorGO1'> </td><td class='AutoAnnotatorGO2'> </td><td class='AutoAnnotatorGO3'> </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"> - </td></tr><tr><td class="AutoAnnotatorPredFeat1"></td><td class="AutoAnnotatorPredFeat2a">Transmembrane helices:</td><td class="AutoAnnotatorPredFeat3"> - </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></div><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>function show_or_hide_plot_1380912466041(){hydrophobicity_datapoints = 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= 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383.5,0.00],[384.5,0.00],[385.5,0.00],[386.5,0.00],[387.5,0.20],[388.5,0.20],[389.5,0.00],[390.5,0.00],[391.5,0.00],[392.5,-0.20],[393.5,-0.20],[394.5,0.20],[395.5,0.20],[396.5,0.00],[397.5,0.00],[398.5,-0.20],[399.5,-0.20],[400.5,-0.20],[401.5,0.00],[402.5,-0.20],[403.5,0.00],[404.5,-0.20],[405.5,-0.20],[406.5,-0.20],[407.5,0.00],[408.5,-0.20],[409.5,0.00],[410.5,0.00],[411.5,0.00],[412.5,0.00],[413.5,0.20],[414.5,-0.20],[415.5,-0.20],[416.5,-0.20],[417.5,-0.20],[418.5,-0.40],[419.5,-0.20],[420.5,-0.20]];dis_datapoints = [];trans_datapoints = [];sec_helix_datapoints = [[3,12],[28,34],[50,67],[81,90],[95,105],[109,121],[144,156],[159,172],[181,188],[193,200],[201,212],[215,218],[224,249],[261,276],[305,314],[359,365],[380,382],[389,391],[401,403]];sec_strand_datapoints = [[39,43],[72,76],[128,134],[282,286],[319,325],[330,334],[371,374],[406,411]];acc_exposed_datapoints = [[1,4],[7,7],[10,11],[15,15],[17,17],[19,19],[21,24],[26,26],[29,29],[33,33],[36,37],[66,67],[90,90],[92,92],[95,96],[99,100],[109,109],[120,120],[123,127],[141,141],[155,156],[158,160],[163,163],[167,167],[170,170],[173,174],[176,177],[179,179],[189,189],[191,193],[197,197],[200,200],[204,204],[207,207],[210,211],[214,214],[218,219],[221,221],[223,224],[251,253],[274,274],[277,279],[313,313],[316,317],[337,341],[343,343],[345,345],[347,347],[350,350],[353,353],[356,356],[364,365],[367,367],[369,369],[380,381],[384,384],[387,387],[397,397],[399,399],[402,402],[412,412],[414,414],[417,417],[420,423]];acc_buried_datapoints = [[5,5],[9,9],[13,13],[16,16],[28,28],[31,31],[35,35],[38,38],[40,50],[53,54],[56,61],[64,65],[69,79],[82,82],[84,86],[88,89],[91,91],[98,98],[101,102],[105,108],[111,115],[117,118],[122,122],[129,137],[142,143],[146,147],[149,151],[153,154],[161,162],[165,165],[168,169],[172,172],[183,187],[198,199],[201,202],[205,205],[209,209],[212,213],[216,217],[225,225],[228,232],[234,238],[240,242],[244,249],[258,258],[260,260],[262,262],[264,266],[268,270],[272,273],[280,280],[282,292],[294,294],[296,296],[298,298],[301,301],[304,311],[315,315],[319,327],[329,334],[346,346],[351,351],[358,359],[362,363],[366,366],[371,375],[378,379],[382,382],[388,388],[391,396],[400,400],[404,410],[415,415]];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 '], [-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)'}},{show: true,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)'}}]};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}];};try {if( $('#AutoAnnotator_container_1380912466041 #hydrophobicity_charge_button').val() =='Show' ){$('#AutoAnnotator_container_1380912466041 #hydrophobicity_charge_container').css('display','block');$('#AutoAnnotator_container_1380912466041 #hydrophobicity_charge_button').val('Hide');var description_html = '<div id=\'AutoAnnotator_plot_selectors\'>';description_html = description_html + '<br> <input type=\'checkbox\' id=\'hydrophobicity_checkbox\' checked=\'checked\'> 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> <input type=\'checkbox\' id=\'charge_checkbox\' checked=\'checked\'> 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> <input type=\'checkbox\' id=\'dis_checkbox\' checked=\'checked\'> 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> <input type=\'checkbox\' id=\'trans_checkbox\' checked=\'checked\'> 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> <input type=\'checkbox\' id=\'sec_checkbox\' checked=\'checked\'> 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> <input type=\'checkbox\' id=\'acc_checkbox\' checked=\'checked\'> 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>';$('#AutoAnnotator_container_1380912466041 #hydrophobicity_charge_explanation').html(description_html);plot_according_to_selectors_1380912466041();$('#AutoAnnotator_container_1380912466041 #AutoAnnotator_plot_selectors').find('input').click(plot_according_to_selectors_1380912466041);}else{$('#AutoAnnotator_container_1380912466041 #hydrophobicity_charge_container').css('display','none');$('#AutoAnnotator_container_1380912466041 #hydrophobicity_charge_button').val('Show');$('#AutoAnnotator_container_1380912466041 #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_1380912466041(){try{var plot_datasets = [[],[]];if($('#AutoAnnotator_container_1380912466041 #hydrophobicity_checkbox').prop('checked') == true){plot_datasets[0] = { color: 'rgba(100,149,237,1)',data: hydrophobicity_datapoints,label: 'Hydrophobicity',lines: { show: true, fill: true, fillColor: 'rgba(100,149,237,0.1)' },yaxis: 1};}if($('#AutoAnnotator_container_1380912466041 #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('#AutoAnnotator_container_1380912466041 #hydrophobicity_charge_placeholder'+ plot_num.toString(), plot_datasets, flot_plot_options[plot_num] );}var screen_width = $('canvas.flot-base').width(); var pos_of_first_tick = 46;var pos_of_last_tick = screen_width - 51;var tick_diff = (screen_width - 97)/199;if($('#AutoAnnotator_container_1380912466041 #dis_checkbox').prop('checked') == true){for ( j = 0 ; j < dis_datapoints.length ; j++ ){$('#AutoAnnotator_container_1380912466041 #hydrophobicity_charge_placeholder' + Math.floor((dis_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_dis\' style=\'left:' + ((pos_of_first_tick - 8 + (dis_datapoints[j][0] - 1)*tick_diff - Math.floor((dis_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px;\'><b>' + (j+1) + '</b></div>');$('#AutoAnnotator_container_1380912466041 #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($('#AutoAnnotator_container_1380912466041 #trans_checkbox').prop('checked') == true){for ( j = 0 ; j < trans_datapoints.length ; j++ ){$('#AutoAnnotator_container_1380912466041 #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($('#AutoAnnotator_container_1380912466041 #sec_checkbox').prop('checked') == true){for ( j = 0 ; j < sec_helix_datapoints.length ; j++ ){$('#AutoAnnotator_container_1380912466041 #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++ ){$('#AutoAnnotator_container_1380912466041 #hydrophobicity_charge_placeholder' + Math.floor((sec_strand_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_sec_strand\' style=\'width:' + (((sec_strand_datapoints[j][1] - sec_strand_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px; left:' + ((pos_of_first_tick + (sec_strand_datapoints[j][0] - 1.5)*tick_diff - Math.floor((sec_strand_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px\'></div>');}}if($('#AutoAnnotator_container_1380912466041 #acc_checkbox').prop('checked') == true){for ( j = 0 ; j < acc_buried_datapoints.length ; j++ ){$('#AutoAnnotator_container_1380912466041 #hydrophobicity_charge_placeholder' + Math.floor((acc_buried_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_acc_buried\' style=\'width:' + (((acc_buried_datapoints[j][1] - acc_buried_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px; left:' + ((pos_of_first_tick + (acc_buried_datapoints[j][0] - 1.5)*tick_diff - Math.floor((acc_buried_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px\'></div>');}for ( j = 0 ; j < acc_exposed_datapoints.length ; j++ ){$('#AutoAnnotator_container_1380912466041 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Revision as of 03:41, 5 October 2013
Erythromycin Esterase Type II (EreB) in RFC[25]
Erythromycin esterase type II from Escherichia coli that degrades macrolid antibiotics. Part is RFC[25] compatible and is flanked by RFC[25] pre- and suffix.
<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>| Protein data table for BioBrick <a href="https://parts.igem.org/wiki/index.php?title=Part:BBa_BBa_K1159000">BBa_BBa_K1159000</a> automatically created by the <a href="http://2013.igem.org/Team:TU-Munich/Results/AutoAnnotator">BioBrick-AutoAnnotator</a> version 1.0 | ||||||||||||||||||||||||||||||||||||||||||||||
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| Nucleotide sequence in RFC 25, so ATGGCCGGC and ACCGGT were added (in italics) to the 5' and 3' ends: (underlined part encodes the protein) ATGGCCGGCAGGTTCGAA ... GTTTATGAAACCGGT ORF from nucleotide position -8 to 1260 (excluding stop-codon) | ||||||||||||||||||||||||||||||||||||||||||||||
Amino acid sequence: (RFC 25 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 <a href="http://2013.igem.org/Team:TU-Munich/Results/Software/FeatureList">list of supported features</a>)
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Amino acid composition:
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Amino acid counting
| Biochemical parameters
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| Plot for hydrophobicity, charge, predicted secondary structure, solvent accessability, transmembrane helices and disulfid bridges <input type='button' id='hydrophobicity_charge_button' onclick='show_or_hide_plot_1380912466041()' value='Show'> | ||||||||||||||||||||||||||||||||||||||||||||||
Codon usage
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Alignments (obtained from <a href='http://predictprotein.org'>PredictProtein.org</a>)
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| Predictions (obtained from <a href='http://predictprotein.org'>PredictProtein.org</a>) | ||||||||||||||||||||||||||||||||||||||||||||||
Subcellular Localization (reliability in brackets)
| Gene Ontology (reliability in brackets)
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Predicted features:
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| 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>. 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>. | ||||||||||||||||||||||||||||||||||||||||||||||
<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>function show_or_hide_plot_1380912466041(){hydrophobicity_datapoints = [[2.5,0.32],[3.5,-0.76],[4.5,-1.82],[5.5,-1.92],[6.5,-0.18],[7.5,-1.52],[8.5,-1.52],[9.5,-1.60],[10.5,-2.06],[11.5,-2.00],[12.5,-1.54],[13.5,-0.28],[14.5,-0.28],[15.5,1.12],[16.5,-0.48],[17.5,-0.80],[18.5,-1.68],[19.5,-1.60],[20.5,-3.06],[21.5,-3.06],[22.5,-2.68],[23.5,-3.06],[24.5,-3.06],[25.5,-1.80],[26.5,-1.88],[27.5,-1.94],[28.5,-0.48],[29.5,-0.68],[30.5,-2.02],[31.5,-0.34],[32.5,0.88],[33.5,0.04],[34.5,0.24],[35.5,0.88],[36.5,-0.92],[37.5,-0.98],[38.5,-0.06],[39.5,1.00],[40.5,1.90],[41.5,2.72],[42.5,1.18],[43.5,-0.36],[44.5,-0.88],[45.5,-2.28],[46.5,-1.64],[47.5,-0.04],[48.5,-0.12],[49.5,-0.66],[50.5,0.54],[51.5,0.54],[52.5,0.40],[53.5,1.94],[54.5,1.74],[55.5,0.54],[56.5,-0.16],[57.5,-0.16],[58.5,-0.16],[59.5,-0.16],[60.5,1.04],[61.5,1.74],[62.5,1.88],[63.5,0.42],[64.5,0.62],[65.5,0.82],[66.5,0.18],[67.5,-0.16],[68.5,0.40],[69.5,0.96],[70.5,0.76],[71.5,1.20],[72.5,1.20],[73.5,0.64],[74.5,1.34],[75.5,0.70],[76.5,0.90],[77.5,0.70],[78.5,0.70],[79.5,0.06],[80.5,-0.56],[81.5,-0.22],[82.5,0.32],[83.5,0.32],[84.5,-0.30],[85.5,0.22],[86.5,0.22],[87.5,-1.32],[88.5,-0.70],[89.5,-0.70],[90.5,-0.60],[91.5,-1.64],[92.5,-1.70],[93.5,-2.32],[94.5,-2.32],[95.5,-1.34],[96.5,-1.28],[97.5,-1.48],[98.5,-0.22],[99.5,1.24],[100.5,-0.44],[101.5,-1.00],[102.5,0.46],[103.5,-0.36],[104.5,-1.38],[105.5,-0.92],[106.5,-0.98],[107.5,-2.24],[108.5,-1.22],[109.5,-1.74],[110.5,-1.56],[111.5,-1.00],[112.5,0.26],[113.5,0.26],[114.5,0.86],[115.5,1.76],[116.5,1.00],[117.5,-0.26],[118.5,-1.28],[119.5,-1.80],[120.5,-3.34],[121.5,-2.08],[122.5,-1.02],[123.5,-1.54],[124.5,-1.54],[125.5,-1.54],[126.5,-1.00],[127.5,-1.50],[128.5,-0.16],[129.5,1.30],[130.5,2.00],[131.5,2.00],[132.5,1.44],[133.5,1.78],[134.5,0.70],[135.5,-0.12],[136.5,-1.72],[137.5,-1.10],[138.5,-2.08],[139.5,-1.92],[140.5,-1.28],[141.5,0.18],[142.5,-0.06],[143.5,-0.68],[144.5,-0.14],[145.5,-0.58],[146.5,-0.44],[147.5,0.72],[148.5,0.78],[149.5,-0.30],[150.5,0.96],[151.5,0.62],[152.5,-1.12],[153.5,-0.62],[154.5,0.44],[155.5,-0.82],[156.5,-2.16],[157.5,-1.96],[158.5,-1.46],[159.5,-1.06],[160.5,-1.00],[161.5,0.68],[162.5,2.28],[163.5,1.22],[164.5,-0.24],[165.5,0.76],[166.5,0.42],[167.5,-1.18],[168.5,0.42],[169.5,1.48],[170.5,0.34],[171.5,-1.00],[172.5,0.60],[173.5,-1.00],[174.5,-1.62],[175.5,-0.28],[176.5,0.34],[177.5,-0.70],[178.5,-0.16],[179.5,-0.60],[180.5,-0.80],[181.5,-0.28],[182.5,0.62],[183.5,0.08],[184.5,1.54],[185.5,0.54],[186.5,-0.52],[187.5,-0.52],[188.5,0.04],[189.5,-1.42],[190.5,-0.94],[191.5,-0.94],[192.5,-2.48],[193.5,-1.84],[194.5,-2.04],[195.5,-1.12],[196.5,-0.56],[197.5,0.06],[198.5,-1.14],[199.5,0.52],[200.5,0.12],[201.5,-0.64],[202.5,0.36],[203.5,0.28],[204.5,0.36],[205.5,-0.90],[206.5,0.76],[207.5,-0.78],[208.5,0.36],[209.5,-0.10],[210.5,1.16],[211.5,0.08],[212.5,1.68],[213.5,0.68],[214.5,1.20],[215.5,0.14],[216.5,-0.32],[217.5,-1.48],[218.5,-0.92],[219.5,-0.92],[220.5,-0.92],[221.5,-0.92],[222.5,-0.92],[223.5,-1.54],[224.5,-2.58],[225.5,-0.98],[226.5,0.56],[227.5,0.18],[228.5,0.62],[229.5,1.12],[230.5,-0.48],[231.5,-1.32],[232.5,-0.30],[233.5,0.86],[234.5,0.24],[235.5,1.70],[236.5,1.08],[237.5,0.44],[238.5,-1.16],[239.5,-0.00],[240.5,-1.46],[241.5,-0.40],[242.5,0.24],[243.5,0.78],[244.5,-0.20],[245.5,1.06],[246.5,1.60],[247.5,1.06],[248.5,1.14],[249.5,1.14],[250.5,0.50],[251.5,-0.02],[252.5,-0.56],[253.5,-0.56],[254.5,-1.18],[255.5,-0.72],[256.5,-1.18],[257.5,-0.12],[258.5,-0.82],[259.5,-0.82],[260.5,-1.98],[261.5,-2.16],[262.5,-2.14],[263.5,-1.00],[264.5,-1.00],[265.5,-0.38],[266.5,0.72],[267.5,1.10],[268.5,0.56],[269.5,0.62],[270.5,1.54],[271.5,-0.08],[272.5,-1.54],[273.5,-1.68],[274.5,-1.74],[275.5,-2.66],[276.5,-2.58],[277.5,-2.58],[278.5,-3.04],[279.5,-1.50],[280.5,-0.44],[281.5,1.10],[282.5,2.64],[283.5,3.78],[284.5,2.30],[285.5,0.70],[286.5,0.22],[287.5,-1.26],[288.5,-0.72],[289.5,-0.78],[290.5,-0.86],[291.5,-1.36],[292.5,-1.04],[293.5,-1.04],[294.5,0.42],[295.5,0.94],[296.5,0.38],[297.5,0.62],[298.5,0.28],[299.5,0.28],[300.5,0.38],[301.5,1.58],[302.5,2.42],[303.5,1.54],[304.5,1.16],[305.5,1.24],[306.5,0.04],[307.5,-1.62],[308.5,-0.54],[309.5,-1.70],[310.5,-2.32],[311.5,-1.26],[312.5,0.54],[313.5,-0.30],[314.5,-0.22],[315.5,-0.22],[316.5,-0.84],[317.5,-1.36],[318.5,-1.44],[319.5,0.02],[320.5,0.64],[321.5,1.80],[322.5,1.28],[323.5,1.28],[324.5,0.26],[325.5,0.18],[326.5,-0.80],[327.5,-1.30],[328.5,-1.28],[329.5,-0.66],[330.5,-0.14],[331.5,0.70],[332.5,1.08],[333.5,0.90],[334.5,-0.16],[335.5,0.32],[336.5,-1.14],[337.5,-1.02],[338.5,-1.48],[339.5,-1.04],[340.5,-1.96],[341.5,-0.70],[342.5,-1.46],[343.5,0.16],[344.5,-0.28],[345.5,-0.90],[346.5,-0.90],[347.5,-0.70],[348.5,-0.78],[349.5,-0.78],[350.5,-0.78],[351.5,-1.66],[352.5,-1.66],[353.5,-3.12],[354.5,-2.50],[355.5,-1.96],[356.5,-0.80],[357.5,-0.80],[358.5,-0.88],[359.5,-0.44],[360.5,0.62],[361.5,-0.38],[362.5,0.24],[363.5,1.52],[364.5,1.08],[365.5,1.02],[366.5,1.04],[367.5,0.42],[368.5,-0.24],[369.5,0.40],[370.5,0.40],[371.5,1.10],[372.5,2.36],[373.5,1.62],[374.5,0.36],[375.5,0.42],[376.5,-0.46],[377.5,-1.72],[378.5,-1.52],[379.5,-0.06],[380.5,-1.66],[381.5,-1.50],[382.5,0.10],[383.5,0.48],[384.5,-0.98],[385.5,0.10],[386.5,1.16],[387.5,-0.64],[388.5,0.24],[389.5,0.24],[390.5,-0.30],[391.5,-0.30],[392.5,0.34],[393.5,0.16],[394.5,0.08],[395.5,0.60],[396.5,-1.00],[397.5,0.02],[398.5,-1.06],[399.5,-1.06],[400.5,-1.06],[401.5,0.20],[402.5,-1.26],[403.5,-0.64],[404.5,1.04],[405.5,1.24],[406.5,-0.02],[407.5,1.58],[408.5,0.96],[409.5,-0.72],[410.5,-1.44],[411.5,-0.90],[412.5,-0.96],[413.5,-0.42],[414.5,-0.34],[415.5,0.66],[416.5,1.66],[417.5,0.56],[418.5,0.02],[419.5,0.58],[420.5,-0.34]];charge_datapoints = 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383.5,0.00],[384.5,0.00],[385.5,0.00],[386.5,0.00],[387.5,0.20],[388.5,0.20],[389.5,0.00],[390.5,0.00],[391.5,0.00],[392.5,-0.20],[393.5,-0.20],[394.5,0.20],[395.5,0.20],[396.5,0.00],[397.5,0.00],[398.5,-0.20],[399.5,-0.20],[400.5,-0.20],[401.5,0.00],[402.5,-0.20],[403.5,0.00],[404.5,-0.20],[405.5,-0.20],[406.5,-0.20],[407.5,0.00],[408.5,-0.20],[409.5,0.00],[410.5,0.00],[411.5,0.00],[412.5,0.00],[413.5,0.20],[414.5,-0.20],[415.5,-0.20],[416.5,-0.20],[417.5,-0.20],[418.5,-0.40],[419.5,-0.20],[420.5,-0.20]];dis_datapoints = [];trans_datapoints = [];sec_helix_datapoints = [[3,12],[28,34],[50,67],[81,90],[95,105],[109,121],[144,156],[159,172],[181,188],[193,200],[201,212],[215,218],[224,249],[261,276],[305,314],[359,365],[380,382],[389,391],[401,403]];sec_strand_datapoints = [[39,43],[72,76],[128,134],[282,286],[319,325],[330,334],[371,374],[406,411]];acc_exposed_datapoints = [[1,4],[7,7],[10,11],[15,15],[17,17],[19,19],[21,24],[26,26],[29,29],[33,33],[36,37],[66,67],[90,90],[92,92],[95,96],[99,100],[109,109],[120,120],[123,127],[141,141],[155,156],[158,160],[163,163],[167,167],[170,170],[173,174],[176,177],[179,179],[189,189],[191,193],[197,197],[200,200],[204,204],[207,207],[210,211],[214,214],[218,219],[221,221],[223,224],[251,253],[274,274],[277,279],[313,313],[316,317],[337,341],[343,343],[345,345],[347,347],[350,350],[353,353],[356,356],[364,365],[367,367],[369,369],[380,381],[384,384],[387,387],[397,397],[399,399],[402,402],[412,412],[414,414],[417,417],[420,423]];acc_buried_datapoints = [[5,5],[9,9],[13,13],[16,16],[28,28],[31,31],[35,35],[38,38],[40,50],[53,54],[56,61],[64,65],[69,79],[82,82],[84,86],[88,89],[91,91],[98,98],[101,102],[105,108],[111,115],[117,118],[122,122],[129,137],[142,143],[146,147],[149,151],[153,154],[161,162],[165,165],[168,169],[172,172],[183,187],[198,199],[201,202],[205,205],[209,209],[212,213],[216,217],[225,225],[228,232],[234,238],[240,242],[244,249],[258,258],[260,260],[262,262],[264,266],[268,270],[272,273],[280,280],[282,292],[294,294],[296,296],[298,298],[301,301],[304,311],[315,315],[319,327],[329,334],[346,346],[351,351],[358,359],[362,363],[366,366],[371,375],[378,379],[382,382],[388,388],[391,396],[400,400],[404,410],[415,415]];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-
phobic '], [-4.5,'hydro-
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)'}},{show: true,ticks: [[0, ], [1,'positive
charge'], [-1,'negative
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)'}}]};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}];};try {if( $('#AutoAnnotator_container_1380912466041 #hydrophobicity_charge_button').val() =='Show' ){$('#AutoAnnotator_container_1380912466041 #hydrophobicity_charge_container').css('display','block');$('#AutoAnnotator_container_1380912466041 #hydrophobicity_charge_button').val('Hide');var description_html = '
';description_html = description_html + '
<input type=\'checkbox\' id=\'hydrophobicity_checkbox\' checked=\'checked\'> 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 + '
<input type=\'checkbox\' id=\'charge_checkbox\' checked=\'checked\'> 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 + '
<input type=\'checkbox\' id=\'dis_checkbox\' checked=\'checked\'> 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 + '
<input type=\'checkbox\' id=\'trans_checkbox\' checked=\'checked\'> 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 + '
<input type=\'checkbox\' id=\'sec_checkbox\' checked=\'checked\'> 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 + '
<input type=\'checkbox\' id=\'acc_checkbox\' checked=\'checked\'> 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 + '
';$('#AutoAnnotator_container_1380912466041 #hydrophobicity_charge_explanation').html(description_html);plot_according_to_selectors_1380912466041();$('#AutoAnnotator_container_1380912466041 #AutoAnnotator_plot_selectors').find('input').click(plot_according_to_selectors_1380912466041);}else{$('#AutoAnnotator_container_1380912466041 #hydrophobicity_charge_container').css('display','none');$('#AutoAnnotator_container_1380912466041 #hydrophobicity_charge_button').val('Show');$('#AutoAnnotator_container_1380912466041 #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_1380912466041(){try{var plot_datasets = [[],[]];if($('#AutoAnnotator_container_1380912466041 #hydrophobicity_checkbox').prop('checked') == true){plot_datasets[0] = { color: 'rgba(100,149,237,1)',data: hydrophobicity_datapoints,label: 'Hydrophobicity',lines: { show: true, fill: true, fillColor: 'rgba(100,149,237,0.1)' },yaxis: 1};}if($('#AutoAnnotator_container_1380912466041 #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('#AutoAnnotator_container_1380912466041 #hydrophobicity_charge_placeholder'+ plot_num.toString(), plot_datasets, flot_plot_options[plot_num] );}var screen_width = $('canvas.flot-base').width(); var pos_of_first_tick = 46;var pos_of_last_tick = screen_width - 51;var tick_diff = (screen_width - 97)/199;if($('#AutoAnnotator_container_1380912466041 #dis_checkbox').prop('checked') == true){for ( j = 0 ; j < dis_datapoints.length ; j++ ){$('#AutoAnnotator_container_1380912466041 #hydrophobicity_charge_placeholder' + Math.floor((dis_datapoints[j][0] - 1)/200) ).append('<input type=\'checkbox\' id=\'hydrophobicity_checkbox\' checked=\'checked\'> 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 + '
<input type=\'checkbox\' id=\'charge_checkbox\' checked=\'checked\'> 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 + '
<input type=\'checkbox\' id=\'dis_checkbox\' checked=\'checked\'> 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 + '
<input type=\'checkbox\' id=\'trans_checkbox\' checked=\'checked\'> 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 + '
<input type=\'checkbox\' id=\'sec_checkbox\' checked=\'checked\'> 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 + '
<input type=\'checkbox\' id=\'acc_checkbox\' checked=\'checked\'> 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 + '
' + (j+1) + '
');$('#AutoAnnotator_container_1380912466041 #hydrophobicity_charge_placeholder' + Math.floor((dis_datapoints[j][1] - 1)/200) ).append('' + (j+1) + '
');}}if($('#AutoAnnotator_container_1380912466041 #trans_checkbox').prop('checked') == true){for ( j = 0 ; j < trans_datapoints.length ; j++ ){$('#AutoAnnotator_container_1380912466041 #hydrophobicity_charge_placeholder' + Math.floor((trans_datapoints[j][0] - 1)/200) ).append('');}}if($('#AutoAnnotator_container_1380912466041 #sec_checkbox').prop('checked') == true){for ( j = 0 ; j < sec_helix_datapoints.length ; j++ ){$('#AutoAnnotator_container_1380912466041 #hydrophobicity_charge_placeholder' + Math.floor((sec_helix_datapoints[j][0] - 1)/200) ).append('');}for ( j = 0 ; j < sec_strand_datapoints.length ; j++ ){$('#AutoAnnotator_container_1380912466041 #hydrophobicity_charge_placeholder' + Math.floor((sec_strand_datapoints[j][0] - 1)/200) ).append('');}}if($('#AutoAnnotator_container_1380912466041 #acc_checkbox').prop('checked') == true){for ( j = 0 ; j < acc_buried_datapoints.length ; j++ ){$('#AutoAnnotator_container_1380912466041 #hydrophobicity_charge_placeholder' + Math.floor((acc_buried_datapoints[j][0] - 1)/200) ).append('');}for ( j = 0 ; j < acc_exposed_datapoints.length ; j++ ){$('#AutoAnnotator_container_1380912466041 #hydrophobicity_charge_placeholder' + Math.floor((acc_exposed_datapoints[j][0] - 1)/200) ).append('');}}}catch(err){txt='There was an error while drawing the selected elements for the plot.\n';txt=txt+'The originating error is:\n' + err + '\n\n';throw(txt);}}</script></html>
Sequence and Features
Assembly Compatibility:
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal BglII site found at 189
Illegal XhoI site found at 599
Illegal XhoI site found at 1189 - 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000INCOMPATIBLE WITH RFC[1000]Illegal SapI.rc site found at 316