Difference between revisions of "Part:BBa K1159108"
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<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>
 
<partinfo>BBa_K1159108 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K1159108 SequenceAndFeatures</partinfo>
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<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_1381261291225'><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1381261291225 --><th id="AutoAnnotatorHeader" colspan="2">Protein data table for BioBrick <a href="https://parts.igem.org/wiki/index.php?title=Part:BBa_<!------------------------Enter BioBrick number here------------------------>">BBa_<!------------------------Enter BioBrick number here------------------------></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">&nbsp;<u><i>ATGGCCGGC</i>GGAGAAAGC&nbsp;...&nbsp;CATGTTGAC<i>ACCGGT</i></u></span><br>&nbsp;<strong>ORF</strong> from nucleotide position -8 to 777 (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;</td><td class="AutoAnnotatorSeqSeq">MAGGESLFKGPRDYNPISSTICHLTNESDGHTTSLYGIGFGPFIITNKHLFRRNNGTLLVQSLHGVFKVKNTTTLQQHL<u>IDGR</u>DMIIIRMPKDFPPFPQK<br>LKFREPQREERICLVTTNFQT<b>TG</b>GGSAGGSGSGSSGGSSGASGTGTAGGTGSGSGTGSG<b>TG</b>MFLPTDYCCRLSDQEYMELVFENGQILAKGQRSNVSLHN<br>QRTKSIMDLYEAEYNEDFMKSIIHGGGGAITNLGDTQVVPQSHVAAAHETNMLESNKHVDTG*</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">Factor Xa cleavage site:&nbsp;</td><td class="AutoAnnotatorSeqFeat3">80 to 83</td></tr><tr><td class="AutoAnnotatorSeqFeat1"></td><td class="AutoAnnotatorSeqFeat2a">RFC25 scar (shown in bold):&nbsp;</td><td class="AutoAnnotatorSeqFeat3">122 to 123, 160 to 161</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">10 (3.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Arg (R)</td><td class="AutoAnnotatorInnerAmino">11 (4.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asn (N)</td><td class="AutoAnnotatorInnerAmino">14 (5.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asp (D)</td><td class="AutoAnnotatorInnerAmino">11 (4.2%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Cys (C)</td><td class="AutoAnnotatorInnerAmino">4 (1.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gln (Q)</td><td class="AutoAnnotatorInnerAmino">12 (4.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Glu (E)</td><td class="AutoAnnotatorInnerAmino">13 (5.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gly (G)</td><td class="AutoAnnotatorInnerAmino">38 (14.5%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">His (H)</td><td class="AutoAnnotatorInnerAmino">10 (3.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ile (I)</td><td class="AutoAnnotatorInnerAmino">15 (5.7%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Leu (L)</td><td class="AutoAnnotatorInnerAmino">19 (7.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Lys (K)</td><td class="AutoAnnotatorInnerAmino">11 (4.2%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Met (M)</td><td class="AutoAnnotatorInnerAmino">8 (3.1%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Phe (F)</td><td class="AutoAnnotatorInnerAmino">12 (4.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Pro (P)</td><td class="AutoAnnotatorInnerAmino">10 (3.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ser (S)</td><td class="AutoAnnotatorInnerAmino">24 (9.2%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Thr (T)</td><td class="AutoAnnotatorInnerAmino">24 (9.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Trp (W)</td><td class="AutoAnnotatorInnerAmino">0 (0.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Tyr (Y)</td><td class="AutoAnnotatorInnerAmino">6 (2.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Val (V)</td><td class="AutoAnnotatorInnerAmino">10 (3.8%)</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">262</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Positively charged (Arg+Lys):</td><td class="AutoAnnotatorAminoCountingInner3">22 (8.4%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Negatively charged (Asp+Glu):</td><td class="AutoAnnotatorAminoCountingInner3">24 (9.2%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Aromatic (Phe+His+Try+Tyr):</td><td class="AutoAnnotatorAminoCountingInner3">28 (10.7%)</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>1209</sub>H<sub>1902</sub>N<sub>352</sub>O<sub>391</sub>S<sub>12</sub></td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Molecular mass [Da]:</td><td class="AutoAnnotatorBiochemParInner3">28009.2</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Theoretical pI:</td><td class="AutoAnnotatorBiochemParInner3">6.55</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">8940 / 9190 (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_1381261291225()' 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></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 (0.73)</td><td class="AutoAnnotatorCodonUsage3">good (0.72)</td><td class="AutoAnnotatorCodonUsage3">good (0.69)</td><td class="AutoAnnotatorCodonUsage3">good (0.74)</td><td class="AutoAnnotatorCodonUsage3">excellent (0.82)</td><td class="AutoAnnotatorCodonUsage3">good (0.69)</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/P04517'>P04517</a> (49% identity on 239 AAs), <a href='http://www.uniprot.org/uniprot/P31999'>P31999</a> (36% identity on 222 AAs)</td></tr><tr><td class="AutoAnnotatorAlignment1"></td><td class="AutoAnnotatorAlignment2">TrEML:</td><td class="AutoAnnotatorAlignment3"><a href='http://www.uniprot.org/uniprot/Q000U0'>Q000U0</a> (49% identity on 239 AAs), <a href='http://www.uniprot.org/uniprot/A4UQV2'>A4UQV2</a> (48% identity on 239 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=1lvm'>1lvm</a> (65% identity on 178 AAs), <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1q31'>1q31</a> (65% identity on 175 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">secreted (100%)</td></tr><tr><td class="AutoAnnotatorLocalization1"></td><td class="AutoAnnotatorLocalization2">Bacteria:</td><td class="AutoAnnotatorLocalization3">secreted (56%)</td></tr><tr><td class="AutoAnnotatorLocalization1"></td><td class="AutoAnnotatorLocalization2">Eukarya:</td><td class="AutoAnnotatorLocalization3">cytosol (20%)</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:0005515'>GO:0005515</a> (70%), <a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0043621'>GO:0043621</a> (13%)</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:0006508'>GO:0006508</a> (32%), <a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0006410'>GO:0006410</a> (26%)</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></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_1381261291225(){hydrophobicity_datapoints = [[2.5,-0.12],[3.5,-0.66],[4.5,-0.26],[5.5,0.38],[6.5,-0.32],[7.5,0.30],[8.5,0.14],[9.5,-1.52],[10.5,-2.78],[11.5,-2.26],[12.5,-2.88],[13.5,-2.88],[14.5,-1.08],[15.5,-0.54],[16.5,-0.44],[17.5,0.12],[18.5,1.34],[19.5,0.94],[20.5,0.46],[21.5,1.38],[22.5,1.38],[23.5,-0.22],[24.5,-1.42],[25.5,-0.94],[26.5,-2.40],[27.5,-2.34],[28.5,-2.28],[29.5,-1.72],[30.5,-1.70],[31.5,-1.16],[32.5,-0.32],[33.5,0.06],[34.5,0.12],[35.5,1.16],[36.5,1.24],[37.5,1.04],[38.5,1.22],[39.5,0.98],[40.5,0.64],[41.5,1.62],[42.5,1.96],[43.5,1.90],[44.5,1.52],[45.5,0.18],[46.5,-1.36],[47.5,-1.50],[48.5,-0.80],[49.5,-1.00],[50.5,-1.12],[51.5,-1.18],[52.5,-2.64],[53.5,-3.28],[54.5,-2.52],[55.5,-0.86],[56.5,0.60],[57.5,2.14],[58.5,1.52],[59.5,1.50],[60.5,1.50],[61.5,0.10],[62.5,-0.82],[63.5,0.72],[64.5,1.44],[65.5,-0.10],[66.5,1.38],[67.5,0.68],[68.5,-0.86],[69.5,-1.56],[70.5,-0.92],[71.5,-1.90],[72.5,-0.36],[73.5,-0.36],[74.5,-0.92],[75.5,-1.42],[76.5,-0.52],[77.5,-0.38],[78.5,-0.38],[79.5,0.24],[80.5,-0.02],[81.5,-1.48],[82.5,-2.00],[83.5,-0.40],[84.5,0.58],[85.5,2.38],[86.5,2.18],[87.5,2.18],[88.5,0.96],[89.5,-0.72],[90.5,-2.32],[91.5,-0.86],[92.5,-1.56],[93.5,-1.56],[94.5,-0.22],[95.5,0.16],[96.5,-1.10],[97.5,-1.56],[98.5,-0.48],[99.5,-1.82],[100.5,-0.94],[101.5,-1.14],[102.5,-1.06],[103.5,-2.14],[104.5,-2.06],[105.5,-3.52],[106.5,-3.32],[107.5,-3.32],[108.5,-3.90],[109.5,-2.30],[110.5,-0.90],[111.5,0.56],[112.5,2.10],[113.5,2.86],[114.5,1.82],[115.5,0.62],[116.5,0.42],[117.5,-1.12],[118.5,-1.12],[119.5,-1.12],[120.5,-0.50],[121.5,-1.14],[122.5,-0.52],[123.5,-0.54],[124.5,-0.04],[125.5,-0.04],[126.5,-0.04],[127.5,-0.12],[128.5,-0.04],[129.5,-0.56],[130.5,-0.56],[131.5,-0.64],[132.5,-0.64],[133.5,-0.64],[134.5,-0.56],[135.5,-0.64],[136.5,-0.64],[137.5,-0.56],[138.5,-0.12],[139.5,-0.20],[140.5,-0.12],[141.5,-0.10],[142.5,-0.10],[143.5,-0.60],[144.5,-0.08],[145.5,-0.08],[146.5,-0.02],[147.5,-0.08],[148.5,-0.02],[149.5,-0.54],[150.5,-0.54],[151.5,-0.62],[152.5,-0.56],[153.5,-0.62],[154.5,-0.54],[155.5,-0.62],[156.5,-0.54],[157.5,-0.60],[158.5,-0.54],[159.5,-0.08],[160.5,0.64],[161.5,1.48],[162.5,1.30],[163.5,1.24],[164.5,0.16],[165.5,-0.66],[166.5,-0.92],[167.5,-0.10],[168.5,-0.86],[169.5,0.60],[170.5,0.70],[171.5,-0.50],[172.5,-1.70],[173.5,-1.50],[174.5,-2.52],[175.5,-1.98],[176.5,-1.98],[177.5,-0.52],[178.5,1.02],[179.5,1.84],[180.5,0.76],[181.5,0.76],[182.5,-0.08],[183.5,-1.62],[184.5,-1.28],[185.5,0.18],[186.5,1.24],[187.5,0.54],[188.5,1.16],[189.5,-0.44],[190.5,-2.10],[191.5,-2.62],[192.5,-2.54],[193.5,-1.62],[194.5,-1.08],[195.5,0.58],[196.5,0.10],[197.5,0.10],[198.5,-1.44],[199.5,-2.18],[200.5,-3.08],[201.5,-3.22],[202.5,-2.68],[203.5,-1.08],[204.5,0.20],[205.5,-0.36],[206.5,1.18],[207.5,1.08],[208.5,-0.52],[209.5,-0.54],[210.5,-0.54],[211.5,-1.56],[212.5,-2.00],[213.5,-2.00],[214.5,-3.06],[215.5,-1.80],[216.5,-1.16],[217.5,-1.24],[218.5,-0.70],[219.5,0.90],[220.5,1.24],[221.5,0.22],[222.5,0.92],[223.5,1.00],[224.5,0.02],[225.5,-0.96],[226.5,0.04],[227.5,1.02],[228.5,0.96],[229.5,0.34],[230.5,1.18],[231.5,0.74],[232.5,-0.86],[233.5,-0.86],[234.5,-0.86],[235.5,-0.78],[236.5,0.14],[237.5,0.52],[238.5,-0.04],[239.5,0.50],[240.5,-0.98],[241.5,-0.98],[242.5,-0.30],[243.5,0.76],[244.5,1.28],[245.5,1.28],[246.5,-0.26],[247.5,-0.76],[248.5,-1.82],[249.5,-1.80],[250.5,-0.40],[251.5,-0.40],[252.5,-0.42],[253.5,-0.42],[254.5,-1.58],[255.5,-2.98],[256.5,-1.44],[257.5,-1.98],[258.5,-1.42],[259.5,-0.72]];charge_datapoints = [[2.5,-0.20],[3.5,-0.20],[4.5,-0.20],[5.5,-0.20],[6.5,0.00],[7.5,0.20],[8.5,0.20],[9.5,0.40],[10.5,0.20],[11.5,0.00],[12.5,0.00],[13.5,0.00],[14.5,-0.20],[15.5,0.00],[16.5,0.00],[17.5,0.00],[18.5,0.00],[19.5,0.00],[20.5,0.10],[21.5,0.10],[22.5,0.10],[23.5,0.10],[24.5,-0.10],[25.5,-0.20],[26.5,-0.40],[27.5,-0.40],[28.5,-0.30],[29.5,-0.10],[30.5,-0.10],[31.5,0.10],[32.5,0.10],[33.5,-0.00],[34.5,-0.00],[35.5,-0.00],[36.5,-0.00],[37.5,-0.00],[38.5,-0.00],[39.5,-0.00],[40.5,-0.00],[41.5,-0.00],[42.5,-0.00],[43.5,-0.00],[44.5,-0.00],[45.5,0.20],[46.5,0.30],[47.5,0.30],[48.5,0.30],[49.5,0.50],[50.5,0.50],[51.5,0.40],[52.5,0.40],[53.5,0.40],[54.5,0.20],[55.5,0.00],[56.5,0.00],[57.5,0.00],[58.5,0.00],[59.5,0.00],[60.5,0.00],[61.5,0.10],[62.5,0.10],[63.5,0.10],[64.5,0.10],[65.5,0.30],[66.5,0.20],[67.5,0.40],[68.5,0.40],[69.5,0.40],[70.5,0.20],[71.5,0.20],[72.5,0.00],[73.5,0.00],[74.5,0.00],[75.5,0.10],[76.5,0.10],[77.5,0.10],[78.5,-0.10],[79.5,-0.10],[80.5,0.00],[81.5,-0.20],[82.5,-0.20],[83.5,0.00],[84.5,0.00],[85.5,-0.20],[86.5,0.20],[87.5,0.20],[88.5,0.20],[89.5,0.40],[90.5,0.20],[91.5,0.00],[92.5,0.00],[93.5,0.00],[94.5,-0.20],[95.5,0.00],[96.5,0.00],[97.5,0.20],[98.5,0.20],[99.5,0.40],[100.5,0.40],[101.5,0.60],[102.5,0.20],[103.5,0.20],[104.5,0.00],[105.5,0.20],[106.5,-0.20],[107.5,-0.20],[108.5,0.00],[109.5,0.00],[110.5,-0.20],[111.5,0.00],[112.5,0.20],[113.5,0.00],[114.5,0.00],[115.5,0.00],[116.5,0.00],[117.5,0.00],[118.5,0.00],[119.5,0.00],[120.5,0.00],[121.5,0.00],[122.5,0.00],[123.5,0.00],[124.5,0.00],[125.5,0.00],[126.5,0.00],[127.5,0.00],[128.5,0.00],[129.5,0.00],[130.5,0.00],[131.5,0.00],[132.5,0.00],[133.5,0.00],[134.5,0.00],[135.5,0.00],[136.5,0.00],[137.5,0.00],[138.5,0.00],[139.5,0.00],[140.5,0.00],[141.5,0.00],[142.5,0.00],[143.5,0.00],[144.5,0.00],[145.5,0.00],[146.5,0.00],[147.5,0.00],[148.5,0.00],[149.5,0.00],[150.5,0.00],[151.5,0.00],[152.5,0.00],[153.5,0.00],[154.5,0.00],[155.5,0.00],[156.5,0.00],[157.5,0.00],[158.5,0.00],[159.5,0.00],[160.5,0.00],[161.5,0.00],[162.5,0.00],[163.5,0.00],[164.5,-0.20],[165.5,-0.20],[166.5,-0.20],[167.5,-0.20],[168.5,0.00],[169.5,0.20],[170.5,0.20],[171.5,0.00],[172.5,0.00],[173.5,-0.40],[174.5,-0.40],[175.5,-0.40],[176.5,-0.40],[177.5,-0.40],[178.5,-0.20],[179.5,-0.20],[180.5,-0.40],[181.5,-0.20],[182.5,-0.20],[183.5,-0.20],[184.5,-0.20],[185.5,0.00],[186.5,0.00],[187.5,0.20],[188.5,0.20],[189.5,0.20],[190.5,0.40],[191.5,0.40],[192.5,0.20],[193.5,0.20],[194.5,0.20],[195.5,0.00],[196.5,0.10],[197.5,0.10],[198.5,0.10],[199.5,0.30],[200.5,0.30],[201.5,0.40],[202.5,0.40],[203.5,0.40],[204.5,0.20],[205.5,0.00],[206.5,-0.20],[207.5,-0.20],[208.5,-0.40],[209.5,-0.40],[210.5,-0.40],[211.5,-0.40],[212.5,-0.40],[213.5,-0.40],[214.5,-0.60],[215.5,-0.40],[216.5,-0.40],[217.5,-0.20],[218.5,-0.00],[219.5,0.20],[220.5,0.20],[221.5,0.30],[222.5,0.10],[223.5,0.10],[224.5,0.10],[225.5,0.10],[226.5,-0.00],[227.5,-0.00],[228.5,-0.00],[229.5,-0.00],[230.5,-0.00],[231.5,-0.00],[232.5,-0.20],[233.5,-0.20],[234.5,-0.20],[235.5,-0.20],[236.5,-0.20],[237.5,-0.00],[238.5,-0.00],[239.5,-0.00],[240.5,0.10],[241.5,0.10],[242.5,0.10],[243.5,0.10],[244.5,0.10],[245.5,0.10],[246.5,-0.10],[247.5,-0.10],[248.5,-0.10],[249.5,-0.10],[250.5,-0.20],[251.5,-0.20],[252.5,-0.20],[253.5,-0.20],[254.5,-0.00],[255.5,0.10],[256.5,0.30],[257.5,0.10],[258.5,0.10],[259.5,-0.10]];dis_datapoints = [];trans_datapoints = [];sec_helix_datapoints = [[16,19]];sec_strand_datapoints = [[20,26],[32,39],[42,46],[49,52],[57,62],[66,70],[73,79],[85,89],[102,103],[111,117],[123,134],[142,146],[162,164],[168,171],[179,182],[202,211],[218,224],[230,239],[243,250]];acc_exposed_datapoints = [[1,3],[5,6],[9,9],[12,13],[29,32],[54,55],[70,71],[73,73],[76,76],[79,79],[81,82],[92,93],[96,96],[99,100],[102,102],[105,105],[107,109],[120,123],[125,125],[137,138],[148,148],[157,159],[167,167],[171,171],[173,176],[179,179],[184,184],[186,186],[190,195],[200,200],[201,201],[204,204],[208,208],[211,217],[225,225],[227,229],[231,232],[234,237],[240,243],[245,246],[249,249],[251,252],[254,258],[260,262]];acc_buried_datapoints = [[10,11],[17,18],[20,22],[24,24],[35,47],[49,51],[56,56],[58,58],[60,60],[62,62],[65,65],[67,67],[69,69],[75,75],[77,77],[80,80],[84,88],[90,91],[97,97],[101,101],[103,103],[112,117],[119,119],[126,126],[128,129],[132,132],[134,134],[139,139],[142,146],[149,149],[152,153],[161,165],[172,172],[180,180],[188,188],[203,203],[207,207],[209,209],[218,218],[223,223],[230,230],[233,233],[239,239],[253,253],[259,259]];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)'}}]};number_of_plots = 2;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( $('#AutoAnnotator_container_1381261291225 #hydrophobicity_charge_button').val() =='Show' ){$('#AutoAnnotator_container_1381261291225 #hydrophobicity_charge_container').css('display','block');$('#AutoAnnotator_container_1381261291225 #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>';$('#AutoAnnotator_container_1381261291225 #hydrophobicity_charge_explanation').html(description_html);plot_according_to_selectors_1381261291225();$('#AutoAnnotator_container_1381261291225 #AutoAnnotator_plot_selectors').find('input').click(plot_according_to_selectors_1381261291225);}else{$('#AutoAnnotator_container_1381261291225 #hydrophobicity_charge_container').css('display','none');$('#AutoAnnotator_container_1381261291225 #hydrophobicity_charge_button').val('Show');$('#AutoAnnotator_container_1381261291225 #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_1381261291225(){try{var plot_datasets = [[],[]];if($('#AutoAnnotator_container_1381261291225 #hydrophobicity_checkbox').prop('checked') == true){plot_datasets[0] = { color: 'rgba(100,149,237,1)',data: hydrophobicity_datapoints,label: 'Hydrophobicity',lines: { show: true, fill: true, fillColor: 'rgba(100,149,237,0.1)' },yaxis: 1};}if($('#AutoAnnotator_container_1381261291225 #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_1381261291225 #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_1381261291225 #dis_checkbox').prop('checked') == true){for ( j = 0 ; j < dis_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381261291225 #hydrophobicity_charge_placeholder' + Math.floor((dis_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_dis\' style=\'left:' + ((pos_of_first_tick - 8 + (dis_datapoints[j][0] - 1)*tick_diff - Math.floor((dis_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px;\'><b>' + (j+1) + '</b></div>');$('#AutoAnnotator_container_1381261291225 #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($('#AutoAnnotator_container_1381261291225 #trans_checkbox').prop('checked') == true){for ( j = 0 ; j < trans_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381261291225 #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($('#AutoAnnotator_container_1381261291225 #sec_checkbox').prop('checked') == true){for ( j = 0 ; j < sec_helix_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381261291225 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<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  

Latest revision as of 19:42, 8 October 2013

N-TEV-Protease_36AALinker_PIF6 (Second part for a light-switchable TEV-Protease) in RFC[25]

This parts encodes a fusion protein consisting the N-terminal half of the TEV Protease as its terminus and first 100 amino acids of PIF6 as its C-terminus. PIF6 interacts with PhyB in the presence of red light. This reaction is reversible by far-red light. Both parts are seperated by a 36 amino acids long flexible linker. This part is flanked by RFC[25] pre- and suffix to allow further protein fusions.

By expressing this part together with its interaction partner BBa_K1159106 that contains the part, which interacts with PIF6, and the C-terminal half of the splitted TEV Protease, they form together a light-switchable TEV Protease system which can be activated by red light and inactivated by far-red light.

Sequence and Features


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 SapI.rc site found at 316

Protein data table for BioBrick BBa_ automatically created by the BioBrick-AutoAnnotator version 1.0
Nucleotide sequence in RFC 25, so ATGGCCGGC and ACCGGT were added (in italics) to the 5' and 3' ends: (underlined part encodes the protein)
 ATGGCCGGCGGAGAAAGC ... CATGTTGACACCGGT
 ORF from nucleotide position -8 to 777 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
1 
101 
201 		MAGGESLFKGPRDYNPISSTICHLTNESDGHTTSLYGIGFGPFIITNKHLFRRNNGTLLVQSLHGVFKVKNTTTLQQHLIDGRDMIIIRMPKDFPPFPQK
LKFREPQREERICLVTTNFQTTGGGSAGGSGSGSSGGSSGASGTGTAGGTGSGSGTGSGTGMFLPTDYCCRLSDQEYMELVFENGQILAKGQRSNVSLHN
QRTKSIMDLYEAEYNEDFMKSIIHGGGGAITNLGDTQVVPQSHVAAAHETNMLESNKHVDTG*
Sequence features: (with their position in the amino acid sequence, see the list of supported features)
Factor Xa cleavage site: 80 to 83
RFC25 scar (shown in bold): 122 to 123, 160 to 161
Amino acid composition:
Ala (A)10 (3.8%)
Arg (R)11 (4.2%)
Asn (N)14 (5.3%)
Asp (D)11 (4.2%)
Cys (C)4 (1.5%)
Gln (Q)12 (4.6%)
Glu (E)13 (5.0%)
Gly (G)38 (14.5%)
His (H)10 (3.8%)
Ile (I)15 (5.7%)
Leu (L)19 (7.3%)
Lys (K)11 (4.2%)
Met (M)8 (3.1%)
Phe (F)12 (4.6%)
Pro (P)10 (3.8%)
Ser (S)24 (9.2%)
Thr (T)24 (9.2%)
Trp (W)0 (0.0%)
Tyr (Y)6 (2.3%)
Val (V)10 (3.8%)
Amino acid counting
Total number:262
Positively charged (Arg+Lys):22 (8.4%)
Negatively charged (Asp+Glu):24 (9.2%)
Aromatic (Phe+His+Try+Tyr):28 (10.7%)
Biochemical parameters
Atomic composition:C1209H1902N352O391S12
Molecular mass [Da]:28009.2
Theoretical pI:6.55
Extinction coefficient at 280 nm [M-1 cm-1]:8940 / 9190 (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 (0.73)good (0.72)good (0.69)good (0.74)excellent (0.82)good (0.69)
Alignments (obtained from PredictProtein.org)
SwissProt:P04517 (49% identity on 239 AAs), P31999 (36% identity on 222 AAs)
TrEML:Q000U0 (49% identity on 239 AAs), A4UQV2 (48% identity on 239 AAs)
PDB:1lvm (65% identity on 178 AAs), 1q31 (65% identity on 175 AAs)
Predictions (obtained from PredictProtein.org)
Subcellular Localization (reliability in brackets)
Archaea:secreted (100%)
Bacteria:secreted (56%)
Eukarya:cytosol (20%)
Gene Ontology (reliability in brackets)
Molecular Function Ontology:GO:0005515 (70%), GO:0043621 (13%)
Biological Process Ontology:GO:0006508 (32%), GO:0006410 (26%)
 
Predicted features:
Disulfid bridges: -
Transmembrane helices: -
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