Difference between revisions of "Part:BBa K1159209"

 
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<span class='h3bb'>Sequence and Features</span>
 
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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_1381264567956'><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1381264567956 --><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 N-Part</strong> using the stop codon in the suffix, so ACCGGT was added (in italics) to the 3' end: (underlined part encodes the protein)<br><span class="AutoAnnotatorSequence">&nbsp;AACA<u>ATGGAAACC&nbsp;...&nbsp;CCAACTAAG<i>ACCGGT</i></u></span><br>&nbsp;<strong>ORF</strong> from nucleotide position 5 to 634 (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">METDTLLLWVLLLWVPGS<b>TG</b>D<b>TG</b>VFTLEDFVGDWRQTAGYNLDQVLEQGGVSSLFQNLGVSVTPIQRIVLSGENGLKIDIHVIIPYEGLSGDQMGQIEKI<br>FKVVYPVDDHHFKVILHYGTLVIDGVTPNMIDYFGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLINPDGSLLFRVTINGVTGWRLCERILA<b>TG</b><u>AHIVM</u><br><u>VDAYKPTK</u>TG*</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">19 to 20, 22 to 23, 194 to 195</td></tr><tr><td class="AutoAnnotatorSeqFeat1"></td><td class="AutoAnnotatorSeqFeat2a">Spy-tag:&nbsp;</td><td class="AutoAnnotatorSeqFeat3">196 to 208</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">5 (2.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Arg (R)</td><td class="AutoAnnotatorInnerAmino">7 (3.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asn (N)</td><td class="AutoAnnotatorInnerAmino">8 (3.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asp (D)</td><td class="AutoAnnotatorInnerAmino">15 (7.1%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Cys (C)</td><td class="AutoAnnotatorInnerAmino">1 (0.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gln (Q)</td><td class="AutoAnnotatorInnerAmino">7 (3.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Glu (E)</td><td class="AutoAnnotatorInnerAmino">9 (4.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gly (G)</td><td class="AutoAnnotatorInnerAmino">25 (11.9%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">His (H)</td><td class="AutoAnnotatorInnerAmino">5 (2.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ile (I)</td><td class="AutoAnnotatorInnerAmino">19 (9.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Leu (L)</td><td class="AutoAnnotatorInnerAmino">22 (10.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Lys (K)</td><td class="AutoAnnotatorInnerAmino">9 (4.3%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Met (M)</td><td class="AutoAnnotatorInnerAmino">4 (1.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Phe (F)</td><td class="AutoAnnotatorInnerAmino">8 (3.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Pro (P)</td><td class="AutoAnnotatorInnerAmino">8 (3.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ser (S)</td><td class="AutoAnnotatorInnerAmino">7 (3.3%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Thr (T)</td><td class="AutoAnnotatorInnerAmino">17 (8.1%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Trp (W)</td><td class="AutoAnnotatorInnerAmino">5 (2.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Tyr (Y)</td><td class="AutoAnnotatorInnerAmino">7 (3.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Val (V)</td><td class="AutoAnnotatorInnerAmino">22 (10.5%)</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">210</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Positively charged (Arg+Lys):</td><td class="AutoAnnotatorAminoCountingInner3">16 (7.6%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Negatively charged (Asp+Glu):</td><td class="AutoAnnotatorAminoCountingInner3">24 (11.4%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Aromatic (Phe+His+Try+Tyr):</td><td class="AutoAnnotatorAminoCountingInner3">25 (11.9%)</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>1061</sub>H<sub>1656</sub>N<sub>270</sub>O<sub>305</sub>S<sub>5</sub></td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Molecular mass [Da]:</td><td class="AutoAnnotatorBiochemParInner3">23234.7</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Theoretical pI:</td><td class="AutoAnnotatorBiochemParInner3">5.01</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">37930 / 37993 (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_1381264567956()' 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 (0.66)</td><td class="AutoAnnotatorCodonUsage3">good (0.68)</td><td class="AutoAnnotatorCodonUsage3">good (0.63)</td><td class="AutoAnnotatorCodonUsage3">excellent (0.84)</td><td class="AutoAnnotatorCodonUsage3">excellent (0.89)</td><td class="AutoAnnotatorCodonUsage3">good (0.80)</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/Q9GV45'>Q9GV45</a> (90% identity on 169 AAs)</td></tr><tr><td class="AutoAnnotatorAlignment1"></td><td class="AutoAnnotatorAlignment2">TrEML:</td><td class="AutoAnnotatorAlignment3">&nbsp;- </td></tr><tr><td class="AutoAnnotatorAlignment1"></td><td class="AutoAnnotatorAlignment2">PDB:</td><td class="AutoAnnotatorAlignment3">&nbsp;- </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 (44%)</td></tr><tr><td class="AutoAnnotatorLocalization1"></td><td class="AutoAnnotatorLocalization2">Eukarya:</td><td class="AutoAnnotatorLocalization3">secreted (31%)</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'> - </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_1381264567956(){hydrophobicity_datapoints = [[2.5,-1.30],[3.5,-0.92],[4.5,0.54],[5.5,1.44],[6.5,1.96],[7.5,2.94],[8.5,2.94],[9.5,2.94],[10.5,2.94],[11.5,2.94],[12.5,2.94],[13.5,1.86],[14.5,1.02],[15.5,0.10],[16.5,0.14],[17.5,-0.78],[18.5,-1.16],[19.5,-1.22],[20.5,-1.14],[21.5,-0.16],[22.5,0.48],[23.5,1.04],[24.5,1.94],[25.5,1.32],[26.5,-0.22],[27.5,-0.22],[28.5,0.76],[29.5,-0.08],[30.5,-0.08],[31.5,0.44],[32.5,-1.02],[33.5,-2.56],[34.5,-2.62],[35.5,-1.56],[36.5,-1.46],[37.5,-0.82],[38.5,-0.82],[39.5,0.08],[40.5,-0.98],[41.5,-1.60],[42.5,-0.50],[43.5,0.96],[44.5,-0.50],[45.5,-0.50],[46.5,0.12],[47.5,-0.80],[48.5,-0.72],[49.5,-0.18],[50.5,0.36],[51.5,1.20],[52.5,1.84],[53.5,0.30],[54.5,-0.24],[55.5,0.68],[56.5,-0.16],[57.5,0.12],[58.5,0.66],[59.5,2.20],[60.5,1.30],[61.5,1.06],[62.5,1.12],[63.5,0.58],[64.5,-1.16],[65.5,-0.12],[66.5,1.04],[67.5,0.90],[68.5,1.44],[69.5,2.26],[70.5,0.66],[71.5,-0.88],[72.5,-1.72],[73.5,-0.80],[74.5,-1.50],[75.5,0.10],[76.5,0.10],[77.5,1.08],[78.5,-0.32],[79.5,1.30],[80.5,1.30],[81.5,2.90],[82.5,1.68],[83.5,2.06],[84.5,0.52],[85.5,-0.46],[86.5,-0.60],[87.5,-0.44],[88.5,-0.26],[89.5,-0.26],[90.5,-0.88],[91.5,-1.26],[92.5,-1.18],[93.5,-1.80],[94.5,-0.20],[95.5,-0.20],[96.5,-1.36],[97.5,-0.38],[98.5,0.88],[99.5,-0.80],[100.5,0.74],[101.5,2.36],[102.5,1.20],[103.5,0.32],[104.5,1.94],[105.5,0.40],[106.5,-1.14],[107.5,-1.52],[108.5,-1.84],[109.5,-2.12],[110.5,-2.20],[111.5,-0.66],[112.5,0.88],[113.5,2.28],[114.5,1.08],[115.5,1.60],[116.5,0.68],[117.5,-0.36],[118.5,-0.36],[119.5,1.12],[120.5,2.28],[121.5,1.66],[122.5,1.72],[123.5,1.80],[124.5,0.82],[125.5,-0.40],[126.5,-0.40],[127.5,0.06],[128.5,0.12],[129.5,-0.44],[130.5,-0.38],[131.5,0.88],[132.5,0.42],[133.5,-1.38],[134.5,-1.00],[135.5,-1.00],[136.5,-2.26],[137.5,-2.26],[138.5,-0.46],[139.5,0.22],[140.5,1.32],[141.5,2.58],[142.5,1.96],[143.5,0.98],[144.5,-0.16],[145.5,-1.78],[146.5,-1.44],[147.5,-0.88],[148.5,0.04],[149.5,0.68],[150.5,1.38],[151.5,0.34],[152.5,1.24],[153.5,0.22],[154.5,-0.34],[155.5,-0.34],[156.5,-0.90],[157.5,-2.44],[158.5,-1.36],[159.5,0.24],[160.5,-0.38],[161.5,-0.38],[162.5,-0.50],[163.5,-0.64],[164.5,-0.64],[165.5,-0.64],[166.5,-0.26],[167.5,-0.06],[168.5,-0.90],[169.5,-1.96],[170.5,-0.50],[171.5,0.58],[172.5,1.84],[173.5,1.02],[174.5,2.02],[175.5,1.12],[176.5,1.26],[177.5,-0.00],[178.5,0.82],[179.5,0.82],[180.5,0.82],[181.5,-0.16],[182.5,0.36],[183.5,-0.46],[184.5,-0.54],[185.5,0.10],[186.5,-0.52],[187.5,-1.24],[188.5,0.56],[189.5,0.56],[190.5,0.42],[191.5,0.98],[192.5,1.80],[193.5,1.26],[194.5,-0.14],[195.5,0.40],[196.5,1.38],[197.5,1.84],[198.5,2.32],[199.5,2.26],[200.5,1.72],[201.5,0.62],[202.5,-0.54],[203.5,-1.70],[204.5,-1.14],[205.5,-2.28],[206.5,-2.16],[207.5,-1.46]];charge_datapoints = [[2.5,-0.40],[3.5,-0.40],[4.5,-0.20],[5.5,-0.20],[6.5,0.00],[7.5,0.00],[8.5,0.00],[9.5,0.00],[10.5,0.00],[11.5,0.00],[12.5,0.00],[13.5,0.00],[14.5,0.00],[15.5,0.00],[16.5,0.00],[17.5,0.00],[18.5,-0.20],[19.5,-0.20],[20.5,-0.20],[21.5,-0.20],[22.5,-0.20],[23.5,0.00],[24.5,0.00],[25.5,-0.20],[26.5,-0.40],[27.5,-0.40],[28.5,-0.40],[29.5,-0.40],[30.5,-0.40],[31.5,-0.20],[32.5,0.00],[33.5,0.00],[34.5,0.00],[35.5,0.20],[36.5,0.20],[37.5,0.00],[38.5,0.00],[39.5,0.00],[40.5,-0.20],[41.5,-0.20],[42.5,-0.20],[43.5,-0.20],[44.5,-0.40],[45.5,-0.20],[46.5,-0.20],[47.5,-0.20],[48.5,-0.20],[49.5,0.00],[50.5,0.00],[51.5,0.00],[52.5,0.00],[53.5,0.00],[54.5,0.00],[55.5,0.00],[56.5,0.00],[57.5,0.00],[58.5,0.00],[59.5,0.00],[60.5,0.00],[61.5,0.00],[62.5,0.00],[63.5,0.00],[64.5,0.20],[65.5,0.20],[66.5,0.20],[67.5,0.20],[68.5,0.20],[69.5,0.00],[70.5,-0.20],[71.5,-0.20],[72.5,-0.20],[73.5,-0.20],[74.5,0.00],[75.5,0.20],[76.5,0.00],[77.5,0.00],[78.5,0.10],[79.5,-0.10],[80.5,-0.10],[81.5,0.10],[82.5,0.10],[83.5,0.00],[84.5,-0.20],[85.5,-0.20],[86.5,-0.20],[87.5,-0.20],[88.5,-0.20],[89.5,-0.20],[90.5,-0.20],[91.5,-0.20],[92.5,-0.20],[93.5,-0.20],[94.5,0.00],[95.5,-0.20],[96.5,0.00],[97.5,0.00],[98.5,0.00],[99.5,0.20],[100.5,0.40],[101.5,0.20],[102.5,0.20],[103.5,0.20],[104.5,0.00],[105.5,-0.20],[106.5,-0.40],[107.5,-0.30],[108.5,-0.20],[109.5,-0.20],[110.5,0.20],[111.5,0.40],[112.5,0.30],[113.5,0.20],[114.5,0.30],[115.5,0.10],[116.5,0.10],[117.5,0.10],[118.5,0.10],[119.5,0.00],[120.5,0.00],[121.5,-0.20],[122.5,-0.20],[123.5,-0.20],[124.5,-0.20],[125.5,-0.20],[126.5,0.00],[127.5,0.00],[128.5,0.00],[129.5,-0.20],[130.5,-0.20],[131.5,-0.20],[132.5,-0.20],[133.5,0.00],[134.5,0.20],[135.5,0.20],[136.5,0.00],[137.5,0.00],[138.5,-0.20],[139.5,-0.20],[140.5,-0.20],[141.5,0.00],[142.5,-0.20],[143.5,-0.20],[144.5,0.00],[145.5,0.20],[146.5,0.20],[147.5,0.40],[148.5,0.40],[149.5,0.20],[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],[157.5,0.20],[158.5,0.20],[159.5,0.20],[160.5,0.00],[161.5,-0.20],[162.5,-0.20],[163.5,-0.20],[164.5,-0.20],[165.5,0.00],[166.5,0.20],[167.5,-0.20],[168.5,-0.20],[169.5,-0.20],[170.5,-0.20],[171.5,-0.20],[172.5,0.00],[173.5,0.20],[174.5,0.20],[175.5,0.20],[176.5,0.20],[177.5,0.20],[178.5,0.00],[179.5,0.00],[180.5,0.00],[181.5,0.00],[182.5,0.00],[183.5,0.20],[184.5,0.20],[185.5,0.20],[186.5,0.00],[187.5,0.20],[188.5,0.00],[189.5,0.00],[190.5,0.00],[191.5,0.20],[192.5,0.00],[193.5,0.00],[194.5,0.10],[195.5,0.10],[196.5,0.10],[197.5,0.10],[198.5,0.10],[199.5,-0.20],[200.5,-0.20],[201.5,-0.20],[202.5,0.00],[203.5,0.00],[204.5,0.20],[205.5,0.40],[206.5,0.40],[207.5,0.20]];dis_datapoints = [];trans_datapoints = [];sec_helix_datapoints = [[4,12],[34,37],[42,47],[51,57],[91,97],[130,133],[185,193]];sec_strand_datapoints = [[13,15],[23,27],[62,71],[77,85],[98,106],[112,117],[121,124],[140,144],[148,155],[160,167],[173,180],[197,200],[201,202]];acc_exposed_datapoints = [[1,4],[16,17],[19,22],[32,33],[35,36],[39,39],[41,41],[43,43],[47,49],[56,57],[59,59],[73,75],[77,77],[87,88],[90,92],[95,95],[99,99],[108,110],[125,125],[132,132],[135,135],[137,137],[139,139],[145,148],[157,160],[164,164],[170,170],[189,189],[195,195],[205,210]];acc_buried_datapoints = [[6,15],[23,23],[25,25],[27,27],[30,31],[34,34],[37,38],[45,46],[51,55],[60,60],[62,63],[65,65],[68,70],[76,76],[78,78],[80,86],[93,94],[97,97],[100,101],[103,105],[107,107],[112,112],[114,123],[126,126],[130,131],[134,134],[140,144],[149,149],[151,151],[153,155],[161,161],[166,167],[172,175],[177,179],[181,182],[184,184],[187,188],[191,193],[196,200],[201,201],[203,203]];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( $('#AutoAnnotator_container_1381264567956 #hydrophobicity_charge_button').val() =='Show' ){$('#AutoAnnotator_container_1381264567956 #hydrophobicity_charge_container').css('display','block');$('#AutoAnnotator_container_1381264567956 #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_1381264567956 #hydrophobicity_charge_explanation').html(description_html);plot_according_to_selectors_1381264567956();$('#AutoAnnotator_container_1381264567956 #AutoAnnotator_plot_selectors').find('input').click(plot_according_to_selectors_1381264567956);}else{$('#AutoAnnotator_container_1381264567956 #hydrophobicity_charge_container').css('display','none');$('#AutoAnnotator_container_1381264567956 #hydrophobicity_charge_button').val('Show');$('#AutoAnnotator_container_1381264567956 #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_1381264567956(){try{var plot_datasets = [[],[]];if($('#AutoAnnotator_container_1381264567956 #hydrophobicity_checkbox').prop('checked') == true){plot_datasets[0] = { color: 'rgba(100,149,237,1)',data: hydrophobicity_datapoints,label: 'Hydrophobicity',lines: { show: true, fill: true, fillColor: 'rgba(100,149,237,0.1)' },yaxis: 1};}if($('#AutoAnnotator_container_1381264567956 #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_1381264567956 #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_1381264567956 #dis_checkbox').prop('checked') == true){for ( j = 0 ; j < dis_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381264567956 #hydrophobicity_charge_placeholder' + Math.floor((dis_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_dis\' style=\'left:' + ((pos_of_first_tick - 8 + (dis_datapoints[j][0] - 1)*tick_diff - Math.floor((dis_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px;\'><b>' + (j+1) + '</b></div>');$('#AutoAnnotator_container_1381264567956 #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($('#AutoAnnotator_container_1381264567956 #trans_checkbox').prop('checked') == true){for ( j = 0 ; j < trans_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381264567956 #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($('#AutoAnnotator_container_1381264567956 #sec_checkbox').prop('checked') == true){for ( j = 0 ; j < sec_helix_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381264567956 #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++ ){$('#AutoAnnotator_container_1381264567956 #hydrophobicity_charge_placeholder' + Math.floor((sec_strand_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_sec_strand\' style=\'width:' + (((sec_strand_datapoints[j][1] - sec_strand_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px; left:' + ((pos_of_first_tick + (sec_strand_datapoints[j][0] - 1.5)*tick_diff - Math.floor((sec_strand_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px\'></div>');}}if($('#AutoAnnotator_container_1381264567956 #acc_checkbox').prop('checked') == true){for ( j = 0 ; j < acc_buried_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381264567956 #hydrophobicity_charge_placeholder' + Math.floor((acc_buried_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_acc_buried\' style=\'width:' + (((acc_buried_datapoints[j][1] - acc_buried_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px; left:' + ((pos_of_first_tick + (acc_buried_datapoints[j][0] - 1.5)*tick_diff - Math.floor((acc_buried_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px\'></div>');}for ( j = 0 ; j < acc_exposed_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381264567956 #hydrophobicity_charge_placeholder' + Math.floor((acc_exposed_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_acc_exposed\' style=\'width:' + (((acc_exposed_datapoints[j][1] - acc_exposed_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px; left:' + ((pos_of_first_tick + (acc_exposed_datapoints[j][0] - 1.5)*tick_diff - Math.floor((acc_exposed_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px\'></div>');}}}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>
  
 
<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  

Latest revision as of 20:36, 8 October 2013

Secretory nLuc_SpyTag fusion (IgKappa-SigP_nLuc_SpyTag) in RFC[25] N-Part

Secretory Fusionprotein consisting N-terminal nLuc and C-terminal SpyTag (IgKappa-SigP_nLuc_SpyTag) in RFC[25] N-Part. This construct is flanked by RFC[25] N-part prefix and suffix. Note: This means only protein fusions to the C-terminus of this part is possible, adding promoters (typically RFC[10]) into the prefix or terminators/IRES (typically RFC[10]) into the suffix of this part is nevertheless possible

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal XhoI site found at 83
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]

Protein data table for BioBrick BBa_ automatically created by the BioBrick-AutoAnnotator version 1.0
Nucleotide sequence in RFC 25 N-Part using the stop codon in the suffix, so ACCGGT was added (in italics) to the 3' end: (underlined part encodes the protein)
 AACAATGGAAACC ... CCAACTAAGACCGGT
 ORF from nucleotide position 5 to 634 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
1 
101 
201 		METDTLLLWVLLLWVPGSTGDTGVFTLEDFVGDWRQTAGYNLDQVLEQGGVSSLFQNLGVSVTPIQRIVLSGENGLKIDIHVIIPYEGLSGDQMGQIEKI
FKVVYPVDDHHFKVILHYGTLVIDGVTPNMIDYFGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLINPDGSLLFRVTINGVTGWRLCERILATGAHIVM
VDAYKPTKTG*
Sequence features: (with their position in the amino acid sequence, see the list of supported features)
RFC25 scar (shown in bold): 19 to 20, 22 to 23, 194 to 195
Spy-tag: 196 to 208
Amino acid composition:
Ala (A)5 (2.4%)
Arg (R)7 (3.3%)
Asn (N)8 (3.8%)
Asp (D)15 (7.1%)
Cys (C)1 (0.5%)
Gln (Q)7 (3.3%)
Glu (E)9 (4.3%)
Gly (G)25 (11.9%)
His (H)5 (2.4%)
Ile (I)19 (9.0%)
Leu (L)22 (10.5%)
Lys (K)9 (4.3%)
Met (M)4 (1.9%)
Phe (F)8 (3.8%)
Pro (P)8 (3.8%)
Ser (S)7 (3.3%)
Thr (T)17 (8.1%)
Trp (W)5 (2.4%)
Tyr (Y)7 (3.3%)
Val (V)22 (10.5%)
Amino acid counting
Total number:210
Positively charged (Arg+Lys):16 (7.6%)
Negatively charged (Asp+Glu):24 (11.4%)
Aromatic (Phe+His+Try+Tyr):25 (11.9%)
Biochemical parameters
Atomic composition:C1061H1656N270O305S5
Molecular mass [Da]:23234.7
Theoretical pI:5.01
Extinction coefficient at 280 nm [M-1 cm-1]:37930 / 37993 (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 (0.66)good (0.68)good (0.63)excellent (0.84)excellent (0.89)good (0.80)
Alignments (obtained from PredictProtein.org)
SwissProt:Q9GV45 (90% identity on 169 AAs)
TrEML: -
PDB: -
Predictions (obtained from PredictProtein.org)
Subcellular Localization (reliability in brackets)
Archaea:secreted (100%)
Bacteria:secreted (44%)
Eukarya:secreted (31%)
Gene Ontology (reliability in brackets)
Molecular Function Ontology: -
Biological Process Ontology: -
 
Predicted features:
Disulfid bridges: -
Transmembrane helices: -
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