Difference between revisions of "Part:BBa K1159210"
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<span class='h3bb'>Sequence and Features</span> | <span class='h3bb'>Sequence and Features</span> | ||
<partinfo>BBa_K1159210 SequenceAndFeatures</partinfo> | <partinfo>BBa_K1159210 SequenceAndFeatures</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_1381265226419'><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1381265226419 --><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"> AACA<u>ATGGAAACC ... GCTCATATT<i>ACCGGT</i></u></span><br> <strong>ORF</strong> from nucleotide position 5 to 934 (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 </td><td class="AutoAnnotatorSeqSeq">METDTLLLWVLLLWVPGS<b>TG</b>D<b>TG</b>VFTLEDFVGDWRQTAGYNLDQVLEQGGVSSLFQNLGVSVTPIQRIVLSGENGLKIDIHVIIPYEGLSGDQMGQIEKI<br>FKVVYPVDDHHFKVILHYGTLVIDGVTPNMIDYFGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLINPDGSLLFRVTINGVTGWRLCERILA<b>TG</b>VDTLS<br>GLSSEQGQSGDMTIEEDSATHIKFSKRDEDGKELAGATMELRDSSGKTISTWISDGQVKDFYLYPGKYTFVETAAPDGYEVATAITFTVNEQGQVTVNGK<br>ATKGDAHITG*</td></tr></table></span></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Sequence features:</strong> (with their position in the amino acid sequence, see the <a href="http://2013.igem.org/Team:TU-Munich/Results/Software/FeatureList">list of supported features</a>)<table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorSeqFeat1"></td><td class="AutoAnnotatorSeqFeat2a">RFC25 scar (shown in bold): </td><td class="AutoAnnotatorSeqFeat3">19 to 20, 22 to 23, 194 to 195</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">12 (3.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Arg (R)</td><td class="AutoAnnotatorInnerAmino">9 (2.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asn (N)</td><td class="AutoAnnotatorInnerAmino">10 (3.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asp (D)</td><td class="AutoAnnotatorInnerAmino">24 (7.7%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Cys (C)</td><td class="AutoAnnotatorInnerAmino">1 (0.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gln (Q)</td><td class="AutoAnnotatorInnerAmino">12 (3.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Glu (E)</td><td class="AutoAnnotatorInnerAmino">18 (5.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gly (G)</td><td class="AutoAnnotatorInnerAmino">37 (11.9%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">His (H)</td><td class="AutoAnnotatorInnerAmino">6 (1.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ile (I)</td><td class="AutoAnnotatorInnerAmino">24 (7.7%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Leu (L)</td><td class="AutoAnnotatorInnerAmino">27 (8.7%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Lys (K)</td><td class="AutoAnnotatorInnerAmino">15 (4.8%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Met (M)</td><td class="AutoAnnotatorInnerAmino">5 (1.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Phe (F)</td><td class="AutoAnnotatorInnerAmino">12 (3.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Pro (P)</td><td class="AutoAnnotatorInnerAmino">9 (2.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ser (S)</td><td class="AutoAnnotatorInnerAmino">17 (5.5%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Thr (T)</td><td class="AutoAnnotatorInnerAmino">29 (9.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Trp (W)</td><td class="AutoAnnotatorInnerAmino">6 (1.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Tyr (Y)</td><td class="AutoAnnotatorInnerAmino">10 (3.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Val (V)</td><td class="AutoAnnotatorInnerAmino">27 (8.7%)</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">310</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Positively charged (Arg+Lys):</td><td class="AutoAnnotatorAminoCountingInner3">24 (7.7%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Negatively charged (Asp+Glu):</td><td class="AutoAnnotatorAminoCountingInner3">42 (13.5%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Aromatic (Phe+His+Try+Tyr):</td><td class="AutoAnnotatorAminoCountingInner3">34 (11.0%)</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>1521</sub>H<sub>2368</sub>N<sub>392</sub>O<sub>473</sub>S<sub>6</sub></td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Molecular mass [Da]:</td><td class="AutoAnnotatorBiochemParInner3">33906.2</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Theoretical pI:</td><td class="AutoAnnotatorBiochemParInner3">4.63</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">47900 / 47963 (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_1381265226419()' 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 (0.71)</td><td class="AutoAnnotatorCodonUsage3">good (0.71)</td><td class="AutoAnnotatorCodonUsage3">good (0.67)</td><td class="AutoAnnotatorCodonUsage3">excellent (0.83)</td><td class="AutoAnnotatorCodonUsage3">excellent (0.85)</td><td class="AutoAnnotatorCodonUsage3">good (0.75)</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 167 AAs)</td></tr><tr><td class="AutoAnnotatorAlignment1"></td><td class="AutoAnnotatorAlignment2">TrEML:</td><td class="AutoAnnotatorAlignment3"><a href='http://www.uniprot.org/uniprot/A2RC81'>A2RC81</a> (50% identity on 251 AAs), <a href='http://www.uniprot.org/uniprot/A2T8Z5'>A2T8Z5</a> (50% identity on 251 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=2x5p'>2x5p</a> (92% identity on 99 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 (49%)</td></tr><tr><td class="AutoAnnotatorLocalization1"></td><td class="AutoAnnotatorLocalization2">Eukarya:</td><td class="AutoAnnotatorLocalization3">secreted (52%)</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'> </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_1381265226419(){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],[193.5,1.74],[194.5,0.28],[195.5,-0.22],[196.5,0.68],[197.5,0.60],[198.5,-0.32],[199.5,1.14],[200.5,1.12],[201.5,0.20],[202.5,-0.34],[203.5,-0.96],[204.5,-1.80],[205.5,-2.34],[206.5,-2.34],[207.5,-1.72],[208.5,-1.72],[209.5,-1.26],[210.5,-0.70],[211.5,0.36],[212.5,-0.26],[213.5,-0.26],[214.5,-1.34],[215.5,-1.36],[216.5,-1.90],[217.5,-1.34],[218.5,-1.28],[219.5,0.32],[220.5,-0.30],[221.5,-0.10],[222.5,-0.12],[223.5,-0.26],[224.5,-2.06],[225.5,-1.98],[226.5,-3.24],[227.5,-3.78],[228.5,-3.08],[229.5,-2.96],[230.5,-2.96],[231.5,-1.50],[232.5,-0.44],[233.5,-0.44],[234.5,0.70],[235.5,1.26],[236.5,0.88],[237.5,-0.18],[238.5,0.66],[239.5,-0.60],[240.5,-1.16],[241.5,-1.70],[242.5,-1.16],[243.5,-2.00],[244.5,-1.88],[245.5,-1.32],[246.5,-0.26],[247.5,-0.26],[248.5,-0.32],[249.5,0.28],[250.5,1.32],[251.5,0.26],[252.5,-0.28],[253.5,-0.22],[254.5,-0.74],[255.5,-0.80],[256.5,-1.42],[257.5,-1.42],[258.5,-0.78],[259.5,-0.34],[260.5,-0.42],[261.5,0.10],[262.5,0.48],[263.5,-0.16],[264.5,-0.68],[265.5,-1.70],[266.5,-1.58],[267.5,-0.70],[268.5,0.22],[269.5,0.30],[270.5,0.42],[271.5,0.92],[272.5,0.72],[273.5,-0.44],[274.5,-0.44],[275.5,-0.38],[276.5,-1.00],[277.5,-2.06],[278.5,-0.90],[279.5,0.16],[280.5,0.10],[281.5,0.72],[282.5,2.32],[283.5,1.34],[284.5,1.54],[285.5,1.54],[286.5,2.02],[287.5,0.42],[288.5,-0.14],[289.5,-1.40],[290.5,-1.34],[291.5,-2.88],[292.5,-1.34],[293.5,-0.78],[294.5,0.76],[295.5,0.14],[296.5,0.76],[297.5,-0.86],[298.5,-0.36],[299.5,-1.34],[300.5,-1.42],[301.5,-1.42],[302.5,-1.34],[303.5,-1.34],[304.5,-1.84],[305.5,-0.16],[306.5,-0.22],[307.5,0.40]];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,-0.20],[195.5,-0.20],[196.5,-0.20],[197.5,-0.20],[198.5,-0.20],[199.5,0.00],[200.5,0.00],[201.5,0.00],[202.5,-0.20],[203.5,-0.20],[204.5,-0.20],[205.5,-0.20],[206.5,-0.20],[207.5,0.00],[208.5,-0.20],[209.5,-0.20],[210.5,-0.20],[211.5,-0.20],[212.5,-0.40],[213.5,-0.40],[214.5,-0.60],[215.5,-0.60],[216.5,-0.60],[217.5,-0.40],[218.5,-0.10],[219.5,0.10],[220.5,0.30],[221.5,0.30],[222.5,0.30],[223.5,0.40],[224.5,0.60],[225.5,0.20],[226.5,-0.00],[227.5,-0.20],[228.5,-0.40],[229.5,-0.40],[230.5,-0.40],[231.5,-0.20],[232.5,-0.00],[233.5,-0.00],[234.5,-0.20],[235.5,-0.00],[236.5,-0.00],[237.5,-0.20],[238.5,-0.20],[239.5,-0.00],[240.5,-0.20],[241.5,-0.20],[242.5,-0.00],[243.5,-0.00],[244.5,-0.00],[245.5,0.20],[246.5,0.20],[247.5,0.20],[248.5,0.20],[249.5,-0.00],[250.5,-0.00],[251.5,-0.00],[252.5,-0.20],[253.5,-0.20],[254.5,-0.20],[255.5,-0.20],[256.5,-0.00],[257.5,-0.00],[258.5,-0.00],[259.5,-0.00],[260.5,-0.00],[261.5,-0.20],[262.5,-0.00],[263.5,-0.00],[264.5,0.20],[265.5,0.20],[266.5,0.20],[267.5,0.20],[268.5,0.20],[269.5,-0.20],[270.5,-0.20],[271.5,-0.20],[272.5,-0.20],[273.5,-0.20],[274.5,-0.20],[275.5,-0.20],[276.5,-0.20],[277.5,-0.40],[278.5,-0.40],[279.5,-0.20],[280.5,-0.20],[281.5,-0.20],[282.5,-0.00],[283.5,-0.00],[284.5,-0.00],[285.5,-0.00],[286.5,-0.00],[287.5,-0.00],[288.5,-0.20],[289.5,-0.20],[290.5,-0.20],[291.5,-0.20],[292.5,-0.20],[293.5,-0.00],[294.5,-0.00],[295.5,-0.00],[296.5,-0.00],[297.5,0.20],[298.5,0.20],[299.5,0.20],[300.5,0.40],[301.5,0.40],[302.5,-0.00],[303.5,-0.00],[304.5,0.10],[305.5,-0.10],[306.5,-0.10],[307.5,0.10]];dis_datapoints = [];trans_datapoints = [];sec_helix_datapoints = [];sec_strand_datapoints = [[7,15],[23,31],[38,46],[53,70],[76,78],[82,88],[95,101],[104,106],[111,117],[121,124],[129,133],[138,144],[148,155],[160,167],[172,178],[184,190],[203,204],[212,215],[221,227],[237,243],[248,253],[257,262],[268,273],[285,290],[294,300]];acc_exposed_datapoints = [[1,3],[17,17],[19,22],[32,37],[39,39],[41,41],[43,43],[47,50],[56,57],[59,59],[61,61],[64,64],[67,67],[71,75],[77,77],[79,79],[81,81],[88,88],[90,93],[96,96],[98,98],[100,100],[102,102],[104,104],[106,106],[108,109],[111,111],[118,119],[124,125],[127,129],[132,132],[134,140],[145,148],[150,150],[157,160],[169,170],[172,172],[180,182],[189,189],[193,195],[197,197],[200,200],[201,201],[203,203],[205,209],[211,211],[216,219],[229,233],[244,247],[255,255],[257,257],[265,265],[267,267],[277,277],[280,280],[284,284],[291,292],[294,294],[298,298],[300,300],[303,305],[307,307],[309,310]];acc_buried_datapoints = [[5,15],[23,23],[25,25],[27,27],[42,42],[46,46],[60,60],[62,62],[76,76],[78,78],[80,80],[82,82],[84,84],[86,86],[89,89],[97,97],[107,107],[112,112],[114,115],[122,123],[144,144],[149,149],[151,151],[162,162],[166,166],[171,171],[173,173],[175,175],[177,179],[185,185],[187,187],[199,199],[212,212],[214,214],[222,222],[224,224],[234,234],[236,237],[239,239],[241,241],[249,249],[252,253],[256,256],[258,258],[260,263],[266,266],[268,268],[270,270],[272,272],[275,276],[278,279],[281,281],[285,285],[287,287],[289,289],[295,295],[297,297]];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 = 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( $('#AutoAnnotator_container_1381265226419 #hydrophobicity_charge_button').val() =='Show' ){$('#AutoAnnotator_container_1381265226419 #hydrophobicity_charge_container').css('display','block');$('#AutoAnnotator_container_1381265226419 #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_1381265226419 #hydrophobicity_charge_explanation').html(description_html);plot_according_to_selectors_1381265226419();$('#AutoAnnotator_container_1381265226419 #AutoAnnotator_plot_selectors').find('input').click(plot_according_to_selectors_1381265226419);}else{$('#AutoAnnotator_container_1381265226419 #hydrophobicity_charge_container').css('display','none');$('#AutoAnnotator_container_1381265226419 #hydrophobicity_charge_button').val('Show');$('#AutoAnnotator_container_1381265226419 #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_1381265226419(){try{var plot_datasets = [[],[]];if($('#AutoAnnotator_container_1381265226419 #hydrophobicity_checkbox').prop('checked') == true){plot_datasets[0] = { color: 'rgba(100,149,237,1)',data: hydrophobicity_datapoints,label: 'Hydrophobicity',lines: { show: true, fill: true, fillColor: 'rgba(100,149,237,0.1)' },yaxis: 1};}if($('#AutoAnnotator_container_1381265226419 #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_1381265226419 #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_1381265226419 #dis_checkbox').prop('checked') == true){for ( j = 0 ; j < dis_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381265226419 #hydrophobicity_charge_placeholder' + Math.floor((dis_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_dis\' style=\'left:' + ((pos_of_first_tick - 8 + (dis_datapoints[j][0] - 1)*tick_diff - Math.floor((dis_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px;\'><b>' + (j+1) + '</b></div>');$('#AutoAnnotator_container_1381265226419 #hydrophobicity_charge_placeholder' + 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<!-- Uncomment this to enable Functional Parameter display | <!-- Uncomment this to enable Functional Parameter display | ||
Latest revision as of 20:47, 8 October 2013
Secretory nLuc_SpyCatcher fusion (IgKappa-SigP_nLuc_SpyCatcher) in RFC[25] N-Part
Secretory Fusionprotein consisting N-terminal nLuc and C-terminal SpyCatcher (IgKappa-SigP_nLuc_SpyCatcher) 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:
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal XhoI site found at 83
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
| Protein data table for BioBrick BBa_ automatically created by the BioBrick-AutoAnnotator version 1.0 | ||||||||||||||||||||||||||||||||||||||||||||||
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| 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 ... GCTCATATTACCGGT ORF from nucleotide position 5 to 934 (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 list of supported features)
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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 | ||||||||||||||||||||||||||||||||||||||||||||||
Codon usage
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Alignments (obtained from PredictProtein.org)
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| Predictions (obtained from PredictProtein.org) | ||||||||||||||||||||||||||||||||||||||||||||||
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 TU-Munich 2013 iGEM team. For more information please see the documentation. If you have any questions, comments or suggestions, please leave us a comment. | ||||||||||||||||||||||||||||||||||||||||||||||