Difference between revisions of "Part:BBa K1159301"
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<span class='h3bb'>Sequence and Features</span> | <span class='h3bb'>Sequence and Features</span> | ||
<partinfo>BBa_K1159301 SequenceAndFeatures</partinfo> | <partinfo>BBa_K1159301 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_1381265402771'><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1381265402771 --><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"> <u><i>ATGGCCGGC</i>GTTAGCAAG ... CTGTATAAA<i>ACCGGT</i></u></span><br> <strong>ORF</strong> from nucleotide position -8 to 720 (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 </td><td class="AutoAnnotatorSeqSeq">MAGVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKLICTTGKLPVPWPTLVTTLGYGVQCFARYPDHMKQHDFFKSAMPEGYVQERT<br>IFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGGVQLADHYQQNTPIGDGPVLLPD<br>NHYLSYQSKLSKDPNEKRDHMVLLEFVTAAGITLGMDELYKTG*</td></tr></table></span></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Sequence features:</strong> (with their position in the amino acid sequence, see the <a href="http://2013.igem.org/Team:TU-Munich/Results/Software/FeatureList">list of supported features</a>)<table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorSeqFeat1"></td><td class="AutoAnnotatorSeqFeat2b">None of the supported features appeared in the sequence</td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Amino acid composition:</strong><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Ala (A)</td><td class="AutoAnnotatorInnerAmino">10 (4.1%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Arg (R)</td><td class="AutoAnnotatorInnerAmino">6 (2.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asn (N)</td><td class="AutoAnnotatorInnerAmino">13 (5.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asp (D)</td><td class="AutoAnnotatorInnerAmino">18 (7.4%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Cys (C)</td><td class="AutoAnnotatorInnerAmino">2 (0.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gln (Q)</td><td class="AutoAnnotatorInnerAmino">8 (3.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Glu (E)</td><td class="AutoAnnotatorInnerAmino">16 (6.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gly (G)</td><td class="AutoAnnotatorInnerAmino">26 (10.7%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">His (H)</td><td class="AutoAnnotatorInnerAmino">9 (3.7%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ile (I)</td><td class="AutoAnnotatorInnerAmino">12 (4.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Leu (L)</td><td class="AutoAnnotatorInnerAmino">22 (9.1%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Lys (K)</td><td class="AutoAnnotatorInnerAmino">21 (8.6%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Met (M)</td><td class="AutoAnnotatorInnerAmino">5 (2.1%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Phe (F)</td><td class="AutoAnnotatorInnerAmino">11 (4.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Pro (P)</td><td class="AutoAnnotatorInnerAmino">10 (4.1%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ser (S)</td><td class="AutoAnnotatorInnerAmino">8 (3.3%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Thr (T)</td><td class="AutoAnnotatorInnerAmino">16 (6.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Trp (W)</td><td class="AutoAnnotatorInnerAmino">1 (0.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Tyr (Y)</td><td class="AutoAnnotatorInnerAmino">12 (4.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Val (V)</td><td class="AutoAnnotatorInnerAmino">17 (7.0%)</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">243</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Positively charged (Arg+Lys):</td><td class="AutoAnnotatorAminoCountingInner3">27 (11.1%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Negatively charged (Asp+Glu):</td><td class="AutoAnnotatorAminoCountingInner3">34 (14.0%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Aromatic (Phe+His+Try+Tyr):</td><td class="AutoAnnotatorAminoCountingInner3">33 (13.6%)</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>1218</sub>H<sub>1882</sub>N<sub>322</sub>O<sub>369</sub>S<sub>7</sub></td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Molecular mass [Da]:</td><td class="AutoAnnotatorBiochemParInner3">27164.7</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Theoretical pI:</td><td class="AutoAnnotatorBiochemParInner3">5.71</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">23380 / 23505 (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_1381265402771()' 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 (0.80)</td><td class="AutoAnnotatorCodonUsage3">good (0.76)</td><td class="AutoAnnotatorCodonUsage3">good (0.63)</td><td class="AutoAnnotatorCodonUsage3">good (0.70)</td><td class="AutoAnnotatorCodonUsage3">excellent (0.81)</td><td class="AutoAnnotatorCodonUsage3">good (0.72)</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/P42212'>P42212</a> (95% identity on 238 AAs), <a href='http://www.uniprot.org/uniprot/Q9U6Y3'>Q9U6Y3</a> (26% identity on 217 AAs)</td></tr><tr><td class="AutoAnnotatorAlignment1"></td><td class="AutoAnnotatorAlignment2">TrEML:</td><td class="AutoAnnotatorAlignment3"><a href='http://www.uniprot.org/uniprot/B6UPG7'>B6UPG7</a> (96% identity on 238 AAs), <a href='http://www.uniprot.org/uniprot/B7UCZ6'>B7UCZ6</a> (96% identity on 238 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=1myw'>1myw</a> (97% identity on 228 AAs), <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1qxt'>1qxt</a> (96% identity on 226 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">cytosol (50%)</td></tr><tr><td class="AutoAnnotatorLocalization1"></td><td class="AutoAnnotatorLocalization2">Eukarya:</td><td class="AutoAnnotatorLocalization3">cytosol (36%)</td></tr></table></td><td class="AutoAnnotatorGOOuter"><strong>Gene Ontology</strong> (reliability in brackets)<br><table class="AutoAnnotatorNoBorder"><tr><td class='AutoAnnotatorGO1'></td><td class='AutoAnnotatorGO2'>Molecular Function Ontology:</td><td class='AutoAnnotatorGO3'> - </td></tr><tr><td class='AutoAnnotatorGO1'></td><td class='AutoAnnotatorGO2'>Biological Process Ontology:</td><td class='AutoAnnotatorGO3'><a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0018298'>GO:0018298</a> (44%), <a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0008218'>GO:0008218</a> (31%)</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_1381265402771(){hydrophobicity_datapoints = [[2.5,1.34],[3.5,0.18],[4.5,-0.26],[5.5,-0.88],[6.5,-2.42],[7.5,-1.50],[8.5,-0.16],[9.5,-0.22],[10.5,0.40],[11.5,1.94],[12.5,2.02],[13.5,1.14],[14.5,2.18],[15.5,3.02],[16.5,3.02],[17.5,1.48],[18.5,2.56],[19.5,0.96],[20.5,0.12],[21.5,-1.42],[22.5,0.12],[23.5,-1.34],[24.5,-0.72],[25.5,-1.28],[26.5,-1.36],[27.5,-1.64],[28.5,-1.10],[29.5,-0.18],[30.5,0.30],[31.5,1.00],[32.5,-0.26],[33.5,-0.18],[34.5,-1.72],[35.5,-1.64],[36.5,-2.26],[37.5,-1.20],[38.5,-1.26],[39.5,-0.82],[40.5,-0.82],[41.5,-0.90],[42.5,-0.50],[43.5,-0.50],[44.5,0.52],[45.5,-0.18],[46.5,1.36],[47.5,1.50],[48.5,2.14],[49.5,1.24],[50.5,1.88],[51.5,1.04],[52.5,-0.64],[53.5,-0.38],[54.5,-0.56],[55.5,0.42],[56.5,0.18],[57.5,0.78],[58.5,-0.30],[59.5,-0.12],[60.5,-0.20],[61.5,0.96],[62.5,1.00],[63.5,1.18],[64.5,2.08],[65.5,1.24],[66.5,0.14],[67.5,0.20],[68.5,1.18],[69.5,-0.28],[70.5,0.30],[71.5,1.12],[72.5,1.56],[73.5,-0.18],[74.5,0.26],[75.5,-0.56],[76.5,-1.82],[77.5,-2.82],[78.5,-1.54],[79.5,-2.06],[80.5,-2.44],[81.5,-2.38],[82.5,-2.44],[83.5,-2.26],[84.5,-0.92],[85.5,-1.00],[86.5,-0.52],[87.5,0.54],[88.5,0.36],[89.5,-0.52],[90.5,-0.44],[91.5,-0.36],[92.5,-0.98],[93.5,-0.52],[94.5,-0.90],[95.5,-0.90],[96.5,-1.72],[97.5,-1.60],[98.5,-1.54],[99.5,-0.28],[100.5,0.98],[101.5,1.10],[102.5,0.54],[103.5,-1.06],[104.5,-1.70],[105.5,-2.96],[106.5,-2.44],[107.5,-2.52],[108.5,-1.96],[109.5,-2.78],[110.5,-1.72],[111.5,-2.16],[112.5,-0.54],[113.5,-1.18],[114.5,0.28],[115.5,-0.78],[116.5,-0.16],[117.5,-1.70],[118.5,-1.06],[119.5,-0.86],[120.5,0.68],[121.5,0.06],[122.5,-0.14],[123.5,0.90],[124.5,-0.56],[125.5,-0.64],[126.5,-0.72],[127.5,0.10],[128.5,0.10],[129.5,0.10],[130.5,-0.10],[131.5,-0.10],[132.5,-0.72],[133.5,-2.32],[134.5,-1.70],[135.5,-2.96],[136.5,-1.28],[137.5,0.18],[138.5,0.80],[139.5,0.24],[140.5,0.16],[141.5,0.02],[142.5,-1.44],[143.5,-1.62],[144.5,-1.68],[145.5,-1.16],[146.5,-2.62],[147.5,-2.08],[148.5,-2.46],[149.5,-2.46],[150.5,-1.36],[151.5,-0.92],[152.5,0.14],[153.5,0.64],[154.5,1.70],[155.5,0.16],[156.5,-0.36],[157.5,-1.96],[158.5,-2.60],[159.5,-3.66],[160.5,-3.04],[161.5,-1.36],[162.5,-1.44],[163.5,-0.30],[164.5,-0.30],[165.5,0.34],[166.5,-1.34],[167.5,0.34],[168.5,-0.92],[169.5,-0.86],[170.5,-2.12],[171.5,-0.44],[172.5,-2.04],[173.5,-1.84],[174.5,-1.28],[175.5,-0.66],[176.5,-0.72],[177.5,-0.72],[178.5,0.74],[179.5,1.18],[180.5,0.56],[181.5,-0.92],[182.5,-0.48],[183.5,-1.94],[184.5,-3.00],[185.5,-3.00],[186.5,-2.50],[187.5,-2.56],[188.5,-0.96],[189.5,-0.34],[190.5,-0.34],[191.5,-0.28],[192.5,-0.28],[193.5,-0.34],[194.5,0.50],[195.5,1.96],[196.5,1.72],[197.5,1.34],[198.5,-0.20],[199.5,-1.60],[200.5,-2.62],[201.5,-1.54],[202.5,-1.00],[203.5,-0.56],[204.5,-0.62],[205.5,-0.52],[206.5,-2.06],[207.5,-1.14],[208.5,-1.04],[209.5,-1.12],[210.5,-1.66],[211.5,-1.20],[212.5,-2.66],[213.5,-3.20],[214.5,-3.20],[215.5,-3.40],[216.5,-3.78],[217.5,-3.72],[218.5,-2.64],[219.5,-1.02],[220.5,0.64],[221.5,2.10],[222.5,2.04],[223.5,2.22],[224.5,2.22],[225.5,1.32],[226.5,0.92],[227.5,1.98],[228.5,1.34],[229.5,1.40],[230.5,1.40],[231.5,1.80],[232.5,1.36],[233.5,1.82],[234.5,0.22],[235.5,-0.34],[236.5,-0.34],[237.5,-0.52],[238.5,-1.68],[239.5,-1.12],[240.5,-0.50]];charge_datapoints = [[2.5,0.00],[3.5,0.20],[4.5,0.20],[5.5,0.00],[6.5,-0.20],[7.5,-0.20],[8.5,-0.40],[9.5,-0.40],[10.5,-0.20],[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,-0.20],[18.5,-0.20],[19.5,-0.40],[20.5,-0.40],[21.5,-0.60],[22.5,-0.40],[23.5,-0.40],[24.5,-0.20],[25.5,-0.10],[26.5,0.30],[27.5,0.30],[28.5,0.30],[29.5,0.30],[30.5,0.20],[31.5,-0.00],[32.5,-0.20],[33.5,-0.20],[34.5,-0.40],[35.5,-0.40],[36.5,-0.60],[37.5,-0.40],[38.5,-0.40],[39.5,-0.20],[40.5,-0.20],[41.5,0.20],[42.5,0.20],[43.5,0.20],[44.5,0.20],[45.5,0.40],[46.5,0.20],[47.5,0.20],[48.5,0.20],[49.5,0.20],[50.5,-0.00],[51.5,-0.00],[52.5,0.20],[53.5,0.20],[54.5,0.20],[55.5,0.20],[56.5,0.20],[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,-0.00],[65.5,-0.00],[66.5,-0.00],[67.5,-0.00],[68.5,-0.00],[69.5,-0.00],[70.5,-0.00],[71.5,-0.00],[72.5,-0.00],[73.5,0.20],[74.5,0.20],[75.5,0.20],[76.5,-0.00],[77.5,0.10],[78.5,-0.10],[79.5,0.10],[80.5,0.10],[81.5,0.40],[82.5,0.10],[83.5,0.10],[84.5,-0.10],[85.5,0.10],[86.5,-0.00],[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,-0.20],[95.5,-0.20],[96.5,-0.00],[97.5,-0.00],[98.5,-0.00],[99.5,-0.00],[100.5,0.20],[101.5,0.20],[102.5,-0.00],[103.5,-0.20],[104.5,-0.20],[105.5,-0.20],[106.5,-0.40],[107.5,-0.00],[108.5,0.20],[109.5,0.40],[110.5,0.40],[111.5,0.20],[112.5,-0.00],[113.5,0.20],[114.5,-0.00],[115.5,-0.20],[116.5,-0.00],[117.5,-0.20],[118.5,-0.40],[119.5,-0.40],[120.5,-0.20],[121.5,-0.20],[122.5,0.20],[123.5,0.20],[124.5,-0.00],[125.5,-0.00],[126.5,0.20],[127.5,-0.00],[128.5,-0.00],[129.5,-0.00],[130.5,-0.00],[131.5,-0.00],[132.5,-0.20],[133.5,-0.40],[134.5,-0.20],[135.5,-0.20],[136.5,-0.40],[137.5,-0.20],[138.5,-0.00],[139.5,0.10],[140.5,0.30],[141.5,0.30],[142.5,0.10],[143.5,0.10],[144.5,-0.00],[145.5,-0.20],[146.5,-0.20],[147.5,-0.00],[148.5,0.10],[149.5,0.10],[150.5,0.10],[151.5,0.10],[152.5,0.10],[153.5,-0.00],[154.5,-0.00],[155.5,-0.20],[156.5,-0.00],[157.5,-0.00],[158.5,0.20],[159.5,0.20],[160.5,0.40],[161.5,0.20],[162.5,0.40],[163.5,0.20],[164.5,0.20],[165.5,0.20],[166.5,0.40],[167.5,0.20],[168.5,0.40],[169.5,0.50],[170.5,0.50],[171.5,0.30],[172.5,0.10],[173.5,-0.30],[174.5,-0.40],[175.5,-0.40],[176.5,-0.40],[177.5,-0.20],[178.5,-0.00],[179.5,-0.00],[180.5,-0.20],[181.5,-0.10],[182.5,-0.10],[183.5,-0.10],[184.5,-0.10],[185.5,0.10],[186.5,-0.00],[187.5,-0.00],[188.5,-0.00],[189.5,-0.00],[190.5,-0.20],[191.5,-0.20],[192.5,-0.20],[193.5,-0.20],[194.5,-0.20],[195.5,-0.00],[196.5,-0.00],[197.5,-0.20],[198.5,-0.20],[199.5,-0.10],[200.5,-0.10],[201.5,-0.10],[202.5,0.10],[203.5,0.10],[204.5,-0.00],[205.5,-0.00],[206.5,0.20],[207.5,0.20],[208.5,0.20],[209.5,0.40],[210.5,0.20],[211.5,-0.00],[212.5,-0.00],[213.5,-0.20],[214.5,-0.20],[215.5,0.20],[216.5,-0.00],[217.5,0.10],[218.5,0.30],[219.5,0.10],[220.5,-0.10],[221.5,0.10],[222.5,-0.20],[223.5,-0.20],[224.5,-0.20],[225.5,-0.20],[226.5,-0.20],[227.5,-0.00],[228.5,-0.00],[229.5,-0.00],[230.5,-0.00],[231.5,-0.00],[232.5,-0.00],[233.5,-0.00],[234.5,-0.20],[235.5,-0.40],[236.5,-0.40],[237.5,-0.40],[238.5,-0.20],[239.5,-0.00],[240.5,0.20]];dis_datapoints = [];trans_datapoints = [];sec_helix_datapoints = [[8,13],[59,68],[87,89],[237,240]];sec_strand_datapoints = [[17,25],[29,34],[44,51],[73,75],[97,104],[108,117],[121,130],[142,144],[152,156],[163,174],[179,187],[203,211],[221,231]];acc_exposed_datapoints = [[1,3],[5,6],[8,9],[12,13],[16,16],[22,22],[26,26],[29,29],[35,35],[37,37],[39,39],[42,42],[44,44],[52,53],[55,55],[72,72],[76,76],[79,80],[82,83],[85,85],[88,88],[92,93],[104,104],[106,106],[116,116],[118,120],[129,129],[132,132],[135,136],[138,138],[142,143],[145,149],[158,162],[175,178],[183,183],[186,187],[189,189],[191,195],[197,197],[200,200],[209,209],[212,219],[233,233],[235,235],[237,238],[240,243]];acc_buried_datapoints = [[7,7],[10,11],[15,15],[17,17],[19,19],[21,21],[23,23],[25,25],[27,27],[30,30],[32,32],[34,34],[36,36],[38,38],[43,43],[45,45],[47,47],[49,49],[51,51],[56,67],[70,71],[73,75],[77,78],[87,87],[90,91],[94,95],[100,101],[103,103],[107,107],[109,109],[111,111],[113,113],[115,115],[117,117],[122,122],[126,126],[128,128],[130,130],[133,133],[137,137],[139,140],[144,144],[150,150],[154,156],[164,164],[166,166],[168,168],[170,172],[174,174],[182,182],[184,184],[198,199],[202,204],[206,206],[208,208],[210,210],[221,221],[223,223],[225,225],[227,227],[229,229],[234,234],[239,239]];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( $('#AutoAnnotator_container_1381265402771 #hydrophobicity_charge_button').val() =='Show' ){$('#AutoAnnotator_container_1381265402771 #hydrophobicity_charge_container').css('display','block');$('#AutoAnnotator_container_1381265402771 #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_1381265402771 #hydrophobicity_charge_explanation').html(description_html);plot_according_to_selectors_1381265402771();$('#AutoAnnotator_container_1381265402771 #AutoAnnotator_plot_selectors').find('input').click(plot_according_to_selectors_1381265402771);}else{$('#AutoAnnotator_container_1381265402771 #hydrophobicity_charge_container').css('display','none');$('#AutoAnnotator_container_1381265402771 #hydrophobicity_charge_button').val('Show');$('#AutoAnnotator_container_1381265402771 #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_1381265402771(){try{var plot_datasets = [[],[]];if($('#AutoAnnotator_container_1381265402771 #hydrophobicity_checkbox').prop('checked') == true){plot_datasets[0] = { color: 'rgba(100,149,237,1)',data: hydrophobicity_datapoints,label: 'Hydrophobicity',lines: { show: true, fill: true, fillColor: 'rgba(100,149,237,0.1)' },yaxis: 1};}if($('#AutoAnnotator_container_1381265402771 #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_1381265402771 #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_1381265402771 #dis_checkbox').prop('checked') == true){for ( j = 0 ; j < dis_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381265402771 #hydrophobicity_charge_placeholder' + Math.floor((dis_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_dis\' style=\'left:' + ((pos_of_first_tick - 8 + (dis_datapoints[j][0] - 1)*tick_diff - Math.floor((dis_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px;\'><b>' + (j+1) + '</b></div>');$('#AutoAnnotator_container_1381265402771 #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($('#AutoAnnotator_container_1381265402771 #trans_checkbox').prop('checked') == true){for ( j = 0 ; j < trans_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381265402771 #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($('#AutoAnnotator_container_1381265402771 #sec_checkbox').prop('checked') == true){for ( j = 0 ; j < sec_helix_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381265402771 #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++ ){$('#AutoAnnotator_container_1381265402771 #hydrophobicity_charge_placeholder' + Math.floor((sec_strand_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_sec_strand\' style=\'width:' + (((sec_strand_datapoints[j][1] - sec_strand_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px; left:' + ((pos_of_first_tick + (sec_strand_datapoints[j][0] - 1.5)*tick_diff - Math.floor((sec_strand_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px\'></div>');}}if($('#AutoAnnotator_container_1381265402771 #acc_checkbox').prop('checked') == true){for ( j = 0 ; j < acc_buried_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381265402771 #hydrophobicity_charge_placeholder' + Math.floor((acc_buried_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_acc_buried\' style=\'width:' + (((acc_buried_datapoints[j][1] - acc_buried_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px; left:' + ((pos_of_first_tick + (acc_buried_datapoints[j][0] - 1.5)*tick_diff - Math.floor((acc_buried_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px\'></div>');}for ( j = 0 ; j < acc_exposed_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381265402771 #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 20:50, 8 October 2013
Super Yellow Fluorescent Protein 2 (SYFP2) in RFC[25]
Improved part of BBa_K864100 which originally cannot be fused to other protein domains. This improved version is flanked by RFC[25] pre- and suffix for further protein fusions.
Sequence and Features
Assembly Compatibility:
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 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, so ATGGCCGGC and ACCGGT were added (in italics) to the 5' and 3' ends: (underlined part encodes the protein) ATGGCCGGCGTTAGCAAG ... CTGTATAAAACCGGT ORF from nucleotide position -8 to 720 (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. | ||||||||||||||||||||||||||||||||||||||||||||||