Difference between revisions of "Part:BBa K1159311"
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===Usage and Biology=== | ===Usage and Biology=== | ||
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<span class='h3bb'>Sequence and Features</span> | <span class='h3bb'>Sequence and Features</span> | ||
<partinfo>BBa_K1159311 SequenceAndFeatures</partinfo> | <partinfo>BBa_K1159311 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_1382698695454'><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1382698695454 --><th id="AutoAnnotatorHeader" colspan="2">Protein data table for BioBrick <a href="https://parts.igem.org/wiki/index.php?title=Part:BBa_K1159311">BBa_K1159311</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>AGTAAAGGA ... CTCTACAAA<i>ACCGGT</i></u></span><br> <strong>ORF</strong> from nucleotide position -8 to 717 (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">MAGSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTI<br>FFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLSPDN<br>HYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYKTG*</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">9 (3.7%)</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 (5.4%)</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">24 (9.9%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">His (H)</td><td class="AutoAnnotatorInnerAmino">10 (4.1%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ile (I)</td><td class="AutoAnnotatorInnerAmino">12 (5.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Leu (L)</td><td class="AutoAnnotatorInnerAmino">19 (7.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Lys (K)</td><td class="AutoAnnotatorInnerAmino">20 (8.3%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Met (M)</td><td class="AutoAnnotatorInnerAmino">6 (2.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Phe (F)</td><td class="AutoAnnotatorInnerAmino">12 (5.0%)</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">11 (4.5%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Thr (T)</td><td class="AutoAnnotatorInnerAmino">17 (7.0%)</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">11 (4.5%)</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">242</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Positively charged (Arg+Lys):</td><td class="AutoAnnotatorAminoCountingInner3">26 (10.7%)</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">34 (14.0%)</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>1211</sub>H<sub>1864</sub>N<sub>322</sub>O<sub>371</sub>S<sub>8</sub></td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Molecular mass [Da]:</td><td class="AutoAnnotatorBiochemParInner3">27126.5</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Theoretical pI:</td><td class="AutoAnnotatorBiochemParInner3">5.67</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">21890 / 22015 (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_1382698695454()' 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 (0.72)</td><td class="AutoAnnotatorCodonUsage3">good (0.76)</td><td class="AutoAnnotatorCodonUsage3">good (0.74)</td><td class="AutoAnnotatorCodonUsage3">excellent (0.82)</td><td class="AutoAnnotatorCodonUsage3">good (0.78)</td><td class="AutoAnnotatorCodonUsage3">good (0.69)</td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Alignments</strong> (obtained from <a href='http://predictprotein.org'>PredictProtein.org</a>)<table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorAlignment1"></td><td class="AutoAnnotatorAlignment2">SwissProt:</td><td class="AutoAnnotatorAlignment3"><a href='http://www.uniprot.org/uniprot/P42212'>P42212</a> (98% identity on 238 AAs), <a href='http://www.uniprot.org/uniprot/Q9U6Y3'>Q9U6Y3</a> (25% 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/B7UCZ6'>B7UCZ6</a> (98% identity on 238 AAs), <a href='http://www.uniprot.org/uniprot/B9U1C3'>B9U1C3</a> (98% identity on 239 AAs), <a href='http://www.uniprot.org/uniprot/Q71RY9'>Q71RY9</a> (98% 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=1gfl'>1gfl</a> (98% identity on 229 AAs), <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1emm'>1emm</a> (97% identity on 221 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 (54%)</td></tr><tr><td class="AutoAnnotatorLocalization1"></td><td class="AutoAnnotatorLocalization2">Eukarya:</td><td class="AutoAnnotatorLocalization3">cytosol (37%)</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="http://2013.igem.org/Team:TU-Munich/excanvas.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_1382698695454(){hydrophobicity_datapoints = [[2.5,-0.28],[3.5,-0.74],[4.5,-1.80],[5.5,-2.42],[6.5,-1.50],[7.5,-0.16],[8.5,-0.22],[9.5,0.40],[10.5,1.94],[11.5,2.02],[12.5,1.14],[13.5,2.18],[14.5,3.02],[15.5,3.02],[16.5,1.48],[17.5,2.56],[18.5,0.96],[19.5,0.12],[20.5,-1.42],[21.5,0.12],[22.5,-1.34],[23.5,-0.72],[24.5,-1.28],[25.5,-1.36],[26.5,-1.64],[27.5,-1.10],[28.5,-0.18],[29.5,0.30],[30.5,1.00],[31.5,-0.26],[32.5,-0.18],[33.5,-1.72],[34.5,-1.64],[35.5,-2.26],[36.5,-1.20],[37.5,-1.26],[38.5,-0.82],[39.5,-0.82],[40.5,-0.90],[41.5,-0.50],[42.5,-0.50],[43.5,0.52],[44.5,-0.18],[45.5,1.16],[46.5,1.30],[47.5,1.94],[48.5,1.04],[49.5,1.68],[50.5,1.04],[51.5,-0.64],[52.5,-0.38],[53.5,-0.56],[54.5,0.42],[55.5,0.18],[56.5,0.78],[57.5,-0.30],[58.5,-0.12],[59.5,-0.20],[60.5,0.96],[61.5,1.00],[62.5,1.18],[63.5,2.08],[64.5,1.18],[65.5,0.08],[66.5,0.14],[67.5,1.12],[68.5,-0.34],[69.5,0.30],[70.5,1.12],[71.5,1.04],[72.5,-0.70],[73.5,-0.26],[74.5,-1.08],[75.5,-2.34],[76.5,-2.82],[77.5,-1.54],[78.5,-2.06],[79.5,-2.44],[80.5,-2.38],[81.5,-2.44],[82.5,-2.26],[83.5,-0.92],[84.5,-1.00],[85.5,-0.52],[86.5,0.54],[87.5,0.36],[88.5,-0.52],[89.5,-0.44],[90.5,-0.36],[91.5,-0.98],[92.5,-0.52],[93.5,-0.90],[94.5,-0.90],[95.5,-1.72],[96.5,-1.60],[97.5,-1.54],[98.5,-0.28],[99.5,0.98],[100.5,1.10],[101.5,0.54],[102.5,-1.06],[103.5,-1.70],[104.5,-2.96],[105.5,-2.44],[106.5,-2.52],[107.5,-1.96],[108.5,-2.78],[109.5,-1.72],[110.5,-2.16],[111.5,-0.54],[112.5,-1.18],[113.5,0.28],[114.5,-0.78],[115.5,-0.16],[116.5,-1.70],[117.5,-1.06],[118.5,-0.86],[119.5,0.68],[120.5,0.06],[121.5,-0.14],[122.5,0.90],[123.5,-0.56],[124.5,-0.64],[125.5,-0.72],[126.5,0.10],[127.5,0.10],[128.5,0.10],[129.5,-0.10],[130.5,-0.10],[131.5,-0.72],[132.5,-2.32],[133.5,-1.70],[134.5,-2.96],[135.5,-1.28],[136.5,0.18],[137.5,0.80],[138.5,0.24],[139.5,0.16],[140.5,0.02],[141.5,-1.44],[142.5,-1.62],[143.5,-1.68],[144.5,-1.16],[145.5,-2.62],[146.5,-2.08],[147.5,-2.46],[148.5,-2.46],[149.5,-1.36],[150.5,-0.92],[151.5,0.14],[152.5,1.16],[153.5,2.22],[154.5,0.68],[155.5,0.16],[156.5,-1.44],[157.5,-2.60],[158.5,-3.66],[159.5,-3.04],[160.5,-1.36],[161.5,-1.44],[162.5,0.18],[163.5,0.18],[164.5,0.82],[165.5,-0.86],[166.5,0.82],[167.5,-0.92],[168.5,-0.86],[169.5,-2.12],[170.5,-0.44],[171.5,-2.04],[172.5,-1.84],[173.5,-1.28],[174.5,-0.74],[175.5,-0.80],[176.5,-0.80],[177.5,0.66],[178.5,1.10],[179.5,0.56],[180.5,-0.92],[181.5,-0.48],[182.5,-1.94],[183.5,-3.00],[184.5,-3.00],[185.5,-2.50],[186.5,-2.56],[187.5,-0.96],[188.5,-0.34],[189.5,-0.34],[190.5,-0.28],[191.5,-0.28],[192.5,-0.34],[193.5,0.50],[194.5,1.04],[195.5,0.80],[196.5,0.42],[197.5,-1.12],[198.5,-2.52],[199.5,-2.62],[200.5,-1.54],[201.5,-1.00],[202.5,-0.44],[203.5,-0.50],[204.5,-0.40],[205.5,-0.80],[206.5,0.12],[207.5,0.10],[208.5,0.02],[209.5,-0.52],[210.5,-1.20],[211.5,-2.66],[212.5,-3.20],[213.5,-3.20],[214.5,-3.40],[215.5,-3.78],[216.5,-3.72],[217.5,-2.64],[218.5,-1.02],[219.5,0.64],[220.5,2.10],[221.5,2.04],[222.5,2.22],[223.5,2.22],[224.5,1.32],[225.5,0.92],[226.5,1.98],[227.5,1.34],[228.5,1.40],[229.5,1.40],[230.5,0.40],[231.5,-0.04],[232.5,0.42],[233.5,-1.18],[234.5,-1.74],[235.5,-0.34],[236.5,-0.52],[237.5,-1.68],[238.5,-1.12],[239.5,-0.50]];charge_datapoints = [[2.5,0.20],[3.5,0.20],[4.5,0.00],[5.5,-0.20],[6.5,-0.20],[7.5,-0.40],[8.5,-0.40],[9.5,-0.20],[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,-0.20],[17.5,-0.20],[18.5,-0.40],[19.5,-0.40],[20.5,-0.60],[21.5,-0.40],[22.5,-0.40],[23.5,-0.20],[24.5,-0.10],[25.5,0.30],[26.5,0.30],[27.5,0.30],[28.5,0.30],[29.5,0.20],[30.5,-0.00],[31.5,-0.20],[32.5,-0.20],[33.5,-0.40],[34.5,-0.40],[35.5,-0.60],[36.5,-0.40],[37.5,-0.40],[38.5,-0.20],[39.5,-0.20],[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],[51.5,0.20],[52.5,0.20],[53.5,0.20],[54.5,0.20],[55.5,0.20],[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,-0.00],[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],[72.5,0.20],[73.5,0.20],[74.5,0.20],[75.5,-0.00],[76.5,0.10],[77.5,-0.10],[78.5,0.10],[79.5,0.10],[80.5,0.40],[81.5,0.10],[82.5,0.10],[83.5,-0.10],[84.5,0.10],[85.5,-0.00],[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,-0.20],[95.5,-0.00],[96.5,-0.00],[97.5,-0.00],[98.5,-0.00],[99.5,0.20],[100.5,0.20],[101.5,-0.00],[102.5,-0.20],[103.5,-0.20],[104.5,-0.20],[105.5,-0.40],[106.5,-0.00],[107.5,0.20],[108.5,0.40],[109.5,0.40],[110.5,0.20],[111.5,-0.00],[112.5,0.20],[113.5,-0.00],[114.5,-0.20],[115.5,-0.00],[116.5,-0.20],[117.5,-0.40],[118.5,-0.40],[119.5,-0.20],[120.5,-0.20],[121.5,0.20],[122.5,0.20],[123.5,-0.00],[124.5,-0.00],[125.5,0.20],[126.5,-0.00],[127.5,-0.00],[128.5,-0.00],[129.5,-0.00],[130.5,-0.00],[131.5,-0.20],[132.5,-0.40],[133.5,-0.20],[134.5,-0.20],[135.5,-0.40],[136.5,-0.20],[137.5,-0.00],[138.5,0.10],[139.5,0.30],[140.5,0.30],[141.5,0.10],[142.5,0.10],[143.5,-0.00],[144.5,-0.20],[145.5,-0.20],[146.5,-0.00],[147.5,0.10],[148.5,0.10],[149.5,0.10],[150.5,0.10],[151.5,0.10],[152.5,-0.00],[153.5,-0.00],[154.5,-0.20],[155.5,-0.00],[156.5,-0.00],[157.5,0.20],[158.5,0.20],[159.5,0.40],[160.5,0.20],[161.5,0.40],[162.5,0.20],[163.5,0.20],[164.5,0.20],[165.5,0.40],[166.5,0.20],[167.5,0.40],[168.5,0.50],[169.5,0.50],[170.5,0.30],[171.5,0.10],[172.5,-0.30],[173.5,-0.40],[174.5,-0.40],[175.5,-0.40],[176.5,-0.20],[177.5,-0.00],[178.5,-0.00],[179.5,-0.20],[180.5,-0.10],[181.5,-0.10],[182.5,-0.10],[183.5,-0.10],[184.5,0.10],[185.5,-0.00],[186.5,-0.00],[187.5,-0.00],[188.5,-0.00],[189.5,-0.20],[190.5,-0.20],[191.5,-0.20],[192.5,-0.20],[193.5,-0.20],[194.5,-0.00],[195.5,-0.00],[196.5,-0.20],[197.5,-0.20],[198.5,-0.10],[199.5,-0.10],[200.5,-0.10],[201.5,0.10],[202.5,0.10],[203.5,-0.00],[204.5,-0.00],[205.5,-0.00],[206.5,-0.00],[207.5,-0.00],[208.5,0.20],[209.5,-0.00],[210.5,-0.00],[211.5,-0.00],[212.5,-0.20],[213.5,-0.20],[214.5,0.20],[215.5,-0.00],[216.5,0.10],[217.5,0.30],[218.5,0.10],[219.5,-0.10],[220.5,0.10],[221.5,-0.20],[222.5,-0.20],[223.5,-0.20],[224.5,-0.20],[225.5,-0.20],[226.5,-0.00],[227.5,-0.00],[228.5,-0.00],[229.5,-0.00],[230.5,0.10],[231.5,0.10],[232.5,0.10],[233.5,-0.10],[234.5,-0.30],[235.5,-0.40],[236.5,-0.40],[237.5,-0.20],[238.5,-0.00],[239.5,0.20]];dis_datapoints = [];trans_datapoints = [];sec_helix_datapoints = [[58,67],[86,88],[237,239]];sec_strand_datapoints = [[9,10],[15,24],[28,34],[43,50],[72,74],[96,103],[107,117],[120,130],[141,142],[150,155],[162,173],[178,185],[202,211],[219,230]];acc_exposed_datapoints = [[1,2],[4,8],[11,12],[15,15],[21,21],[25,25],[28,28],[34,34],[36,36],[38,38],[41,41],[43,43],[52,52],[54,54],[71,71],[75,75],[78,79],[81,82],[84,84],[87,87],[91,92],[103,103],[105,105],[115,115],[117,119],[128,128],[131,131],[134,135],[137,137],[140,140],[142,142],[144,144],[146,148],[157,160],[174,177],[185,188],[191,194],[196,196],[199,199],[211,218],[230,230],[232,232],[234,234],[236,237],[239,242]];acc_buried_datapoints = [[9,10],[14,14],[16,16],[18,18],[20,20],[22,22],[24,24],[26,26],[29,29],[31,31],[33,33],[35,35],[37,37],[42,42],[44,44],[46,46],[48,48],[50,50],[55,66],[69,70],[72,73],[76,77],[86,86],[89,90],[93,95],[99,100],[102,102],[106,106],[108,108],[110,110],[112,112],[114,114],[116,116],[121,121],[125,125],[127,127],[129,129],[132,132],[136,136],[138,139],[143,143],[152,155],[163,163],[165,165],[167,167],[169,171],[173,173],[181,181],[183,183],[197,198],[200,200],[201,203],[205,205],[207,207],[209,209],[220,220],[222,222],[224,224],[226,226],[228,228]];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( $('#AutoAnnotator_container_1382698695454 #hydrophobicity_charge_button').val() =='Show' ){$('#AutoAnnotator_container_1382698695454 #hydrophobicity_charge_container').css('display','block');$('#AutoAnnotator_container_1382698695454 #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_1382698695454 #hydrophobicity_charge_explanation').html(description_html);plot_according_to_selectors_1382698695454();$('#AutoAnnotator_container_1382698695454 #AutoAnnotator_plot_selectors').find('input').click(plot_according_to_selectors_1382698695454);}else{$('#AutoAnnotator_container_1382698695454 #hydrophobicity_charge_container').css('display','none');$('#AutoAnnotator_container_1382698695454 #hydrophobicity_charge_button').val('Show');$('#AutoAnnotator_container_1382698695454 #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_1382698695454(){try{var plot_datasets = [[],[]];if($('#AutoAnnotator_container_1382698695454 #hydrophobicity_checkbox').prop('checked') == true){plot_datasets[0] = { color: 'rgba(100,149,237,1)',data: hydrophobicity_datapoints,label: 'Hydrophobicity',lines: { show: true, fill: true, fillColor: 'rgba(100,149,237,0.1)' },yaxis: 1};}if($('#AutoAnnotator_container_1382698695454 #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_1382698695454 #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_1382698695454 #dis_checkbox').prop('checked') == true){for ( j = 0 ; j < dis_datapoints.length ; j++ ){$('#AutoAnnotator_container_1382698695454 #hydrophobicity_charge_placeholder' + Math.floor((dis_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_dis\' style=\'left:' + ((pos_of_first_tick - 8 + (dis_datapoints[j][0] - 1)*tick_diff - Math.floor((dis_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px;\'><b>' + (j+1) + '</b></div>');$('#AutoAnnotator_container_1382698695454 #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($('#AutoAnnotator_container_1382698695454 #trans_checkbox').prop('checked') == true){for ( j = 0 ; j < trans_datapoints.length ; j++ ){$('#AutoAnnotator_container_1382698695454 #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($('#AutoAnnotator_container_1382698695454 #sec_checkbox').prop('checked') == true){for ( j = 0 ; j < sec_helix_datapoints.length ; j++ ){$('#AutoAnnotator_container_1382698695454 #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++ ){$('#AutoAnnotator_container_1382698695454 #hydrophobicity_charge_placeholder' + Math.floor((sec_strand_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_sec_strand\' style=\'width:' + (((sec_strand_datapoints[j][1] - sec_strand_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px; left:' + ((pos_of_first_tick + (sec_strand_datapoints[j][0] - 1.5)*tick_diff - Math.floor((sec_strand_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px\'></div>');}}if($('#AutoAnnotator_container_1382698695454 #acc_checkbox').prop('checked') == true){for ( j = 0 ; j < acc_buried_datapoints.length ; j++ ){$('#AutoAnnotator_container_1382698695454 #hydrophobicity_charge_placeholder' + Math.floor((acc_buried_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_acc_buried\' style=\'width:' + (((acc_buried_datapoints[j][1] - acc_buried_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px; left:' + ((pos_of_first_tick + (acc_buried_datapoints[j][0] - 1.5)*tick_diff - Math.floor((acc_buried_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px\'></div>');}for ( j = 0 ; j < acc_exposed_datapoints.length ; j++ ){$('#AutoAnnotator_container_1382698695454 #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 11:00, 25 October 2013
GFPmut1
This part codes for GFPmut1 which is flanked by RFC[25] pre- and suffix.
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]
- 1000INCOMPATIBLE WITH RFC[1000]Illegal BsaI.rc site found at 641
| Protein data table for BioBrick BBa_K1159311 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) ATGGCCGGCAGTAAAGGA ... CTCTACAAAACCGGT ORF from nucleotide position -8 to 717 (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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