Difference between revisions of "Part:BBa K1159105"

 
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<span class='h3bb'>Sequence and Features</span>
 
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<html><!--- Please copy this table containing parameters for BBa_ at the end of the parametrs section ahead of the references. ---><style type="text/css">table#AutoAnnotator {border:1px solid black; width:100%; border-collapse:collapse;} th#AutoAnnotatorHeader { border:1px solid black; width:100%; background-color: rgb(221, 221, 221);} td.AutoAnnotator1col { width:100%; border:1px solid black; } span.AutoAnnotatorSequence { font-family:'Courier New', Arial; } td.AutoAnnotatorSeqNum { text-align:right; width:2%; } td.AutoAnnotatorSeqSeq { width:98% } td.AutoAnnotatorSeqFeat1 { width:3% } td.AutoAnnotatorSeqFeat2a { width:27% } td.AutoAnnotatorSeqFeat2b { width:97% } td.AutoAnnotatorSeqFeat3 { width:70% } table.AutoAnnotatorNoBorder { border:0px; width:100%; border-collapse:collapse; } table.AutoAnnotatorWithBorder { border:1px solid black; width:100%; border-collapse:collapse; } td.AutoAnnotatorOuterAmino { border:0px solid black; width:20% } td.AutoAnnotatorInnerAmino { border:1px solid black; width:50% } td.AutoAnnotatorAminoCountingOuter { border:1px solid black; width:40%;  } td.AutoAnnotatorBiochemParOuter { border:1px solid black; width:60%; } td.AutoAnnotatorAminoCountingInner1 { width: 7.5% } td.AutoAnnotatorAminoCountingInner2 { width:62.5% } td.AutoAnnotatorAminoCountingInner3 { width:30% } td.AutoAnnotatorBiochemParInner1 { width: 5% } td.AutoAnnotatorBiochemParInner2 { width:55% } td.AutoAnnotatorBiochemParInner3 { width:40% } td.AutoAnnotatorCodonUsage1 { width: 3% } td.AutoAnnotatorCodonUsage2 { width:14.2% } td.AutoAnnotatorCodonUsage3 { width:13.8% } td.AutoAnnotatorAlignment1 { width: 3% } td.AutoAnnotatorAlignment2 { width: 10% } td.AutoAnnotatorAlignment3 { width: 87% } td.AutoAnnotatorLocalizationOuter {border:1px solid black; width:40%} td.AutoAnnotatorGOOuter {border:1px solid black; width:60%} td.AutoAnnotatorLocalization1 { width: 7.5% } td.AutoAnnotatorLocalization2 { width: 22.5% } td.AutoAnnotatorLocalization3 { width: 70% } td.AutoAnnotatorGO1 { width: 5% } td.AutoAnnotatorGO2 { width: 35% } td.AutoAnnotatorGO3 { width: 60% } td.AutoAnnotatorPredFeat1 { width:3% } td.AutoAnnotatorPredFeat2a { width:27% } td.AutoAnnotatorPredFeat3 { width:70% } div.AutoAnnotator_trans { position:absolute; background:rgb(11,140,143); background-color:rgba(11,140,143, 0.8); height:5px; top:100px; } div.AutoAnnotator_sec_helix { position:absolute; background:rgb(102,0,102); background-color:rgba(102,0,102, 0.8); height:5px; top:110px; } div.AutoAnnotator_sec_strand { position:absolute; background:rgb(245,170,26); background-color:rgba(245,170,26, 1); height:5px; top:110px; } div.AutoAnnotator_acc_buried { position:absolute; background:rgb(89,168,15); background-color:rgba(89,168,15, 0.8); height:5px; top:120px; } div.AutoAnnotator_acc_exposed { position:absolute; background:rgb(0, 0, 255); background-color:rgba(0, 0, 255, 0.8); height:5px; top:120px; } div.AutoAnnotator_dis { position:absolute; text-align:center; font-family:Arial,Helvetica,sans-serif; background:rgb(255, 200, 0); background-color:rgba(255, 200, 0, 1); height:16px; width:16px; top:80px; border-radius:50%; } </style><div id='AutoAnnotator_container_1381259770036'><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1381259770036 --><th id="AutoAnnotatorHeader" colspan="2">Protein data table for BioBrick <a href="https://parts.igem.org/wiki/index.php?title=Part:BBa_<!------------------------Enter BioBrick number here------------------------>">BBa_<!------------------------Enter BioBrick number here------------------------></a> automatically created by the <a href="http://2013.igem.org/Team:TU-Munich/Results/AutoAnnotator">BioBrick-AutoAnnotator</a> version 1.0</th></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Nucleotide sequence</strong> in <strong>RFC 25</strong>, so ATGGCCGGC and ACCGGT were added (in italics) to the 5' and 3' ends: (underlined part encodes the protein)<br><span class="AutoAnnotatorSequence">&nbsp;<u><i>ATGGCCGGC</i>GCAACTTCA&nbsp;...&nbsp;TCAGGTCAA<i>ACCGGT</i></u></span><br>&nbsp;<strong>ORF</strong> from nucleotide position -8 to 453 (excluding stop-codon)</td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Amino acid sequence:</strong> (RFC 25 scars in shown in bold, other sequence features underlined; both given below)<br><span class="AutoAnnotatorSequence"><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorSeqNum">1&nbsp;<br>101&nbsp;</td><td class="AutoAnnotatorSeqSeq">MAGATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQRTDKYGRGLAYIYADGK<br>MVNEALVRQGLAKVAYVYKPNNTHEQHLRKSEAQAKKEKLNIWSEDNADSGQTG*</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">15 (9.7%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Arg (R)</td><td class="AutoAnnotatorInnerAmino">5 (3.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asn (N)</td><td class="AutoAnnotatorInnerAmino">6 (3.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asp (D)</td><td class="AutoAnnotatorInnerAmino">8 (5.2%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Cys (C)</td><td class="AutoAnnotatorInnerAmino">0 (0.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gln (Q)</td><td class="AutoAnnotatorInnerAmino">6 (3.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Glu (E)</td><td class="AutoAnnotatorInnerAmino">12 (7.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gly (G)</td><td class="AutoAnnotatorInnerAmino">12 (7.8%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">His (H)</td><td class="AutoAnnotatorInnerAmino">4 (2.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ile (I)</td><td class="AutoAnnotatorInnerAmino">5 (3.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Leu (L)</td><td class="AutoAnnotatorInnerAmino">11 (7.1%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Lys (K)</td><td class="AutoAnnotatorInnerAmino">23 (14.9%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Met (M)</td><td class="AutoAnnotatorInnerAmino">5 (3.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Phe (F)</td><td class="AutoAnnotatorInnerAmino">3 (1.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Pro (P)</td><td class="AutoAnnotatorInnerAmino">6 (3.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ser (S)</td><td class="AutoAnnotatorInnerAmino">5 (3.2%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Thr (T)</td><td class="AutoAnnotatorInnerAmino">11 (7.1%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Trp (W)</td><td class="AutoAnnotatorInnerAmino">1 (0.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Tyr (Y)</td><td class="AutoAnnotatorInnerAmino">7 (4.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Val (V)</td><td class="AutoAnnotatorInnerAmino">9 (5.8%)</td></tr></table></td></tr></table></td></tr><tr><td class="AutoAnnotatorAminoCountingOuter"><strong>Amino acid counting</strong><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Total number:</td><td class="AutoAnnotatorAminoCountingInner3">154</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Positively charged (Arg+Lys):</td><td class="AutoAnnotatorAminoCountingInner3">28 (18.2%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Negatively charged (Asp+Glu):</td><td class="AutoAnnotatorAminoCountingInner3">20 (13.0%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Aromatic (Phe+His+Try+Tyr):</td><td class="AutoAnnotatorAminoCountingInner3">15 (9.7%)</td></tr></table></td><td class="AutoAnnotatorBiochemParOuter"><strong>Biochemical parameters</strong><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Atomic composition:</td><td class="AutoAnnotatorBiochemParInner3">C<sub>763</sub>H<sub>1231</sub>N<sub>213</sub>O<sub>230</sub>S<sub>5</sub></td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Molecular mass [Da]:</td><td class="AutoAnnotatorBiochemParInner3">17228.8</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Theoretical pI:</td><td class="AutoAnnotatorBiochemParInner3">9.48</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">15930 / 15930 (all Cys red/ox)</td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Plot for hydrophobicity, charge, predicted secondary structure, solvent accessability, transmembrane helices and disulfid bridges</strong>&nbsp;<input type='button' id='hydrophobicity_charge_button' onclick='show_or_hide_plot_1381259770036()' 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></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 (0.79)</td><td class="AutoAnnotatorCodonUsage3">excellent (0.83)</td><td class="AutoAnnotatorCodonUsage3">excellent (0.82)</td><td class="AutoAnnotatorCodonUsage3">excellent (0.81)</td><td class="AutoAnnotatorCodonUsage3">good (0.72)</td><td class="AutoAnnotatorCodonUsage3">acceptable (0.60)</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/P00644'>P00644</a> (99% identity on 150 AAs), <a href='http://www.uniprot.org/uniprot/Q5HHM4'>Q5HHM4</a> (98% identity on 150 AAs), <a href='http://www.uniprot.org/uniprot/Q6GB41'>Q6GB41</a> (98% identity on 150 AAs), <a href='http://www.uniprot.org/uniprot/Q6GIK1'>Q6GIK1</a> (98% identity on 150 AAs), <a href='http://www.uniprot.org/uniprot/Q7A6P2'>Q7A6P2</a> (98% identity on 150 AAs), <a href='http://www.uniprot.org/uniprot/Q8NXI6'>Q8NXI6</a> (98% identity on 150 AAs), <a href='http://www.uniprot.org/uniprot/Q99VJ0'>Q99VJ0</a> (98% identity on 150 AAs)</td></tr><tr><td class="AutoAnnotatorAlignment1"></td><td class="AutoAnnotatorAlignment2">TrEML:</td><td class="AutoAnnotatorAlignment3"><a href='http://www.uniprot.org/uniprot/A3QSR2'>A3QSR2</a> (98% identity on 140 AAs), <a href='http://www.uniprot.org/uniprot/A3QSR3'>A3QSR3</a> (98% identity on 140 AAs), <a href='http://www.uniprot.org/uniprot/A3QSR6'>A3QSR6</a> (98% identity on 140 AAs), <a href='http://www.uniprot.org/uniprot/A5A513'>A5A513</a> (98% identity on 148 AAs), <a href='http://www.uniprot.org/uniprot/A5A520'>A5A520</a> (98% identity on 148 AAs), <a href='http://www.uniprot.org/uniprot/A5A523'>A5A523</a> (98% identity on 148 AAs), <a href='http://www.uniprot.org/uniprot/A5IQZ5'>A5IQZ5</a> (98% identity on 150 AAs), <a href='http://www.uniprot.org/uniprot/A6QFA0'>A6QFA0</a> (98% identity on 150 AAs), <a href='http://www.uniprot.org/uniprot/A6TZS0'>A6TZS0</a> (98% identity on 150 AAs), <a href='http://www.uniprot.org/uniprot/A7WZZ3'>A7WZZ3</a> (98% identity on 150 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=1ey0'>1ey0</a> (100% identity on 136 AAs), <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1eyd'>1eyd</a> (100% identity on 136 AAs), <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1nsn'>1nsn</a> (100% identity on 138 AAs), <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1snc'>1snc</a> (100% identity on 135 AAs), <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1sta'>1sta</a> (100% identity on 135 AAs), <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1stb'>1stb</a> (100% identity on 136 AAs), <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1stg'>1stg</a> (100% identity on 136 AAs), <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1sth'>1sth</a> (100% identity on 136 AAs), <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1stn'>1stn</a> (100% identity on 136 AAs), <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1sty'>1sty</a> (100% identity on 136 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">cytosol (100%)</td></tr><tr><td class="AutoAnnotatorLocalization1"></td><td class="AutoAnnotatorLocalization2">Bacteria:</td><td class="AutoAnnotatorLocalization3">secreted (55%)</td></tr><tr><td class="AutoAnnotatorLocalization1"></td><td class="AutoAnnotatorLocalization2">Eukarya:</td><td class="AutoAnnotatorLocalization3">cytosol (24%)</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:0030541'>GO:0030541</a> (28%)</td></tr><tr><td class='AutoAnnotatorGO1'> </td><td class='AutoAnnotatorGO2'> </td><td class='AutoAnnotatorGO3'>&nbsp;</td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Predicted features:</strong><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorPredFeat1"></td><td class="AutoAnnotatorPredFeat2a">Disulfid bridges:</td><td class="AutoAnnotatorPredFeat3">&nbsp;- </td></tr><tr><td class="AutoAnnotatorPredFeat1"></td><td class="AutoAnnotatorPredFeat2a">Transmembrane helices:</td><td class="AutoAnnotatorPredFeat3">&nbsp;- </td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"> The BioBrick-AutoAnnotator was created by <a href="http://2013.igem.org/Team:TU-Munich">TU-Munich 2013</a> iGEM team. For more information please see the <a href="http://2013.igem.org/Team:TU-Munich/Results/Software">documentation</a>.<br>If you have any questions, comments or suggestions, please leave us a <a href="http://2013.igem.org/Team:TU-Munich/Results/AutoAnnotator">comment</a>.</td></tr></table></div><br><!-- IMPORTANT: DON'T REMOVE THIS LINE, OTHERWISE NOT SUPPORTED FOR IE BEFORE 9 --><!--[if lte IE 8]><script language="javascript" type="text/javascript" src="excanvas.min.js"></script><![endif]--><script type='text/javascript' src='http://code.jquery.com/jquery-1.10.0.min.js'></script><script type='text/javascript' src='http://2013.igem.org/Team:TU-Munich/Flot.js?action=raw&ctype=text/js'></script><script>function show_or_hide_plot_1381259770036(){hydrophobicity_datapoints = [[2.5,0.88],[3.5,0.34],[4.5,-0.16],[5.5,-0.86],[6.5,-2.00],[7.5,-1.10],[8.5,-1.58],[9.5,-2.22],[10.5,-2.14],[11.5,-1.68],[12.5,-2.08],[13.5,-1.58],[14.5,-0.04],[15.5,1.56],[16.5,1.10],[17.5,1.10],[18.5,2.14],[19.5,0.68],[20.5,-0.30],[21.5,-0.22],[22.5,-0.72],[23.5,-0.78],[24.5,-0.86],[25.5,-0.02],[26.5,1.06],[27.5,0.94],[28.5,-0.68],[29.5,0.02],[30.5,-1.44],[31.5,-2.14],[32.5,-1.50],[33.5,-0.86],[34.5,-0.22],[35.5,-0.42],[36.5,0.66],[37.5,1.04],[38.5,1.94],[39.5,2.22],[40.5,2.42],[41.5,1.52],[42.5,0.44],[43.5,-1.02],[44.5,-2.00],[45.5,-2.08],[46.5,-2.58],[47.5,-2.58],[48.5,-2.66],[49.5,-3.30],[50.5,-2.60],[51.5,-1.12],[52.5,-1.50],[53.5,-1.50],[54.5,-0.98],[55.5,-0.98],[56.5,-2.14],[57.5,-2.14],[58.5,-1.00],[59.5,-0.90],[60.5,-0.46],[61.5,0.42],[62.5,0.98],[63.5,-0.16],[64.5,-0.78],[65.5,-0.76],[66.5,-0.48],[67.5,-1.04],[68.5,-0.96],[69.5,0.18],[70.5,-0.98],[71.5,-2.60],[72.5,-1.00],[73.5,-1.00],[74.5,-0.52],[75.5,-0.44],[76.5,0.90],[77.5,-0.70],[78.5,-0.78],[79.5,-1.70],[80.5,-1.70],[81.5,-3.16],[82.5,-2.60],[83.5,-2.52],[84.5,-3.22],[85.5,-2.78],[86.5,-1.96],[87.5,-2.72],[88.5,-2.10],[89.5,-0.56],[90.5,0.06],[91.5,-0.12],[92.5,1.68],[93.5,1.50],[94.5,1.10],[95.5,0.04],[96.5,0.22],[97.5,-1.46],[98.5,-0.82],[99.5,-0.34],[100.5,-0.34],[101.5,-0.96],[102.5,0.18],[103.5,0.56],[104.5,0.56],[105.5,0.36],[106.5,0.36],[107.5,-0.08],[108.5,-0.08],[109.5,-0.56],[110.5,-0.44],[111.5,1.10],[112.5,1.54],[113.5,0.52],[114.5,1.00],[115.5,1.52],[116.5,-0.10],[117.5,-0.78],[118.5,-1.22],[119.5,-2.76],[120.5,-2.64],[121.5,-2.50],[122.5,-2.88],[123.5,-2.88],[124.5,-2.82],[125.5,-1.92],[126.5,-2.18],[127.5,-2.26],[128.5,-1.72],[129.5,-1.78],[130.5,-2.18],[131.5,-1.98],[132.5,-0.84],[133.5,-1.46],[134.5,-1.54],[135.5,-2.60],[136.5,-2.68],[137.5,-2.28],[138.5,-2.20],[139.5,-0.52],[140.5,0.00],[141.5,0.62],[142.5,-0.84],[143.5,-0.84],[144.5,-2.44],[145.5,-1.90],[146.5,-2.44],[147.5,-1.90],[148.5,-1.28],[149.5,-1.28],[150.5,-1.78],[151.5,-1.16]];charge_datapoints = [[2.5,0.00],[3.5,0.00],[4.5,0.00],[5.5,0.20],[6.5,0.40],[7.5,0.40],[8.5,0.50],[9.5,0.70],[10.5,0.30],[11.5,0.10],[12.5,0.10],[13.5,-0.00],[14.5,-0.20],[15.5,-0.00],[16.5,0.20],[17.5,0.20],[18.5,0.20],[19.5,-0.00],[20.5,-0.00],[21.5,-0.40],[22.5,-0.40],[23.5,-0.40],[24.5,-0.00],[25.5,-0.00],[26.5,0.20],[27.5,0.20],[28.5,0.40],[29.5,0.20],[30.5,0.20],[31.5,0.20],[32.5,0.20],[33.5,-0.00],[34.5,-0.00],[35.5,0.20],[36.5,0.20],[37.5,0.20],[38.5,0.20],[39.5,0.20],[40.5,-0.20],[41.5,-0.20],[42.5,-0.20],[43.5,-0.40],[44.5,-0.40],[45.5,-0.00],[46.5,0.10],[47.5,0.10],[48.5,0.50],[49.5,0.70],[50.5,0.50],[51.5,0.40],[52.5,0.20],[53.5,0.20],[54.5,-0.00],[55.5,-0.00],[56.5,-0.00],[57.5,-0.00],[58.5,-0.20],[59.5,-0.20],[60.5,-0.20],[61.5,-0.20],[62.5,-0.00],[63.5,0.20],[64.5,0.40],[65.5,0.40],[66.5,0.40],[67.5,0.20],[68.5,-0.00],[69.5,-0.20],[70.5,-0.00],[71.5,0.20],[72.5,0.40],[73.5,0.20],[74.5,0.20],[75.5,-0.20],[76.5,-0.40],[77.5,-0.60],[78.5,-0.20],[79.5,-0.20],[80.5,-0.00],[81.5,0.20],[82.5,0.40],[83.5,-0.00],[84.5,0.20],[85.5,0.20],[86.5,-0.00],[87.5,0.20],[88.5,0.40],[89.5,0.20],[90.5,0.20],[91.5,0.20],[92.5,-0.00],[93.5,-0.00],[94.5,-0.00],[95.5,-0.20],[96.5,-0.20],[97.5,-0.00],[98.5,-0.00],[99.5,-0.00],[100.5,0.20],[101.5,-0.00],[102.5,-0.20],[103.5,-0.20],[104.5,-0.20],[105.5,-0.00],[106.5,0.20],[107.5,0.20],[108.5,0.20],[109.5,0.20],[110.5,0.20],[111.5,0.20],[112.5,0.20],[113.5,0.20],[114.5,0.20],[115.5,-0.00],[116.5,0.20],[117.5,0.20],[118.5,0.20],[119.5,0.20],[120.5,0.20],[121.5,0.10],[122.5,-0.10],[123.5,-0.10],[124.5,-0.00],[125.5,-0.00],[126.5,0.10],[127.5,0.50],[128.5,0.50],[129.5,0.20],[130.5,0.20],[131.5,-0.00],[132.5,-0.20],[133.5,-0.00],[134.5,0.40],[135.5,0.20],[136.5,0.40],[137.5,0.40],[138.5,0.20],[139.5,-0.00],[140.5,0.20],[141.5,-0.00],[142.5,-0.20],[143.5,-0.40],[144.5,-0.40],[145.5,-0.40],[146.5,-0.60],[147.5,-0.40],[148.5,-0.20],[149.5,-0.20],[150.5,-0.20],[151.5,-0.00]];dis_datapoints 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[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( $('#AutoAnnotator_container_1381259770036 #hydrophobicity_charge_button').val() =='Show' ){$('#AutoAnnotator_container_1381259770036 #hydrophobicity_charge_container').css('display','block');$('#AutoAnnotator_container_1381259770036 #hydrophobicity_charge_button').val('Hide');var description_html = '<div id=\'AutoAnnotator_plot_selectors\'>';description_html = description_html + '<br>&nbsp;<input type=\'checkbox\' id=\'hydrophobicity_checkbox\' checked=\'checked\'>&nbsp;Moving average over 5 amino acids for hydrophobicity (<img src=\'https://static.igem.org/mediawiki/2013/e/e9/TUM13_hydrophobicity_icon.png\' alt=\'blue graph\' height=\'10\'></img>)';description_html = 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structure: Helices (<img src=\'https://static.igem.org/mediawiki/2013/b/bf/TUM13_helix_icon.png\' alt=\'violet bars\' height=\'10\'></img>) and beta-strands (<img src=\'https://static.igem.org/mediawiki/2013/b/bf/TUM13_strand_icon.png\' alt=\'yellow bars\' height=\'10\'></img>)';description_html = description_html + '<br>&nbsp;<input type=\'checkbox\' id=\'acc_checkbox\' checked=\'checked\'>&nbsp;Predicted solvent accessability: Exposed (<img src=\'https://static.igem.org/mediawiki/2013/1/16/TUM13_exposed_icon.png\' alt=\'blue bars\' height=\'10\'></img>) and buried (<img src=\'https://static.igem.org/mediawiki/2013/0/0b/TUM13_buried_icon.png\' alt=\'green bars\' height=\'10\'></img>) residues';description_html = description_html + '<br></div>';$('#AutoAnnotator_container_1381259770036 #hydrophobicity_charge_explanation').html(description_html);plot_according_to_selectors_1381259770036();$('#AutoAnnotator_container_1381259770036 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<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  

Revision as of 19:17, 8 October 2013

Mature Nuclease NucA from Staphylococcus aureus (Thermonuclease) in RFC[25]

Thermonuclease is a endo-exonuclease from Staphylococcus aureus that degrades dsDNA, ssDNA, dsRNA and ssRNA. This part is coding the mature form of the nuclease, also called NucA. This part is flanked by RFC[25] pre- and suffix for further protein fusions.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]

Protein data table for BioBrick BBa_ automatically created by the BioBrick-AutoAnnotator version 1.0
Nucleotide sequence in RFC 25, so ATGGCCGGC and ACCGGT were added (in italics) to the 5' and 3' ends: (underlined part encodes the protein)
 ATGGCCGGCGCAACTTCA ... TCAGGTCAAACCGGT
 ORF from nucleotide position -8 to 453 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
1 
101 		MAGATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQRTDKYGRGLAYIYADGK
MVNEALVRQGLAKVAYVYKPNNTHEQHLRKSEAQAKKEKLNIWSEDNADSGQTG*
Sequence features: (with their position in the amino acid sequence, see the list of supported features)
None of the supported features appeared in the sequence
Amino acid composition:
Ala (A)15 (9.7%)
Arg (R)5 (3.2%)
Asn (N)6 (3.9%)
Asp (D)8 (5.2%)
Cys (C)0 (0.0%)
Gln (Q)6 (3.9%)
Glu (E)12 (7.8%)
Gly (G)12 (7.8%)
His (H)4 (2.6%)
Ile (I)5 (3.2%)
Leu (L)11 (7.1%)
Lys (K)23 (14.9%)
Met (M)5 (3.2%)
Phe (F)3 (1.9%)
Pro (P)6 (3.9%)
Ser (S)5 (3.2%)
Thr (T)11 (7.1%)
Trp (W)1 (0.6%)
Tyr (Y)7 (4.5%)
Val (V)9 (5.8%)
Amino acid counting
Total number:154
Positively charged (Arg+Lys):28 (18.2%)
Negatively charged (Asp+Glu):20 (13.0%)
Aromatic (Phe+His+Try+Tyr):15 (9.7%)
Biochemical parameters
Atomic composition:C763H1231N213O230S5
Molecular mass [Da]:17228.8
Theoretical pI:9.48
Extinction coefficient at 280 nm [M-1 cm-1]:15930 / 15930 (all Cys red/ox)
Plot for hydrophobicity, charge, predicted secondary structure, solvent accessability, transmembrane helices and disulfid bridges 
Codon usage
Organism:E. coliB. subtilisS. cerevisiaeA. thalianaP. patensMammals
Codon quality (CAI):good (0.79)excellent (0.83)excellent (0.82)excellent (0.81)good (0.72)acceptable (0.60)
Alignments (obtained from PredictProtein.org)
SwissProt:P00644 (99% identity on 150 AAs), Q5HHM4 (98% identity on 150 AAs), Q6GB41 (98% identity on 150 AAs), Q6GIK1 (98% identity on 150 AAs), Q7A6P2 (98% identity on 150 AAs), Q8NXI6 (98% identity on 150 AAs), Q99VJ0 (98% identity on 150 AAs)
TrEML:A3QSR2 (98% identity on 140 AAs), A3QSR3 (98% identity on 140 AAs), A3QSR6 (98% identity on 140 AAs), A5A513 (98% identity on 148 AAs), A5A520 (98% identity on 148 AAs), A5A523 (98% identity on 148 AAs), A5IQZ5 (98% identity on 150 AAs), A6QFA0 (98% identity on 150 AAs), A6TZS0 (98% identity on 150 AAs), A7WZZ3 (98% identity on 150 AAs)
PDB:1ey0 (100% identity on 136 AAs), 1eyd (100% identity on 136 AAs), 1nsn (100% identity on 138 AAs), 1snc (100% identity on 135 AAs), 1sta (100% identity on 135 AAs), 1stb (100% identity on 136 AAs), 1stg (100% identity on 136 AAs), 1sth (100% identity on 136 AAs), 1stn (100% identity on 136 AAs), 1sty (100% identity on 136 AAs)
Predictions (obtained from PredictProtein.org)
Subcellular Localization (reliability in brackets)
Archaea:cytosol (100%)
Bacteria:secreted (55%)
Eukarya:cytosol (24%)
Gene Ontology (reliability in brackets)
Molecular Function Ontology: -
Biological Process Ontology:GO:0030541 (28%)
 
Predicted features:
Disulfid bridges: -
Transmembrane helices: -
The BioBrick-AutoAnnotator was created by TU-Munich 2013 iGEM team. For more information please see the documentation.
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