Difference between revisions of "Part:BBa K2842680"
| Line 47: | Line 47: | ||
===Functional Parameters=== | ===Functional Parameters=== | ||
<partinfo>BBa_K2332312 parameters</partinfo> | <partinfo>BBa_K2332312 parameters</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_1539807777240'><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1539807777240 --><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 10</strong>: (underlined part encodes the protein)<br><span class="AutoAnnotatorSequence"> GCTTCTACAAACGCGGCTTCTTCCAAAGAGACCTAATACGACTCACTATAGGGGTTGTGAGCGGATAACAACCCAAGACAAGGAGGAGTACCA<u>ATGATCAAG ... CGCTTGGCT</u>TAAGTGACAGTTGAAAAGCGAAAAAAAAACCCCGCCCCTGACAGGGCGGGGTTTTTTTTGGTCTCAACGGACGACGCCGGTTACTACATTGA</span><br> <strong>ORF</strong> from nucleotide position 94 to 1032 (excluding stop-codon)</td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Amino acid sequence:</strong> (RFC 25 scars in shown in bold, other sequence features underlined; both given below)<br><span class="AutoAnnotatorSequence"><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorSeqNum">1 <br>101 <br>201 <br>301 </td><td class="AutoAnnotatorSeqSeq">MIKIATRKYLGKQNVYDIGVERDHNFALKNGFIASNCYNGGRASMASSEDVIKEFMRFKVRMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPF<br>AWDILSPQFQYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASTERMYPEDGA<br>LKGEIKMRLKLKDGGHYDAEVKTTYMAKKPVQLPGAYKTDIKLDITSHNEDYTIVEQYERAEGRHSTGAGSSSESGS<u>WSHPQFEK</u>AEYCVYGDTMVETED<br>GKIKIEDLYKRLA*</td></tr></table></span></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Sequence features:</strong> (with their position in the amino acid sequence, see the <a href="http://2013.igem.org/Team:TU-Munich/Results/Software/FeatureList">list of supported features</a>)<table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorSeqFeat1"></td><td class="AutoAnnotatorSeqFeat2a"><i>Strep</i>-tag II: </td><td class="AutoAnnotatorSeqFeat3">278 to 285</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">18 (5.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Arg (R)</td><td class="AutoAnnotatorInnerAmino">13 (4.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asn (N)</td><td class="AutoAnnotatorInnerAmino">9 (2.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asp (D)</td><td class="AutoAnnotatorInnerAmino">19 (6.1%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Cys (C)</td><td class="AutoAnnotatorInnerAmino">2 (0.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gln (Q)</td><td class="AutoAnnotatorInnerAmino">10 (3.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Glu (E)</td><td class="AutoAnnotatorInnerAmino">29 (9.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gly (G)</td><td class="AutoAnnotatorInnerAmino">32 (10.2%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">His (H)</td><td class="AutoAnnotatorInnerAmino">7 (2.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ile (I)</td><td class="AutoAnnotatorInnerAmino">15 (4.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Leu (L)</td><td class="AutoAnnotatorInnerAmino">16 (5.1%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Lys (K)</td><td class="AutoAnnotatorInnerAmino">30 (9.6%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Met (M)</td><td class="AutoAnnotatorInnerAmino">11 (3.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Phe (F)</td><td class="AutoAnnotatorInnerAmino">13 (4.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Pro (P)</td><td class="AutoAnnotatorInnerAmino">13 (4.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ser (S)</td><td class="AutoAnnotatorInnerAmino">20 (6.4%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Thr (T)</td><td class="AutoAnnotatorInnerAmino">17 (5.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Trp (W)</td><td class="AutoAnnotatorInnerAmino">4 (1.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Tyr (Y)</td><td class="AutoAnnotatorInnerAmino">17 (5.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Val (V)</td><td class="AutoAnnotatorInnerAmino">18 (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">313</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Positively charged (Arg+Lys):</td><td class="AutoAnnotatorAminoCountingInner3">43 (13.7%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Negatively charged (Asp+Glu):</td><td class="AutoAnnotatorAminoCountingInner3">48 (15.3%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Aromatic (Phe+His+Try+Tyr):</td><td class="AutoAnnotatorAminoCountingInner3">41 (13.1%)</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>1569</sub>H<sub>2417</sub>N<sub>419</sub>O<sub>483</sub>S<sub>13</sub></td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Molecular mass [Da]:</td><td class="AutoAnnotatorBiochemParInner3">35294.7</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Theoretical pI:</td><td class="AutoAnnotatorBiochemParInner3">5.90</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">47330 / 47455 (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_1539807777240()' 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 (0.72)</td><td class="AutoAnnotatorCodonUsage3">good (0.67)</td><td class="AutoAnnotatorCodonUsage3">good (0.75)</td><td class="AutoAnnotatorCodonUsage3">good (0.79)</td><td class="AutoAnnotatorCodonUsage3">good (0.71)</td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Alignments</strong> (obtained from <a href='http://predictprotein.org'>PredictProtein.org</a>)<br> There were no alignments for this protein in the data base. The BLAST search was initialized and should be ready in a few hours.</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="AutoAnnotator1col" colspan="2"> There were no predictions for this protein in the data base. The prediction was initialized and should be ready in a few hours.</td><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>var jqAutoAnnotator = jQuery.noConflict(true);function show_or_hide_plot_1539807777240(){hydrophobicity_datapoints = [[2.5,1.76],[3.5,1.24],[4.5,-0.56],[5.5,-0.56],[6.5,-1.72],[7.5,-1.32],[8.5,-1.26],[9.5,-1.14],[10.5,-1.06],[11.5,-1.50],[12.5,-1.42],[13.5,-1.60],[14.5,-1.52],[15.5,0.08],[16.5,0.70],[17.5,0.70],[18.5,0.26],[19.5,0.06],[20.5,-1.54],[21.5,-2.10],[22.5,-3.64],[23.5,-2.38],[24.5,-1.12],[25.5,0.34],[26.5,0.20],[27.5,0.20],[28.5,-0.44],[29.5,-0.24],[30.5,-0.10],[31.5,1.04],[32.5,1.58],[33.5,0.96],[34.5,0.90],[35.5,-0.26],[36.5,-1.32],[37.5,-1.24],[38.5,-0.62],[39.5,-2.02],[40.5,-1.40],[41.5,-0.86],[42.5,-0.40],[43.5,0.04],[44.5,0.78],[45.5,0.26],[46.5,-0.28],[47.5,-1.36],[48.5,-0.88],[49.5,0.18],[50.5,-0.44],[51.5,-0.44],[52.5,0.82],[53.5,0.36],[54.5,-1.44],[55.5,-0.10],[56.5,-0.18],[57.5,0.10],[58.5,-1.18],[59.5,0.10],[60.5,-1.16],[61.5,-0.46],[62.5,-1.46],[63.5,0.28],[64.5,-0.80],[65.5,-0.18],[66.5,-0.74],[67.5,-1.28],[68.5,-1.56],[69.5,-1.56],[70.5,-0.58],[71.5,-0.64],[72.5,-0.02],[73.5,-1.28],[74.5,-0.66],[75.5,-2.26],[76.5,-1.64],[77.5,-2.46],[78.5,-2.08],[79.5,-2.26],[80.5,-2.26],[81.5,-2.26],[82.5,-1.50],[83.5,-1.88],[84.5,-1.76],[85.5,-0.70],[86.5,-1.40],[87.5,-0.50],[88.5,-0.58],[89.5,0.40],[90.5,-0.10],[91.5,-0.10],[92.5,-0.94],[93.5,-0.24],[94.5,-1.40],[95.5,-0.50],[96.5,-0.04],[97.5,0.60],[98.5,1.04],[99.5,1.18],[100.5,-0.28],[101.5,0.94],[102.5,1.14],[103.5,0.62],[104.5,0.48],[105.5,0.48],[106.5,0.14],[107.5,-1.32],[108.5,-1.42],[109.5,-1.18],[110.5,-0.64],[111.5,-1.98],[112.5,-0.92],[113.5,-0.92],[114.5,0.00],[115.5,-0.62],[116.5,-0.48],[117.5,-1.16],[118.5,-0.54],[119.5,-2.08],[120.5,-0.40],[121.5,-0.08],[122.5,-0.46],[123.5,-1.08],[124.5,0.38],[125.5,-1.30],[126.5,-0.22],[127.5,0.32],[128.5,1.14],[129.5,0.06],[130.5,0.14],[131.5,-0.70],[132.5,0.02],[133.5,-1.32],[134.5,-1.18],[135.5,-1.18],[136.5,-2.00],[137.5,-1.72],[138.5,-0.56],[139.5,-1.08],[140.5,0.18],[141.5,0.38],[142.5,-1.16],[143.5,-1.62],[144.5,-1.00],[145.5,-0.72],[146.5,0.82],[147.5,1.38],[148.5,2.30],[149.5,2.24],[150.5,0.70],[151.5,-0.84],[152.5,-0.86],[153.5,-1.86],[154.5,-0.96],[155.5,-0.96],[156.5,-0.96],[157.5,-0.88],[158.5,-1.42],[159.5,-1.62],[160.5,-0.02],[161.5,0.42],[162.5,-0.28],[163.5,1.26],[164.5,-0.08],[165.5,-0.22],[166.5,-0.86],[167.5,-0.16],[168.5,-1.14],[169.5,-1.06],[170.5,-1.26],[171.5,-0.68],[172.5,-0.76],[173.5,-1.32],[174.5,-0.70],[175.5,-1.58],[176.5,-0.42],[177.5,0.12],[178.5,0.12],[179.5,-0.58],[180.5,-1.04],[181.5,-2.02],[182.5,-2.02],[183.5,-1.40],[184.5,-0.80],[185.5,-0.72],[186.5,-0.22],[187.5,-0.76],[188.5,-0.82],[189.5,-1.34],[190.5,-1.54],[191.5,-1.52],[192.5,-1.62],[193.5,-1.80],[194.5,-1.80],[195.5,-1.60],[196.5,-2.06],[197.5,-1.44],[198.5,-0.36],[199.5,-0.44],[200.5,0.18],[201.5,-0.44],[202.5,0.10],[203.5,-1.44],[204.5,-0.28],[205.5,-1.10],[206.5,0.36],[207.5,-1.32],[208.5,0.22],[209.5,-0.94],[210.5,-0.74],[211.5,-1.58],[212.5,-0.88],[213.5,-2.28],[214.5,-1.76],[215.5,-1.76],[216.5,-1.32],[217.5,-1.94],[218.5,-0.46],[219.5,-0.98],[220.5,-0.42],[221.5,-0.92],[222.5,-0.48],[223.5,-0.94],[224.5,0.20],[225.5,-0.44],[226.5,-1.08],[227.5,-1.14],[228.5,-0.68],[229.5,-1.74],[230.5,-0.20],[231.5,0.26],[232.5,0.50],[233.5,0.02],[234.5,0.46],[235.5,-1.08],[236.5,-0.90],[237.5,-1.52],[238.5,-0.98],[239.5,-1.50],[240.5,0.04],[241.5,-0.52],[242.5,1.08],[243.5,0.04],[244.5,0.66],[245.5,-0.74],[246.5,-0.74],[247.5,-2.34],[248.5,-2.90],[249.5,-3.00],[250.5,-2.50],[251.5,-0.90],[252.5,0.64],[253.5,0.64],[254.5,0.20],[255.5,0.08],[256.5,-1.52],[257.5,-3.26],[258.5,-2.20],[259.5,-2.20],[260.5,-2.02],[261.5,-2.22],[262.5,-1.96],[263.5,-2.48],[264.5,-1.92],[265.5,-1.92],[266.5,-0.66],[267.5,-0.10],[268.5,-0.10],[269.5,-0.12],[270.5,-0.20],[271.5,-1.26],[272.5,-1.34],[273.5,-1.26],[274.5,-1.26],[275.5,-1.28],[276.5,-0.74],[277.5,-1.22],[278.5,-1.46],[279.5,-2.00],[280.5,-1.26],[281.5,-1.80],[282.5,-1.94],[283.5,-1.26],[284.5,-1.26],[285.5,-2.08],[286.5,-0.88],[287.5,0.74],[288.5,0.12],[289.5,0.74],[290.5,0.30],[291.5,-0.34],[292.5,-0.80],[293.5,0.30],[294.5,-0.32],[295.5,0.24],[296.5,-0.32],[297.5,-1.40],[298.5,-2.32],[299.5,-2.40],[300.5,-1.36],[301.5,-1.44],[302.5,0.16],[303.5,-0.46],[304.5,-0.38],[305.5,-0.52],[306.5,0.00],[307.5,-1.68],[308.5,-1.88],[309.5,-0.42],[310.5,-0.82]];charge_datapoints = [[2.5,0.20],[3.5,0.20],[4.5,0.40],[5.5,0.40],[6.5,0.40],[7.5,0.40],[8.5,0.40],[9.5,0.40],[10.5,0.20],[11.5,0.20],[12.5,0.20],[13.5,0.20],[14.5,-0.20],[15.5,-0.20],[16.5,-0.20],[17.5,-0.20],[18.5,-0.40],[19.5,0.00],[20.5,-0.20],[21.5,-0.10],[22.5,-0.10],[23.5,0.10],[24.5,-0.10],[25.5,0.10],[26.5,0.20],[27.5,0.20],[28.5,0.20],[29.5,0.20],[30.5,0.20],[31.5,0.00],[32.5,0.00],[33.5,0.00],[34.5,0.00],[35.5,0.00],[36.5,0.00],[37.5,0.00],[38.5,0.00],[39.5,0.20],[40.5,0.20],[41.5,0.20],[42.5,0.20],[43.5,0.20],[44.5,0.00],[45.5,0.00],[46.5,-0.20],[47.5,-0.40],[48.5,-0.40],[49.5,-0.40],[50.5,-0.20],[51.5,-0.20],[52.5,0.00],[53.5,0.00],[54.5,0.20],[55.5,0.00],[56.5,0.40],[57.5,0.40],[58.5,0.60],[59.5,0.40],[60.5,0.20],[61.5,0.00],[62.5,0.00],[63.5,-0.20],[64.5,-0.20],[65.5,0.00],[66.5,0.10],[67.5,-0.10],[68.5,-0.10],[69.5,-0.30],[70.5,-0.30],[71.5,-0.60],[72.5,-0.40],[73.5,-0.60],[74.5,-0.40],[75.5,-0.60],[76.5,-0.40],[77.5,-0.20],[78.5,0.00],[79.5,0.00],[80.5,0.00],[81.5,0.00],[82.5,-0.20],[83.5,-0.20],[84.5,-0.20],[85.5,0.00],[86.5,0.20],[87.5,0.20],[88.5,0.40],[89.5,0.40],[90.5,0.40],[91.5,0.40],[92.5,0.40],[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,-0.20],[103.5,-0.20],[104.5,-0.20],[105.5,0.00],[106.5,0.00],[107.5,0.00],[108.5,0.00],[109.5,0.00],[110.5,0.00],[111.5,0.20],[112.5,0.20],[113.5,0.20],[114.5,0.20],[115.5,0.40],[116.5,0.30],[117.5,0.30],[118.5,0.30],[119.5,0.10],[120.5,-0.10],[121.5,-0.20],[122.5,-0.40],[123.5,-0.40],[124.5,-0.20],[125.5,0.00],[126.5,0.00],[127.5,0.20],[128.5,0.20],[129.5,0.20],[130.5,-0.20],[131.5,-0.20],[132.5,-0.20],[133.5,0.00],[134.5,0.00],[135.5,0.00],[136.5,0.20],[137.5,0.20],[138.5,0.00],[139.5,0.00],[140.5,0.20],[141.5,-0.20],[142.5,-0.40],[143.5,-0.40],[144.5,-0.40],[145.5,-0.40],[146.5,-0.20],[147.5,0.00],[148.5,0.00],[149.5,0.00],[150.5,0.00],[151.5,-0.20],[152.5,-0.20],[153.5,-0.20],[154.5,-0.20],[155.5,-0.20],[156.5,-0.20],[157.5,-0.20],[158.5,-0.40],[159.5,-0.40],[160.5,-0.40],[161.5,-0.20],[162.5,0.00],[163.5,0.20],[164.5,0.40],[165.5,0.40],[166.5,0.60],[167.5,0.40],[168.5,0.40],[169.5,0.20],[170.5,0.20],[171.5,0.00],[172.5,0.00],[173.5,-0.20],[174.5,-0.20],[175.5,-0.20],[176.5,-0.20],[177.5,-0.20],[178.5,0.00],[179.5,0.20],[180.5,0.40],[181.5,0.40],[182.5,0.40],[183.5,0.40],[184.5,0.20],[185.5,-0.20],[186.5,-0.20],[187.5,-0.20],[188.5,-0.20],[189.5,-0.40],[190.5,0.00],[191.5,0.00],[192.5,0.00],[193.5,0.00],[194.5,0.00],[195.5,-0.40],[196.5,-0.40],[197.5,-0.40],[198.5,-0.40],[199.5,0.00],[200.5,0.20],[201.5,0.00],[202.5,0.00],[203.5,0.20],[204.5,0.00],[205.5,0.20],[206.5,0.40],[207.5,0.60],[208.5,0.40],[209.5,0.60],[210.5,0.20],[211.5,0.20],[212.5,0.00],[213.5,0.10],[214.5,-0.10],[215.5,-0.10],[216.5,-0.10],[217.5,-0.30],[218.5,-0.40],[219.5,-0.20],[220.5,0.00],[221.5,0.00],[222.5,0.20],[223.5,0.20],[224.5,0.00],[225.5,0.20],[226.5,0.40],[227.5,0.40],[228.5,0.40],[229.5,0.40],[230.5,0.20],[231.5,0.00],[232.5,0.00],[233.5,0.00],[234.5,0.00],[235.5,0.20],[236.5,0.20],[237.5,0.00],[238.5,0.00],[239.5,0.20],[240.5,0.00],[241.5,-0.20],[242.5,0.00],[243.5,0.00],[244.5,-0.20],[245.5,-0.10],[246.5,0.10],[247.5,-0.10],[248.5,-0.30],[249.5,-0.30],[250.5,-0.40],[251.5,-0.40],[252.5,-0.20],[253.5,-0.20],[254.5,-0.20],[255.5,-0.20],[256.5,-0.40],[257.5,-0.20],[258.5,0.00],[259.5,-0.20],[260.5,-0.20],[261.5,0.20],[262.5,0.10],[263.5,0.10],[264.5,0.30],[265.5,0.30],[266.5,0.10],[267.5,0.00],[268.5,0.00],[269.5,0.00],[270.5,0.00],[271.5,-0.20],[272.5,-0.20],[273.5,-0.20],[274.5,-0.20],[275.5,-0.20],[276.5,0.00],[277.5,0.10],[278.5,0.10],[279.5,0.10],[280.5,0.10],[281.5,-0.10],[282.5,0.00],[283.5,0.00],[284.5,-0.20],[285.5,-0.20],[286.5,0.00],[287.5,-0.20],[288.5,-0.20],[289.5,0.00],[290.5,-0.20],[291.5,-0.20],[292.5,-0.20],[293.5,-0.20],[294.5,-0.40],[295.5,-0.20],[296.5,-0.40],[297.5,-0.60],[298.5,-0.60],[299.5,-0.20],[300.5,-0.20],[301.5,0.20],[302.5,0.40],[303.5,0.20],[304.5,-0.20],[305.5,-0.20],[306.5,-0.40],[307.5,-0.20],[308.5,0.20],[309.5,0.40],[310.5,0.40]];dis_datapoints = undefined;trans_datapoints = undefined;sec_helix_datapoints = undefined;sec_strand_datapoints = undefined;acc_exposed_datapoints = undefined;acc_buried_datapoints = undefined;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] = jqAutoAnnotator.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( jqAutoAnnotator('#AutoAnnotator_container_1539807777240 #hydrophobicity_charge_button').val() =='Show' ){jqAutoAnnotator('#AutoAnnotator_container_1539807777240 #hydrophobicity_charge_container').css('display','block');jqAutoAnnotator('#AutoAnnotator_container_1539807777240 #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>';jqAutoAnnotator('#AutoAnnotator_container_1539807777240 #hydrophobicity_charge_explanation').html(description_html);plot_according_to_selectors_1539807777240();jqAutoAnnotator('#AutoAnnotator_container_1539807777240 #AutoAnnotator_plot_selectors').find('input').click(plot_according_to_selectors_1539807777240);}else{jqAutoAnnotator('#AutoAnnotator_container_1539807777240 #hydrophobicity_charge_container').css('display','none');jqAutoAnnotator('#AutoAnnotator_container_1539807777240 #hydrophobicity_charge_button').val('Show');jqAutoAnnotator('#AutoAnnotator_container_1539807777240 #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_1539807777240(){try{var plot_datasets = [[],[]];if(jqAutoAnnotator('#AutoAnnotator_container_1539807777240 #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(jqAutoAnnotator('#AutoAnnotator_container_1539807777240 #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 ++){jqAutoAnnotator.plot('#AutoAnnotator_container_1539807777240 #hydrophobicity_charge_placeholder'+ plot_num.toString(), plot_datasets, flot_plot_options[plot_num] );}var screen_width = jqAutoAnnotator('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(jqAutoAnnotator('#AutoAnnotator_container_1539807777240 #dis_checkbox').prop('checked') == true){for ( j = 0 ; j < dis_datapoints.length ; j++ ){jqAutoAnnotator('#AutoAnnotator_container_1539807777240 #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>');jqAutoAnnotator('#AutoAnnotator_container_1539807777240 #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(jqAutoAnnotator('#AutoAnnotator_container_1539807777240 #trans_checkbox').prop('checked') == true){for ( j = 0 ; j < trans_datapoints.length ; j++ ){jqAutoAnnotator('#AutoAnnotator_container_1539807777240 #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(jqAutoAnnotator('#AutoAnnotator_container_1539807777240 #sec_checkbox').prop('checked') == true){for ( j = 0 ; j < sec_helix_datapoints.length ; j++ ){jqAutoAnnotator('#AutoAnnotator_container_1539807777240 #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++ ){jqAutoAnnotator('#AutoAnnotator_container_1539807777240 #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(jqAutoAnnotator('#AutoAnnotator_container_1539807777240 #acc_checkbox').prop('checked') == true){for ( j = 0 ; j < acc_buried_datapoints.length ; j++ ){jqAutoAnnotator('#AutoAnnotator_container_1539807777240 #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++ ){jqAutoAnnotator('#AutoAnnotator_container_1539807777240 #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> | |
Revision as of 20:48, 17 October 2018
Intein Monomer 1: RFP reporter flanked with orthogonal inteins
| Intein Monomer 1 | |
|---|---|
| Function | Standardised blue-white screening |
| Use in | E. coli cells |
| Chassis Tested | DH5α cells, BL21* cells |
| Abstraction Hierarchy | Composite Device |
| Related Device | BBa_K2842690 |
| RFC standard | RFC10,RFC12,RFC21,RFC23 & RFC25 compatible |
| Backbone | pSB1C3 |
| Submitted by | [http://2018.igem.org/Team:UCL UCL iGEM 2018] |
(1) BsaI digested Intein Passenger BBa_K2842669
(2) BsaI digested RFP inteins BBa_K2842680
(3) BsaI digested GFP inteins BBa_K2842690
*edited to show relevant bands
Functional Parameters
| Protein data table for BioBrick BBa_ automatically created by the BioBrick-AutoAnnotator version 1.0 | ||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Nucleotide sequence in RFC 10: (underlined part encodes the protein) GCTTCTACAAACGCGGCTTCTTCCAAAGAGACCTAATACGACTCACTATAGGGGTTGTGAGCGGATAACAACCCAAGACAAGGAGGAGTACCAATGATCAAG ... CGCTTGGCTTAAGTGACAGTTGAAAAGCGAAAAAAAAACCCCGCCCCTGACAGGGCGGGGTTTTTTTTGGTCTCAACGGACGACGCCGGTTACTACATTGA ORF from nucleotide position 94 to 1032 (excluding stop-codon) | ||||||||||||||||||||||||||||||||||||||||||||||
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
| ||||||||||||||||||||||||||||||||||||||||||||||
Sequence features: (with their position in the amino acid sequence, see the list of supported features)
| ||||||||||||||||||||||||||||||||||||||||||||||
Amino acid composition:
| ||||||||||||||||||||||||||||||||||||||||||||||
Amino acid counting
| Biochemical parameters
| |||||||||||||||||||||||||||||||||||||||||||||
| Plot for hydrophobicity, charge, predicted secondary structure, solvent accessability, transmembrane helices and disulfid bridges | ||||||||||||||||||||||||||||||||||||||||||||||
Codon usage
| ||||||||||||||||||||||||||||||||||||||||||||||
| Alignments (obtained from PredictProtein.org) There were no alignments for this protein in the data base. The BLAST search was initialized and should be ready in a few hours. | ||||||||||||||||||||||||||||||||||||||||||||||
| Predictions (obtained from PredictProtein.org) | ||||||||||||||||||||||||||||||||||||||||||||||
| There were no predictions for this protein in the data base. The prediction was initialized and should be ready in a few hours. | ||||||||||||||||||||||||||||||||||||||||||||||
| 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. | ||||||||||||||||||||||||||||||||||||||||||||||
References
-
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 site found at 1165
Illegal BsaI.rc site found at 28
Illegal SapI site found at 903
Illegal SapI.rc site found at 213