Difference between revisions of "Part:BBa K1351021"
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<partinfo>BBa_K1351021 short</partinfo> | <partinfo>BBa_K1351021 short</partinfo> | ||
| − | Mutant of the Biobrick | + | Mutant of the Biobrick [https://parts.igem.org/Part:BBa_E1010 BBa_E1010]. In order to make it compatible with the Freiburg-Standard RFC25, two AgeI-Restriction sites were deleted. |
monomeric RFP: Red Fluorescent Protein. | monomeric RFP: Red Fluorescent Protein. | ||
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[[File:LMU14_E1010mut-Pellet.jpg|thumb|right|The left eppendorf tube contains a pink bacterial pellet of ''E. coli'' containing the BioBrick BBa_K1351021 in [https://parts.igem.org/wiki/index.php?title=Part:BBa_K1351040 pBS0K-pPspac], a ''B. subtilis'' expression vector. On the right, you can see ''E. coli'' with the empty vector]] | [[File:LMU14_E1010mut-Pellet.jpg|thumb|right|The left eppendorf tube contains a pink bacterial pellet of ''E. coli'' containing the BioBrick BBa_K1351021 in [https://parts.igem.org/wiki/index.php?title=Part:BBa_K1351040 pBS0K-pPspac], a ''B. subtilis'' expression vector. On the right, you can see ''E. coli'' with the empty vector]] | ||
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This part is used in the 2014 LMU-Munich iGEM project [http://2014.igem.org/Team:LMU-Munich BaKillus]. | This part is used in the 2014 LMU-Munich iGEM project [http://2014.igem.org/Team:LMU-Munich BaKillus]. | ||
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| + | === BioBrick AutoAnnotator === | ||
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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_1414675305031'><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1414675305031 --><th id="AutoAnnotatorHeader" colspan="2">Protein data table for BioBrick <a href="https://parts.igem.org/wiki/index.php?title=Part:BBa_<!------------------------Enter BioBrick number here------------------------>">BBa_<!------------------------Enter BioBrick number here------------------------></a> automatically created by the <a href="http://2013.igem.org/Team:TU-Munich/Results/AutoAnnotator">BioBrick-AutoAnnotator</a> version 1.0</th></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Nucleotide sequence</strong> in <strong>RFC 25</strong>, so ATGGCCGGC and ACCGGT were added (in italics) to the 5' and 3' ends: (underlined part encodes the protein)<br><span class="AutoAnnotatorSequence"> <u><i>ATGGCCGGC</i>ATGGCTTCC ... ACCTGTGCT<i>ACCGGT</i></u></span><br> <strong>ORF</strong> from nucleotide position -8 to 681 (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">MAGMASSEDVIKEFMRFKVRMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQFQYGSKAYVKHPADIPDYLKLSFPEGFKWERVM<br>NFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASTERMYPEDGALKGEIKMRLKLKDGGHYDAEVKTTYMAKKPVQLPGAYKTDI<br>KLDITSHNEDYTIVEQYERAEGRHSTCATG*</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">13 (5.7%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Arg (R)</td><td class="AutoAnnotatorInnerAmino">9 (3.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asn (N)</td><td class="AutoAnnotatorInnerAmino">4 (1.7%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asp (D)</td><td class="AutoAnnotatorInnerAmino">14 (6.1%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Cys (C)</td><td class="AutoAnnotatorInnerAmino">1 (0.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gln (Q)</td><td class="AutoAnnotatorInnerAmino">8 (3.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Glu (E)</td><td class="AutoAnnotatorInnerAmino">22 (9.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gly (G)</td><td class="AutoAnnotatorInnerAmino">24 (10.4%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">His (H)</td><td class="AutoAnnotatorInnerAmino">5 (2.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ile (I)</td><td class="AutoAnnotatorInnerAmino">9 (3.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Leu (L)</td><td class="AutoAnnotatorInnerAmino">12 (5.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Lys (K)</td><td class="AutoAnnotatorInnerAmino">22 (9.6%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Met (M)</td><td class="AutoAnnotatorInnerAmino">10 (4.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Phe (F)</td><td class="AutoAnnotatorInnerAmino">10 (4.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Pro (P)</td><td class="AutoAnnotatorInnerAmino">12 (5.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ser (S)</td><td class="AutoAnnotatorInnerAmino">12 (5.2%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Thr (T)</td><td class="AutoAnnotatorInnerAmino">15 (6.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Trp (W)</td><td class="AutoAnnotatorInnerAmino">3 (1.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Tyr (Y)</td><td class="AutoAnnotatorInnerAmino">11 (4.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Val (V)</td><td class="AutoAnnotatorInnerAmino">14 (6.1%)</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">230</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Positively charged (Arg+Lys):</td><td class="AutoAnnotatorAminoCountingInner3">31 (13.5%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Negatively charged (Asp+Glu):</td><td class="AutoAnnotatorAminoCountingInner3">36 (15.7%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Aromatic (Phe+His+Try+Tyr):</td><td class="AutoAnnotatorAminoCountingInner3">29 (12.6%)</td></tr></table></td><td class="AutoAnnotatorBiochemParOuter"><strong>Biochemical parameters</strong><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Atomic composition:</td><td class="AutoAnnotatorBiochemParInner3">C<sub>1152</sub>H<sub>1778</sub>N<sub>304</sub>O<sub>353</sub>S<sub>11</sub></td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Molecular mass [Da]:</td><td class="AutoAnnotatorBiochemParInner3">25887.3</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Theoretical pI:</td><td class="AutoAnnotatorBiochemParInner3">5.65</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">32890 / 32953 (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_1414675305031()' 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">excellent (0.84)</td><td class="AutoAnnotatorCodonUsage3">good (0.72)</td><td class="AutoAnnotatorCodonUsage3">good (0.68)</td><td class="AutoAnnotatorCodonUsage3">good (0.74)</td><td class="AutoAnnotatorCodonUsage3">good (0.79)</td><td class="AutoAnnotatorCodonUsage3">good (0.72)</td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Alignments</strong> (obtained from <a href='http://predictprotein.org'>PredictProtein.org</a>)<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_1414675305031(){hydrophobicity_datapoints = [[2.5,1.40],[3.5,0.86],[4.5,0.34],[5.5,-0.28],[6.5,-1.36],[7.5,-0.88],[8.5,0.18],[9.5,-0.44],[10.5,-0.44],[11.5,0.82],[12.5,0.36],[13.5,-1.44],[14.5,-0.10],[15.5,-0.18],[16.5,0.10],[17.5,-1.18],[18.5,0.10],[19.5,-1.16],[20.5,-0.46],[21.5,-1.46],[22.5,0.28],[23.5,-0.80],[24.5,-0.18],[25.5,-0.74],[26.5,-1.28],[27.5,-1.56],[28.5,-1.56],[29.5,-0.58],[30.5,-0.64],[31.5,-0.02],[32.5,-1.28],[33.5,-0.66],[34.5,-2.26],[35.5,-1.64],[36.5,-2.46],[37.5,-2.08],[38.5,-2.26],[39.5,-2.26],[40.5,-2.26],[41.5,-1.50],[42.5,-1.88],[43.5,-1.76],[44.5,-0.70],[45.5,-1.40],[46.5,-0.50],[47.5,-0.58],[48.5,0.40],[49.5,-0.10],[50.5,-0.10],[51.5,-0.94],[52.5,-0.24],[53.5,-1.40],[54.5,-0.50],[55.5,-0.04],[56.5,0.60],[57.5,1.04],[58.5,1.18],[59.5,-0.28],[60.5,0.94],[61.5,1.14],[62.5,0.62],[63.5,0.48],[64.5,0.48],[65.5,0.14],[66.5,-1.32],[67.5,-1.42],[68.5,-1.18],[69.5,-0.64],[70.5,-1.98],[71.5,-0.92],[72.5,-0.92],[73.5,-0.00],[74.5,-0.62],[75.5,-0.48],[76.5,-1.16],[77.5,-0.54],[78.5,-2.08],[79.5,-0.40],[80.5,-0.08],[81.5,-0.46],[82.5,-1.08],[83.5,0.38],[84.5,-1.30],[85.5,-0.22],[86.5,0.32],[87.5,1.14],[88.5,0.06],[89.5,0.14],[90.5,-0.70],[91.5,0.02],[92.5,-1.32],[93.5,-1.18],[94.5,-1.18],[95.5,-2.00],[96.5,-1.72],[97.5,-0.56],[98.5,-1.08],[99.5,0.18],[100.5,0.38],[101.5,-1.16],[102.5,-1.62],[103.5,-1.00],[104.5,-0.72],[105.5,0.82],[106.5,1.38],[107.5,2.30],[108.5,2.24],[109.5,0.70],[110.5,-0.84],[111.5,-0.86],[112.5,-1.86],[113.5,-0.96],[114.5,-0.96],[115.5,-0.96],[116.5,-0.88],[117.5,-1.42],[118.5,-1.62],[119.5,-0.02],[120.5,0.42],[121.5,-0.28],[122.5,1.26],[123.5,-0.08],[124.5,-0.22],[125.5,-0.86],[126.5,-0.16],[127.5,-1.14],[128.5,-1.06],[129.5,-1.26],[130.5,-0.68],[131.5,-0.76],[132.5,-1.32],[133.5,-0.70],[134.5,-1.58],[135.5,-0.42],[136.5,0.12],[137.5,0.12],[138.5,-0.58],[139.5,-1.04],[140.5,-2.02],[141.5,-2.02],[142.5,-1.40],[143.5,-0.80],[144.5,-0.72],[145.5,-0.22],[146.5,-0.76],[147.5,-0.82],[148.5,-1.34],[149.5,-1.54],[150.5,-1.52],[151.5,-1.62],[152.5,-1.80],[153.5,-1.80],[154.5,-1.60],[155.5,-2.06],[156.5,-1.44],[157.5,-0.36],[158.5,-0.44],[159.5,0.18],[160.5,-0.44],[161.5,0.10],[162.5,-1.44],[163.5,-0.28],[164.5,-1.10],[165.5,0.36],[166.5,-1.32],[167.5,0.22],[168.5,-0.94],[169.5,-0.74],[170.5,-1.58],[171.5,-0.88],[172.5,-2.28],[173.5,-1.76],[174.5,-1.76],[175.5,-1.32],[176.5,-1.94],[177.5,-0.46],[178.5,-0.98],[179.5,-0.42],[180.5,-0.92],[181.5,-0.48],[182.5,-0.94],[183.5,0.20],[184.5,-0.44],[185.5,-1.08],[186.5,-1.14],[187.5,-0.68],[188.5,-1.74],[189.5,-0.20],[190.5,0.26],[191.5,0.50],[192.5,0.02],[193.5,0.46],[194.5,-1.08],[195.5,-0.90],[196.5,-1.52],[197.5,-0.98],[198.5,-1.50],[199.5,0.04],[200.5,-0.52],[201.5,1.08],[202.5,0.04],[203.5,0.66],[204.5,-0.74],[205.5,-0.74],[206.5,-2.34],[207.5,-2.90],[208.5,-3.00],[209.5,-2.50],[210.5,-0.90],[211.5,0.64],[212.5,0.64],[213.5,0.20],[214.5,0.08],[215.5,-1.52],[216.5,-3.26],[217.5,-2.20],[218.5,-2.20],[219.5,-2.02],[220.5,-2.22],[221.5,-1.96],[222.5,-2.48],[223.5,-1.92],[224.5,-1.34],[225.5,-0.08],[226.5,0.42],[227.5,0.50]];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,-0.40],[9.5,-0.20],[10.5,-0.20],[11.5,0.00],[12.5,0.00],[13.5,0.20],[14.5,0.00],[15.5,0.40],[16.5,0.40],[17.5,0.60],[18.5,0.40],[19.5,0.20],[20.5,0.00],[21.5,0.00],[22.5,-0.20],[23.5,-0.20],[24.5,0.00],[25.5,0.10],[26.5,-0.10],[27.5,-0.10],[28.5,-0.30],[29.5,-0.30],[30.5,-0.60],[31.5,-0.40],[32.5,-0.60],[33.5,-0.40],[34.5,-0.60],[35.5,-0.40],[36.5,-0.20],[37.5,0.00],[38.5,0.00],[39.5,0.00],[40.5,0.00],[41.5,-0.20],[42.5,-0.20],[43.5,-0.20],[44.5,0.00],[45.5,0.20],[46.5,0.20],[47.5,0.40],[48.5,0.40],[49.5,0.40],[50.5,0.40],[51.5,0.40],[52.5,0.20],[53.5,0.20],[54.5,0.20],[55.5,0.00],[56.5,0.00],[57.5,0.00],[58.5,0.00],[59.5,-0.20],[60.5,-0.20],[61.5,-0.20],[62.5,-0.20],[63.5,-0.20],[64.5,0.00],[65.5,0.00],[66.5,0.00],[67.5,0.00],[68.5,0.00],[69.5,0.00],[70.5,0.20],[71.5,0.20],[72.5,0.20],[73.5,0.20],[74.5,0.40],[75.5,0.30],[76.5,0.30],[77.5,0.30],[78.5,0.10],[79.5,-0.10],[80.5,-0.20],[81.5,-0.40],[82.5,-0.40],[83.5,-0.20],[84.5,0.00],[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],[92.5,0.00],[93.5,0.00],[94.5,0.00],[95.5,0.20],[96.5,0.20],[97.5,0.00],[98.5,0.00],[99.5,0.20],[100.5,-0.20],[101.5,-0.40],[102.5,-0.40],[103.5,-0.40],[104.5,-0.40],[105.5,-0.20],[106.5,0.00],[107.5,0.00],[108.5,0.00],[109.5,0.00],[110.5,-0.20],[111.5,-0.20],[112.5,-0.20],[113.5,-0.20],[114.5,-0.20],[115.5,-0.20],[116.5,-0.20],[117.5,-0.40],[118.5,-0.40],[119.5,-0.40],[120.5,-0.20],[121.5,0.00],[122.5,0.20],[123.5,0.40],[124.5,0.40],[125.5,0.60],[126.5,0.40],[127.5,0.40],[128.5,0.20],[129.5,0.20],[130.5,0.00],[131.5,0.00],[132.5,-0.20],[133.5,-0.20],[134.5,-0.20],[135.5,-0.20],[136.5,-0.20],[137.5,0.00],[138.5,0.20],[139.5,0.40],[140.5,0.40],[141.5,0.40],[142.5,0.40],[143.5,0.20],[144.5,-0.20],[145.5,-0.20],[146.5,-0.20],[147.5,-0.20],[148.5,-0.40],[149.5,0.00],[150.5,0.00],[151.5,0.00],[152.5,0.00],[153.5,0.00],[154.5,-0.40],[155.5,-0.40],[156.5,-0.40],[157.5,-0.40],[158.5,0.00],[159.5,0.20],[160.5,0.00],[161.5,0.00],[162.5,0.20],[163.5,0.00],[164.5,0.20],[165.5,0.40],[166.5,0.60],[167.5,0.40],[168.5,0.60],[169.5,0.20],[170.5,0.20],[171.5,0.00],[172.5,0.10],[173.5,-0.10],[174.5,-0.10],[175.5,-0.10],[176.5,-0.30],[177.5,-0.40],[178.5,-0.20],[179.5,0.00],[180.5,0.00],[181.5,0.20],[182.5,0.20],[183.5,0.00],[184.5,0.20],[185.5,0.40],[186.5,0.40],[187.5,0.40],[188.5,0.40],[189.5,0.20],[190.5,0.00],[191.5,0.00],[192.5,0.00],[193.5,0.00],[194.5,0.20],[195.5,0.20],[196.5,0.00],[197.5,0.00],[198.5,0.20],[199.5,0.00],[200.5,-0.20],[201.5,0.00],[202.5,0.00],[203.5,-0.20],[204.5,-0.10],[205.5,0.10],[206.5,-0.10],[207.5,-0.30],[208.5,-0.30],[209.5,-0.40],[210.5,-0.40],[211.5,-0.20],[212.5,-0.20],[213.5,-0.20],[214.5,-0.20],[215.5,-0.40],[216.5,-0.20],[217.5,0.00],[218.5,-0.20],[219.5,-0.20],[220.5,0.20],[221.5,0.10],[222.5,0.10],[223.5,0.30],[224.5,0.30],[225.5,0.10],[226.5,0.00],[227.5,0.00]];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_1414675305031 #hydrophobicity_charge_button').val() =='Show' ){jqAutoAnnotator('#AutoAnnotator_container_1414675305031 #hydrophobicity_charge_container').css('display','block');jqAutoAnnotator('#AutoAnnotator_container_1414675305031 #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_1414675305031 #hydrophobicity_charge_explanation').html(description_html);plot_according_to_selectors_1414675305031();jqAutoAnnotator('#AutoAnnotator_container_1414675305031 #AutoAnnotator_plot_selectors').find('input').click(plot_according_to_selectors_1414675305031);}else{jqAutoAnnotator('#AutoAnnotator_container_1414675305031 #hydrophobicity_charge_container').css('display','none');jqAutoAnnotator('#AutoAnnotator_container_1414675305031 #hydrophobicity_charge_button').val('Show');jqAutoAnnotator('#AutoAnnotator_container_1414675305031 #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_1414675305031(){try{var plot_datasets = [[],[]];if(jqAutoAnnotator('#AutoAnnotator_container_1414675305031 #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_1414675305031 #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_1414675305031 #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_1414675305031 #dis_checkbox').prop('checked') == true){for ( j = 0 ; j < dis_datapoints.length ; j++ ){jqAutoAnnotator('#AutoAnnotator_container_1414675305031 #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_1414675305031 #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_1414675305031 #trans_checkbox').prop('checked') == true){for ( j = 0 ; j < trans_datapoints.length ; j++ ){jqAutoAnnotator('#AutoAnnotator_container_1414675305031 #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_1414675305031 #sec_checkbox').prop('checked') == true){for ( j = 0 ; j < sec_helix_datapoints.length ; j++ ){jqAutoAnnotator('#AutoAnnotator_container_1414675305031 #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_1414675305031 #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_1414675305031 #acc_checkbox').prop('checked') == true){for ( j = 0 ; j < acc_buried_datapoints.length ; j++ ){jqAutoAnnotator('#AutoAnnotator_container_1414675305031 #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_1414675305031 #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:' + 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Revision as of 12:43, 30 October 2014
Monomeric Red Fluorescent Protein from Discosoma striata
Mutant of the Biobrick BBa_E1010. In order to make it compatible with the Freiburg-Standard RFC25, two AgeI-Restriction sites were deleted.
monomeric RFP: Red Fluorescent Protein.
Excitation peak: 584 nm Emission peak: 607 nm
Usage and Biology
This part was created in order to enhance the [http://2012.igem.org/Team:LMU-Munich/Bacillus_BioBricks Bacillus BioBrick Box] by adding different fluorescent proteins in order to have more reporters available in B. subtilis. It still works very well in E. coli, the rather weak coloring you see on the pictures is due to the fact, that a rather homogenous and weak B. subtilis expression vector (pBS0K-Pspac) was used in E. coli
BBa_K1351021 in the B. subtilis expression vector pBS0K-Pspac in E. coli
The left eppendorf tube contains a pink bacterial pellet of E. coli containing the BioBrick BBa_K1351021 in pBS0K-pPspac, a B. subtilis expression vector. On the right, you can see E. coli with the empty vector
Design
This part was generated in a modified version of RFC25, where a strong Shine Dalgarno Sequence (SD) is included, and has the following prefix and suffix:
| prefix with EcoRI, NotI, XbaI, SD and NgoMIV: | GAATTCGCGGCCGCTTCTAGAGTAAGGAGGAGCCGGC |
| suffix with AgeI, SpeI, NotI and PstI: | ACCGGTTAATACTAGTAGCGGCCGCTGCAG |
Sites of restriction enzymes generating compatible overhangs have the same color:
EcoRI and PstI in blue, NotI in green, XbaI and SpeI in red, NgoMIV and AgeI in orange. Shine-Dalgarno sequence and stop codons are underlined.
This part is used in the 2014 LMU-Munich iGEM project [http://2014.igem.org/Team:LMU-Munich BaKillus].
BioBrick AutoAnnotator
| Protein data table for BioBrick BBa_ automatically created by the BioBrick-AutoAnnotator version 1.0 | ||||||||||||||||||||||||||||||||||||||||||||||
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| Nucleotide sequence in RFC 25, so ATGGCCGGC and ACCGGT were added (in italics) to the 5' and 3' ends: (underlined part encodes the protein) ATGGCCGGCATGGCTTCC ... ACCTGTGCTACCGGT ORF from nucleotide position -8 to 681 (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) 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. | ||||||||||||||||||||||||||||||||||||||||||||||
Sequence and Features
Assembly Compatibility:
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]