Difference between revisions of "Part:BBa E0040"
(rollbackEdits.php mass rollback) |
|||
| Line 61: | Line 61: | ||
Yeast- and FACS optimized GFP: <html><a href="https://parts.igem.org/Part:BBa_K194001" target="_blank">BBa_K194001</a> | Yeast- and FACS optimized GFP: <html><a href="https://parts.igem.org/Part:BBa_K194001" target="_blank">BBa_K194001</a> | ||
Yeast- and FACS optimized, fast degradable GFP: <html><a href="https://parts.igem.org/Part:BBa_K194002" target="_blank">BBa_K194002</a> | Yeast- and FACS optimized, fast degradable GFP: <html><a href="https://parts.igem.org/Part:BBa_K194002" target="_blank">BBa_K194002</a> | ||
| + | |||
| + | <html><!--- Please copy this table containing parameters for BBa_E0040 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><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1380155648870 --><th id="AutoAnnotatorHeader" colspan="2">Protein data table for BioBrick <a href="https://parts.igem.org/wiki/index.php?title=Part:BBa_E0040">BBa_E0040</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"> <u>ATGCGTAAA ... CTATACAAA</u>TAATAA</span><br> <strong>ORF</strong> from nucleotide position 1 to 714 (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">MRKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFGYGVQCFARYPDHMKQHDFFKSAMPEGYVQERTIFF<br>KDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHY<br>LSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK*</td></tr></table></span></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Sequence features:</strong> (with their position in the amino acid sequence, see the <a href="http://2013.igem.org/Team:TU-Munich/Results/Software/FeatureList">list of supported features</a>)<table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorSeqFeat1"></td><td class="AutoAnnotatorSeqFeat2b">None of the supported features appeared in the sequence</td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Amino acid composition:</strong><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Ala (A)</td><td class="AutoAnnotatorInnerAmino">9 (3.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Arg (R)</td><td class="AutoAnnotatorInnerAmino">7 (2.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asn (N)</td><td class="AutoAnnotatorInnerAmino">13 (5.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asp (D)</td><td class="AutoAnnotatorInnerAmino">18 (7.6%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Cys (C)</td><td class="AutoAnnotatorInnerAmino">2 (0.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gln (Q)</td><td class="AutoAnnotatorInnerAmino">8 (3.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Glu (E)</td><td class="AutoAnnotatorInnerAmino">16 (6.7%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gly (G)</td><td class="AutoAnnotatorInnerAmino">23 (9.7%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">His (H)</td><td class="AutoAnnotatorInnerAmino">10 (4.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ile (I)</td><td class="AutoAnnotatorInnerAmino">12 (5.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Leu (L)</td><td class="AutoAnnotatorInnerAmino">19 (8.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Lys (K)</td><td class="AutoAnnotatorInnerAmino">20 (8.4%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Met (M)</td><td class="AutoAnnotatorInnerAmino">6 (2.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Phe (F)</td><td class="AutoAnnotatorInnerAmino">13 (5.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Pro (P)</td><td class="AutoAnnotatorInnerAmino">10 (4.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ser (S)</td><td class="AutoAnnotatorInnerAmino">8 (3.4%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Thr (T)</td><td class="AutoAnnotatorInnerAmino">15 (6.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Trp (W)</td><td class="AutoAnnotatorInnerAmino">1 (0.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Tyr (Y)</td><td class="AutoAnnotatorInnerAmino">11 (4.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Val (V)</td><td class="AutoAnnotatorInnerAmino">17 (7.1%)</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">238</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Positively charged (Arg+Lys):</td><td class="AutoAnnotatorAminoCountingInner3">27 (11.3%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Negatively charged (Asp+Glu):</td><td class="AutoAnnotatorAminoCountingInner3">34 (14.3%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Aromatic (Phe+His+Try+Tyr):</td><td class="AutoAnnotatorAminoCountingInner3">35 (14.7%)</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>1207</sub>H<sub>1853</sub>N<sub>321</sub>O<sub>362</sub>S<sub>8</sub></td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Molecular mass [Da]:</td><td class="AutoAnnotatorBiochemParInner3">26909.4</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Theoretical pI:</td><td class="AutoAnnotatorBiochemParInner3">5.80</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Extinction coefficient at 280 nm [M<sup>-1</sup> cm<sup>-1</sup>]:</td><td class="AutoAnnotatorBiochemParInner3">21890 / 22015 (all Cys red/ox)</td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Plot for hydrophobicity, charge, predicted secondary structure, solvent accessability, transmembrane helices and disulfid bridges</strong> <input type='button' id='hydrophobicity_charge_button' onclick='show_or_hide_plot()' value='Show'><span id="hydrophobicity_charge_explanation"></span><div id="hydrophobicity_charge_container" style='display:none'><div id="hydrophobicity_charge_placeholder0" style="width:100%;height:150px"></div><div id="hydrophobicity_charge_placeholder1" style="width:100%;height:150px"></div></div></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Codon usage</strong><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorCodonUsage1"></td><td class="AutoAnnotatorCodonUsage2">Organism:</td><td class="AutoAnnotatorCodonUsage3"><i>E. coli</i></td><td class="AutoAnnotatorCodonUsage3"><i>B. subtilis</i></td><td class="AutoAnnotatorCodonUsage3"><i>S. cerevisiae</i></td><td class="AutoAnnotatorCodonUsage3"><i>A. thaliana</i></td><td class="AutoAnnotatorCodonUsage3"><i>P. patens</i></td><td class="AutoAnnotatorCodonUsage3">Mammals</td></tr><tr><td class="AutoAnnotatorCodonUsage1"></td><td class="AutoAnnotatorCodonUsage2">Codon quality (<a href="http://en.wikipedia.org/wiki/Codon_Adaptation_Index">CAI</a>):</td><td class="AutoAnnotatorCodonUsage3">good (0.72)</td><td class="AutoAnnotatorCodonUsage3">good (0.76)</td><td class="AutoAnnotatorCodonUsage3">good (0.75)</td><td class="AutoAnnotatorCodonUsage3">excellent (0.82)</td><td class="AutoAnnotatorCodonUsage3">good (0.77)</td><td class="AutoAnnotatorCodonUsage3">good (0.68)</td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Alignments</strong> (obtained from <a href='http://predictprotein.org'>PredictProtein.org</a>)<table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorAlignment1"></td><td class="AutoAnnotatorAlignment2">SwissProt:</td><td class="AutoAnnotatorAlignment3"><a href='http://www.uniprot.org/uniprot/P42212'>P42212</a> (98% identity on 238 AAs), <a href='http://www.uniprot.org/uniprot/Q9U6Y3'>Q9U6Y3</a> (25% identity on 217 AAs)</td></tr><tr><td class="AutoAnnotatorAlignment1"></td><td class="AutoAnnotatorAlignment2">TrEML:</td><td class="AutoAnnotatorAlignment3"><a href='http://www.uniprot.org/uniprot/B6UPG7'>B6UPG7</a> (99% identity on 238 AAs), <a href='http://www.uniprot.org/uniprot/B9U1C3'>B9U1C3</a> (98% identity on 238 AAs), <a href='http://www.uniprot.org/uniprot/J8VIQ3'>J8VIQ3</a> (98% identity on 238 AAs), <a href='http://www.uniprot.org/uniprot/Q71RY9'>Q71RY9</a> (98% identity on 238 AAs), <a href='http://www.uniprot.org/uniprot/Q8GHE2'>Q8GHE2</a> (98% identity on 238 AAs)</td></tr><tr><td class="AutoAnnotatorAlignment1"></td><td class="AutoAnnotatorAlignment2">PDB:</td><td class="AutoAnnotatorAlignment3"><a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1gfl'>1gfl</a> (98% identity on 229 AAs), <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=3vht'>3vht</a> (98% identity on 228 AAs)</td></tr></table></td></tr><tr><th id='AutoAnnotatorHeader' colspan="2"><strong>Predictions</strong> (obtained from <a href='http://predictprotein.org'>PredictProtein.org</a>)</th></tr><tr><td class="AutoAnnotatorLocalizationOuter"><strong>Subcellular Localization</strong> (reliability in brackets)<table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorLocalization1"></td><td class="AutoAnnotatorLocalization2">Archaea:</td><td class="AutoAnnotatorLocalization3">secreted (99%)</td></tr><tr><td class="AutoAnnotatorLocalization1"></td><td class="AutoAnnotatorLocalization2">Bacteria:</td><td class="AutoAnnotatorLocalization3">cytosol (62%)</td></tr><tr><td class="AutoAnnotatorLocalization1"></td><td class="AutoAnnotatorLocalization2">Eukarya:</td><td class="AutoAnnotatorLocalization3">cytosol (36%)</td></tr></table></td><td class="AutoAnnotatorGOOuter"><strong>Gene Ontology</strong> (reliability in brackets)<br><table class="AutoAnnotatorNoBorder"><tr><td class='AutoAnnotatorGO1'></td><td class='AutoAnnotatorGO2'>Molecular Function Ontology:</td><td class='AutoAnnotatorGO3'> - </td></tr><tr><td class='AutoAnnotatorGO1'></td><td class='AutoAnnotatorGO2'>Biological Process Ontology:</td><td class='AutoAnnotatorGO3'><a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0018298'>GO:0018298</a> (45%), <a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0008218'>GO:0008218</a> (32%)</td></tr><tr><td class='AutoAnnotatorGO1'> </td><td class='AutoAnnotatorGO2'> </td><td class='AutoAnnotatorGO3'> </td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Predicted features:</strong><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorPredFeat1"></td><td class="AutoAnnotatorPredFeat2a">Disulfid bridges:</td><td class="AutoAnnotatorPredFeat3"> - </td></tr><tr><td class="AutoAnnotatorPredFeat1"></td><td class="AutoAnnotatorPredFeat2a">Transmembrane helices:</td><td class="AutoAnnotatorPredFeat3"> - </td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"> The BioBrick-AutoAnnotator was created by <a href="http://2013.igem.org/Team:TU-Munich">TU-Munich 2013</a> iGEM team. For more information please see the <a href="http://2013.igem.org/Team:TU-Munich/Results/Software">documentation</a>.<br>If you have any questions, comments or suggestions, please leave us a <a href="http://2013.igem.org/Team:TU-Munich/Results/AutoAnnotator">comment</a>.</td></tr></table><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>var hydrophobicity_datapoints = [[2.5,-2.08],[3.5,-3.16],[4.5,-1.50],[5.5,-0.16],[6.5,-0.22],[7.5,0.40],[8.5,1.94],[9.5,2.02],[10.5,1.14],[11.5,2.18],[12.5,3.02],[13.5,3.02],[14.5,1.48],[15.5,2.56],[16.5,0.96],[17.5,0.12],[18.5,-1.42],[19.5,0.12],[20.5,-1.34],[21.5,-0.72],[22.5,-1.28],[23.5,-1.36],[24.5,-1.64],[25.5,-1.10],[26.5,-0.18],[27.5,0.30],[28.5,1.00],[29.5,-0.26],[30.5,-0.18],[31.5,-1.72],[32.5,-1.64],[33.5,-2.26],[34.5,-1.20],[35.5,-1.26],[36.5,-0.82],[37.5,-0.82],[38.5,-0.90],[39.5,-0.50],[40.5,-0.50],[41.5,0.52],[42.5,-0.18],[43.5,1.16],[44.5,1.30],[45.5,1.94],[46.5,1.04],[47.5,1.68],[48.5,1.04],[49.5,-0.64],[50.5,-0.38],[51.5,-0.56],[52.5,0.42],[53.5,0.18],[54.5,0.78],[55.5,-0.30],[56.5,-0.12],[57.5,-0.20],[58.5,0.96],[59.5,1.00],[60.5,1.18],[61.5,1.88],[62.5,1.04],[63.5,-0.06],[64.5,0.00],[65.5,0.98],[66.5,-0.28],[67.5,0.30],[68.5,1.12],[69.5,1.56],[70.5,-0.18],[71.5,0.26],[72.5,-0.56],[73.5,-1.82],[74.5,-2.82],[75.5,-1.54],[76.5,-2.06],[77.5,-2.44],[78.5,-2.38],[79.5,-2.44],[80.5,-2.26],[81.5,-0.92],[82.5,-1.00],[83.5,-0.52],[84.5,0.54],[85.5,0.36],[86.5,-0.52],[87.5,-0.44],[88.5,-0.36],[89.5,-0.98],[90.5,-0.52],[91.5,-0.90],[92.5,-0.90],[93.5,-1.72],[94.5,-1.60],[95.5,-1.54],[96.5,-0.28],[97.5,0.98],[98.5,1.10],[99.5,0.54],[100.5,-1.06],[101.5,-1.70],[102.5,-2.96],[103.5,-2.44],[104.5,-2.52],[105.5,-1.96],[106.5,-2.78],[107.5,-1.72],[108.5,-2.16],[109.5,-0.54],[110.5,-1.18],[111.5,0.28],[112.5,-0.78],[113.5,-0.16],[114.5,-1.70],[115.5,-1.06],[116.5,-0.86],[117.5,0.68],[118.5,0.06],[119.5,-0.14],[120.5,0.90],[121.5,-0.56],[122.5,-0.64],[123.5,-0.72],[124.5,0.10],[125.5,0.10],[126.5,0.10],[127.5,-0.10],[128.5,-0.10],[129.5,-0.72],[130.5,-2.32],[131.5,-1.70],[132.5,-2.96],[133.5,-1.28],[134.5,0.18],[135.5,0.80],[136.5,0.24],[137.5,0.16],[138.5,0.02],[139.5,-1.44],[140.5,-1.62],[141.5,-1.68],[142.5,-1.16],[143.5,-2.62],[144.5,-2.08],[145.5,-2.46],[146.5,-2.46],[147.5,-1.36],[148.5,-0.92],[149.5,0.14],[150.5,1.16],[151.5,2.22],[152.5,0.68],[153.5,0.16],[154.5,-1.44],[155.5,-2.60],[156.5,-3.66],[157.5,-3.04],[158.5,-1.36],[159.5,-1.44],[160.5,0.18],[161.5,0.18],[162.5,0.82],[163.5,-0.86],[164.5,0.82],[165.5,-0.92],[166.5,-0.86],[167.5,-2.12],[168.5,-0.44],[169.5,-2.04],[170.5,-1.84],[171.5,-1.28],[172.5,-0.74],[173.5,-0.80],[174.5,-0.80],[175.5,0.66],[176.5,1.10],[177.5,0.56],[178.5,-0.92],[179.5,-0.48],[180.5,-1.94],[181.5,-3.00],[182.5,-3.00],[183.5,-2.50],[184.5,-2.56],[185.5,-0.96],[186.5,-0.34],[187.5,-0.34],[188.5,-0.28],[189.5,-0.28],[190.5,-0.34],[191.5,0.50],[192.5,1.96],[193.5,1.72],[194.5,1.34],[195.5,-0.20],[196.5,-1.60],[197.5,-2.62],[198.5,-1.54],[199.5,-1.00],[200.5,-0.44],[201.5,-0.50],[202.5,-0.40],[203.5,-0.80],[204.5,0.12],[205.5,0.10],[206.5,0.02],[207.5,-0.52],[208.5,-1.20],[209.5,-2.66],[210.5,-3.20],[211.5,-3.20],[212.5,-3.40],[213.5,-3.78],[214.5,-3.72],[215.5,-2.64],[216.5,-1.02],[217.5,0.64],[218.5,2.10],[219.5,2.04],[220.5,2.22],[221.5,2.22],[222.5,1.32],[223.5,0.92],[224.5,1.98],[225.5,1.34],[226.5,1.40],[227.5,1.40],[228.5,0.40],[229.5,-0.04],[230.5,0.42],[231.5,-1.18],[232.5,-1.74],[233.5,-0.34],[234.5,-0.52],[235.5,-1.68]];var charge_datapoints = [[2.5,0.20],[3.5,0.00],[4.5,-0.20],[5.5,-0.40],[6.5,-0.40],[7.5,-0.20],[8.5,0.00],[9.5,0.00],[10.5,0.00],[11.5,0.00],[12.5,0.00],[13.5,0.00],[14.5,-0.20],[15.5,-0.20],[16.5,-0.40],[17.5,-0.40],[18.5,-0.60],[19.5,-0.40],[20.5,-0.40],[21.5,-0.20],[22.5,-0.10],[23.5,0.30],[24.5,0.30],[25.5,0.30],[26.5,0.30],[27.5,0.20],[28.5,-0.00],[29.5,-0.20],[30.5,-0.20],[31.5,-0.40],[32.5,-0.40],[33.5,-0.60],[34.5,-0.40],[35.5,-0.40],[36.5,-0.20],[37.5,-0.20],[38.5,0.20],[39.5,0.20],[40.5,0.20],[41.5,0.20],[42.5,0.40],[43.5,0.20],[44.5,0.20],[45.5,0.20],[46.5,0.20],[47.5,-0.00],[48.5,-0.00],[49.5,0.20],[50.5,0.20],[51.5,0.20],[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,-0.00],[59.5,-0.00],[60.5,-0.00],[61.5,-0.00],[62.5,-0.00],[63.5,-0.00],[64.5,-0.00],[65.5,-0.00],[66.5,-0.00],[67.5,-0.00],[68.5,-0.00],[69.5,-0.00],[70.5,0.20],[71.5,0.20],[72.5,0.20],[73.5,-0.00],[74.5,0.10],[75.5,-0.10],[76.5,0.10],[77.5,0.10],[78.5,0.40],[79.5,0.10],[80.5,0.10],[81.5,-0.10],[82.5,0.10],[83.5,-0.00],[84.5,0.20],[85.5,0.20],[86.5,0.20],[87.5,-0.20],[88.5,-0.20],[89.5,-0.20],[90.5,-0.20],[91.5,-0.20],[92.5,-0.20],[93.5,-0.00],[94.5,-0.00],[95.5,-0.00],[96.5,-0.00],[97.5,0.20],[98.5,0.20],[99.5,-0.00],[100.5,-0.20],[101.5,-0.20],[102.5,-0.20],[103.5,-0.40],[104.5,-0.00],[105.5,0.20],[106.5,0.40],[107.5,0.40],[108.5,0.20],[109.5,-0.00],[110.5,0.20],[111.5,-0.00],[112.5,-0.20],[113.5,-0.00],[114.5,-0.20],[115.5,-0.40],[116.5,-0.40],[117.5,-0.20],[118.5,-0.20],[119.5,0.20],[120.5,0.20],[121.5,-0.00],[122.5,-0.00],[123.5,0.20],[124.5,-0.00],[125.5,-0.00],[126.5,-0.00],[127.5,-0.00],[128.5,-0.00],[129.5,-0.20],[130.5,-0.40],[131.5,-0.20],[132.5,-0.20],[133.5,-0.40],[134.5,-0.20],[135.5,-0.00],[136.5,0.10],[137.5,0.30],[138.5,0.30],[139.5,0.10],[140.5,0.10],[141.5,-0.00],[142.5,-0.20],[143.5,-0.20],[144.5,-0.00],[145.5,0.10],[146.5,0.10],[147.5,0.10],[148.5,0.10],[149.5,0.10],[150.5,-0.00],[151.5,-0.00],[152.5,-0.20],[153.5,-0.00],[154.5,-0.00],[155.5,0.20],[156.5,0.20],[157.5,0.40],[158.5,0.20],[159.5,0.40],[160.5,0.20],[161.5,0.20],[162.5,0.20],[163.5,0.40],[164.5,0.20],[165.5,0.40],[166.5,0.50],[167.5,0.50],[168.5,0.30],[169.5,0.10],[170.5,-0.30],[171.5,-0.40],[172.5,-0.40],[173.5,-0.40],[174.5,-0.20],[175.5,-0.00],[176.5,-0.00],[177.5,-0.20],[178.5,-0.10],[179.5,-0.10],[180.5,-0.10],[181.5,-0.10],[182.5,0.10],[183.5,-0.00],[184.5,-0.00],[185.5,-0.00],[186.5,-0.00],[187.5,-0.20],[188.5,-0.20],[189.5,-0.20],[190.5,-0.20],[191.5,-0.20],[192.5,-0.00],[193.5,-0.00],[194.5,-0.20],[195.5,-0.20],[196.5,-0.10],[197.5,-0.10],[198.5,-0.10],[199.5,0.10],[200.5,0.10],[201.5,-0.00],[202.5,-0.00],[203.5,-0.00],[204.5,-0.00],[205.5,-0.00],[206.5,0.20],[207.5,-0.00],[208.5,-0.00],[209.5,-0.00],[210.5,-0.20],[211.5,-0.20],[212.5,0.20],[213.5,-0.00],[214.5,0.10],[215.5,0.30],[216.5,0.10],[217.5,-0.10],[218.5,0.10],[219.5,-0.20],[220.5,-0.20],[221.5,-0.20],[222.5,-0.20],[223.5,-0.20],[224.5,-0.00],[225.5,-0.00],[226.5,-0.00],[227.5,-0.00],[228.5,0.10],[229.5,0.10],[230.5,0.10],[231.5,-0.10],[232.5,-0.30],[233.5,-0.40],[234.5,-0.40],[235.5,-0.20]];var dis_datapoints = [];var trans_datapoints = [];var sec_helix_datapoints = [[5,9],[57,65],[84,86]];var sec_strand_datapoints = [[13,22],[25,31],[41,48],[70,72],[94,101],[105,114],[118,128],[139,140],[148,153],[160,171],[176,183],[200,200],[201,208],[217,228]];var acc_exposed_datapoints = [[1,6],[9,11],[13,13],[19,19],[23,23],[26,26],[32,32],[34,34],[36,36],[39,39],[41,41],[50,50],[52,52],[69,69],[73,73],[76,77],[79,80],[82,82],[85,85],[90,90],[101,101],[103,103],[113,113],[115,117],[126,126],[129,129],[132,133],[135,135],[138,138],[140,140],[142,142],[144,146],[155,159],[172,175],[180,180],[183,186],[189,192],[194,194],[197,197],[209,216],[230,230],[232,232],[234,235],[237,238]];var acc_buried_datapoints = [[8,8],[12,12],[14,14],[16,16],[18,18],[20,20],[22,22],[24,24],[27,27],[29,29],[31,31],[33,33],[35,35],[40,40],[42,42],[44,44],[46,46],[48,48],[53,64],[67,68],[70,72],[75,75],[83,84],[87,88],[91,92],[97,98],[100,100],[104,104],[106,106],[108,108],[112,112],[114,114],[119,119],[123,123],[125,125],[127,127],[130,130],[134,134],[136,137],[150,150],[152,152],[161,161],[163,163],[165,165],[167,169],[171,171],[179,179],[181,181],[193,193],[195,196],[199,200],[201,201],[203,203],[205,205],[207,207],[218,218],[220,220],[222,222],[224,224],[226,226]];var 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)'}}]};var number_of_plots = 2;for ( plot_num = 1 ; plot_num < number_of_plots ; plot_num ++){flot_plot_options[plot_num] = $.extend(true, {} ,flot_plot_options[0]);flot_plot_options[plot_num].xaxes = [{min: plot_num*200,max: (plot_num + 1)*200,ticks: [ [plot_num*200 + 0.5, (plot_num*200 + 1).toString()], [plot_num*200 + 24.5, (plot_num*200 + 25).toString()], [plot_num*200 + 49.5, (plot_num*200 + 50).toString()], [plot_num*200 + 74.5, (plot_num*200 + 75).toString()], [plot_num*200 + 99.5, (plot_num*200 + 100).toString()], [plot_num*200 + 124.5, (plot_num*200 + 125).toString()], [plot_num*200 + 149.5, (plot_num*200 + 150).toString()], [plot_num*200 + 174.5, (plot_num*200 + 175).toString()], [plot_num*200 + 199.5, (plot_num*200 + 200).toString()] ],tickLength: -5}];};function show_or_hide_plot(){try {if( $('#hydrophobicity_charge_button').val() =='Show' ){$('#hydrophobicity_charge_container').css('display','block');$('#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>';$('#hydrophobicity_charge_explanation').html(description_html);plot_according_to_selectors();$('#AutoAnnotator_plot_selectors').find('input').click(plot_according_to_selectors);}else{$('#hydrophobicity_charge_container').css('display','none');$('#hydrophobicity_charge_button').val('Show');$('#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(){try{var plot_datasets = [[],[]];if($('#hydrophobicity_checkbox').prop('checked') == true){plot_datasets[0] = { color: 'rgba(100,149,237,1)',data: hydrophobicity_datapoints,label: 'Hydrophobicity',lines: { show: true, fill: true, fillColor: 'rgba(100,149,237,0.1)' },yaxis: 1};}if($('#charge_checkbox').prop('checked') == true){plot_datasets[1] = {color: 'rgba(255,99,71,1)',data: charge_datapoints,label: 'Charge',lines: { show: true, fill: true, fillColor: 'rgba(255,99,71,0.1)' },yaxis: 2};}for (plot_num = 0 ; plot_num < number_of_plots ; plot_num ++){$.plot('#hydrophobicity_charge_placeholder'+ plot_num.toString(), plot_datasets, flot_plot_options[plot_num] );}var screen_width = $('canvas.flot-base').width(); var pos_of_first_tick = 46;var pos_of_last_tick = screen_width - 51;var tick_diff = (screen_width - 97)/199;if($('#dis_checkbox').prop('checked') == true){for ( j = 0 ; j < dis_datapoints.length ; j++ ){$('#hydrophobicity_charge_placeholder' + Math.floor((dis_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_dis\' style=\'left:' + ((pos_of_first_tick - 8 + (dis_datapoints[j][0] - 1)*tick_diff - Math.floor((dis_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px;\'><b>' + (j+1) + '</b></div>');$('#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($('#trans_checkbox').prop('checked') == true){for ( j = 0 ; j < trans_datapoints.length ; j++ ){$('#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($('#sec_checkbox').prop('checked') == true){for ( j = 0 ; j < sec_helix_datapoints.length ; j++ ){$('#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++ ){$('#hydrophobicity_charge_placeholder' + Math.floor((sec_strand_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_sec_strand\' style=\'width:' + (((sec_strand_datapoints[j][1] - sec_strand_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px; left:' + ((pos_of_first_tick + (sec_strand_datapoints[j][0] - 1.5)*tick_diff - Math.floor((sec_strand_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px\'></div>');}}if($('#acc_checkbox').prop('checked') == true){for ( j = 0 ; j < acc_buried_datapoints.length ; j++ ){$('#hydrophobicity_charge_placeholder' + Math.floor((acc_buried_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_acc_buried\' style=\'width:' + (((acc_buried_datapoints[j][1] - acc_buried_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px; left:' + ((pos_of_first_tick + (acc_buried_datapoints[j][0] - 1.5)*tick_diff - Math.floor((acc_buried_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px\'></div>');}for ( j = 0 ; j < acc_exposed_datapoints.length ; j++ ){$('#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 00:37, 26 September 2013
green fluorescent protein derived from jellyfish Aequeora victoria wild-type GFP (SwissProt: P42212
GFP (mut3b) [note that this part does not have a barcode]
Usage and Biology
Untagged version of gfp from Repressilator reporter. See the design page for more source information.
The original citation for GFPmut3b is as follows:
Cormack, B.P., Valdivia, R.H., and S. Falkow. FACS-optimized mutants of green fluorescent protein (GFP). Gene 173: 33-38 (1996).
Here's the link: http://www.sciencedirect.com/science/article/pii/0378111995006850
Fluorescence wavelengths
Cormack et al.Cormack report the following excitation and emission data for GFPmut3 -
- Excitation max - 501nm
- Emission max - 511nm
Latency
Cormack et al.Cormack report detectable fluorescence within 8 mins. Please add maturation time data for E0040 here.
References
<biblio>
- Cormack pmid=10659856
</biblio>
Part Characteristics in Cell-Free Chassis
| Parameter | Value and Description |
|---|---|
| Calibration | A conversion factor of 79.429 from Au to concentraion in nM |
| Half-life | 33 hours in the cell-free chassis, with a degradation constant of 0.0210 (in hours) |
Purificaton
GFPmut3b can be purified for calibration after the addition of a his-tag. The detailed [http://2007.igem.org/Imperial/Wet_Lab/Protocols/Prot1.6 protocols]and [http://2007.igem.org/Imperial/Wet_Lab/Results/Res1.6 results]for the purification can be found.
Calibration
The fluorescence of purified GFPmut3B was calibrated in the cell-free chassis. The derived [http://2007.igem.org/Imperial/Wet_Lab/Results/Res1.3 calilbration curve]allows the determination of the concentration of GFPmut3b in the cell-free chassis. [http://2007.igem.org/Imperial/Wet_Lab/Protocols/Prot1.3 Detailed protocols]for generating the calibration curve are available. Other calibration curves for are also available on the results page.
Degradation
The degradation of GFPmut3B in the cell-free chassis was also characterized. Purified GFPmut3B was allowed to degrade in the cell-free chassis and the fluorescence was measured over time. [http://2007.igem.org/Imperial/Wet_Lab/Protocols/Prot1.4 Detailed protocols]and [http://2007.igem.org/Imperial/Wet_Lab/Results/Res1.4 results]are attached.
From the semi-log plot, the degradation constant (in minutes) was derived to be 0.0003501, which is equivalent to GFPmut3b having a half-life of 33 hours in the cell-free chassis.
Improvements
Yeast- and FACS optimized GFP: BBa_K194001 Yeast- and FACS optimized, fast degradable GFP: BBa_K194002
| Protein data table for BioBrick BBa_E0040 automatically created by the BioBrick-AutoAnnotator version 1.0 | ||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Nucleotide sequence in RFC 10: (underlined part encodes the protein) ATGCGTAAA ... CTATACAAATAATAA ORF from nucleotide position 1 to 714 (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)
| ||||||||||||||||||||||||||||||||||||||||||||||
| Predictions (obtained from PredictProtein.org) | ||||||||||||||||||||||||||||||||||||||||||||||
Subcellular Localization (reliability in brackets)
| Gene Ontology (reliability in brackets)
| |||||||||||||||||||||||||||||||||||||||||||||
Predicted features:
| ||||||||||||||||||||||||||||||||||||||||||||||
| 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. | ||||||||||||||||||||||||||||||||||||||||||||||