Difference between revisions of "Part:BBa K1981001"
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<partinfo>BBa_K1981001 short</partinfo> | <partinfo>BBa_K1981001 short</partinfo> | ||
− | Autoinducer 2 import ATP-binding protein LsrA. Part of the ABC transporter complex LsrABCD involved in autoinducer 2 (AI-2) import. | + | Autoinducer 2 import ATP-binding protein LsrA. Part of the ABC transporter complex LsrABCD involved in autoinducer 2 (AI-2) import. It's responsible for regulation of uptake and processing of the quorum-sensing AI-2 and responsible for energy coupling to the transport system (Probable). This protein is essential for aerobic growth. In the absence of AI-2, it is repressed by LsrR. It can be induced by AI-2, via releasing of the LsrR repressor. In the absence of glucose, it was induced by cAMP-CRP by direct binding to the upstream region of the <i>lsr</i> promoter. |
<!-- Add more about the biology of this part here | <!-- Add more about the biology of this part here | ||
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===Characterization=== | ===Characterization=== | ||
The colony PCR verification result for <i>lsrA</i> is shown in <b>Figure 1</b>. | The colony PCR verification result for <i>lsrA</i> is shown in <b>Figure 1</b>. | ||
− | [[File:T--NKU China--lsrA Colony PCR.jpeg]] | + | <div>[[File:T--NKU China--lsrA Colony PCR.jpeg|400px|thumb|center|<b>Figure 1:</b> Colony PCR Verification for <i>lsrA</i>]]</div> |
===Protein-Data Table=== | ===Protein-Data Table=== | ||
<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_1476451634389'><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1476451634389 --><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_K1981001<!------------------------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"> <u>ATGACGATA ... GTAGCGGAA</u>TGA</span><br> <strong>ORF</strong> from nucleotide position 1 to 1197 (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">MTIEENICIGLKEKKKKLKVQIQQLISSLGWDIALNKLGGTLSIAQQQLVEIVRGLIREAEILILDEPTSTLTTHEIKSLFVLMKSLQEKGIGMIYITHR<br>FPEIFEIANKVAILRDGMVVSQGDVCDYTYDMLMEGLLPKGYKQKEKIEVVQETAKTKKILEVVDINGHAFENISFTVHAGEVVGVAGIIGSGRTELAEA<br>IFGLKAIKSGSILLEGKSIDTCSLHKRLSEGLVYVPEDRARNGIFSIASVKENIAAATSLYQNNRFFINQEKESALVNSFIEQFRIVVQNMNKELASLSG<br>GNQQKVVLAKYLACNPKIIILDEPTRGIDAKARLEVYETIKKMKREGLAILLISSDVEEIVQLVNRVYVMRNGRFVSHMEKEQLSVNEVTRLAYGGVAE*</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">26 (6.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Arg (R)</td><td class="AutoAnnotatorInnerAmino">17 (4.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asn (N)</td><td class="AutoAnnotatorInnerAmino">18 (4.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asp (D)</td><td class="AutoAnnotatorInnerAmino">12 (3.0%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Cys (C)</td><td class="AutoAnnotatorInnerAmino">4 (1.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gln (Q)</td><td class="AutoAnnotatorInnerAmino">18 (4.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Glu (E)</td><td class="AutoAnnotatorInnerAmino">38 (9.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gly (G)</td><td class="AutoAnnotatorInnerAmino">29 (7.3%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">His (H)</td><td class="AutoAnnotatorInnerAmino">6 (1.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ile (I)</td><td class="AutoAnnotatorInnerAmino">42 (10.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Leu (L)</td><td class="AutoAnnotatorInnerAmino">41 (10.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Lys (K)</td><td class="AutoAnnotatorInnerAmino">33 (8.3%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Met (M)</td><td class="AutoAnnotatorInnerAmino">10 (2.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Phe (F)</td><td class="AutoAnnotatorInnerAmino">12 (3.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Pro (P)</td><td class="AutoAnnotatorInnerAmino">6 (1.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ser (S)</td><td class="AutoAnnotatorInnerAmino">25 (6.3%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Thr (T)</td><td class="AutoAnnotatorInnerAmino">17 (4.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Trp (W)</td><td class="AutoAnnotatorInnerAmino">1 (0.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Tyr (Y)</td><td class="AutoAnnotatorInnerAmino">10 (2.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Val (V)</td><td class="AutoAnnotatorInnerAmino">34 (8.5%)</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">399</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Positively charged (Arg+Lys):</td><td class="AutoAnnotatorAminoCountingInner3">50 (12.5%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Negatively charged (Asp+Glu):</td><td class="AutoAnnotatorAminoCountingInner3">50 (12.5%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Aromatic (Phe+His+Try+Tyr):</td><td class="AutoAnnotatorAminoCountingInner3">29 (7.3%)</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>1984</sub>H<sub>3262</sub>N<sub>532</sub>O<sub>588</sub>S<sub>14</sub></td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Molecular mass [Da]:</td><td class="AutoAnnotatorBiochemParInner3">44425.8</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Theoretical pI:</td><td class="AutoAnnotatorBiochemParInner3">7.03</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">20400 / 20650 (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_1476451634389()' 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 (0.70)</td><td class="AutoAnnotatorCodonUsage3">good (0.74)</td><td class="AutoAnnotatorCodonUsage3">good (0.66)</td><td class="AutoAnnotatorCodonUsage3">good (0.75)</td><td class="AutoAnnotatorCodonUsage3">good (0.77)</td><td class="AutoAnnotatorCodonUsage3">good (0.66)</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_1476451634389(){hydrophobicity_datapoints = [[2.5,-0.26],[3.5,-1.34],[4.5,-0.30],[5.5,-0.70],[6.5,0.90],[7.5,1.52],[8.5,2.98],[9.5,1.30],[10.5,0.10],[11.5,-1.58],[12.5,-2.28],[13.5,-3.82],[14.5,-3.82],[15.5,-2.36],[16.5,-2.36],[17.5,-0.74],[18.5,-0.66],[19.5,1.02],[20.5,-0.44],[21.5,-0.36],[22.5,-0.44],[23.5,1.16],[24.5,0.10],[25.5,0.64],[26.5,2.10],[27.5,1.26],[28.5,0.18],[29.5,-0.36],[30.5,0.70],[31.5,0.30],[32.5,1.14],[33.5,0.62],[34.5,0.54],[35.5,0.40],[36.5,-0.04],[37.5,-0.88],[38.5,-0.32],[39.5,1.22],[40.5,0.30],[41.5,1.28],[42.5,1.72],[43.5,1.16],[44.5,-0.30],[45.5,-0.84],[46.5,-0.98],[47.5,-0.50],[48.5,-0.50],[49.5,1.10],[50.5,2.64],[51.5,0.98],[52.5,0.06],[53.5,1.52],[54.5,1.52],[55.5,-0.22],[56.5,-0.02],[57.5,0.42],[58.5,-1.04],[59.5,-1.04],[60.5,0.62],[61.5,2.22],[62.5,2.62],[63.5,2.62],[64.5,1.02],[65.5,-0.06],[66.5,-1.10],[67.5,-2.02],[68.5,-1.46],[69.5,-0.00],[70.5,0.18],[71.5,0.18],[72.5,-0.30],[73.5,-0.86],[74.5,-0.72],[75.5,-1.36],[76.5,-1.38],[77.5,0.02],[78.5,1.28],[79.5,1.22],[80.5,2.76],[81.5,3.30],[82.5,1.76],[83.5,1.04],[84.5,0.96],[85.5,-0.50],[86.5,-1.58],[87.5,-1.58],[88.5,-1.50],[89.5,-1.36],[90.5,-0.74],[91.5,0.34],[92.5,2.02],[93.5,1.84],[94.5,1.84],[95.5,1.78],[96.5,0.76],[97.5,-1.04],[98.5,-0.22],[99.5,-1.44],[100.5,-2.00],[101.5,-0.46],[102.5,1.00],[103.5,-0.26],[104.5,0.96],[105.5,2.02],[106.5,0.42],[107.5,-0.92],[108.5,0.62],[109.5,0.08],[110.5,0.62],[111.5,2.08],[112.5,1.96],[113.5,0.42],[114.5,-0.02],[115.5,-0.54],[116.5,-0.46],[117.5,1.28],[118.5,1.82],[119.5,1.20],[120.5,0.74],[121.5,-0.80],[122.5,-0.80],[123.5,-0.14],[124.5,-0.14],[125.5,-0.32],[126.5,0.24],[127.5,-0.86],[128.5,-2.06],[129.5,-0.98],[130.5,0.04],[131.5,0.56],[132.5,0.12],[133.5,0.74],[134.5,1.12],[135.5,1.12],[136.5,0.42],[137.5,0.34],[138.5,0.34],[139.5,-0.68],[140.5,-2.22],[141.5,-2.60],[142.5,-2.60],[143.5,-3.22],[144.5,-3.74],[145.5,-2.06],[146.5,-2.06],[147.5,-0.44],[148.5,1.10],[149.5,1.18],[150.5,-0.42],[151.5,0.14],[152.5,-0.34],[153.5,-1.96],[154.5,-1.40],[155.5,-1.48],[156.5,-2.12],[157.5,-1.58],[158.5,-0.04],[159.5,-0.60],[160.5,1.02],[161.5,2.64],[162.5,1.04],[163.5,1.18],[164.5,1.18],[165.5,0.26],[166.5,-1.22],[167.5,-0.16],[168.5,-0.50],[169.5,-0.50],[170.5,-1.12],[171.5,0.42],[172.5,-0.10],[173.5,-0.10],[174.5,0.46],[175.5,2.00],[176.5,0.46],[177.5,0.98],[178.5,0.34],[179.5,-0.22],[180.5,-0.22],[181.5,1.26],[182.5,0.82],[183.5,1.74],[184.5,2.80],[185.5,1.88],[186.5,1.94],[187.5,2.92],[188.5,2.00],[189.5,1.48],[190.5,1.48],[191.5,-0.32],[192.5,-1.36],[193.5,-1.98],[194.5,-1.06],[195.5,-0.62],[196.5,-0.42],[197.5,0.08],[198.5,1.68],[199.5,1.48],[200.5,1.04],[201.5,2.50],[202.5,1.36],[203.5,0.82],[204.5,1.16],[205.5,0.46],[206.5,-0.46],[207.5,0.24],[208.5,-0.28],[209.5,-0.28],[210.5,1.26],[211.5,2.18],[212.5,1.56],[213.5,1.64],[214.5,-0.04],[215.5,-0.96],[216.5,-0.82],[217.5,-0.82],[218.5,-0.88],[219.5,0.40],[220.5,0.40],[221.5,0.26],[222.5,0.32],[223.5,-0.32],[224.5,-1.72],[225.5,-0.80],[226.5,-1.72],[227.5,-1.78],[228.5,-1.08],[229.5,0.58],[230.5,0.66],[231.5,0.56],[232.5,2.10],[233.5,1.86],[234.5,0.40],[235.5,-1.14],[236.5,-1.78],[237.5,-2.26],[238.5,-2.84],[239.5,-2.84],[240.5,-2.22],[241.5,-0.42],[242.5,-0.22],[243.5,0.52],[244.5,2.12],[245.5,2.56],[246.5,1.50],[247.5,1.78],[248.5,1.16],[249.5,-0.44],[250.5,-1.50],[251.5,-0.44],[252.5,-0.92],[253.5,0.22],[254.5,1.28],[255.5,1.84],[256.5,0.78],[257.5,1.18],[258.5,0.56],[259.5,-0.50],[260.5,-1.06],[261.5,-1.60],[262.5,-3.26],[263.5,-2.44],[264.5,-1.18],[265.5,0.42],[266.5,0.42],[267.5,0.62],[268.5,-0.64],[269.5,-1.98],[270.5,-3.58],[271.5,-3.04],[272.5,-1.98],[273.5,-0.52],[274.5,1.10],[275.5,1.10],[276.5,1.10],[277.5,1.30],[278.5,1.44],[279.5,-0.10],[280.5,-0.10],[281.5,0.62],[282.5,-0.84],[283.5,-0.84],[284.5,0.70],[285.5,2.24],[286.5,0.98],[287.5,1.18],[288.5,0.66],[289.5,-0.88],[290.5,-2.50],[291.5,-2.50],[292.5,-1.04],[293.5,-1.06],[294.5,-0.52],[295.5,1.02],[296.5,1.56],[297.5,0.72],[298.5,0.28],[299.5,-0.26],[300.5,-1.72],[301.5,-2.26],[302.5,-2.96],[303.5,-2.04],[304.5,-0.50],[305.5,0.96],[306.5,2.02],[307.5,2.02],[308.5,0.92],[309.5,0.84],[310.5,0.44],[311.5,0.58],[312.5,0.66],[313.5,0.60],[314.5,-0.94],[315.5,-0.40],[316.5,-0.00],[317.5,1.60],[318.5,2.68],[319.5,2.76],[320.5,1.16],[321.5,-0.06],[322.5,-1.10],[323.5,-2.76],[324.5,-2.14],[325.5,-0.54],[326.5,-0.92],[327.5,-0.42],[328.5,-0.30],[329.5,0.14],[330.5,-1.66],[331.5,-0.20],[332.5,-1.26],[333.5,0.36],[334.5,-0.26],[335.5,-0.06],[336.5,-0.96],[337.5,0.64],[338.5,-0.98],[339.5,-1.50],[340.5,-0.42],[341.5,-1.06],[342.5,-2.86],[343.5,-2.78],[344.5,-2.08],[345.5,-1.70],[346.5,-0.56],[347.5,1.24],[348.5,2.70],[349.5,3.54],[350.5,3.68],[351.5,3.16],[352.5,2.10],[353.5,0.64],[354.5,0.72],[355.5,-0.88],[356.5,-1.42],[357.5,-0.36],[358.5,1.18],[359.5,-0.36],[360.5,1.10],[361.5,2.64],[362.5,1.04],[363.5,-0.70],[364.5,0.84],[365.5,-0.18],[366.5,-0.18],[367.5,0.90],[368.5,0.90],[369.5,-0.64],[370.5,-0.46],[371.5,-2.20],[372.5,-2.02],[373.5,-0.28],[374.5,0.26],[375.5,-0.30],[376.5,0.98],[377.5,-0.28],[378.5,-1.90],[379.5,-2.44],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= 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_1476451634389 #hydrophobicity_charge_button').val() =='Show' ){jqAutoAnnotator('#AutoAnnotator_container_1476451634389 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- 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_1476451634389 #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_1476451634389 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((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> | <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_1476451634389'><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1476451634389 --><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_K1981001<!------------------------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"> <u>ATGACGATA ... GTAGCGGAA</u>TGA</span><br> <strong>ORF</strong> from nucleotide position 1 to 1197 (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">MTIEENICIGLKEKKKKLKVQIQQLISSLGWDIALNKLGGTLSIAQQQLVEIVRGLIREAEILILDEPTSTLTTHEIKSLFVLMKSLQEKGIGMIYITHR<br>FPEIFEIANKVAILRDGMVVSQGDVCDYTYDMLMEGLLPKGYKQKEKIEVVQETAKTKKILEVVDINGHAFENISFTVHAGEVVGVAGIIGSGRTELAEA<br>IFGLKAIKSGSILLEGKSIDTCSLHKRLSEGLVYVPEDRARNGIFSIASVKENIAAATSLYQNNRFFINQEKESALVNSFIEQFRIVVQNMNKELASLSG<br>GNQQKVVLAKYLACNPKIIILDEPTRGIDAKARLEVYETIKKMKREGLAILLISSDVEEIVQLVNRVYVMRNGRFVSHMEKEQLSVNEVTRLAYGGVAE*</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">26 (6.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Arg (R)</td><td class="AutoAnnotatorInnerAmino">17 (4.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asn (N)</td><td class="AutoAnnotatorInnerAmino">18 (4.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asp (D)</td><td class="AutoAnnotatorInnerAmino">12 (3.0%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Cys (C)</td><td class="AutoAnnotatorInnerAmino">4 (1.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gln (Q)</td><td class="AutoAnnotatorInnerAmino">18 (4.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Glu (E)</td><td class="AutoAnnotatorInnerAmino">38 (9.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gly (G)</td><td class="AutoAnnotatorInnerAmino">29 (7.3%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">His (H)</td><td class="AutoAnnotatorInnerAmino">6 (1.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ile (I)</td><td class="AutoAnnotatorInnerAmino">42 (10.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Leu (L)</td><td class="AutoAnnotatorInnerAmino">41 (10.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Lys (K)</td><td class="AutoAnnotatorInnerAmino">33 (8.3%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Met (M)</td><td class="AutoAnnotatorInnerAmino">10 (2.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Phe (F)</td><td class="AutoAnnotatorInnerAmino">12 (3.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Pro (P)</td><td class="AutoAnnotatorInnerAmino">6 (1.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ser (S)</td><td class="AutoAnnotatorInnerAmino">25 (6.3%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Thr (T)</td><td class="AutoAnnotatorInnerAmino">17 (4.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Trp (W)</td><td class="AutoAnnotatorInnerAmino">1 (0.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Tyr (Y)</td><td class="AutoAnnotatorInnerAmino">10 (2.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Val (V)</td><td class="AutoAnnotatorInnerAmino">34 (8.5%)</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">399</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Positively charged (Arg+Lys):</td><td class="AutoAnnotatorAminoCountingInner3">50 (12.5%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Negatively charged (Asp+Glu):</td><td class="AutoAnnotatorAminoCountingInner3">50 (12.5%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Aromatic (Phe+His+Try+Tyr):</td><td class="AutoAnnotatorAminoCountingInner3">29 (7.3%)</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>1984</sub>H<sub>3262</sub>N<sub>532</sub>O<sub>588</sub>S<sub>14</sub></td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Molecular mass [Da]:</td><td class="AutoAnnotatorBiochemParInner3">44425.8</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Theoretical pI:</td><td class="AutoAnnotatorBiochemParInner3">7.03</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">20400 / 20650 (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_1476451634389()' 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 (0.70)</td><td class="AutoAnnotatorCodonUsage3">good (0.74)</td><td class="AutoAnnotatorCodonUsage3">good (0.66)</td><td class="AutoAnnotatorCodonUsage3">good (0.75)</td><td class="AutoAnnotatorCodonUsage3">good (0.77)</td><td class="AutoAnnotatorCodonUsage3">good (0.66)</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_1476451634389(){hydrophobicity_datapoints = [[2.5,-0.26],[3.5,-1.34],[4.5,-0.30],[5.5,-0.70],[6.5,0.90],[7.5,1.52],[8.5,2.98],[9.5,1.30],[10.5,0.10],[11.5,-1.58],[12.5,-2.28],[13.5,-3.82],[14.5,-3.82],[15.5,-2.36],[16.5,-2.36],[17.5,-0.74],[18.5,-0.66],[19.5,1.02],[20.5,-0.44],[21.5,-0.36],[22.5,-0.44],[23.5,1.16],[24.5,0.10],[25.5,0.64],[26.5,2.10],[27.5,1.26],[28.5,0.18],[29.5,-0.36],[30.5,0.70],[31.5,0.30],[32.5,1.14],[33.5,0.62],[34.5,0.54],[35.5,0.40],[36.5,-0.04],[37.5,-0.88],[38.5,-0.32],[39.5,1.22],[40.5,0.30],[41.5,1.28],[42.5,1.72],[43.5,1.16],[44.5,-0.30],[45.5,-0.84],[46.5,-0.98],[47.5,-0.50],[48.5,-0.50],[49.5,1.10],[50.5,2.64],[51.5,0.98],[52.5,0.06],[53.5,1.52],[54.5,1.52],[55.5,-0.22],[56.5,-0.02],[57.5,0.42],[58.5,-1.04],[59.5,-1.04],[60.5,0.62],[61.5,2.22],[62.5,2.62],[63.5,2.62],[64.5,1.02],[65.5,-0.06],[66.5,-1.10],[67.5,-2.02],[68.5,-1.46],[69.5,-0.00],[70.5,0.18],[71.5,0.18],[72.5,-0.30],[73.5,-0.86],[74.5,-0.72],[75.5,-1.36],[76.5,-1.38],[77.5,0.02],[78.5,1.28],[79.5,1.22],[80.5,2.76],[81.5,3.30],[82.5,1.76],[83.5,1.04],[84.5,0.96],[85.5,-0.50],[86.5,-1.58],[87.5,-1.58],[88.5,-1.50],[89.5,-1.36],[90.5,-0.74],[91.5,0.34],[92.5,2.02],[93.5,1.84],[94.5,1.84],[95.5,1.78],[96.5,0.76],[97.5,-1.04],[98.5,-0.22],[99.5,-1.44],[100.5,-2.00],[101.5,-0.46],[102.5,1.00],[103.5,-0.26],[104.5,0.96],[105.5,2.02],[106.5,0.42],[107.5,-0.92],[108.5,0.62],[109.5,0.08],[110.5,0.62],[111.5,2.08],[112.5,1.96],[113.5,0.42],[114.5,-0.02],[115.5,-0.54],[116.5,-0.46],[117.5,1.28],[118.5,1.82],[119.5,1.20],[120.5,0.74],[121.5,-0.80],[122.5,-0.80],[123.5,-0.14],[124.5,-0.14],[125.5,-0.32],[126.5,0.24],[127.5,-0.86],[128.5,-2.06],[129.5,-0.98],[130.5,0.04],[131.5,0.56],[132.5,0.12],[133.5,0.74],[134.5,1.12],[135.5,1.12],[136.5,0.42],[137.5,0.34],[138.5,0.34],[139.5,-0.68],[140.5,-2.22],[141.5,-2.60],[142.5,-2.60],[143.5,-3.22],[144.5,-3.74],[145.5,-2.06],[146.5,-2.06],[147.5,-0.44],[148.5,1.10],[149.5,1.18],[150.5,-0.42],[151.5,0.14],[152.5,-0.34],[153.5,-1.96],[154.5,-1.40],[155.5,-1.48],[156.5,-2.12],[157.5,-1.58],[158.5,-0.04],[159.5,-0.60],[160.5,1.02],[161.5,2.64],[162.5,1.04],[163.5,1.18],[164.5,1.18],[165.5,0.26],[166.5,-1.22],[167.5,-0.16],[168.5,-0.50],[169.5,-0.50],[170.5,-1.12],[171.5,0.42],[172.5,-0.10],[173.5,-0.10],[174.5,0.46],[175.5,2.00],[176.5,0.46],[177.5,0.98],[178.5,0.34],[179.5,-0.22],[180.5,-0.22],[181.5,1.26],[182.5,0.82],[183.5,1.74],[184.5,2.80],[185.5,1.88],[186.5,1.94],[187.5,2.92],[188.5,2.00],[189.5,1.48],[190.5,1.48],[191.5,-0.32],[192.5,-1.36],[193.5,-1.98],[194.5,-1.06],[195.5,-0.62],[196.5,-0.42],[197.5,0.08],[198.5,1.68],[199.5,1.48],[200.5,1.04],[201.5,2.50],[202.5,1.36],[203.5,0.82],[204.5,1.16],[205.5,0.46],[206.5,-0.46],[207.5,0.24],[208.5,-0.28],[209.5,-0.28],[210.5,1.26],[211.5,2.18],[212.5,1.56],[213.5,1.64],[214.5,-0.04],[215.5,-0.96],[216.5,-0.82],[217.5,-0.82],[218.5,-0.88],[219.5,0.40],[220.5,0.40],[221.5,0.26],[222.5,0.32],[223.5,-0.32],[224.5,-1.72],[225.5,-0.80],[226.5,-1.72],[227.5,-1.78],[228.5,-1.08],[229.5,0.58],[230.5,0.66],[231.5,0.56],[232.5,2.10],[233.5,1.86],[234.5,0.40],[235.5,-1.14],[236.5,-1.78],[237.5,-2.26],[238.5,-2.84],[239.5,-2.84],[240.5,-2.22],[241.5,-0.42],[242.5,-0.22],[243.5,0.52],[244.5,2.12],[245.5,2.56],[246.5,1.50],[247.5,1.78],[248.5,1.16],[249.5,-0.44],[250.5,-1.50],[251.5,-0.44],[252.5,-0.92],[253.5,0.22],[254.5,1.28],[255.5,1.84],[256.5,0.78],[257.5,1.18],[258.5,0.56],[259.5,-0.50],[260.5,-1.06],[261.5,-1.60],[262.5,-3.26],[263.5,-2.44],[264.5,-1.18],[265.5,0.42],[266.5,0.42],[267.5,0.62],[268.5,-0.64],[269.5,-1.98],[270.5,-3.58],[271.5,-3.04],[272.5,-1.98],[273.5,-0.52],[274.5,1.10],[275.5,1.10],[276.5,1.10],[277.5,1.30],[278.5,1.44],[279.5,-0.10],[280.5,-0.10],[281.5,0.62],[282.5,-0.84],[283.5,-0.84],[284.5,0.70],[285.5,2.24],[286.5,0.98],[287.5,1.18],[288.5,0.66],[289.5,-0.88],[290.5,-2.50],[291.5,-2.50],[292.5,-1.04],[293.5,-1.06],[294.5,-0.52],[295.5,1.02],[296.5,1.56],[297.5,0.72],[298.5,0.28],[299.5,-0.26],[300.5,-1.72],[301.5,-2.26],[302.5,-2.96],[303.5,-2.04],[304.5,-0.50],[305.5,0.96],[306.5,2.02],[307.5,2.02],[308.5,0.92],[309.5,0.84],[310.5,0.44],[311.5,0.58],[312.5,0.66],[313.5,0.60],[314.5,-0.94],[315.5,-0.40],[316.5,-0.00],[317.5,1.60],[318.5,2.68],[319.5,2.76],[320.5,1.16],[321.5,-0.06],[322.5,-1.10],[323.5,-2.76],[324.5,-2.14],[325.5,-0.54],[326.5,-0.92],[327.5,-0.42],[328.5,-0.30],[329.5,0.14],[330.5,-1.66],[331.5,-0.20],[332.5,-1.26],[333.5,0.36],[334.5,-0.26],[335.5,-0.06],[336.5,-0.96],[337.5,0.64],[338.5,-0.98],[339.5,-1.50],[340.5,-0.42],[341.5,-1.06],[342.5,-2.86],[343.5,-2.78],[344.5,-2.08],[345.5,-1.70],[346.5,-0.56],[347.5,1.24],[348.5,2.70],[349.5,3.54],[350.5,3.68],[351.5,3.16],[352.5,2.10],[353.5,0.64],[354.5,0.72],[355.5,-0.88],[356.5,-1.42],[357.5,-0.36],[358.5,1.18],[359.5,-0.36],[360.5,1.10],[361.5,2.64],[362.5,1.04],[363.5,-0.70],[364.5,0.84],[365.5,-0.18],[366.5,-0.18],[367.5,0.90],[368.5,0.90],[369.5,-0.64],[370.5,-0.46],[371.5,-2.20],[372.5,-2.02],[373.5,-0.28],[374.5,0.26],[375.5,-0.30],[376.5,0.98],[377.5,-0.28],[378.5,-1.90],[379.5,-2.44],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= 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: 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Latest revision as of 01:42, 15 October 2016
lsrA
Autoinducer 2 import ATP-binding protein LsrA. Part of the ABC transporter complex LsrABCD involved in autoinducer 2 (AI-2) import. It's responsible for regulation of uptake and processing of the quorum-sensing AI-2 and responsible for energy coupling to the transport system (Probable). This protein is essential for aerobic growth. In the absence of AI-2, it is repressed by LsrR. It can be induced by AI-2, via releasing of the LsrR repressor. In the absence of glucose, it was induced by cAMP-CRP by direct binding to the upstream region of the lsr promoter.
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
Usage and Biology
AI-2 “Consumer” was constructed by overexpressing the lsrACDB gene in Bacillus amyloliquefaciens LL3.
Characterization
The colony PCR verification result for lsrA is shown in Figure 1.
Protein-Data Table
Protein data table for BioBrick BBa_K1981001 automatically created by the BioBrick-AutoAnnotator version 1.0 | ||||||||||||||||||||||||||||||||||||||||||||||
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Nucleotide sequence in RFC 10: (underlined part encodes the protein) ATGACGATA ... GTAGCGGAATGA ORF from nucleotide position 1 to 1197 (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. |