Difference between revisions of "Part:BBa K1981004"
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===Protein-Data Table===
 
===Protein-Data Table===
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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_1476453507167'><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1476453507167 --><th id="AutoAnnotatorHeader" colspan="2">Protein data table for BioBrick <a href="https://parts.igem.org/wiki/index.php?title=Part:BBa_<!------------------------Enter BioBrick number here------------------------>">BBa_<!------------------------Enter BioBrick number here------------------------></a> automatically created by the <a href="http://2013.igem.org/Team:TU-Munich/Results/AutoAnnotator">BioBrick-AutoAnnotator</a> version 1.0</th></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Nucleotide sequence</strong> in <strong>RFC 10</strong>: (underlined part encodes the protein)<br><span class="AutoAnnotatorSequence">&nbsp;<u>ATGAAGTAT&nbsp;...&nbsp;GAAATGTCA</u>TGA</span><br>&nbsp;<strong>ORF</strong> from nucleotide position 1 to 987 (excluding stop-codon)</td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Amino acid sequence:</strong> (RFC 25 scars in shown in bold, other sequence features underlined; both given below)<br><span class="AutoAnnotatorSequence"><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorSeqNum">1&nbsp;<br>101&nbsp;<br>201&nbsp;<br>301&nbsp;</td><td class="AutoAnnotatorSeqSeq">MKYLYRWEGVLIVLLLIEFILFSFINSDFLNISNLLFSTNDFLFIAIAAIPMTFVIVTGGIDVSVGSIMGLTSILIGVLWMNGIPILFAVIIALIISCLA<br>GALNGLIIKMTDVEPLVVTLGTMFLYGGIALVISGGAGASGYEGISGLPDTYVQLANGSFIGIPNLLWLLISLTIVYTILFHRTIYGRYVKLTGANENTA<br>KYTGIKTKKVVIIAYILSGLGGGLGGVFLTAYFGSARADIGSETILPIITAVVLGGTLITGGKGSIFGTVLASIFIGLMQYGLQMTGLTNEQSNVVIGII<br>LILSVIMRHFKLHQFLAGKRQSWHKGEMS*</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">20 (6.1%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Arg (R)</td><td class="AutoAnnotatorInnerAmino">6 (1.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asn (N)</td><td class="AutoAnnotatorInnerAmino">12 (3.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asp (D)</td><td class="AutoAnnotatorInnerAmino">6 (1.8%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Cys (C)</td><td class="AutoAnnotatorInnerAmino">1 (0.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gln (Q)</td><td class="AutoAnnotatorInnerAmino">6 (1.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Glu (E)</td><td class="AutoAnnotatorInnerAmino">8 (2.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gly (G)</td><td class="AutoAnnotatorInnerAmino">43 (13.1%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">His (H)</td><td class="AutoAnnotatorInnerAmino">4 (1.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ile (I)</td><td class="AutoAnnotatorInnerAmino">47 (14.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Leu (L)</td><td class="AutoAnnotatorInnerAmino">46 (14.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Lys (K)</td><td class="AutoAnnotatorInnerAmino">11 (3.3%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Met (M)</td><td class="AutoAnnotatorInnerAmino">10 (3.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Phe (F)</td><td class="AutoAnnotatorInnerAmino">18 (5.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Pro (P)</td><td class="AutoAnnotatorInnerAmino">6 (1.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ser (S)</td><td class="AutoAnnotatorInnerAmino">22 (6.7%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Thr (T)</td><td class="AutoAnnotatorInnerAmino">23 (7.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Trp (W)</td><td class="AutoAnnotatorInnerAmino">4 (1.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Tyr (Y)</td><td class="AutoAnnotatorInnerAmino">12 (3.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Val (V)</td><td class="AutoAnnotatorInnerAmino">24 (7.3%)</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">329</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Positively charged (Arg+Lys):</td><td class="AutoAnnotatorAminoCountingInner3">17 (5.2%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Negatively charged (Asp+Glu):</td><td class="AutoAnnotatorAminoCountingInner3">14 (4.3%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Aromatic (Phe+His+Try+Tyr):</td><td class="AutoAnnotatorAminoCountingInner3">38 (11.6%)</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>1647</sub>H<sub>2626</sub>N<sub>388</sub>O<sub>433</sub>S<sub>11</sub></td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Molecular mass [Da]:</td><td class="AutoAnnotatorBiochemParInner3">35144.0</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Theoretical pI:</td><td class="AutoAnnotatorBiochemParInner3">8.87</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">39880 / 39943 (all Cys red/ox)</td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Plot for hydrophobicity, charge, predicted secondary structure, solvent accessability, transmembrane helices and disulfid bridges</strong>&nbsp;<input type='button' id='hydrophobicity_charge_button' onclick='show_or_hide_plot_1476453507167()' 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 (0.68)</td><td class="AutoAnnotatorCodonUsage3">good (0.73)</td><td class="AutoAnnotatorCodonUsage3">good (0.69)</td><td class="AutoAnnotatorCodonUsage3">good (0.75)</td><td class="AutoAnnotatorCodonUsage3">good (0.69)</td><td class="AutoAnnotatorCodonUsage3">acceptable (0.55)</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>&nbsp;&nbsp;&nbsp;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">&nbsp;&nbsp;&nbsp;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_1476453507167(){hydrophobicity_datapoints = [[2.5,-0.16],[3.5,-1.44],[4.5,-0.84],[5.5,-1.28],[6.5,-2.12],[7.5,-1.02],[8.5,0.64],[9.5,1.72],[10.5,3.26],[11.5,4.10],[12.5,4.02],[13.5,4.02],[14.5,4.02],[15.5,2.48],[16.5,2.28],[17.5,2.42],[18.5,2.42],[19.5,2.08],[20.5,2.62],[21.5,2.62],[22.5,2.62],[23.5,1.16],[24.5,0.44],[25.5,-0.10],[26.5,-0.10],[27.5,-0.24],[28.5,-0.24],[29.5,0.82],[30.5,1.36],[31.5,0.10],[32.5,0.10],[33.5,1.56],[34.5,1.22],[35.5,1.22],[36.5,1.78],[37.5,0.32],[38.5,-1.14],[39.5,-1.14],[40.5,-0.22],[41.5,0.48],[42.5,2.08],[43.5,3.14],[44.5,3.48],[45.5,3.08],[46.5,2.88],[47.5,2.88],[48.5,2.20],[49.5,1.68],[50.5,1.18],[51.5,1.38],[52.5,1.32],[53.5,2.54],[54.5,3.00],[55.5,3.00],[56.5,2.36],[57.5,1.44],[58.5,1.44],[59.5,-0.10],[60.5,0.88],[61.5,0.80],[62.5,1.72],[63.5,0.74],[64.5,1.28],[65.5,1.34],[66.5,1.88],[67.5,0.96],[68.5,1.80],[69.5,1.82],[70.5,0.76],[71.5,1.28],[72.5,2.12],[73.5,2.26],[74.5,2.32],[75.5,3.32],[76.5,3.18],[77.5,2.24],[78.5,1.72],[79.5,1.10],[80.5,0.18],[81.5,0.32],[82.5,0.18],[83.5,0.70],[84.5,2.16],[85.5,2.80],[86.5,2.26],[87.5,3.42],[88.5,3.42],[89.5,3.56],[90.5,3.36],[91.5,3.76],[92.5,3.82],[93.5,3.82],[94.5,2.76],[95.5,2.90],[96.5,2.90],[97.5,2.36],[98.5,1.38],[99.5,1.90],[100.5,2.16],[101.5,0.70],[102.5,0.26],[103.5,1.10],[104.5,1.64],[105.5,1.78],[106.5,1.70],[107.5,2.16],[108.5,1.26],[109.5,-0.34],[110.5,-0.40],[111.5,-0.32],[112.5,-1.02],[113.5,-0.12],[114.5,1.42],[115.5,1.42],[116.5,1.98],[117.5,3.06],[118.5,2.22],[119.5,1.24],[120.5,0.78],[121.5,1.48],[122.5,1.48],[123.5,1.30],[124.5,1.36],[125.5,0.90],[126.5,1.24],[127.5,0.84],[128.5,1.86],[129.5,2.78],[130.5,3.76],[131.5,2.70],[132.5,2.26],[133.5,1.42],[134.5,0.94],[135.5,-0.04],[136.5,0.48],[137.5,0.40],[138.5,0.40],[139.5,-0.22],[140.5,-0.84],[141.5,-1.28],[142.5,-0.22],[143.5,-0.30],[144.5,-0.12],[145.5,1.34],[146.5,1.10],[147.5,-0.50],[148.5,-0.48],[149.5,-0.66],[150.5,-0.58],[151.5,-0.96],[152.5,0.50],[153.5,1.00],[154.5,0.56],[155.5,-0.36],[156.5,0.18],[157.5,-0.02],[158.5,0.52],[159.5,1.14],[160.5,2.12],[161.5,1.96],[162.5,0.70],[163.5,0.56],[164.5,1.40],[165.5,0.32],[166.5,1.40],[167.5,2.86],[168.5,3.00],[169.5,2.08],[170.5,3.02],[171.5,2.12],[172.5,2.26],[173.5,2.20],[174.5,2.10],[175.5,1.20],[176.5,2.24],[177.5,2.10],[178.5,1.82],[179.5,1.44],[180.5,0.68],[181.5,-0.36],[182.5,-0.22],[183.5,-1.04],[184.5,-0.48],[185.5,-0.48],[186.5,-0.60],[187.5,-0.66],[188.5,-1.18],[189.5,-0.34],[190.5,0.42],[191.5,0.60],[192.5,0.12],[193.5,0.20],[194.5,-1.26],[195.5,-1.82],[196.5,-1.88],[197.5,-1.88],[198.5,-1.96],[199.5,-1.52],[200.5,-0.96],[201.5,-0.90],[202.5,-0.36],[203.5,-0.36],[204.5,-0.24],[205.5,-0.88],[206.5,-1.58],[207.5,-1.64],[208.5,-0.02],[209.5,1.02],[210.5,2.70],[211.5,3.84],[212.5,2.74],[213.5,2.80],[214.5,2.66],[215.5,1.60],[216.5,1.16],[217.5,2.18],[218.5,1.20],[219.5,0.36],[220.5,0.44],[221.5,1.28],[222.5,0.44],[223.5,0.44],[224.5,1.36],[225.5,2.00],[226.5,2.00],[227.5,1.94],[228.5,2.38],[229.5,1.28],[230.5,1.28],[231.5,0.44],[232.5,0.42],[233.5,0.42],[234.5,-0.22],[235.5,-0.42],[236.5,-1.04],[237.5,0.02],[238.5,-0.42],[239.5,0.32],[240.5,-0.74],[241.5,-0.18],[242.5,-0.18],[243.5,0.66],[244.5,0.50],[245.5,2.10],[246.5,3.14],[247.5,2.10],[248.5,1.70],[249.5,2.86],[250.5,2.80],[251.5,2.66],[252.5,2.72],[253.5,2.28],[254.5,1.30],[255.5,1.22],[256.5,1.36],[257.5,1.30],[258.5,1.30],[259.5,1.36],[260.5,-0.18],[261.5,-1.16],[262.5,-1.18],[263.5,-0.20],[264.5,0.44],[265.5,1.14],[266.5,1.08],[267.5,2.08],[268.5,1.94],[269.5,1.74],[270.5,1.66],[271.5,2.70],[272.5,2.42],[273.5,2.56],[274.5,2.12],[275.5,3.04],[276.5,2.52],[277.5,1.26],[278.5,0.10],[279.5,0.10],[280.5,0.10],[281.5,-0.98],[282.5,0.10],[283.5,0.22],[284.5,0.22],[285.5,0.22],[286.5,0.78],[287.5,-0.30],[288.5,-0.86],[289.5,-1.48],[290.5,-2.40],[291.5,-2.96],[292.5,-1.42],[293.5,0.12],[294.5,1.72],[295.5,1.80],[296.5,3.40],[297.5,3.46],[298.5,3.38],[299.5,3.38],[300.5,4.22],[301.5,3.16],[302.5,3.10],[303.5,3.24],[304.5,2.72],[305.5,1.06],[306.5,0.58],[307.5,0.30],[308.5,-1.38],[309.5,-1.00],[310.5,-0.74],[311.5,-0.80],[312.5,-0.80],[313.5,0.74],[314.5,0.34],[315.5,0.90],[316.5,0.82],[317.5,-0.64],[318.5,-2.10],[319.5,-2.62],[320.5,-2.72],[321.5,-2.58],[322.5,-2.46],[323.5,-1.84],[324.5,-2.38],[325.5,-1.82],[326.5,-1.34]];charge_datapoints = [[2.5,0.20],[3.5,0.40],[4.5,0.20],[5.5,0.00],[6.5,0.00],[7.5,0.00],[8.5,-0.20],[9.5,-0.20],[10.5,0.00],[11.5,0.00],[12.5,0.00],[13.5,0.00],[14.5,0.00],[15.5,-0.20],[16.5,-0.20],[17.5,-0.20],[18.5,-0.20],[19.5,-0.20],[20.5,0.00],[21.5,0.00],[22.5,0.00],[23.5,0.00],[24.5,0.00],[25.5,-0.20],[26.5,-0.20],[27.5,-0.20],[28.5,-0.20],[29.5,-0.20],[30.5,0.00],[31.5,0.00],[32.5,0.00],[33.5,0.00],[34.5,0.00],[35.5,0.00],[36.5,0.00],[37.5,0.00],[38.5,-0.20],[39.5,-0.20],[40.5,-0.20],[41.5,-0.20],[42.5,-0.20],[43.5,0.00],[44.5,0.00],[45.5,0.00],[46.5,0.00],[47.5,0.00],[48.5,0.00],[49.5,0.00],[50.5,0.00],[51.5,0.00],[52.5,0.00],[53.5,0.00],[54.5,0.00],[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],[70.5,0.00],[71.5,0.00],[72.5,0.00],[73.5,0.00],[74.5,0.00],[75.5,0.00],[76.5,0.00],[77.5,0.00],[78.5,0.00],[79.5,0.00],[80.5,0.00],[81.5,0.00],[82.5,0.00],[83.5,0.00],[84.5,0.00],[85.5,0.00],[86.5,0.00],[87.5,0.00],[88.5,0.00],[89.5,0.00],[90.5,0.00],[91.5,0.00],[92.5,0.00],[93.5,0.00],[94.5,0.00],[95.5,0.00],[96.5,0.00],[97.5,0.00],[98.5,0.00],[99.5,0.00],[100.5,0.00],[101.5,0.00],[102.5,0.00],[103.5,0.00],[104.5,0.00],[105.5,0.00],[106.5,0.20],[107.5,0.20],[108.5,0.20],[109.5,0.00],[110.5,0.00],[111.5,-0.40],[112.5,-0.40],[113.5,-0.40],[114.5,-0.20],[115.5,-0.20],[116.5,0.00],[117.5,0.00],[118.5,0.00],[119.5,0.00],[120.5,0.00],[121.5,0.00],[122.5,0.00],[123.5,0.00],[124.5,0.00],[125.5,0.00],[126.5,0.00],[127.5,0.00],[128.5,0.00],[129.5,0.00],[130.5,0.00],[131.5,0.00],[132.5,0.00],[133.5,0.00],[134.5,0.00],[135.5,0.00],[136.5,0.00],[137.5,0.00],[138.5,0.00],[139.5,0.00],[140.5,-0.20],[141.5,-0.20],[142.5,-0.20],[143.5,-0.20],[144.5,-0.20],[145.5,0.00],[146.5,0.00],[147.5,-0.20],[148.5,-0.20],[149.5,-0.20],[150.5,-0.20],[151.5,-0.20],[152.5,0.00],[153.5,0.00],[154.5,0.00],[155.5,0.00],[156.5,0.00],[157.5,0.00],[158.5,0.00],[159.5,0.00],[160.5,0.00],[161.5,0.00],[162.5,0.00],[163.5,0.00],[164.5,0.00],[165.5,0.00],[166.5,0.00],[167.5,0.00],[168.5,0.00],[169.5,0.00],[170.5,0.00],[171.5,0.00],[172.5,0.00],[173.5,0.00],[174.5,0.00],[175.5,0.00],[176.5,0.00],[177.5,0.00],[178.5,0.00],[179.5,0.10],[180.5,0.30],[181.5,0.30],[182.5,0.30],[183.5,0.30],[184.5,0.20],[185.5,0.20],[186.5,0.20],[187.5,0.20],[188.5,0.40],[189.5,0.40],[190.5,0.20],[191.5,0.20],[192.5,0.20],[193.5,0.00],[194.5,-0.20],[195.5,-0.20],[196.5,-0.20],[197.5,-0.20],[198.5,0.00],[199.5,0.20],[200.5,0.20],[201.5,0.20],[202.5,0.20],[203.5,0.20],[204.5,0.20],[205.5,0.40],[206.5,0.60],[207.5,0.60],[208.5,0.40],[209.5,0.40],[210.5,0.20],[211.5,0.00],[212.5,0.00],[213.5,0.00],[214.5,0.00],[215.5,0.00],[216.5,0.00],[217.5,0.00],[218.5,0.00],[219.5,0.00],[220.5,0.00],[221.5,0.00],[222.5,0.00],[223.5,0.00],[224.5,0.00],[225.5,0.00],[226.5,0.00],[227.5,0.00],[228.5,0.00],[229.5,0.00],[230.5,0.00],[231.5,0.00],[232.5,0.00],[233.5,0.00],[234.5,0.20],[235.5,0.20],[236.5,0.00],[237.5,0.00],[238.5,0.00],[239.5,-0.20],[240.5,-0.40],[241.5,-0.20],[242.5,-0.20],[243.5,-0.20],[244.5,-0.20],[245.5,0.00],[246.5,0.00],[247.5,0.00],[248.5,0.00],[249.5,0.00],[250.5,0.00],[251.5,0.00],[252.5,0.00],[253.5,0.00],[254.5,0.00],[255.5,0.00],[256.5,0.00],[257.5,0.00],[258.5,0.00],[259.5,0.00],[260.5,0.20],[261.5,0.20],[262.5,0.20],[263.5,0.20],[264.5,0.20],[265.5,0.00],[266.5,0.00],[267.5,0.00],[268.5,0.00],[269.5,0.00],[270.5,0.00],[271.5,0.00],[272.5,0.00],[273.5,0.00],[274.5,0.00],[275.5,0.00],[276.5,0.00],[277.5,0.00],[278.5,0.00],[279.5,0.00],[280.5,0.00],[281.5,0.00],[282.5,0.00],[283.5,0.00],[284.5,0.00],[285.5,0.00],[286.5,0.00],[287.5,0.00],[288.5,-0.20],[289.5,-0.20],[290.5,-0.20],[291.5,-0.20],[292.5,-0.20],[293.5,0.00],[294.5,0.00],[295.5,0.00],[296.5,0.00],[297.5,0.00],[298.5,0.00],[299.5,0.00],[300.5,0.00],[301.5,0.00],[302.5,0.00],[303.5,0.00],[304.5,0.00],[305.5,0.20],[306.5,0.30],[307.5,0.30],[308.5,0.50],[309.5,0.50],[310.5,0.40],[311.5,0.30],[312.5,0.30],[313.5,0.10],[314.5,0.10],[315.5,0.00],[316.5,0.20],[317.5,0.40],[318.5,0.40],[319.5,0.40],[320.5,0.40],[321.5,0.30],[322.5,0.30],[323.5,0.30],[324.5,0.10],[325.5,0.10],[326.5,0.00]];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&nbsp;&nbsp;'], [-4.5,'hydro-<br>philic&nbsp;&nbsp;']],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>&nbsp;charge'], [-1,'negative<br>&nbsp;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_1476453507167 #hydrophobicity_charge_button').val() =='Show' ){jqAutoAnnotator('#AutoAnnotator_container_1476453507167 #hydrophobicity_charge_container').css('display','block');jqAutoAnnotator('#AutoAnnotator_container_1476453507167 #hydrophobicity_charge_button').val('Hide');var description_html = '<div id=\'AutoAnnotator_plot_selectors\'>';description_html = description_html + '<br>&nbsp;<input type=\'checkbox\' id=\'hydrophobicity_checkbox\' checked=\'checked\'>&nbsp;Moving average over 5 amino acids for hydrophobicity (<img src=\'https://static.igem.org/mediawiki/2013/e/e9/TUM13_hydrophobicity_icon.png\' alt=\'blue graph\' height=\'10\'></img>)';description_html = description_html + '<br>&nbsp;<input type=\'checkbox\' id=\'charge_checkbox\' checked=\'checked\'>&nbsp;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>&nbsp;<input type=\'checkbox\' id=\'dis_checkbox\' checked=\'checked\'>&nbsp;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>&nbsp;<input type=\'checkbox\' id=\'trans_checkbox\' checked=\'checked\'>&nbsp;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>&nbsp;<input type=\'checkbox\' id=\'sec_checkbox\' checked=\'checked\'>&nbsp;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>&nbsp;<input type=\'checkbox\' id=\'acc_checkbox\' checked=\'checked\'>&nbsp;Predicted solvent accessability: Exposed (<img src=\'https://static.igem.org/mediawiki/2013/1/16/TUM13_exposed_icon.png\' alt=\'blue bars\' height=\'10\'></img>) and buried (<img src=\'https://static.igem.org/mediawiki/2013/0/0b/TUM13_buried_icon.png\' alt=\'green bars\' height=\'10\'></img>) residues';description_html = description_html + '<br></div>';jqAutoAnnotator('#AutoAnnotator_container_1476453507167 #hydrophobicity_charge_explanation').html(description_html);plot_according_to_selectors_1476453507167();jqAutoAnnotator('#AutoAnnotator_container_1476453507167 #AutoAnnotator_plot_selectors').find('input').click(plot_according_to_selectors_1476453507167);}else{jqAutoAnnotator('#AutoAnnotator_container_1476453507167 #hydrophobicity_charge_container').css('display','none');jqAutoAnnotator('#AutoAnnotator_container_1476453507167 #hydrophobicity_charge_button').val('Show');jqAutoAnnotator('#AutoAnnotator_container_1476453507167 #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_1476453507167(){try{var plot_datasets = [[],[]];if(jqAutoAnnotator('#AutoAnnotator_container_1476453507167 #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_1476453507167 #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_1476453507167 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Revision as of 13:59, 14 October 2016


lsrD

Autoinducer 2 import system permease protein LsrD. Part of the ABC transporter complex LsrABCD involved in autoinducer 2 (AI-2) import. Regulation of uptake and processing of the quorum-sensing AI-2. Probably responsible for the translocation of the substrate across the membrane. Share the same promoter with lsrA. In the absence of AI-2, repressed by LsrR. Induced by AI-2, via release of the LsrR repressor. In the absence of glucose, induced by cAMP-CRP by direct binding to the upstream region of the lsr promoter.

Sequence and Features


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


Usage and Biology

AI-2 “Consumer” was constructed by overexpressing the lsrACDB, lsrFG and lsrK genes in Bacillus amyloliquefaciens LL3.

This part is originated from Bacillus thuringiensis serovar thuringiensis str. IS5056.

Characterization

Protein-Data Table

Protein data table for BioBrick BBa_ automatically created by the BioBrick-AutoAnnotator version 1.0
Nucleotide sequence in RFC 10: (underlined part encodes the protein)
 ATGAAGTAT ... GAAATGTCATGA
 ORF from nucleotide position 1 to 987 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
1 
101 
201 
301 		MKYLYRWEGVLIVLLLIEFILFSFINSDFLNISNLLFSTNDFLFIAIAAIPMTFVIVTGGIDVSVGSIMGLTSILIGVLWMNGIPILFAVIIALIISCLA
GALNGLIIKMTDVEPLVVTLGTMFLYGGIALVISGGAGASGYEGISGLPDTYVQLANGSFIGIPNLLWLLISLTIVYTILFHRTIYGRYVKLTGANENTA
KYTGIKTKKVVIIAYILSGLGGGLGGVFLTAYFGSARADIGSETILPIITAVVLGGTLITGGKGSIFGTVLASIFIGLMQYGLQMTGLTNEQSNVVIGII
LILSVIMRHFKLHQFLAGKRQSWHKGEMS*
Sequence features: (with their position in the amino acid sequence, see the list of supported features)
None of the supported features appeared in the sequence
Amino acid composition:
Ala (A)20 (6.1%)
Arg (R)6 (1.8%)
Asn (N)12 (3.6%)
Asp (D)6 (1.8%)
Cys (C)1 (0.3%)
Gln (Q)6 (1.8%)
Glu (E)8 (2.4%)
Gly (G)43 (13.1%)
His (H)4 (1.2%)
Ile (I)47 (14.3%)
Leu (L)46 (14.0%)
Lys (K)11 (3.3%)
Met (M)10 (3.0%)
Phe (F)18 (5.5%)
Pro (P)6 (1.8%)
Ser (S)22 (6.7%)
Thr (T)23 (7.0%)
Trp (W)4 (1.2%)
Tyr (Y)12 (3.6%)
Val (V)24 (7.3%)
Amino acid counting
Total number:329
Positively charged (Arg+Lys):17 (5.2%)
Negatively charged (Asp+Glu):14 (4.3%)
Aromatic (Phe+His+Try+Tyr):38 (11.6%)
Biochemical parameters
Atomic composition:C1647H2626N388O433S11
Molecular mass [Da]:35144.0
Theoretical pI:8.87
Extinction coefficient at 280 nm [M-1 cm-1]:39880 / 39943 (all Cys red/ox)
Plot for hydrophobicity, charge, predicted secondary structure, solvent accessability, transmembrane helices and disulfid bridges 
Codon usage
Organism:E. coliB. subtilisS. cerevisiaeA. thalianaP. patensMammals
Codon quality (CAI):good (0.68)good (0.73)good (0.69)good (0.75)good (0.69)acceptable (0.55)
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.
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