Difference between revisions of "Part:BBa K1981002"
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<partinfo>BBa_K1981002 short</partinfo> | <partinfo>BBa_K1981002 short</partinfo> | ||
| − | Autoinducer 2-binding protein LsrB. Membrane channel protein. Part of the ABC transporter complex LsrABCD involved in autoinducer 2 (AI-2) import. | + | Autoinducer 2-binding protein LsrB. Membrane channel protein. 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. It can bind AI-2 and deliver it to the LsrC and LsrD permeases (Probable). It shares the same promoter with <i>lsrA</i>. 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. |
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<!-- Add more about the biology of this part here | <!-- Add more about the biology of this part here | ||
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===Usage and Biology=== | ===Usage and Biology=== | ||
| + | AI-2 “Consumer” was constructed by overexpressing the <i>lsrACDB</i> gene in <i>Bacillus amyloliquefaciens LL3</i>. | ||
| + | <div>This part is originated from <i>Bacillus thuringiensis</i> serovar thuringiensis str. IS5056.</div> | ||
| + | |||
===Characterization=== | ===Characterization=== | ||
| − | === | + | |
| + | ===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_1476452617211'><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1476452617211 --><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_K1981002<!------------------------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>ATGAAGAGA ... TATAATTTT</u>TAG</span><br> <strong>ORF</strong> from nucleotide position 1 to 1041 (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">MKRKLGIVLIVCICLIGLIACSSQTADKKKADDVKFAFIPKLTGVGFFTSGGEGAKEMGDKLGVQVKYDGPSEASVSGQVKYINNFINQNYDALMVSSTS<br>VDGLSQSLQRAKKKGMTVLTWDSDVNPKDRSFYISQGTPDQLANLLIEMTSKQIGDKGKVAFFYSSPTVTDQNQWVTKAKEIIKKKYPNWEIVTTQYGEN<br>NAQKSLSVGENILKTYPDINAVICPDATALPAMAQAAENLKMDKKVVVTGFSTPNVMRDYVKRGTVQQFGLWDVKQQGALATYVANEIVVKGKKLKVGDS<br>FEVKGIGKVKVEPNSIQGYDYEAEGNGIIVLPERVVFTKDNIDKYNF*</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">23 (6.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Arg (R)</td><td class="AutoAnnotatorInnerAmino">6 (1.7%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asn (N)</td><td class="AutoAnnotatorInnerAmino">19 (5.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asp (D)</td><td class="AutoAnnotatorInnerAmino">22 (6.3%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Cys (C)</td><td class="AutoAnnotatorInnerAmino">4 (1.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gln (Q)</td><td class="AutoAnnotatorInnerAmino">19 (5.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Glu (E)</td><td class="AutoAnnotatorInnerAmino">15 (4.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gly (G)</td><td class="AutoAnnotatorInnerAmino">29 (8.4%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">His (H)</td><td class="AutoAnnotatorInnerAmino">0 (0.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ile (I)</td><td class="AutoAnnotatorInnerAmino">23 (6.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Leu (L)</td><td class="AutoAnnotatorInnerAmino">21 (6.1%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Lys (K)</td><td class="AutoAnnotatorInnerAmino">39 (11.2%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Met (M)</td><td class="AutoAnnotatorInnerAmino">8 (2.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Phe (F)</td><td class="AutoAnnotatorInnerAmino">13 (3.7%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Pro (P)</td><td class="AutoAnnotatorInnerAmino">12 (3.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ser (S)</td><td class="AutoAnnotatorInnerAmino">22 (6.3%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Thr (T)</td><td class="AutoAnnotatorInnerAmino">20 (5.8%)</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">13 (3.7%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Val (V)</td><td class="AutoAnnotatorInnerAmino">35 (10.1%)</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">347</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Positively charged (Arg+Lys):</td><td class="AutoAnnotatorAminoCountingInner3">45 (13.0%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Negatively charged (Asp+Glu):</td><td class="AutoAnnotatorAminoCountingInner3">37 (10.7%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Aromatic (Phe+His+Try+Tyr):</td><td class="AutoAnnotatorAminoCountingInner3">30 (8.6%)</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>1706</sub>H<sub>2724</sub>N<sub>446</sub>O<sub>515</sub>S<sub>12</sub></td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Molecular mass [Da]:</td><td class="AutoAnnotatorBiochemParInner3">38107.8</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Theoretical pI:</td><td class="AutoAnnotatorBiochemParInner3">9.02</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">41370 / 41620 (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_1476452617211()' 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 (0.75)</td><td class="AutoAnnotatorCodonUsage3">good (0.79)</td><td class="AutoAnnotatorCodonUsage3">good (0.73)</td><td class="AutoAnnotatorCodonUsage3">good (0.76)</td><td class="AutoAnnotatorCodonUsage3">good (0.72)</td><td class="AutoAnnotatorCodonUsage3">acceptable (0.59)</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_1476452617211(){hydrophobicity_datapoints = [[2.5,-1.32],[3.5,-1.78],[4.5,-0.10],[5.5,1.64],[6.5,3.18],[7.5,3.32],[8.5,4.24],[9.5,3.84],[10.5,3.90],[11.5,3.64],[12.5,3.50],[13.5,3.56],[14.5,2.98],[15.5,2.84],[16.5,3.24],[17.5,2.84],[18.5,2.44],[19.5,2.36],[20.5,1.44],[21.5,-0.16],[22.5,-0.66],[23.5,-0.80],[24.5,-1.34],[25.5,-1.96],[26.5,-2.04],[27.5,-2.68],[28.5,-2.68],[29.5,-2.68],[30.5,-2.60],[31.5,-0.98],[32.5,-0.98],[33.5,-0.78],[34.5,0.28],[35.5,1.54],[36.5,1.60],[37.5,2.06],[38.5,0.72],[39.5,1.12],[40.5,0.42],[41.5,-0.56],[42.5,0.60],[43.5,1.30],[44.5,1.10],[45.5,1.80],[46.5,1.74],[47.5,0.74],[48.5,0.74],[49.5,0.10],[50.5,-1.16],[51.5,-1.10],[52.5,-0.58],[53.5,-1.28],[54.5,-1.90],[55.5,-0.82],[56.5,-0.82],[57.5,-1.88],[58.5,-1.88],[59.5,-0.42],[60.5,-0.88],[61.5,0.04],[62.5,0.04],[63.5,1.66],[64.5,0.12],[65.5,-0.06],[66.5,-1.60],[67.5,-0.98],[68.5,-2.14],[69.5,-1.52],[70.5,-1.96],[71.5,-0.90],[72.5,-0.98],[73.5,0.18],[74.5,0.18],[75.5,0.80],[76.5,-0.26],[77.5,0.74],[78.5,-0.88],[79.5,-0.98],[80.5,-0.00],[81.5,-0.00],[82.5,-1.54],[83.5,-0.20],[84.5,0.96],[85.5,-0.64],[86.5,-0.64],[87.5,-0.64],[88.5,-1.46],[89.5,-3.06],[90.5,-2.00],[91.5,-0.54],[92.5,0.54],[93.5,1.64],[94.5,2.18],[95.5,1.66],[96.5,0.76],[97.5,0.22],[98.5,0.22],[99.5,-0.32],[100.5,-0.24],[101.5,0.66],[102.5,0.66],[103.5,-0.88],[104.5,-0.34],[105.5,0.50],[106.5,-0.96],[107.5,-1.70],[108.5,-0.64],[109.5,-1.26],[110.5,-2.80],[111.5,-2.88],[112.5,-2.06],[113.5,-2.04],[114.5,-1.40],[115.5,0.22],[116.5,1.76],[117.5,1.70],[118.5,1.14],[119.5,0.58],[120.5,-0.42],[121.5,-1.88],[122.5,-0.90],[123.5,-1.42],[124.5,-1.04],[125.5,-1.66],[126.5,-1.66],[127.5,-3.40],[128.5,-2.86],[129.5,-1.98],[130.5,-1.46],[131.5,0.14],[132.5,0.88],[133.5,0.34],[134.5,-0.30],[135.5,-0.18],[136.5,-1.40],[137.5,-1.94],[138.5,-1.94],[139.5,-1.10],[140.5,-0.60],[141.5,-0.98],[142.5,0.48],[143.5,1.94],[144.5,2.08],[145.5,1.02],[146.5,2.10],[147.5,1.20],[148.5,0.28],[149.5,-1.40],[150.5,-1.40],[151.5,-0.88],[152.5,-0.82],[153.5,-1.36],[154.5,-1.36],[155.5,-0.74],[156.5,-2.42],[157.5,-1.50],[158.5,-0.44],[159.5,0.90],[160.5,1.54],[161.5,2.06],[162.5,1.06],[163.5,0.54],[164.5,-0.34],[165.5,-1.04],[166.5,0.06],[167.5,0.08],[168.5,-0.46],[169.5,-0.84],[170.5,-1.40],[171.5,-2.94],[172.5,-2.98],[173.5,-1.44],[174.5,-0.88],[175.5,-0.96],[176.5,0.10],[177.5,-0.50],[178.5,-2.04],[179.5,-1.00],[180.5,0.68],[181.5,-0.46],[182.5,-0.46],[183.5,-0.54],[184.5,-1.70],[185.5,-2.92],[186.5,-2.84],[187.5,-2.24],[188.5,-2.16],[189.5,-1.00],[190.5,0.16],[191.5,0.72],[192.5,0.76],[193.5,0.76],[194.5,-0.40],[195.5,-1.32],[196.5,-1.88],[197.5,-2.44],[198.5,-2.44],[199.5,-1.82],[200.5,-2.44],[201.5,-2.52],[202.5,-1.98],[203.5,-0.52],[204.5,-1.04],[205.5,0.50],[206.5,1.20],[207.5,0.66],[208.5,-0.80],[209.5,0.26],[210.5,0.18],[211.5,-0.52],[212.5,0.04],[213.5,0.48],[214.5,-0.74],[215.5,-2.20],[216.5,-0.52],[217.5,-1.08],[218.5,-0.46],[219.5,0.70],[220.5,2.30],[221.5,1.90],[222.5,2.28],[223.5,1.22],[224.5,0.74],[225.5,-0.30],[226.5,-0.44],[227.5,0.64],[228.5,1.02],[229.5,1.02],[230.5,1.54],[231.5,1.54],[232.5,0.08],[233.5,0.76],[234.5,0.76],[235.5,-0.32],[236.5,-1.38],[237.5,0.08],[238.5,-1.06],[239.5,-1.04],[240.5,-1.04],[241.5,-1.12],[242.5,-2.66],[243.5,-1.04],[244.5,-0.58],[245.5,0.96],[246.5,1.60],[247.5,2.30],[248.5,2.02],[249.5,1.02],[250.5,0.04],[251.5,-0.14],[252.5,-0.76],[253.5,-0.48],[254.5,0.06],[255.5,-0.70],[256.5,-1.08],[257.5,-0.64],[258.5,-0.64],[259.5,-1.80],[260.5,-1.80],[261.5,-1.18],[262.5,-1.06],[263.5,-1.06],[264.5,-0.98],[265.5,-0.78],[266.5,-0.14],[267.5,-0.08],[268.5,-0.16],[269.5,0.36],[270.5,0.36],[271.5,0.64],[272.5,-0.06],[273.5,-1.52],[274.5,-2.04],[275.5,-1.42],[276.5,-1.90],[277.5,-0.36],[278.5,0.70],[279.5,1.26],[280.5,1.08],[281.5,1.56],[282.5,1.16],[283.5,0.10],[284.5,-0.46],[285.5,0.70],[286.5,0.70],[287.5,1.18],[288.5,1.10],[289.5,1.72],[290.5,0.04],[291.5,-1.58],[292.5,-1.66],[293.5,-1.66],[294.5,-0.74],[295.5,-0.04],[296.5,0.04],[297.5,-0.88],[298.5,0.46],[299.5,-1.08],[300.5,-0.16],[301.5,-0.24],[302.5,-0.16],[303.5,0.18],[304.5,0.80],[305.5,-0.82],[306.5,0.80],[307.5,0.10],[308.5,0.04],[309.5,-0.58],[310.5,-0.12],[311.5,-1.66],[312.5,-1.04],[313.5,-0.98],[314.5,-0.98],[315.5,-0.74],[316.5,-0.30],[317.5,-0.84],[318.5,-2.00],[319.5,-2.00],[320.5,-1.56],[321.5,-2.00],[322.5,-1.38],[323.5,-1.82],[324.5,-1.20],[325.5,-0.66],[326.5,0.94],[327.5,1.86],[328.5,3.32],[329.5,3.08],[330.5,1.48],[331.5,-0.32],[332.5,-0.32],[333.5,-0.24],[334.5,0.64],[335.5,1.20],[336.5,1.32],[337.5,-0.22],[338.5,-1.76],[339.5,-1.42],[340.5,-1.98],[341.5,-1.98],[342.5,-1.54],[343.5,-1.54],[344.5,-1.88]];charge_datapoints = [[2.5,0.60],[3.5,0.60],[4.5,0.40],[5.5,0.20],[6.5,0.00],[7.5,0.00],[8.5,0.00],[9.5,0.00],[10.5,0.00],[11.5,0.00],[12.5,0.00],[13.5,0.00],[14.5,0.00],[15.5,0.00],[16.5,0.00],[17.5,0.00],[18.5,0.00],[19.5,0.00],[20.5,0.00],[21.5,0.00],[22.5,0.00],[23.5,0.00],[24.5,-0.20],[25.5,0.00],[26.5,0.20],[27.5,0.40],[28.5,0.40],[29.5,0.40],[30.5,0.00],[31.5,-0.20],[32.5,-0.20],[33.5,-0.20],[34.5,0.00],[35.5,0.20],[36.5,0.20],[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,-0.20],[51.5,-0.20],[52.5,-0.20],[53.5,0.00],[54.5,-0.20],[55.5,0.00],[56.5,0.00],[57.5,-0.20],[58.5,-0.20],[59.5,0.00],[60.5,0.00],[61.5,0.00],[62.5,0.20],[63.5,0.00],[64.5,0.20],[65.5,0.20],[66.5,0.00],[67.5,0.00],[68.5,0.00],[69.5,-0.20],[70.5,-0.40],[71.5,-0.20],[72.5,-0.20],[73.5,-0.20],[74.5,-0.20],[75.5,0.00],[76.5,0.00],[77.5,0.00],[78.5,0.20],[79.5,0.20],[80.5,0.20],[81.5,0.20],[82.5,0.20],[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,-0.20],[90.5,-0.20],[91.5,-0.20],[92.5,-0.20],[93.5,-0.20],[94.5,0.00],[95.5,0.00],[96.5,0.00],[97.5,0.00],[98.5,0.00],[99.5,-0.20],[100.5,-0.20],[101.5,-0.20],[102.5,-0.20],[103.5,-0.20],[104.5,0.00],[105.5,0.00],[106.5,0.00],[107.5,0.20],[108.5,0.20],[109.5,0.40],[110.5,0.60],[111.5,0.80],[112.5,0.60],[113.5,0.60],[114.5,0.40],[115.5,0.20],[116.5,0.00],[117.5,0.00],[118.5,0.00],[119.5,-0.20],[120.5,-0.20],[121.5,-0.40],[122.5,-0.40],[123.5,-0.40],[124.5,-0.20],[125.5,0.00],[126.5,0.00],[127.5,0.20],[128.5,0.20],[129.5,0.20],[130.5,0.00],[131.5,0.20],[132.5,0.00],[133.5,0.00],[134.5,0.00],[135.5,0.00],[136.5,0.00],[137.5,-0.20],[138.5,-0.20],[139.5,-0.20],[140.5,-0.20],[141.5,-0.20],[142.5,0.00],[143.5,0.00],[144.5,0.00],[145.5,-0.20],[146.5,-0.20],[147.5,-0.20],[148.5,-0.20],[149.5,0.00],[150.5,0.20],[151.5,0.20],[152.5,0.20],[153.5,0.00],[154.5,0.00],[155.5,0.00],[156.5,0.20],[157.5,0.20],[158.5,0.40],[159.5,0.20],[160.5,0.20],[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,-0.20],[169.5,-0.20],[170.5,-0.20],[171.5,-0.20],[172.5,-0.20],[173.5,0.00],[174.5,0.00],[175.5,0.20],[176.5,0.20],[177.5,0.40],[178.5,0.20],[179.5,0.20],[180.5,0.00],[181.5,0.20],[182.5,0.20],[183.5,0.60],[184.5,0.60],[185.5,0.60],[186.5,0.40],[187.5,0.20],[188.5,-0.20],[189.5,-0.20],[190.5,-0.20],[191.5,-0.20],[192.5,-0.20],[193.5,0.00],[194.5,0.00],[195.5,0.00],[196.5,-0.20],[197.5,-0.20],[198.5,-0.20],[199.5,-0.20],[200.5,-0.20],[201.5,0.20],[202.5,0.20],[203.5,0.20],[204.5,0.20],[205.5,0.20],[206.5,0.00],[207.5,-0.20],[208.5,-0.20],[209.5,-0.20],[210.5,-0.20],[211.5,0.00],[212.5,0.20],[213.5,0.20],[214.5,0.20],[215.5,0.00],[216.5,-0.20],[217.5,-0.20],[218.5,-0.20],[219.5,-0.20],[220.5,0.00],[221.5,0.00],[222.5,0.00],[223.5,-0.20],[224.5,-0.20],[225.5,-0.20],[226.5,-0.20],[227.5,-0.20],[228.5,0.00],[229.5,0.00],[230.5,0.00],[231.5,0.00],[232.5,0.00],[233.5,0.00],[234.5,0.00],[235.5,-0.20],[236.5,-0.20],[237.5,-0.20],[238.5,0.00],[239.5,0.00],[240.5,0.00],[241.5,0.20],[242.5,0.40],[243.5,0.20],[244.5,0.20],[245.5,0.40],[246.5,0.20],[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],[255.5,0.20],[256.5,0.00],[257.5,0.00],[258.5,0.00],[259.5,0.20],[260.5,0.20],[261.5,0.40],[262.5,0.40],[263.5,0.40],[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,-0.20],[271.5,-0.20],[272.5,0.00],[273.5,0.00],[274.5,0.00],[275.5,0.20],[276.5,0.20],[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,-0.20],[285.5,-0.20],[286.5,-0.20],[287.5,-0.20],[288.5,0.00],[289.5,0.20],[290.5,0.40],[291.5,0.60],[292.5,0.60],[293.5,0.60],[294.5,0.60],[295.5,0.40],[296.5,0.00],[297.5,0.00],[298.5,-0.20],[299.5,-0.40],[300.5,-0.40],[301.5,0.00],[302.5,0.00],[303.5,0.00],[304.5,0.20],[305.5,0.40],[306.5,0.20],[307.5,0.40],[308.5,0.40],[309.5,0.20],[310.5,0.00],[311.5,0.00],[312.5,-0.20],[313.5,-0.20],[314.5,0.00],[315.5,0.00],[316.5,0.00],[317.5,-0.20],[318.5,-0.20],[319.5,-0.40],[320.5,-0.40],[321.5,-0.60],[322.5,-0.40],[323.5,-0.40],[324.5,-0.20],[325.5,-0.20],[326.5,0.00],[327.5,0.00],[328.5,0.00],[329.5,0.00],[330.5,-0.20],[331.5,0.00],[332.5,0.00],[333.5,0.00],[334.5,0.00],[335.5,0.20],[336.5,0.20],[337.5,0.00],[338.5,0.00],[339.5,0.00],[340.5,-0.20],[341.5,-0.20],[342.5,0.00],[343.5,0.00],[344.5,0.00]];dis_datapoints = undefined;trans_datapoints = undefined;sec_helix_datapoints = undefined;sec_strand_datapoints = undefined;acc_exposed_datapoints = undefined;acc_buried_datapoints = undefined;flot_plot_options = []; flot_plot_options[0] = {grid: {borderWidth: {top: 0,right: 0,bottom: 0,left: 0}},legend: {show: false},xaxes: [{show: true,min: 0,max: 200,ticks: [[0.5, '1'], [24.5, '25'], [49.5, '50'], [74.5, '75'], [99.5, '100'], [124.5, '125'], [149.5, '150'], [174.5, '175'], [199.5, '200']],tickLength: -5}],yaxes: [{show: true,ticks: [[0, '0'], [4.5,'hydro-<br>phobic '], [-4.5,'hydro-<br>philic ']],min: -4.5,max: +4.5,font: {size: 12,lineHeight: 14,style: 'italic',weight: 'bold',family: 'sans-serif',variant: 'small-caps',color: 'rgba(100,149,237,1)'}},{show: true,ticks: [[0, ''], [1,'positive<br> charge'], [-1,'negative<br> charge']],position: 'right',min: -1,max: 1,font: {size: 12,lineHeight: 14,style: 'italic',weight: 'bold',family: 'sans-serif',variant: 'small-caps',color: 'rgba(255,99,71,1)'}}]};number_of_plots = 2;for ( plot_num = 1 ; plot_num < number_of_plots ; plot_num ++){flot_plot_options[plot_num] = jqAutoAnnotator.extend(true, {} ,flot_plot_options[0]);flot_plot_options[plot_num].xaxes = [{min: plot_num*200,max: (plot_num + 1)*200,ticks: [ [plot_num*200 + 0.5, (plot_num*200 + 1).toString()], [plot_num*200 + 24.5, (plot_num*200 + 25).toString()], [plot_num*200 + 49.5, (plot_num*200 + 50).toString()], [plot_num*200 + 74.5, (plot_num*200 + 75).toString()], [plot_num*200 + 99.5, (plot_num*200 + 100).toString()], [plot_num*200 + 124.5, (plot_num*200 + 125).toString()], [plot_num*200 + 149.5, (plot_num*200 + 150).toString()], [plot_num*200 + 174.5, (plot_num*200 + 175).toString()], [plot_num*200 + 199.5, (plot_num*200 + 200).toString()] ],tickLength: -5}];};try {if( jqAutoAnnotator('#AutoAnnotator_container_1476452617211 #hydrophobicity_charge_button').val() =='Show' ){jqAutoAnnotator('#AutoAnnotator_container_1476452617211 #hydrophobicity_charge_container').css('display','block');jqAutoAnnotator('#AutoAnnotator_container_1476452617211 #hydrophobicity_charge_button').val('Hide');var description_html = '<div id=\'AutoAnnotator_plot_selectors\'>';description_html = description_html + '<br> <input type=\'checkbox\' id=\'hydrophobicity_checkbox\' checked=\'checked\'> Moving average over 5 amino acids for hydrophobicity (<img src=\'https://static.igem.org/mediawiki/2013/e/e9/TUM13_hydrophobicity_icon.png\' alt=\'blue graph\' height=\'10\'></img>)';description_html = description_html + '<br> <input type=\'checkbox\' id=\'charge_checkbox\' checked=\'checked\'> Moving average over 5 amino acids for charge (<img src=\'https://static.igem.org/mediawiki/2013/3/3e/TUM13_charge_icon.png\' alt=\'red graph\' height=\'10\'></img>)';description_html = description_html + '<br> <input type=\'checkbox\' id=\'dis_checkbox\' checked=\'checked\'> Predicted disulfid bridges (<img src=\'https://static.igem.org/mediawiki/2013/2/28/TUM13_dis_icon.png\' alt=\'yellow circle\' height=\'10\'></img>) with the number of the bridge in the center';description_html = description_html + '<br> <input type=\'checkbox\' id=\'trans_checkbox\' checked=\'checked\'> Predicted transmembrane helices (<img src=\'https://static.igem.org/mediawiki/2013/7/78/TUM13_trans_icon.png\' alt=\'turquois bars\' height=\'10\'></img>)';description_html = description_html + '<br> <input type=\'checkbox\' id=\'sec_checkbox\' checked=\'checked\'> Predicted secondary structure: Helices (<img src=\'https://static.igem.org/mediawiki/2013/b/bf/TUM13_helix_icon.png\' alt=\'violet bars\' height=\'10\'></img>) and beta-strands (<img src=\'https://static.igem.org/mediawiki/2013/b/bf/TUM13_strand_icon.png\' alt=\'yellow bars\' height=\'10\'></img>)';description_html = description_html + '<br> <input type=\'checkbox\' id=\'acc_checkbox\' checked=\'checked\'> Predicted solvent accessability: Exposed (<img src=\'https://static.igem.org/mediawiki/2013/1/16/TUM13_exposed_icon.png\' alt=\'blue bars\' height=\'10\'></img>) and buried (<img src=\'https://static.igem.org/mediawiki/2013/0/0b/TUM13_buried_icon.png\' alt=\'green bars\' height=\'10\'></img>) residues';description_html = description_html + '<br></div>';jqAutoAnnotator('#AutoAnnotator_container_1476452617211 #hydrophobicity_charge_explanation').html(description_html);plot_according_to_selectors_1476452617211();jqAutoAnnotator('#AutoAnnotator_container_1476452617211 #AutoAnnotator_plot_selectors').find('input').click(plot_according_to_selectors_1476452617211);}else{jqAutoAnnotator('#AutoAnnotator_container_1476452617211 #hydrophobicity_charge_container').css('display','none');jqAutoAnnotator('#AutoAnnotator_container_1476452617211 #hydrophobicity_charge_button').val('Show');jqAutoAnnotator('#AutoAnnotator_container_1476452617211 #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_1476452617211(){try{var plot_datasets = [[],[]];if(jqAutoAnnotator('#AutoAnnotator_container_1476452617211 #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_1476452617211 #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_1476452617211 #hydrophobicity_charge_placeholder'+ plot_num.toString(), plot_datasets, flot_plot_options[plot_num] );}var screen_width = jqAutoAnnotator('canvas.flot-base').width(); var pos_of_first_tick = 46;var pos_of_last_tick = screen_width - 51;var tick_diff = (screen_width - 97)/199;if(jqAutoAnnotator('#AutoAnnotator_container_1476452617211 #dis_checkbox').prop('checked') == true){for ( j = 0 ; j < dis_datapoints.length ; j++ ){jqAutoAnnotator('#AutoAnnotator_container_1476452617211 #hydrophobicity_charge_placeholder' + Math.floor((dis_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_dis\' style=\'left:' + ((pos_of_first_tick - 8 + (dis_datapoints[j][0] - 1)*tick_diff - Math.floor((dis_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px;\'><b>' + (j+1) + '</b></div>');jqAutoAnnotator('#AutoAnnotator_container_1476452617211 #hydrophobicity_charge_placeholder' + Math.floor((dis_datapoints[j][1] - 1)/200) ).append('<div class=\'AutoAnnotator_dis\' style=\'left:' + ((pos_of_first_tick - 8 + (dis_datapoints[j][1] - 1)*tick_diff - Math.floor((dis_datapoints[j][1] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px;\'><b>' + (j+1) + '</b></div>');}}if(jqAutoAnnotator('#AutoAnnotator_container_1476452617211 #trans_checkbox').prop('checked') == true){for ( j = 0 ; j < trans_datapoints.length ; j++ ){jqAutoAnnotator('#AutoAnnotator_container_1476452617211 #hydrophobicity_charge_placeholder' + Math.floor((trans_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_trans\' style=\'width:' + (((trans_datapoints[j][1] - trans_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px ;left:' + ((pos_of_first_tick + (trans_datapoints[j][0] - 1.5)*tick_diff - Math.floor((trans_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px\'></div>');}}if(jqAutoAnnotator('#AutoAnnotator_container_1476452617211 #sec_checkbox').prop('checked') == true){for ( j = 0 ; j < sec_helix_datapoints.length ; j++ ){jqAutoAnnotator('#AutoAnnotator_container_1476452617211 #hydrophobicity_charge_placeholder' + Math.floor((sec_helix_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_sec_helix\' style=\'width:' + (((sec_helix_datapoints[j][1] - sec_helix_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px; left:' + ((pos_of_first_tick + (sec_helix_datapoints[j][0] - 1.5)*tick_diff - Math.floor((sec_helix_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px\'></div>');}for ( j = 0 ; j < sec_strand_datapoints.length ; j++ ){jqAutoAnnotator('#AutoAnnotator_container_1476452617211 #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_1476452617211 #acc_checkbox').prop('checked') == true){for ( j = 0 ; j < acc_buried_datapoints.length ; j++ ){jqAutoAnnotator('#AutoAnnotator_container_1476452617211 #hydrophobicity_charge_placeholder' + Math.floor((acc_buried_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_acc_buried\' style=\'width:' + (((acc_buried_datapoints[j][1] - acc_buried_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px; left:' + ((pos_of_first_tick + (acc_buried_datapoints[j][0] - 1.5)*tick_diff - Math.floor((acc_buried_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px\'></div>');}for ( j = 0 ; j < acc_exposed_datapoints.length ; j++ ){jqAutoAnnotator('#AutoAnnotator_container_1476452617211 #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> | ||
Latest revision as of 01:36, 15 October 2016
lsrB
Autoinducer 2-binding protein LsrB. Membrane channel protein. 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. It can bind AI-2 and deliver it to the LsrC and LsrD permeases (Probable). It shares the same promoter with lsrA. 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
Assembly Compatibility:
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
Usage and Biology
AI-2 “Consumer” was constructed by overexpressing the lsrACDB gene 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_K1981002 automatically created by the BioBrick-AutoAnnotator version 1.0 | ||||||||||||||||||||||||||||||||||||||||||||||
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| Nucleotide sequence in RFC 10: (underlined part encodes the protein) ATGAAGAGA ... TATAATTTTTAG ORF from nucleotide position 1 to 1041 (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. | ||||||||||||||||||||||||||||||||||||||||||||||