Difference between revisions of "Part:BBa K1981003"
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<partinfo>BBa_K1981003 short</partinfo> | <partinfo>BBa_K1981003 short</partinfo> | ||
| − | Autoinducer 2 import system permease protein LsrC. Part of the ABC transporter complex LsrABCD involved in autoinducer 2 (AI-2) import. | + | Autoinducer 2 import system permease protein LsrC. 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 it is probably responsible for the translocation of the substrate across the membrane. 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. |
<!-- 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=== | ||
| − | === | + | The restriction enzyme digestion verification result for <i>lsrC</i> is shown in <b>Figure 1</b>. |
| + | <div>[[File:T--NKU China--lsrC Colony PCR.jpeg|1000px|thumb|center|<b>Figure 1:</b> Restriction Enzyme Digestion Verification for <i>lsrC</i>]]</div> | ||
| + | |||
| + | ===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_1476453209278'><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1476453209278 --><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_K1981003<!------------------------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>ATGAAACAC ... ATGAACCTT</u>TGA</span><br> <strong>ORF</strong> from nucleotide position 1 to 951 (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">MKHMLKMHETSIILLLLIYIAIVGMINPSFIQFNSLSLLMKSSVILVVLAIGQSFVLFTKNIDVSVGSIMGLSAAVCGMLLTNGYNAFMSILAAIMLGAI<br>IGFINGIGVAKFRVPAIIMTLGMLGIVRGAMLIFTGGKWIEDIPNDFKQLSSIIILGLPITVWFVFIILLLLYFFLRKVPLGRYFYAVGDNEDGARLIGI<br>PVNKVKIYAFMISGISAALAGCIFVMNIGFVPNQTGTGLELQVIAAAVLGGIHLKGGTGSIFGAALGALFLEVISSSLVFLKIPAFWNNAISGFLLLLII<br>ILDSVMRKWKAKRRMNL*</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 (8.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Arg (R)</td><td class="AutoAnnotatorInnerAmino">8 (2.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asn (N)</td><td class="AutoAnnotatorInnerAmino">14 (4.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asp (D)</td><td class="AutoAnnotatorInnerAmino">6 (1.9%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Cys (C)</td><td class="AutoAnnotatorInnerAmino">2 (0.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gln (Q)</td><td class="AutoAnnotatorInnerAmino">5 (1.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Glu (E)</td><td class="AutoAnnotatorInnerAmino">5 (1.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gly (G)</td><td class="AutoAnnotatorInnerAmino">33 (10.4%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">His (H)</td><td class="AutoAnnotatorInnerAmino">3 (0.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ile (I)</td><td class="AutoAnnotatorInnerAmino">45 (14.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Leu (L)</td><td class="AutoAnnotatorInnerAmino">45 (14.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Lys (K)</td><td class="AutoAnnotatorInnerAmino">15 (4.7%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Met (M)</td><td class="AutoAnnotatorInnerAmino">16 (5.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Phe (F)</td><td class="AutoAnnotatorInnerAmino">22 (6.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Pro (P)</td><td class="AutoAnnotatorInnerAmino">8 (2.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ser (S)</td><td class="AutoAnnotatorInnerAmino">21 (6.6%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Thr (T)</td><td class="AutoAnnotatorInnerAmino">9 (2.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Trp (W)</td><td class="AutoAnnotatorInnerAmino">4 (1.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Tyr (Y)</td><td class="AutoAnnotatorInnerAmino">6 (1.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Val (V)</td><td class="AutoAnnotatorInnerAmino">24 (7.6%)</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">317</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Positively charged (Arg+Lys):</td><td class="AutoAnnotatorAminoCountingInner3">23 (7.3%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Negatively charged (Asp+Glu):</td><td class="AutoAnnotatorAminoCountingInner3">11 (3.5%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Aromatic (Phe+His+Try+Tyr):</td><td class="AutoAnnotatorAminoCountingInner3">35 (11.0%)</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>1611</sub>H<sub>2593</sub>N<sub>385</sub>O<sub>395</sub>S<sub>18</sub></td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Molecular mass [Da]:</td><td class="AutoAnnotatorBiochemParInner3">34252.7</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Theoretical pI:</td><td class="AutoAnnotatorBiochemParInner3">9.89</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">30940 / 31065 (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_1476453209278()' 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 (0.71)</td><td class="AutoAnnotatorCodonUsage3">good (0.61)</td><td class="AutoAnnotatorCodonUsage3">good (0.71)</td><td class="AutoAnnotatorCodonUsage3">good (0.76)</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_1476453209278(){hydrophobicity_datapoints = [[2.5,0.10],[3.5,-1.06],[4.5,0.10],[5.5,0.10],[6.5,-0.98],[7.5,-1.88],[8.5,-1.26],[9.5,-0.74],[10.5,0.80],[11.5,2.26],[12.5,3.16],[13.5,4.08],[14.5,3.94],[15.5,3.94],[16.5,2.92],[17.5,3.06],[18.5,2.66],[19.5,2.80],[20.5,2.74],[21.5,2.92],[22.5,2.40],[23.5,2.94],[24.5,1.34],[25.5,0.18],[26.5,0.10],[27.5,0.28],[28.5,0.28],[29.5,0.28],[30.5,1.16],[31.5,0.62],[32.5,-0.10],[33.5,-0.24],[34.5,0.30],[35.5,0.50],[36.5,1.96],[37.5,2.50],[38.5,0.96],[39.5,0.96],[40.5,0.04],[41.5,0.12],[42.5,0.64],[43.5,2.18],[44.5,3.18],[45.5,4.18],[46.5,4.10],[47.5,3.56],[48.5,3.70],[49.5,2.78],[50.5,1.24],[51.5,0.32],[52.5,0.52],[53.5,0.46],[54.5,1.30],[55.5,2.56],[56.5,2.58],[57.5,1.24],[58.5,-0.30],[59.5,-0.16],[60.5,-1.42],[61.5,-0.44],[62.5,0.18],[63.5,1.72],[64.5,0.74],[65.5,1.28],[66.5,1.34],[67.5,1.88],[68.5,0.96],[69.5,1.80],[70.5,1.80],[71.5,1.26],[72.5,1.24],[73.5,2.16],[74.5,1.90],[75.5,1.98],[76.5,2.00],[77.5,2.40],[78.5,2.32],[79.5,1.68],[80.5,1.06],[81.5,0.60],[82.5,-0.42],[83.5,-1.88],[84.5,-1.38],[85.5,-0.12],[86.5,0.34],[87.5,0.44],[88.5,2.04],[89.5,2.44],[90.5,2.24],[91.5,2.22],[92.5,3.28],[93.5,2.76],[94.5,2.76],[95.5,2.32],[96.5,2.32],[97.5,2.32],[98.5,2.84],[99.5,2.00],[100.5,2.64],[101.5,3.18],[102.5,1.58],[103.5,0.60],[104.5,1.58],[105.5,0.94],[106.5,0.88],[107.5,1.94],[108.5,1.24],[109.5,0.90],[110.5,0.08],[111.5,0.08],[112.5,-0.60],[113.5,0.54],[114.5,0.88],[115.5,2.68],[116.5,2.22],[117.5,2.40],[118.5,2.80],[119.5,1.82],[120.5,1.30],[121.5,1.68],[122.5,1.74],[123.5,1.88],[124.5,2.80],[125.5,1.52],[126.5,0.68],[127.5,1.12],[128.5,0.60],[129.5,0.52],[130.5,2.32],[131.5,2.96],[132.5,2.46],[133.5,2.00],[134.5,1.16],[135.5,-0.52],[136.5,-1.26],[137.5,-0.22],[138.5,-0.84],[139.5,-1.46],[140.5,0.22],[141.5,0.08],[142.5,-1.52],[143.5,-1.52],[144.5,-0.26],[145.5,-1.94],[146.5,-2.32],[147.5,-0.86],[148.5,-0.32],[149.5,-1.04],[150.5,0.64],[151.5,2.24],[152.5,2.38],[153.5,3.30],[154.5,3.38],[155.5,3.24],[156.5,2.02],[157.5,2.02],[158.5,1.12],[159.5,2.04],[160.5,1.10],[161.5,1.98],[162.5,1.92],[163.5,2.62],[164.5,2.68],[165.5,3.76],[166.5,3.96],[167.5,3.88],[168.5,4.08],[169.5,3.94],[170.5,2.78],[171.5,2.58],[172.5,2.38],[173.5,2.38],[174.5,0.72],[175.5,0.20],[176.5,0.48],[177.5,-0.40],[178.5,-0.40],[179.5,0.42],[180.5,0.30],[181.5,-0.80],[182.5,0.08],[183.5,-0.94],[184.5,-0.50],[185.5,1.24],[186.5,1.42],[187.5,0.16],[188.5,-0.28],[189.5,-1.34],[190.5,-2.88],[191.5,-2.88],[192.5,-1.82],[193.5,-2.02],[194.5,-0.56],[195.5,1.04],[196.5,1.04],[197.5,1.58],[198.5,2.16],[199.5,2.24],[200.5,0.64],[201.5,-0.06],[202.5,-0.12],[203.5,-0.58],[204.5,-0.52],[205.5,-0.08],[206.5,1.06],[207.5,0.78],[208.5,1.94],[209.5,1.94],[210.5,2.04],[211.5,1.60],[212.5,1.94],[213.5,1.40],[214.5,0.86],[215.5,1.38],[216.5,2.22],[217.5,1.68],[218.5,1.76],[219.5,1.90],[220.5,2.44],[221.5,2.24],[222.5,2.72],[223.5,3.18],[224.5,1.98],[225.5,1.98],[226.5,1.34],[227.5,1.06],[228.5,1.52],[229.5,1.90],[230.5,0.30],[231.5,-0.32],[232.5,-1.02],[233.5,-1.94],[234.5,-1.76],[235.5,-1.14],[236.5,0.32],[237.5,-0.24],[238.5,0.60],[239.5,0.04],[240.5,0.96],[241.5,1.10],[242.5,2.16],[243.5,1.76],[244.5,2.82],[245.5,2.82],[246.5,2.68],[247.5,2.24],[248.5,1.80],[249.5,2.34],[250.5,0.86],[251.5,0.86],[252.5,0.16],[253.5,0.16],[254.5,-0.82],[255.5,-0.32],[256.5,-1.16],[257.5,-0.54],[258.5,0.44],[259.5,1.08],[260.5,1.14],[261.5,1.58],[262.5,2.10],[263.5,1.96],[264.5,1.32],[265.5,1.76],[266.5,2.16],[267.5,2.36],[268.5,2.36],[269.5,1.74],[270.5,2.22],[271.5,2.36],[272.5,1.64],[273.5,0.72],[274.5,1.26],[275.5,1.18],[276.5,1.12],[277.5,1.84],[278.5,2.76],[279.5,2.14],[280.5,2.28],[281.5,1.12],[282.5,0.92],[283.5,0.72],[284.5,1.32],[285.5,-0.28],[286.5,-0.66],[287.5,-0.66],[288.5,-0.32],[289.5,-0.30],[290.5,0.32],[291.5,1.58],[292.5,1.98],[293.5,1.84],[294.5,2.76],[295.5,3.60],[296.5,3.94],[297.5,4.08],[298.5,4.22],[299.5,4.22],[300.5,2.76],[301.5,1.70],[302.5,1.64],[303.5,1.12],[304.5,-0.54],[305.5,-0.62],[306.5,-0.64],[307.5,-2.26],[308.5,-2.28],[309.5,-2.16],[310.5,-2.28],[311.5,-3.00],[312.5,-1.84],[313.5,-2.90],[314.5,-1.36]];charge_datapoints = [[2.5,0.30],[3.5,0.50],[4.5,0.30],[5.5,0.30],[6.5,0.10],[7.5,0.10],[8.5,-0.10],[9.5,-0.10],[10.5,-0.20],[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,-0.00],[25.5,-0.00],[26.5,-0.00],[27.5,-0.00],[28.5,-0.00],[29.5,-0.00],[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],[57.5,0.20],[58.5,0.20],[59.5,0.20],[60.5,-0.00],[61.5,-0.00],[62.5,-0.20],[63.5,-0.20],[64.5,-0.20],[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,-0.00],[107.5,-0.00],[108.5,0.20],[109.5,0.20],[110.5,0.40],[111.5,0.40],[112.5,0.40],[113.5,0.20],[114.5,0.20],[115.5,0.00],[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],[125.5,0.20],[126.5,0.20],[127.5,0.20],[128.5,0.20],[129.5,0.20],[130.5,0.00],[131.5,0.00],[132.5,0.00],[133.5,0.00],[134.5,0.00],[135.5,0.20],[136.5,0.20],[137.5,0.20],[138.5,0.00],[139.5,-0.20],[140.5,-0.40],[141.5,-0.40],[142.5,-0.40],[143.5,-0.40],[144.5,-0.20],[145.5,0.00],[146.5,0.00],[147.5,0.00],[148.5,0.20],[149.5,0.20],[150.5,0.00],[151.5,0.00],[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],[174.5,0.20],[175.5,0.40],[176.5,0.40],[177.5,0.40],[178.5,0.40],[179.5,0.20],[180.5,0.20],[181.5,0.20],[182.5,0.20],[183.5,0.20],[184.5,0.20],[185.5,0.00],[186.5,0.00],[187.5,-0.20],[188.5,-0.20],[189.5,-0.40],[190.5,-0.60],[191.5,-0.60],[192.5,-0.40],[193.5,-0.20],[194.5,-0.00],[195.5,0.20],[196.5,0.20],[197.5,0.20],[198.5,-0.00],[199.5,-0.00],[200.5,-0.00],[201.5,0.20],[202.5,0.20],[203.5,0.40],[204.5,0.40],[205.5,0.40],[206.5,0.20],[207.5,0.20],[208.5,-0.00],[209.5,-0.00],[210.5,-0.00],[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,-0.00],[235.5,-0.00],[236.5,-0.00],[237.5,-0.20],[238.5,-0.20],[239.5,-0.20],[240.5,-0.20],[241.5,-0.20],[242.5,-0.00],[243.5,-0.00],[244.5,-0.00],[245.5,-0.00],[246.5,-0.00],[247.5,-0.00],[248.5,-0.00],[249.5,-0.00],[250.5,0.10],[251.5,0.10],[252.5,0.30],[253.5,0.30],[254.5,0.30],[255.5,0.20],[256.5,0.20],[257.5,-0.00],[258.5,-0.00],[259.5,-0.00],[260.5,-0.00],[261.5,-0.00],[262.5,-0.00],[263.5,-0.00],[264.5,-0.00],[265.5,-0.00],[266.5,-0.00],[267.5,-0.00],[268.5,-0.00],[269.5,-0.20],[270.5,-0.20],[271.5,-0.20],[272.5,-0.20],[273.5,-0.20],[274.5,-0.00],[275.5,-0.00],[276.5,-0.00],[277.5,-0.00],[278.5,-0.00],[279.5,0.20],[280.5,0.20],[281.5,0.20],[282.5,0.20],[283.5,0.20],[284.5,-0.00],[285.5,-0.00],[286.5,-0.00],[287.5,-0.00],[288.5,-0.00],[289.5,-0.00],[290.5,-0.00],[291.5,-0.00],[292.5,-0.00],[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,-0.20],[301.5,-0.20],[302.5,-0.20],[303.5,-0.20],[304.5,-0.00],[305.5,0.40],[306.5,0.40],[307.5,0.60],[308.5,0.60],[309.5,0.60],[310.5,0.60],[311.5,0.80],[312.5,0.60],[313.5,0.60],[314.5,0.40]];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_1476453209278 #hydrophobicity_charge_button').val() =='Show' ){jqAutoAnnotator('#AutoAnnotator_container_1476453209278 #hydrophobicity_charge_container').css('display','block');jqAutoAnnotator('#AutoAnnotator_container_1476453209278 #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_1476453209278 #hydrophobicity_charge_explanation').html(description_html);plot_according_to_selectors_1476453209278();jqAutoAnnotator('#AutoAnnotator_container_1476453209278 #AutoAnnotator_plot_selectors').find('input').click(plot_according_to_selectors_1476453209278);}else{jqAutoAnnotator('#AutoAnnotator_container_1476453209278 #hydrophobicity_charge_container').css('display','none');jqAutoAnnotator('#AutoAnnotator_container_1476453209278 #hydrophobicity_charge_button').val('Show');jqAutoAnnotator('#AutoAnnotator_container_1476453209278 #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_1476453209278(){try{var plot_datasets = [[],[]];if(jqAutoAnnotator('#AutoAnnotator_container_1476453209278 #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_1476453209278 #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_1476453209278 #hydrophobicity_charge_placeholder'+ plot_num.toString(), plot_datasets, flot_plot_options[plot_num] );}var 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Latest revision as of 01:38, 15 October 2016
lsrC
Autoinducer 2 import system permease protein LsrC. 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 it is probably responsible for the translocation of the substrate across the membrane. 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]
- 1000INCOMPATIBLE WITH RFC[1000]Illegal SapI.rc site found at 120
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
The restriction enzyme digestion verification result for lsrC is shown in Figure 1.
Protein-Data Table
| Protein data table for BioBrick BBa_K1981003 automatically created by the BioBrick-AutoAnnotator version 1.0 | ||||||||||||||||||||||||||||||||||||||||||||||
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| Nucleotide sequence in RFC 10: (underlined part encodes the protein) ATGAAACAC ... ATGAACCTTTGA ORF from nucleotide position 1 to 951 (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. | ||||||||||||||||||||||||||||||||||||||||||||||