Difference between revisions of "Part:BBa K1981007"
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<partinfo>BBa_K1981007 short</partinfo> | <partinfo>BBa_K1981007 short</partinfo> | ||
| − | + | 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase. It is nvolved in the synthesis of autoinducer 2 (AI-2) which is secreted by bacteria and is used to communicate both the cell density and the metabolic potential of the environment. It catalyzes the irreversible cleavage of the glycosidic bond in both 5'-methylthioadenosine (MTA) and S-adenosylhomocysteine (SAH/AdoHcy) to adenine and the corresponding thioribose, 5'-methylthioribose and S-ribosylhomocysteine, respectively.It can also use 5'-isobutylthioadenosine, 5'-n-butylthioadenosine, S-adenosyl-D-homocysteine, decarboxylated adenosylhomocysteine, deaminated adenosylhomocysteine and S-2-aza-adenosylhomocysteine as substrates. | |
<!-- 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=== | ||
| + | The AI-2 “supplier” was constructed by overexpressing the <i>mtn</i> gene. | ||
| + | <div>This part was originated from <i>Escherichia coli</i> strain K12.</div> | ||
| + | |||
===Characterization=== | ===Characterization=== | ||
| + | The restriction enzyme digestion verification result for <i>mtn</i> is shown in <b>Figure 1</b>. | ||
| + | <div>[[File:T--NKU China--luxS mtn lsrK RDV.jpeg|800px|thumb|center|<b>Figure 1:</b> Restriction Enzyme Digestion Verification for <i>mtn</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_1476456270820'><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1476456270820 --><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"> <u>ATGAAAATC ... GCACATGGC</u>TAA</span><br> <strong>ORF</strong> from nucleotide position 1 to 696 (excluding stop-codon)</td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Amino acid sequence:</strong> (RFC 25 scars in shown in bold, other sequence features underlined; both given below)<br><span class="AutoAnnotatorSequence"><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorSeqNum">1 <br>101 <br>201 </td><td class="AutoAnnotatorSeqSeq">MKIGIIGAMEEEVTLLRDKIENRQTISLGGCEIY<b>TG</b>QLNGTEVALLKSGIGKVAAALGATLLLEHCKPDVIINTGSAGGLAPTLKVGDIVVSDEARYHDA<br>DVTAFGYEYGQLPGCPAGFKADDKLIAAAEACIAELNLNAVRGLIVSGDAFINGSVGLAKIRHNFPQAIAVEMEATAIAHVCHNFNVPFVVVRAISDVAD<br>QQSHLSFDEFLAVAAKQSSLMVESLVQKLAHG*</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="AutoAnnotatorSeqFeat2a">RFC25 scar (shown in bold): </td><td class="AutoAnnotatorSeqFeat3">35 to 36</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">32 (13.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Arg (R)</td><td class="AutoAnnotatorInnerAmino">6 (2.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asn (N)</td><td class="AutoAnnotatorInnerAmino">9 (3.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asp (D)</td><td class="AutoAnnotatorInnerAmino">12 (5.2%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Cys (C)</td><td class="AutoAnnotatorInnerAmino">5 (2.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gln (Q)</td><td class="AutoAnnotatorInnerAmino">8 (3.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Glu (E)</td><td class="AutoAnnotatorInnerAmino">15 (6.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gly (G)</td><td class="AutoAnnotatorInnerAmino">22 (9.5%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">His (H)</td><td class="AutoAnnotatorInnerAmino">7 (3.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ile (I)</td><td class="AutoAnnotatorInnerAmino">18 (7.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Leu (L)</td><td class="AutoAnnotatorInnerAmino">23 (9.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Lys (K)</td><td class="AutoAnnotatorInnerAmino">11 (4.7%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Met (M)</td><td class="AutoAnnotatorInnerAmino">4 (1.7%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Phe (F)</td><td class="AutoAnnotatorInnerAmino">8 (3.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Pro (P)</td><td class="AutoAnnotatorInnerAmino">6 (2.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ser (S)</td><td class="AutoAnnotatorInnerAmino">12 (5.2%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Thr (T)</td><td class="AutoAnnotatorInnerAmino">9 (3.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Trp (W)</td><td class="AutoAnnotatorInnerAmino">0 (0.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Tyr (Y)</td><td class="AutoAnnotatorInnerAmino">4 (1.7%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Val (V)</td><td class="AutoAnnotatorInnerAmino">21 (9.1%)</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">232</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Positively charged (Arg+Lys):</td><td class="AutoAnnotatorAminoCountingInner3">17 (7.3%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Negatively charged (Asp+Glu):</td><td class="AutoAnnotatorAminoCountingInner3">27 (11.6%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Aromatic (Phe+His+Try+Tyr):</td><td class="AutoAnnotatorAminoCountingInner3">19 (8.2%)</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>1079</sub>H<sub>1738</sub>N<sub>292</sub>O<sub>329</sub>S<sub>9</sub></td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Molecular mass [Da]:</td><td class="AutoAnnotatorBiochemParInner3">24354.0</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Theoretical pI:</td><td class="AutoAnnotatorBiochemParInner3">5.09</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">5960 / 6273 (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_1476456270820()' 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">excellent (0.82)</td><td class="AutoAnnotatorCodonUsage3">excellent (0.81)</td><td class="AutoAnnotatorCodonUsage3">good (0.63)</td><td class="AutoAnnotatorCodonUsage3">good (0.68)</td><td class="AutoAnnotatorCodonUsage3">good (0.80)</td><td class="AutoAnnotatorCodonUsage3">good (0.70)</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="AutoAnnotatorLocalizationOuter"><strong>Subcellular Localization</strong> (reliability in brackets)<table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorLocalization1"></td><td class="AutoAnnotatorLocalization2">Archaea:</td><td class="AutoAnnotatorLocalization3"> - </td></tr><tr><td class="AutoAnnotatorLocalization1"></td><td class="AutoAnnotatorLocalization2">Bacteria:</td><td class="AutoAnnotatorLocalization3"> - </td></tr><tr><td class="AutoAnnotatorLocalization1"></td><td class="AutoAnnotatorLocalization2">Eukarya:</td><td class="AutoAnnotatorLocalization3"> - </td></tr></table></td><td class="AutoAnnotatorGOOuter"><strong>Gene Ontology</strong> (reliability in brackets)<br><table class="AutoAnnotatorNoBorder"><tr><td class='AutoAnnotatorGO1'></td><td class='AutoAnnotatorGO2'>Molecular Function Ontology:</td><td class='AutoAnnotatorGO3'><a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=0005515 0.'>0005515 0.</a> (NaN%), <a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=0004731 0.'>0004731 0.</a> (NaN%)</td></tr><tr><td class='AutoAnnotatorGO1'></td><td class='AutoAnnotatorGO2'>Biological Process Ontology:</td><td class='AutoAnnotatorGO3'><a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=0009164 0.'>0009164 0.</a> (NaN%), <a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=0009086 0.'>0009086 0.</a> (NaN%)</td></tr><tr><td class='AutoAnnotatorGO1'> </td><td class='AutoAnnotatorGO2'> </td><td class='AutoAnnotatorGO3'> </td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Predicted features:</strong><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorPredFeat1"></td><td class="AutoAnnotatorPredFeat2a">Disulfid bridges:</td><td class="AutoAnnotatorPredFeat3"> - </td></tr><tr><td class="AutoAnnotatorPredFeat1"></td><td class="AutoAnnotatorPredFeat2a">Transmembrane helices:</td><td class="AutoAnnotatorPredFeat3"> - </td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"> The BioBrick-AutoAnnotator was created by <a href="http://2013.igem.org/Team:TU-Munich">TU-Munich 2013</a> iGEM team. For more information please see the <a href="http://2013.igem.org/Team:TU-Munich/Results/Software">documentation</a>.<br>If you have any questions, comments or suggestions, please leave us a <a href="http://2013.igem.org/Team:TU-Munich/Results/AutoAnnotator">comment</a>.</td></tr></table></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_1476456270820(){hydrophobicity_datapoints = [[2.5,1.32],[3.5,1.84],[4.5,2.54],[5.5,2.00],[6.5,2.46],[7.5,0.86],[8.5,-0.74],[9.5,-1.36],[10.5,-0.88],[11.5,-1.40],[12.5,0.06],[13.5,1.52],[14.5,1.32],[15.5,-0.22],[16.5,-0.86],[17.5,-0.72],[18.5,-2.18],[19.5,-1.98],[20.5,-2.18],[21.5,-2.10],[22.5,-3.14],[23.5,-1.54],[24.5,-1.00],[25.5,0.66],[26.5,1.28],[27.5,1.34],[28.5,0.94],[29.5,0.40],[30.5,0.54],[31.5,0.36],[32.5,0.30],[33.5,-0.28],[34.5,-0.28],[35.5,-0.42],[36.5,-0.86],[37.5,-0.80],[38.5,-0.86],[39.5,-0.86],[40.5,-0.78],[41.5,0.28],[42.5,1.12],[43.5,2.02],[44.5,1.94],[45.5,0.94],[46.5,0.50],[47.5,0.64],[48.5,-0.20],[49.5,-0.20],[50.5,0.80],[51.5,1.24],[52.5,0.70],[53.5,1.14],[54.5,2.68],[55.5,1.76],[56.5,1.76],[57.5,1.26],[58.5,1.66],[59.5,1.66],[60.5,2.50],[61.5,1.44],[62.5,0.94],[63.5,0.68],[64.5,-0.86],[65.5,-1.94],[66.5,-1.94],[67.5,-0.46],[68.5,-0.06],[69.5,1.62],[70.5,1.24],[71.5,1.80],[72.5,0.88],[73.5,-0.18],[74.5,-0.72],[75.5,-0.10],[76.5,-0.04],[77.5,0.80],[78.5,1.32],[79.5,0.64],[80.5,0.58],[81.5,1.42],[82.5,-0.12],[83.5,0.36],[84.5,0.60],[85.5,0.04],[86.5,0.18],[87.5,1.80],[88.5,1.80],[89.5,1.72],[90.5,1.72],[91.5,0.12],[92.5,-0.36],[93.5,-2.10],[94.5,-2.20],[95.5,-2.14],[96.5,-2.14],[97.5,-2.14],[98.5,-1.94],[99.5,-0.84],[100.5,-0.34],[101.5,0.72],[102.5,0.92],[103.5,1.54],[104.5,0.44],[105.5,-0.12],[106.5,-0.74],[107.5,-1.38],[108.5,-2.00],[109.5,-0.98],[110.5,-0.60],[111.5,-0.42],[112.5,0.16],[113.5,0.54],[114.5,0.14],[115.5,0.38],[116.5,1.02],[117.5,-0.26],[118.5,0.42],[119.5,-0.64],[120.5,-1.26],[121.5,-2.60],[122.5,-1.06],[123.5,-0.52],[124.5,0.54],[125.5,1.60],[126.5,2.74],[127.5,1.28],[128.5,0.74],[129.5,0.88],[130.5,1.42],[131.5,1.42],[132.5,1.42],[133.5,1.82],[134.5,0.62],[135.5,0.48],[136.5,-0.58],[137.5,0.48],[138.5,0.56],[139.5,0.36],[140.5,-0.48],[141.5,0.98],[142.5,1.52],[143.5,1.52],[144.5,2.26],[145.5,2.26],[146.5,0.80],[147.5,0.26],[148.5,-0.02],[149.5,1.04],[150.5,0.42],[151.5,1.04],[152.5,0.52],[153.5,0.80],[154.5,-0.18],[155.5,1.28],[156.5,1.72],[157.5,1.10],[158.5,1.16],[159.5,0.34],[160.5,-1.06],[161.5,-2.12],[162.5,-0.78],[163.5,-2.00],[164.5,-1.80],[165.5,-0.80],[166.5,0.80],[167.5,0.60],[168.5,1.76],[169.5,1.76],[170.5,1.78],[171.5,0.18],[172.5,0.18],[173.5,-0.80],[174.5,0.26],[175.5,0.78],[176.5,1.84],[177.5,0.84],[178.5,1.82],[179.5,1.96],[180.5,0.42],[181.5,-0.64],[182.5,0.56],[183.5,-0.98],[184.5,-0.64],[185.5,-0.32],[186.5,0.94],[187.5,1.22],[188.5,2.76],[189.5,2.76],[190.5,2.18],[191.5,1.98],[192.5,2.04],[193.5,1.04],[194.5,-0.50],[195.5,1.24],[196.5,1.24],[197.5,-0.36],[198.5,-0.90],[199.5,-0.90],[200.5,-1.90],[201.5,-2.90],[202.5,-1.44],[203.5,-0.90],[204.5,0.36],[205.5,-0.18],[206.5,-0.24],[207.5,-0.44],[208.5,0.48],[209.5,0.28],[210.5,1.82],[211.5,2.88],[212.5,2.68],[213.5,1.14],[214.5,0.08],[215.5,-0.92],[216.5,-1.44],[217.5,-1.04],[218.5,0.12],[219.5,1.66],[220.5,1.12],[221.5,1.12],[222.5,1.12],[223.5,1.58],[224.5,0.04],[225.5,-0.04],[226.5,0.88],[227.5,0.48],[228.5,-1.00],[229.5,-0.38]];charge_datapoints = [[2.5,0.20],[3.5,0.20],[4.5,0.00],[5.5,0.00],[6.5,0.00],[7.5,-0.20],[8.5,-0.40],[9.5,-0.60],[10.5,-0.60],[11.5,-0.60],[12.5,-0.40],[13.5,-0.20],[14.5,0.20],[15.5,-0.00],[16.5,0.20],[17.5,0.20],[18.5,-0.00],[19.5,-0.20],[20.5,0.20],[21.5,-0.00],[22.5,-0.00],[23.5,0.20],[24.5,0.20],[25.5,-0.00],[26.5,-0.00],[27.5,-0.00],[28.5,-0.00],[29.5,-0.20],[30.5,-0.20],[31.5,-0.20],[32.5,-0.20],[33.5,-0.20],[34.5,-0.00],[35.5,-0.00],[36.5,-0.00],[37.5,-0.00],[38.5,-0.00],[39.5,-0.20],[40.5,-0.20],[41.5,-0.20],[42.5,-0.20],[43.5,-0.20],[44.5,0.20],[45.5,0.20],[46.5,0.20],[47.5,0.20],[48.5,0.20],[49.5,0.20],[50.5,0.20],[51.5,0.20],[52.5,0.20],[53.5,0.20],[54.5,-0.00],[55.5,-0.00],[56.5,-0.00],[57.5,-0.00],[58.5,-0.00],[59.5,-0.00],[60.5,-0.00],[61.5,-0.20],[62.5,-0.10],[63.5,-0.10],[64.5,0.10],[65.5,0.10],[66.5,0.10],[67.5,-0.00],[68.5,-0.00],[69.5,-0.20],[70.5,-0.20],[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],[82.5,0.20],[83.5,0.20],[84.5,0.20],[85.5,-0.00],[86.5,-0.00],[87.5,-0.20],[88.5,-0.20],[89.5,-0.20],[90.5,-0.20],[91.5,-0.40],[92.5,-0.40],[93.5,-0.20],[94.5,-0.20],[95.5,0.10],[96.5,0.10],[97.5,0.10],[98.5,-0.30],[99.5,-0.30],[100.5,-0.40],[101.5,-0.20],[102.5,-0.20],[103.5,-0.00],[104.5,-0.00],[105.5,-0.20],[106.5,-0.20],[107.5,-0.20],[108.5,-0.20],[109.5,-0.20],[110.5,-0.00],[111.5,-0.00],[112.5,-0.00],[113.5,-0.00],[114.5,-0.00],[115.5,-0.00],[116.5,-0.00],[117.5,0.20],[118.5,0.20],[119.5,-0.00],[120.5,-0.20],[121.5,-0.00],[122.5,-0.20],[123.5,-0.20],[124.5,-0.00],[125.5,0.20],[126.5,-0.00],[127.5,-0.20],[128.5,-0.20],[129.5,-0.20],[130.5,-0.20],[131.5,-0.20],[132.5,-0.20],[133.5,-0.20],[134.5,-0.20],[135.5,-0.20],[136.5,-0.20],[137.5,-0.00],[138.5,-0.00],[139.5,0.20],[140.5,0.20],[141.5,0.20],[142.5,0.20],[143.5,0.20],[144.5,-0.00],[145.5,-0.00],[146.5,-0.20],[147.5,-0.20],[148.5,-0.20],[149.5,-0.20],[150.5,-0.20],[151.5,-0.00],[152.5,-0.00],[153.5,-0.00],[154.5,-0.00],[155.5,-0.00],[156.5,-0.00],[157.5,0.20],[158.5,0.20],[159.5,0.40],[160.5,0.50],[161.5,0.50],[162.5,0.30],[163.5,0.30],[164.5,0.10],[165.5,-0.00],[166.5,-0.00],[167.5,-0.00],[168.5,-0.00],[169.5,-0.20],[170.5,-0.20],[171.5,-0.40],[172.5,-0.40],[173.5,-0.40],[174.5,-0.20],[175.5,-0.20],[176.5,-0.00],[177.5,0.10],[178.5,0.10],[179.5,0.10],[180.5,0.20],[181.5,0.20],[182.5,0.10],[183.5,0.10],[184.5,0.10],[185.5,-0.00],[186.5,-0.00],[187.5,-0.00],[188.5,-0.00],[189.5,-0.00],[190.5,0.20],[191.5,0.20],[192.5,0.20],[193.5,0.20],[194.5,-0.00],[195.5,-0.20],[196.5,-0.20],[197.5,-0.40],[198.5,-0.40],[199.5,-0.20],[200.5,-0.20],[201.5,-0.10],[202.5,0.10],[203.5,0.10],[204.5,0.10],[205.5,-0.10],[206.5,-0.40],[207.5,-0.40],[208.5,-0.40],[209.5,-0.40],[210.5,-0.20],[211.5,-0.00],[212.5,-0.00],[213.5,0.20],[214.5,0.20],[215.5,0.20],[216.5,0.20],[217.5,0.20],[218.5,-0.00],[219.5,-0.00],[220.5,-0.20],[221.5,-0.20],[222.5,-0.20],[223.5,-0.20],[224.5,-0.20],[225.5,0.20],[226.5,0.20],[227.5,0.20],[228.5,0.30],[229.5,0.30]];dis_datapoints = [];trans_datapoints = [];sec_helix_datapoints = [];sec_strand_datapoints = [];acc_exposed_datapoints = [];acc_buried_datapoints = [];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_1476456270820 #hydrophobicity_charge_button').val() =='Show' ){jqAutoAnnotator('#AutoAnnotator_container_1476456270820 #hydrophobicity_charge_container').css('display','block');jqAutoAnnotator('#AutoAnnotator_container_1476456270820 #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_1476456270820 #hydrophobicity_charge_explanation').html(description_html);plot_according_to_selectors_1476456270820();jqAutoAnnotator('#AutoAnnotator_container_1476456270820 #AutoAnnotator_plot_selectors').find('input').click(plot_according_to_selectors_1476456270820);}else{jqAutoAnnotator('#AutoAnnotator_container_1476456270820 #hydrophobicity_charge_container').css('display','none');jqAutoAnnotator('#AutoAnnotator_container_1476456270820 #hydrophobicity_charge_button').val('Show');jqAutoAnnotator('#AutoAnnotator_container_1476456270820 #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_1476456270820(){try{var plot_datasets = [[],[]];if(jqAutoAnnotator('#AutoAnnotator_container_1476456270820 #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_1476456270820 #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_1476456270820 #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_1476456270820 #dis_checkbox').prop('checked') == true){for ( j = 0 ; j < dis_datapoints.length ; j++ ){jqAutoAnnotator('#AutoAnnotator_container_1476456270820 #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_1476456270820 #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_1476456270820 #trans_checkbox').prop('checked') == true){for ( j = 0 ; j < trans_datapoints.length ; j++ ){jqAutoAnnotator('#AutoAnnotator_container_1476456270820 #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_1476456270820 #sec_checkbox').prop('checked') == true){for ( j = 0 ; j < sec_helix_datapoints.length ; j++ ){jqAutoAnnotator('#AutoAnnotator_container_1476456270820 #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_1476456270820 #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_1476456270820 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((pos_of_first_tick + (acc_exposed_datapoints[j][0] - 1.5)*tick_diff - Math.floor((acc_exposed_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px\'></div>');}}}catch(err){txt='There was an error while drawing the selected elements for the plot.\n';txt=txt+'The originating error is:\n' + err + '\n\n';throw(txt);}}</script></html> | ||
Latest revision as of 01:47, 15 October 2016
mtn
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase. It is nvolved in the synthesis of autoinducer 2 (AI-2) which is secreted by bacteria and is used to communicate both the cell density and the metabolic potential of the environment. It catalyzes the irreversible cleavage of the glycosidic bond in both 5'-methylthioadenosine (MTA) and S-adenosylhomocysteine (SAH/AdoHcy) to adenine and the corresponding thioribose, 5'-methylthioribose and S-ribosylhomocysteine, respectively.It can also use 5'-isobutylthioadenosine, 5'-n-butylthioadenosine, S-adenosyl-D-homocysteine, decarboxylated adenosylhomocysteine, deaminated adenosylhomocysteine and S-2-aza-adenosylhomocysteine as substrates.
Sequence and Features
Assembly Compatibility:
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal AgeI site found at 475
- 1000COMPATIBLE WITH RFC[1000]
Usage and Biology
The AI-2 “supplier” was constructed by overexpressing the mtn gene.
This part was originated from Escherichia coli strain K12.
Characterization
The restriction enzyme digestion verification result for mtn is shown in Figure 1.
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) ATGAAAATC ... GCACATGGCTAA ORF from nucleotide position 1 to 696 (excluding stop-codon) | ||||||||||||||||||||||||||||||||||||||||||||||
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
| ||||||||||||||||||||||||||||||||||||||||||||||
Sequence features: (with their position in the amino acid sequence, see the list of supported features)
| ||||||||||||||||||||||||||||||||||||||||||||||
Amino acid composition:
| ||||||||||||||||||||||||||||||||||||||||||||||
Amino acid counting
| Biochemical parameters
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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) | ||||||||||||||||||||||||||||||||||||||||||||||
Subcellular Localization (reliability in brackets)
| Gene Ontology (reliability in brackets)
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Predicted features:
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