Difference between revisions of "Part:BBa K1159012"

Latest revision as of 14:51, 8 October 2013

Secretory Catechol-2,3-dioxygenase (SERK-SigP_XylE) in RFC[25] N-Part

This part encodes for the enzyme catechol-2,3-dioxygenase (metapyrocatechase), which converts catechol to the bright yellow product 2-hydroxy-cis,cis-muconic semialdehyde. This part is fused with a N-terminal signal peptide for secretion (signal peptide from SERK Receptor of Physcomitrella patens). This construct is flanked by RFC[25] N-part prefix and suffix. Note: This means only protein fusions to the C-terminus of this part is possible, adding promoters (typically RFC[10]) into the prefix or terminators/IRES (typically RFC[10]) into the suffix of this part is nevertheless possible.

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
COMPATIBLE WITH RFC[21]
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
COMPATIBLE WITH RFC[1000]

Protein data table for BioBrick BBa_ automatically created by the BioBrick-AutoAnnotator version 1.0

Nucleotide sequence in RFC 25 N-Part using the stop codon in the suffix, so ACCGGT was added (in italics) to the 3' end: (underlined part encodes the protein)
AACAATGCCTGGT ... GTGCTGACCACCGGT
ORF from nucleotide position 5 to 1030 (excluding stop-codon)

Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)

1
101
201
301

MPGEVAWWRPLFLIALMPIGVLSNAEGDALNTTGNKGVMRPGHVQLRVLDMSKALEHYVELLGLIEMDRDDQGRVYLKAWTEVDKFSLVLREADEPGMDF
MGFKVVDEDALRQLERDLMAYGCAVEQLPAGELNSCGRRVRFQAPSGHHFELYADKEYTGKWGLNDVNPEAWPRDLKGMAAVRFDHALMYGDELPATYDL
FTKVLGFYLAEQVLDENGTRVAQFLSLSTKAHDVAFIHHPEKGRLHHVSFHLETWEDLLRAADLISMTDTSIDIGPTRHGLTHGKTIYFFDPSGNRNEVF
CGGDYNYPDHKPVTWTTDQLGKAIFYHDRILNERFMTVLTTG*

Sequence features: (with their position in the amino acid sequence, see the list of supported features)

RFC25 scar (shown in bold):

33 to 34

Amino acid composition:

Ala (A)	25 (7.3%)
Arg (R)	20 (5.8%)
Asn (N)	11 (3.2%)
Asp (D)	28 (8.2%)

Cys (C)	3 (0.9%)
Gln (Q)	8 (2.3%)
Glu (E)	23 (6.7%)
Gly (G)	29 (8.5%)

His (H)	15 (4.4%)
Ile (I)	10 (2.9%)
Leu (L)	39 (11.4%)
Lys (K)	14 (4.1%)

Met (M)	12 (3.5%)
Phe (F)	17 (5.0%)
Pro (P)	15 (4.4%)
Ser (S)	11 (3.2%)

Thr (T)	20 (5.8%)
Trp (W)	7 (2.0%)
Tyr (Y)	12 (3.5%)
Val (V)	23 (6.7%)

Amino acid counting

	Total number:	342
	Positively charged (Arg+Lys):	34 (9.9%)
	Negatively charged (Asp+Glu):	51 (14.9%)
	Aromatic (Phe+His+Try+Tyr):	51 (14.9%)

Biochemical parameters

	Atomic composition:	C₁₇₄₂H₂₆₅₈N₄₇₂O₅₀₇S₁₅
	Molecular mass [Da]:	38806.0
	Theoretical pI:	5.28
	Extinction coefficient at 280 nm [M^-1 cm^-1]:	56380 / 56568 (all Cys red/ox)

Plot for hydrophobicity, charge, predicted secondary structure, solvent accessability, transmembrane helices and disulfid bridges

Codon usage

	Organism:	E. coli	B. subtilis	S. cerevisiae	A. thaliana	P. patens	Mammals
	Codon quality (CAI):	good (0.73)	good (0.70)	acceptable (0.55)	good (0.65)	excellent (0.83)	good (0.78)

Alignments (obtained from PredictProtein.org)

	SwissProt:	P06622 (100% identity on 306 AAs), P27887 (94% identity on 306 AAs)
	TrEML:	D2XKL2 (100% identity on 306 AAs), G5DRD2 (100% identity on 215 AAs), J9ZVS6 (100% identity on 270 AAs), J9ZVW6 (100% identity on 270 AAs), J9ZX53 (100% identity on 270 AAs), Q38Q96 (100% identity on 293 AAs), Q7AXV1 (100% identity on 306 AAs), Q7BH44 (100% identity on 306 AAs), J9ZVF5 (99% identity on 270 AAs), Q5EGN5 (99% identity on 237 AAs)
	PDB:	1mpy (100% identity on 306 AAs), 3hpv (48% identity on 296 AAs)

Predictions (obtained from PredictProtein.org)

Subcellular Localization (reliability in brackets)

	Archaea:	cytosol (100%)
	Bacteria:	cytosol (84%)
	Eukarya:	secreted (43%)

Gene Ontology (reliability in brackets)

	Molecular Function Ontology:	-
	Biological Process Ontology:	GO:0019439 (49%), GO:0055114 (35%)

Predicted features:

	Disulfid bridges:	-
	Transmembrane helices:	-

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.

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 <span class='h3bb'>Sequence and Features</span>
 <partinfo>BBa_K1159012 SequenceAndFeatures</partinfo>
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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_1381243831471'><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1381243831471 --><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 25 N-Part</strong> using the stop codon in the suffix, so ACCGGT was added (in italics) to the 3' end: (underlined part encodes the protein)<br><span class="AutoAnnotatorSequence">&nbsp;AACA<u>ATGCCTGGT&nbsp;...&nbsp;GTGCTGACC<i>ACCGGT</i></u></span><br>&nbsp;<strong>ORF</strong> from nucleotide position 5 to 1030 (excluding stop-codon)</td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Amino acid sequence:</strong> (RFC 25 scars in shown in bold, other sequence features underlined; both given below)<br><span class="AutoAnnotatorSequence"><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorSeqNum">1&nbsp;<br>101&nbsp;<br>201&nbsp;<br>301&nbsp;</td><td class="AutoAnnotatorSeqSeq">MPGEVAWWRPLFLIALMPIGVLSNAEGDALNT<b>TG</b>NKGVMRPGHVQLRVLDMSKALEHYVELLGLIEMDRDDQGRVYLKAWTEVDKFSLVLREADEPGMDF<br>MGFKVVDEDALRQLERDLMAYGCAVEQLPAGELNSCGRRVRFQAPSGHHFELYADKEYTGKWGLNDVNPEAWPRDLKGMAAVRFDHALMYGDELPATYDL<br>FTKVLGFYLAEQVLDENGTRVAQFLSLSTKAHDVAFIHHPEKGRLHHVSFHLETWEDLLRAADLISMTDTSIDIGPTRHGLTHGKTIYFFDPSGNRNEVF<br>CGGDYNYPDHKPVTWTTDQLGKAIFYHDRILNERFMTVLTTG*</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):&nbsp;</td><td class="AutoAnnotatorSeqFeat3">33 to 34</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">25 (7.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Arg (R)</td><td class="AutoAnnotatorInnerAmino">20 (5.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asn (N)</td><td class="AutoAnnotatorInnerAmino">11 (3.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asp (D)</td><td class="AutoAnnotatorInnerAmino">28 (8.2%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Cys (C)</td><td class="AutoAnnotatorInnerAmino">3 (0.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gln (Q)</td><td class="AutoAnnotatorInnerAmino">8 (2.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Glu (E)</td><td class="AutoAnnotatorInnerAmino">23 (6.7%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gly (G)</td><td class="AutoAnnotatorInnerAmino">29 (8.5%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">His (H)</td><td class="AutoAnnotatorInnerAmino">15 (4.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ile (I)</td><td class="AutoAnnotatorInnerAmino">10 (2.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Leu (L)</td><td class="AutoAnnotatorInnerAmino">39 (11.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Lys (K)</td><td class="AutoAnnotatorInnerAmino">14 (4.1%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Met (M)</td><td class="AutoAnnotatorInnerAmino">12 (3.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Phe (F)</td><td class="AutoAnnotatorInnerAmino">17 (5.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Pro (P)</td><td class="AutoAnnotatorInnerAmino">15 (4.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ser (S)</td><td class="AutoAnnotatorInnerAmino">11 (3.2%)</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">7 (2.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Tyr (Y)</td><td class="AutoAnnotatorInnerAmino">12 (3.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Val (V)</td><td class="AutoAnnotatorInnerAmino">23 (6.7%)</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">342</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Positively charged (Arg+Lys):</td><td class="AutoAnnotatorAminoCountingInner3">34 (9.9%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Negatively charged (Asp+Glu):</td><td class="AutoAnnotatorAminoCountingInner3">51 (14.9%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Aromatic (Phe+His+Try+Tyr):</td><td class="AutoAnnotatorAminoCountingInner3">51 (14.9%)</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>1742</sub>H<sub>2658</sub>N<sub>472</sub>O<sub>507</sub>S<sub>15</sub></td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Molecular mass [Da]:</td><td class="AutoAnnotatorBiochemParInner3">38806.0</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Theoretical pI:</td><td class="AutoAnnotatorBiochemParInner3">5.28</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">56380 / 56568 (all Cys red/ox)</td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Plot for hydrophobicity, charge, predicted secondary structure, solvent accessability, transmembrane helices and disulfid bridges</strong>&nbsp;<input type='button' id='hydrophobicity_charge_button' onclick='show_or_hide_plot_1381243831471()' 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 (0.73)</td><td class="AutoAnnotatorCodonUsage3">good (0.70)</td><td class="AutoAnnotatorCodonUsage3">acceptable (0.55)</td><td class="AutoAnnotatorCodonUsage3">good (0.65)</td><td class="AutoAnnotatorCodonUsage3">excellent (0.83)</td><td class="AutoAnnotatorCodonUsage3">good (0.78)</td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Alignments</strong> (obtained from <a href='http://predictprotein.org'>PredictProtein.org</a>)<table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorAlignment1"></td><td class="AutoAnnotatorAlignment2">SwissProt:</td><td class="AutoAnnotatorAlignment3"><a href='http://www.uniprot.org/uniprot/P06622'>P06622</a> (100% identity on 306 AAs), <a href='http://www.uniprot.org/uniprot/P27887'>P27887</a> (94% identity on 306 AAs)</td></tr><tr><td class="AutoAnnotatorAlignment1"></td><td class="AutoAnnotatorAlignment2">TrEML:</td><td class="AutoAnnotatorAlignment3"><a href='http://www.uniprot.org/uniprot/D2XKL2'>D2XKL2</a> (100% identity on 306 AAs), <a href='http://www.uniprot.org/uniprot/G5DRD2'>G5DRD2</a> (100% identity on 215 AAs), <a href='http://www.uniprot.org/uniprot/J9ZVS6'>J9ZVS6</a> (100% identity on 270 AAs), <a href='http://www.uniprot.org/uniprot/J9ZVW6'>J9ZVW6</a> (100% identity on 270 AAs), <a href='http://www.uniprot.org/uniprot/J9ZX53'>J9ZX53</a> (100% identity on 270 AAs), <a href='http://www.uniprot.org/uniprot/Q38Q96'>Q38Q96</a> (100% identity on 293 AAs), <a href='http://www.uniprot.org/uniprot/Q7AXV1'>Q7AXV1</a> (100% identity on 306 AAs), <a href='http://www.uniprot.org/uniprot/Q7BH44'>Q7BH44</a> (100% identity on 306 AAs), <a href='http://www.uniprot.org/uniprot/J9ZVF5'>J9ZVF5</a> (99% identity on 270 AAs), <a href='http://www.uniprot.org/uniprot/Q5EGN5'>Q5EGN5</a> (99% identity on 237 AAs)</td></tr><tr><td class="AutoAnnotatorAlignment1"></td><td class="AutoAnnotatorAlignment2">PDB:</td><td class="AutoAnnotatorAlignment3"><a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1mpy'>1mpy</a> (100% identity on 306 AAs), <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=3hpv'>3hpv</a> (48% identity on 296 AAs)</td></tr></table></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">cytosol (100%)</td></tr><tr><td class="AutoAnnotatorLocalization1"></td><td class="AutoAnnotatorLocalization2">Bacteria:</td><td class="AutoAnnotatorLocalization3">cytosol (84%)</td></tr><tr><td class="AutoAnnotatorLocalization1"></td><td class="AutoAnnotatorLocalization2">Eukarya:</td><td class="AutoAnnotatorLocalization3">secreted (43%)</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'> - </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=GO:0019439'>GO:0019439</a> (49%), <a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0055114'>GO:0055114</a> (35%)</td></tr><tr><td class='AutoAnnotatorGO1'> </td><td class='AutoAnnotatorGO2'> </td><td class='AutoAnnotatorGO3'>&nbsp;</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">&nbsp;- </td></tr><tr><td class="AutoAnnotatorPredFeat1"></td><td class="AutoAnnotatorPredFeat2a">Transmembrane helices:</td><td class="AutoAnnotatorPredFeat3">&nbsp;- </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="excanvas.min.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>function show_or_hide_plot_1381243831471(){hydrophobicity_datapoints = [[2.5,0.12],[3.5,0.10],[4.5,0.24],[5.5,0.14],[6.5,-0.06],[7.5,-1.22],[8.5,-0.82],[9.5,-0.08],[10.5,0.86],[11.5,2.66],[12.5,3.34],[13.5,3.34],[14.5,3.16],[15.5,2.08],[16.5,2.08],[17.5,1.64],[18.5,1.72],[19.5,2.10],[20.5,2.26],[21.5,0.66],[22.5,1.10],[23.5,-0.44],[24.5,-1.28],[25.5,-1.82],[26.5,-0.76],[27.5,-0.36],[28.5,-0.36],[29.5,-0.42],[30.5,0.14],[31.5,-0.30],[32.5,-1.76],[33.5,-1.84],[34.5,-1.78],[35.5,-0.80],[36.5,-0.34],[37.5,-0.54],[38.5,-0.08],[39.5,-0.08],[40.5,-1.56],[41.5,-1.10],[42.5,-0.90],[43.5,0.18],[44.5,-0.64],[45.5,0.84],[46.5,0.76],[47.5,0.76],[48.5,0.38],[49.5,1.12],[50.5,-0.50],[51.5,-0.90],[52.5,0.56],[53.5,-0.52],[54.5,-1.00],[55.5,-0.48],[56.5,-0.00],[57.5,-1.46],[58.5,-0.00],[59.5,1.40],[60.5,1.58],[61.5,1.50],[62.5,3.10],[63.5,1.64],[64.5,1.26],[65.5,0.64],[66.5,-1.02],[67.5,-2.62],[68.5,-2.62],[69.5,-3.70],[70.5,-3.08],[71.5,-3.08],[72.5,-1.54],[73.5,-1.10],[74.5,0.36],[75.5,-0.34],[76.5,0.92],[77.5,-0.10],[78.5,0.02],[79.5,-1.44],[80.5,0.18],[81.5,-0.88],[82.5,-1.48],[83.5,-0.78],[84.5,-0.24],[85.5,-0.32],[86.5,1.22],[87.5,2.76],[88.5,1.30],[89.5,0.76],[90.5,0.36],[91.5,-1.18],[92.5,-2.64],[93.5,-2.06],[94.5,-1.44],[95.5,-1.42],[96.5,-1.42],[97.5,-0.16],[98.5,0.54],[99.5,0.54],[100.5,0.72],[101.5,0.64],[102.5,0.92],[103.5,1.38],[104.5,0.76],[105.5,-0.50],[106.5,-0.42],[107.5,-0.90],[108.5,-0.98],[109.5,-1.18],[110.5,-1.18],[111.5,0.28],[112.5,-0.78],[113.5,-2.44],[114.5,-2.24],[115.5,-0.78],[116.5,-1.16],[117.5,-0.10],[118.5,0.54],[119.5,1.16],[120.5,0.90],[121.5,0.88],[122.5,1.36],[123.5,0.92],[124.5,0.30],[125.5,0.56],[126.5,-0.12],[127.5,-0.60],[128.5,0.02],[129.5,0.02],[130.5,0.02],[131.5,-0.36],[132.5,-0.88],[133.5,-0.30],[134.5,0.32],[135.5,-1.34],[136.5,-1.54],[137.5,-0.54],[138.5,-1.94],[139.5,-1.30],[140.5,-1.10],[141.5,0.16],[142.5,-1.00],[143.5,-0.26],[144.5,-0.90],[145.5,-0.84],[146.5,-1.84],[147.5,-0.96],[148.5,-1.50],[149.5,-0.66],[150.5,-0.28],[151.5,0.72],[152.5,-0.54],[153.5,-0.62],[154.5,-2.08],[155.5,-2.08],[156.5,-2.58],[157.5,-1.96],[158.5,-1.96],[159.5,-1.44],[160.5,-1.26],[161.5,-0.36],[162.5,-0.98],[163.5,-0.90],[164.5,0.12],[165.5,-0.50],[166.5,-1.58],[167.5,-1.58],[168.5,-0.52],[169.5,-1.54],[170.5,-1.16],[171.5,-1.74],[172.5,-1.74],[173.5,-1.34],[174.5,-1.94],[175.5,-1.70],[176.5,-0.42],[177.5,0.64],[178.5,0.24],[179.5,1.86],[180.5,1.04],[181.5,1.22],[182.5,0.16],[183.5,-0.84],[184.5,-1.32],[185.5,0.34],[186.5,0.16],[187.5,0.60],[188.5,1.16],[189.5,0.10],[190.5,-1.36],[191.5,-0.98],[192.5,-1.04],[193.5,-0.60],[194.5,-0.04],[195.5,0.40],[196.5,-1.06],[197.5,0.02],[198.5,0.22],[199.5,0.22],[200.5,-0.30],[201.5,1.24],[202.5,1.24],[203.5,0.60],[204.5,1.30],[205.5,1.82],[206.5,1.74],[207.5,1.34],[208.5,0.72],[209.5,-0.54],[210.5,0.56],[211.5,0.56],[212.5,-0.50],[213.5,-0.50],[214.5,-0.50],[215.5,-1.42],[216.5,-2.32],[217.5,-2.52],[218.5,-0.98],[219.5,0.08],[220.5,-0.54],[221.5,0.16],[222.5,1.82],[223.5,0.82],[224.5,1.22],[225.5,1.76],[226.5,1.06],[227.5,-0.48],[228.5,0.04],[229.5,-1.36],[230.5,-1.90],[231.5,-0.92],[232.5,0.22],[233.5,0.42],[234.5,1.96],[235.5,2.02],[236.5,0.54],[237.5,-0.14],[238.5,-1.40],[239.5,-3.08],[240.5,-2.52],[241.5,-2.78],[242.5,-1.70],[243.5,-1.64],[244.5,-1.50],[245.5,-0.58],[246.5,0.16],[247.5,-0.04],[248.5,-0.04],[249.5,1.36],[250.5,-0.18],[251.5,-0.16],[252.5,-0.90],[253.5,-0.96],[254.5,-2.42],[255.5,-0.96],[256.5,-0.06],[257.5,-0.78],[258.5,0.28],[259.5,1.34],[260.5,-0.12],[261.5,-0.12],[262.5,1.68],[263.5,1.16],[264.5,1.18],[265.5,1.74],[266.5,0.28],[267.5,-0.76],[268.5,-0.76],[269.5,-0.24],[270.5,-0.80],[271.5,0.80],[272.5,0.86],[273.5,0.70],[274.5,-0.34],[275.5,-0.54],[276.5,-2.08],[277.5,-2.08],[278.5,-1.00],[279.5,-1.00],[280.5,-0.74],[281.5,-0.18],[282.5,-0.88],[283.5,-1.78],[284.5,-0.74],[285.5,-0.36],[286.5,0.28],[287.5,1.62],[288.5,1.06],[289.5,-0.16],[290.5,-0.06],[291.5,-0.70],[292.5,-1.96],[293.5,-2.16],[294.5,-2.54],[295.5,-3.08],[296.5,-2.16],[297.5,-0.90],[298.5,0.50],[299.5,1.12],[300.5,1.74],[301.5,0.20],[302.5,-0.62],[303.5,-1.82],[304.5,-2.00],[305.5,-2.24],[306.5,-2.24],[307.5,-2.62],[308.5,-2.70],[309.5,-2.76],[310.5,-1.60],[311.5,-1.04],[312.5,-0.58],[313.5,0.06],[314.5,0.24],[315.5,-1.30],[316.5,-1.86],[317.5,-0.92],[318.5,-0.86],[319.5,-1.50],[320.5,-0.44],[321.5,1.16],[322.5,0.96],[323.5,0.78],[324.5,0.92],[325.5,-0.14],[326.5,-1.94],[327.5,-1.60],[328.5,-0.58],[329.5,-0.64],[330.5,-0.64],[331.5,-0.64],[332.5,-0.98],[333.5,-1.36],[334.5,-0.80],[335.5,0.74],[336.5,2.40],[337.5,1.70],[338.5,1.18],[339.5,1.24]];charge_datapoints = [[2.5,-0.20],[3.5,-0.20],[4.5,-0.20],[5.5,-0.20],[6.5,0.20],[7.5,0.20],[8.5,0.20],[9.5,0.20],[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,-0.20],[24.5,-0.20],[25.5,-0.40],[26.5,-0.40],[27.5,-0.40],[28.5,-0.20],[29.5,-0.20],[30.5,0.00],[31.5,0.00],[32.5,0.00],[33.5,0.20],[34.5,0.20],[35.5,0.20],[36.5,0.20],[37.5,0.40],[38.5,0.20],[39.5,0.20],[40.5,0.30],[41.5,0.30],[42.5,0.10],[43.5,0.10],[44.5,0.30],[45.5,0.20],[46.5,0.20],[47.5,0.00],[48.5,0.00],[49.5,-0.20],[50.5,0.00],[51.5,0.00],[52.5,0.20],[53.5,0.00],[54.5,0.10],[55.5,-0.10],[56.5,-0.10],[57.5,-0.30],[58.5,-0.10],[59.5,-0.20],[60.5,-0.20],[61.5,-0.20],[62.5,0.00],[63.5,-0.20],[64.5,-0.20],[65.5,-0.40],[66.5,-0.20],[67.5,-0.40],[68.5,-0.40],[69.5,-0.40],[70.5,-0.20],[71.5,-0.20],[72.5,0.00],[73.5,0.20],[74.5,0.20],[75.5,0.40],[76.5,0.20],[77.5,0.20],[78.5,0.20],[79.5,0.00],[80.5,-0.20],[81.5,-0.40],[82.5,-0.20],[83.5,-0.20],[84.5,0.00],[85.5,0.00],[86.5,0.20],[87.5,0.00],[88.5,0.20],[89.5,0.00],[90.5,0.00],[91.5,-0.20],[92.5,-0.40],[93.5,-0.60],[94.5,-0.40],[95.5,-0.40],[96.5,-0.40],[97.5,-0.20],[98.5,-0.20],[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,-0.20],[106.5,-0.60],[107.5,-0.60],[108.5,-0.60],[109.5,-0.20],[110.5,-0.00],[111.5,0.20],[112.5,-0.00],[113.5,0.20],[114.5,-0.20],[115.5,-0.20],[116.5,-0.20],[117.5,-0.00],[118.5,-0.20],[119.5,-0.00],[120.5,-0.00],[121.5,-0.00],[122.5,-0.00],[123.5,-0.20],[124.5,-0.20],[125.5,-0.20],[126.5,-0.20],[127.5,-0.20],[128.5,-0.00],[129.5,-0.20],[130.5,-0.20],[131.5,-0.20],[132.5,-0.20],[133.5,-0.20],[134.5,-0.00],[135.5,0.20],[136.5,0.40],[137.5,0.40],[138.5,0.60],[139.5,0.60],[140.5,0.40],[141.5,0.20],[142.5,0.20],[143.5,-0.00],[144.5,-0.00],[145.5,0.10],[146.5,0.20],[147.5,0.20],[148.5,-0.00],[149.5,-0.00],[150.5,-0.10],[151.5,-0.20],[152.5,-0.40],[153.5,-0.00],[154.5,-0.20],[155.5,-0.20],[156.5,-0.20],[157.5,-0.00],[158.5,-0.00],[159.5,0.20],[160.5,0.20],[161.5,0.20],[162.5,0.20],[163.5,-0.20],[164.5,-0.20],[165.5,-0.20],[166.5,-0.20],[167.5,-0.40],[168.5,-0.20],[169.5,-0.20],[170.5,-0.20],[171.5,-0.00],[172.5,-0.00],[173.5,-0.00],[174.5,0.20],[175.5,0.20],[176.5,-0.00],[177.5,0.20],[178.5,0.20],[179.5,-0.00],[180.5,0.20],[181.5,0.20],[182.5,-0.00],[183.5,0.10],[184.5,0.10],[185.5,-0.10],[186.5,-0.10],[187.5,0.10],[188.5,-0.00],[189.5,-0.20],[190.5,-0.40],[191.5,-0.40],[192.5,-0.40],[193.5,-0.40],[194.5,-0.20],[195.5,-0.00],[196.5,-0.20],[197.5,-0.20],[198.5,-0.20],[199.5,-0.20],[200.5,-0.00],[201.5,0.20],[202.5,0.20],[203.5,0.20],[204.5,0.20],[205.5,-0.00],[206.5,-0.00],[207.5,-0.00],[208.5,-0.20],[209.5,-0.20],[210.5,-0.20],[211.5,-0.20],[212.5,-0.40],[213.5,-0.40],[214.5,-0.40],[215.5,-0.40],[216.5,-0.40],[217.5,-0.00],[218.5,0.20],[219.5,0.20],[220.5,0.20],[221.5,0.20],[222.5,-0.00],[223.5,-0.00],[224.5,-0.00],[225.5,-0.00],[226.5,-0.00],[227.5,0.20],[228.5,0.20],[229.5,0.30],[230.5,0.10],[231.5,0.10],[232.5,-0.10],[233.5,-0.10],[234.5,-0.20],[235.5,0.10],[236.5,0.20],[237.5,0.20],[238.5,-0.00],[239.5,0.20],[240.5,0.10],[241.5,0.20],[242.5,0.20],[243.5,0.50],[244.5,0.40],[245.5,0.40],[246.5,0.20],[247.5,0.20],[248.5,0.20],[249.5,0.10],[250.5,-0.10],[251.5,-0.10],[252.5,-0.10],[253.5,-0.40],[254.5,-0.60],[255.5,-0.40],[256.5,-0.40],[257.5,-0.20],[258.5,-0.00],[259.5,0.20],[260.5,-0.00],[261.5,-0.00],[262.5,-0.20],[263.5,-0.20],[264.5,-0.20],[265.5,-0.00],[266.5,-0.20],[267.5,-0.20],[268.5,-0.20],[269.5,-0.20],[270.5,-0.40],[271.5,-0.20],[272.5,-0.20],[273.5,-0.20],[274.5,-0.20],[275.5,0.20],[276.5,0.30],[277.5,0.30],[278.5,0.30],[279.5,0.30],[280.5,0.20],[281.5,0.10],[282.5,0.30],[283.5,0.30],[284.5,0.30],[285.5,0.20],[286.5,0.20],[287.5,-0.00],[288.5,-0.20],[289.5,-0.20],[290.5,-0.20],[291.5,-0.20],[292.5,-0.20],[293.5,0.20],[294.5,0.20],[295.5,-0.00],[296.5,-0.00],[297.5,-0.00],[298.5,-0.20],[299.5,-0.20],[300.5,-0.00],[301.5,-0.20],[302.5,-0.20],[303.5,-0.20],[304.5,-0.20],[305.5,-0.20],[306.5,-0.20],[307.5,-0.10],[308.5,0.10],[309.5,0.10],[310.5,0.10],[311.5,0.30],[312.5,0.20],[313.5,-0.00],[314.5,-0.00],[315.5,-0.20],[316.5,-0.20],[317.5,-0.20],[318.5,-0.20],[319.5,-0.00],[320.5,0.20],[321.5,0.20],[322.5,0.20],[323.5,0.20],[324.5,0.10],[325.5,-0.10],[326.5,0.10],[327.5,0.10],[328.5,0.10],[329.5,-0.00],[330.5,-0.00],[331.5,-0.00],[332.5,-0.00],[333.5,-0.00],[334.5,-0.00],[335.5,0.20],[336.5,-0.00],[337.5,-0.00],[338.5,-0.00],[339.5,-0.00]];dis_datapoints = [];trans_datapoints = [];sec_helix_datapoints = [[51,62],[108,120],[194,200],[201,205],[255,267],[333,335]];sec_strand_datapoints = [[12,16],[38,48],[65,68],[74,79],[86,91],[99,105],[124,126],[138,143],[149,154],[186,191],[208,212],[220,226],[232,238],[245,252],[272,273],[285,290],[296,300]];acc_exposed_datapoints = [[1,4],[6,6],[26,26],[28,29],[31,33],[52,53],[69,72],[82,82],[84,84],[94,96],[108,109],[112,112],[116,116],[120,120],[122,122],[124,124],[127,127],[129,129],[131,132],[134,135],[146,146],[156,161],[165,166],[170,170],[175,175],[177,177],[195,195],[199,199],[215,219],[230,230],[241,242],[256,257],[260,260],[263,263],[266,267],[269,269],[271,271],[304,304],[309,309],[311,311],[314,314],[316,316],[318,319],[322,322],[328,329],[333,333],[337,337],[340,342]];acc_buried_datapoints = [[11,22],[38,39],[41,48],[51,51],[54,55],[57,59],[61,64],[67,67],[75,77],[79,80],[86,90],[98,98],[100,103],[105,105],[110,111],[114,115],[118,118],[123,123],[125,125],[139,140],[142,142],[144,144],[148,154],[182,182],[184,191],[194,194],[197,198],[200,200],[201,202],[204,210],[213,213],[221,227],[231,237],[243,243],[245,252],[255,255],[258,259],[261,262],[265,265],[272,272],[274,282],[284,292],[294,301],[323,325],[335,336]];flot_plot_options = []; flot_plot_options[0] = {grid: {borderWidth: {top: 0,right: 0,bottom: 0,left: 0}},legend: {show: false},xaxes: [{show: true,min: 0,max: 200,ticks: [[0.5, '1'], [24.5, '25'], [49.5, '50'], [74.5, '75'], [99.5, '100'], [124.5, '125'], [149.5, '150'], [174.5, '175'], [199.5, '200']],tickLength: -5}],yaxes: [{show: true,ticks: [[0, '0'], [4.5,'hydro-<br>phobic&nbsp;&nbsp;'], [-4.5,'hydro-<br>philic&nbsp;&nbsp;']],min: -4.5,max: +4.5,font: {size: 12,lineHeight: 14,style: 'italic',weight: 'bold',family: 'sans-serif',variant: 'small-caps',color: 'rgba(100,149,237,1)'}},{show: true,ticks: [[0, ''], [1,'positive<br>&nbsp;charge'], [-1,'negative<br>&nbsp;charge']],position: 'right',min: -1,max: 1,font: {size: 12,lineHeight: 14,style: 'italic',weight: 'bold',family: 'sans-serif',variant: 'small-caps',color: 'rgba(255,99,71,1)'}}]};number_of_plots = 2;for ( plot_num = 1 ; plot_num < number_of_plots ; plot_num ++){flot_plot_options[plot_num] = $.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( $('#AutoAnnotator_container_1381243831471 #hydrophobicity_charge_button').val() =='Show' ){$('#AutoAnnotator_container_1381243831471 #hydrophobicity_charge_container').css('display','block');$('#AutoAnnotator_container_1381243831471 #hydrophobicity_charge_button').val('Hide');var description_html = '<div id=\'AutoAnnotator_plot_selectors\'>';description_html = description_html + '<br>&nbsp;<input type=\'checkbox\' id=\'hydrophobicity_checkbox\' checked=\'checked\'>&nbsp;Moving average over 5 amino acids for hydrophobicity (<img src=\'https://static.igem.org/mediawiki/2013/e/e9/TUM13_hydrophobicity_icon.png\' alt=\'blue graph\' height=\'10\'></img>)';description_html = description_html + '<br>&nbsp;<input type=\'checkbox\' id=\'charge_checkbox\' checked=\'checked\'>&nbsp;Moving average over 5 amino acids for charge (<img src=\'https://static.igem.org/mediawiki/2013/3/3e/TUM13_charge_icon.png\' alt=\'red graph\' height=\'10\'></img>)';description_html = description_html + '<br>&nbsp;<input type=\'checkbox\' id=\'dis_checkbox\' checked=\'checked\'>&nbsp;Predicted disulfid bridges (<img src=\'https://static.igem.org/mediawiki/2013/2/28/TUM13_dis_icon.png\' alt=\'yellow circle\' height=\'10\'></img>) with the number of the bridge in the center';description_html = description_html + '<br>&nbsp;<input type=\'checkbox\' id=\'trans_checkbox\' checked=\'checked\'>&nbsp;Predicted transmembrane helices (<img src=\'https://static.igem.org/mediawiki/2013/7/78/TUM13_trans_icon.png\' alt=\'turquois bars\' height=\'10\'></img>)';description_html = description_html + '<br>&nbsp;<input type=\'checkbox\' id=\'sec_checkbox\' checked=\'checked\'>&nbsp;Predicted secondary structure: Helices (<img src=\'https://static.igem.org/mediawiki/2013/b/bf/TUM13_helix_icon.png\' alt=\'violet bars\' height=\'10\'></img>) and beta-strands (<img src=\'https://static.igem.org/mediawiki/2013/b/bf/TUM13_strand_icon.png\' alt=\'yellow bars\' height=\'10\'></img>)';description_html = description_html + '<br>&nbsp;<input type=\'checkbox\' id=\'acc_checkbox\' checked=\'checked\'>&nbsp;Predicted solvent accessability: Exposed (<img src=\'https://static.igem.org/mediawiki/2013/1/16/TUM13_exposed_icon.png\' alt=\'blue bars\' height=\'10\'></img>) and buried (<img src=\'https://static.igem.org/mediawiki/2013/0/0b/TUM13_buried_icon.png\' alt=\'green bars\' height=\'10\'></img>) residues';description_html = description_html + '<br></div>';$('#AutoAnnotator_container_1381243831471 #hydrophobicity_charge_explanation').html(description_html);plot_according_to_selectors_1381243831471();$('#AutoAnnotator_container_1381243831471 #AutoAnnotator_plot_selectors').find('input').click(plot_according_to_selectors_1381243831471);}else{$('#AutoAnnotator_container_1381243831471 #hydrophobicity_charge_container').css('display','none');$('#AutoAnnotator_container_1381243831471 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 <!-- Uncomment this to enable Functional Parameter display