Difference between revisions of "Part:BBa K1088018"

Revision as of 10:14, 25 October 2013

LacI repressor from E. coli

Coding region for the LacI protein. LacI binds to the lac promoter BBa_R0010 and inhibits transcription. IPTG binds LacI and inhibits its function, and thus promotes transcription from the lac promoter.

SDU2013_Characterization_LacIPlac_2.2.png

FACS results and growth curves of lacI(N) and lacI:LVA carrying strains. Two triplicates of MG1655 strains carrying either pSB1C3-Pcon-lacI(N)-term-Plac-dxs(B. subtilits)-GFP (BBa_K1088026) (lacI(N)) or pSB1C3-Pcon-lacI:LVA-term-Plac-dxs(B. subtilits)-GFP (BBa_K1088009) (lacI:LVA) were grown from OD₆₀₀ 0.005 to approximately 0.2. At this OD the one triplicate of each strain were induced with 1 mM IPTG at time 0 min. FACS measurements were done at times: -30, 0, 30, 60, 90, 120, 150 and 180 min. A) lacI(lva) and lacI(N) strains grew at same pace both with and without induction. B) Per cent of population above fluorescence threshold. Both lacI(lva) and lacI(N) represses the expression, when not induced with IPTG. lacI(lva) reaches a maximum of merely 70-75 % after 150 min, which is both a poor response time and maximum cell per cent fluorescent compared to lacI(N). lacI(N) reaches a maximum just below 100 % at a time between 30 and 60 min. C) Mean GFP fluorescence of entire population. These results reflect what is seen in B, and clearly indicates that overexpression of natural LacI instead of LacI:LVA is the better, when a quick response and high level of expression is wanted.

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 BioBrick-AutoAnnotator Nucleotide sequence in RFC 10: (underlined part encodes the protein)
ATGAAACCA ... AGCGGGCAGTGA
ORF from nucleotide position 1 to 1080 (excluding stop-codon)

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

1
101
201
301

MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVE
RSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAG
WHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTS
VDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRLESGQ*

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

None of the supported features appeared in the sequence

Amino acid composition:

Ala (A)	44 (12.2%)
Arg (R)	19 (5.3%)
Asn (N)	12 (3.3%)
Asp (D)	17 (4.7%)

Cys (C)	3 (0.8%)
Gln (Q)	28 (7.8%)
Glu (E)	15 (4.2%)
Gly (G)	22 (6.1%)

His (H)	7 (1.9%)
Ile (I)	18 (5.0%)
Leu (L)	41 (11.4%)
Lys (K)	11 (3.1%)

Met (M)	10 (2.8%)
Phe (F)	4 (1.1%)
Pro (P)	14 (3.9%)
Ser (S)	32 (8.9%)

Thr (T)	19 (5.3%)
Trp (W)	2 (0.6%)
Tyr (Y)	8 (2.2%)
Val (V)	34 (9.4%)

Amino acid counting

	Total number:	360
	Positively charged (Arg+Lys):	30 (8.3%)
	Negatively charged (Asp+Glu):	32 (8.9%)
	Aromatic (Phe+His+Try+Tyr):	21 (5.8%)

Biochemical parameters

	Atomic composition:	C₁₆₈₄H₂₇₆₂N₄₈₄O₅₂₄S₁₃
	Molecular mass [Da]:	38590.2
	Theoretical pI:	6.39
	Extinction coefficient at 280 nm [M^-1 cm^-1]:	22920 / 23108 (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 (0.79)	good (0.78)	acceptable (0.55)	good (0.60)	good (0.78)	good (0.66)

Alignments (obtained from PredictProtein.org)

	SwissProt:	P03023 (100% identity on 360 AAs), Q9CN88 (32% identity on 325 AAs)
	TrEML:	D8E1B5 (100% identity on 359 AAs), E3PES2 (100% identity on 360 AAs), C6EJI7 (100% identity on 359 AAs), Q3Z584 (100% identity on 360 AAs), C6UB29 (100% identity on 360 AAs), C6ZCU4 (100% identity on 360 AAs), C9QQT3 (100% identity on 359 AAs), G2F6I6 (100% identity on 360 AAs), G2CUK7 (100% identity on 360 AAs), G2CFY7 (100% identity on 360 AAs)
	PDB:	1lbg (99% identity on 357 AAs)

Predictions (obtained from PredictProtein.org)

Subcellular Localization (reliability in brackets)

	Archaea:	cytosol (100%)
	Bacteria:	cytosol (99%)
	Eukarya:	mitochondria (61%)

Gene Ontology (reliability in brackets)

	Molecular Function Ontology:	GO:0043565 (25%), GO:0003700 (29%)
	Biological Process Ontology:	GO:0006355 (34%), GO:0045449 (18%)

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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−	<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_1382695602201'><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1382695602201 --><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>ATGAAACCA ... AGCGGGCAG</u>TGA</span><br> <strong>ORF</strong> from nucleotide position 1 to 1080 (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">MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVE<br>RSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAG<br>WHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTS<br>VDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRLESGQ</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">44 (12.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Arg (R)</td><td class="AutoAnnotatorInnerAmino">19 (5.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asn (N)</td><td class="AutoAnnotatorInnerAmino">12 (3.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asp (D)</td><td class="AutoAnnotatorInnerAmino">17 (4.7%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Cys (C)</td><td class="AutoAnnotatorInnerAmino">3 (0.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gln (Q)</td><td class="AutoAnnotatorInnerAmino">28 (7.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Glu (E)</td><td class="AutoAnnotatorInnerAmino">15 (4.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gly (G)</td><td class="AutoAnnotatorInnerAmino">22 (6.1%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">His (H)</td><td class="AutoAnnotatorInnerAmino">7 (1.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ile (I)</td><td class="AutoAnnotatorInnerAmino">18 (5.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Leu (L)</td><td class="AutoAnnotatorInnerAmino">41 (11.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Lys (K)</td><td class="AutoAnnotatorInnerAmino">11 (3.1%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Met (M)</td><td class="AutoAnnotatorInnerAmino">10 (2.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Phe (F)</td><td class="AutoAnnotatorInnerAmino">4 (1.1%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Pro (P)</td><td class="AutoAnnotatorInnerAmino">14 (3.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ser (S)</td><td class="AutoAnnotatorInnerAmino">32 (8.9%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Thr (T)</td><td class="AutoAnnotatorInnerAmino">19 (5.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Trp (W)</td><td class="AutoAnnotatorInnerAmino">2 (0.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Tyr (Y)</td><td class="AutoAnnotatorInnerAmino">8 (2.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Val (V)</td><td class="AutoAnnotatorInnerAmino">34 (9.4%)</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">360</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Positively charged (Arg+Lys):</td><td class="AutoAnnotatorAminoCountingInner3">30 (8.3%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Negatively charged (Asp+Glu):</td><td class="AutoAnnotatorAminoCountingInner3">32 (8.9%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Aromatic (Phe+His+Try+Tyr):</td><td class="AutoAnnotatorAminoCountingInner3">21 (5.8%)</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>1684</sub>H<sub>2762</sub>N<sub>484</sub>O<sub>524</sub>S<sub>13</sub></td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Molecular mass [Da]:</td><td class="AutoAnnotatorBiochemParInner3">38590.2</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Theoretical pI:</td><td class="AutoAnnotatorBiochemParInner3">6.39</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">22920 / 23108 (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_1382695602201()' 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 (0.79)</td><td class="AutoAnnotatorCodonUsage3">good (0.78)</td><td class="AutoAnnotatorCodonUsage3">acceptable (0.55)</td><td class="AutoAnnotatorCodonUsage3">good (0.60)</td><td class="AutoAnnotatorCodonUsage3">good (0.78)</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>)<table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorAlignment1"></td><td class="AutoAnnotatorAlignment2">SwissProt:</td><td class="AutoAnnotatorAlignment3"><a href='http://www.uniprot.org/uniprot/P03023'>P03023</a> (100% identity on 360 AAs), <a href='http://www.uniprot.org/uniprot/Q9CN88'>Q9CN88</a> (32% identity on 325 AAs)</td></tr><tr><td class="AutoAnnotatorAlignment1"></td><td class="AutoAnnotatorAlignment2">TrEML:</td><td class="AutoAnnotatorAlignment3"><a href='http://www.uniprot.org/uniprot/D8E1B5'>D8E1B5</a> (100% identity on 359 AAs), <a href='http://www.uniprot.org/uniprot/E3PES2'>E3PES2</a> (100% identity on 360 AAs), <a href='http://www.uniprot.org/uniprot/C6EJI7'>C6EJI7</a> (100% identity on 359 AAs), <a href='http://www.uniprot.org/uniprot/Q3Z584'>Q3Z584</a> (100% identity on 360 AAs), <a href='http://www.uniprot.org/uniprot/C6UB29'>C6UB29</a> (100% identity on 360 AAs), <a href='http://www.uniprot.org/uniprot/C6ZCU4'>C6ZCU4</a> (100% identity on 360 AAs), <a href='http://www.uniprot.org/uniprot/C9QQT3'>C9QQT3</a> (100% identity on 359 AAs), <a href='http://www.uniprot.org/uniprot/G2F6I6'>G2F6I6</a> (100% identity on 360 AAs), <a href='http://www.uniprot.org/uniprot/G2CUK7'>G2CUK7</a> (100% identity on 360 AAs), <a href='http://www.uniprot.org/uniprot/G2CFY7'>G2CFY7</a> (100% identity on 360 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=1lbg'>1lbg</a> (99% identity on 357 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 (99%)</td></tr><tr><td class="AutoAnnotatorLocalization1"></td><td class="AutoAnnotatorLocalization2">Eukarya:</td><td class="AutoAnnotatorLocalization3">mitochondria (61%)</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=GO:0043565'>GO:0043565</a> (25%), <a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0003700'>GO:0003700</a> (29%)</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:0006355'>GO:0006355</a> (34%), <a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0045449'>GO:0045449</a> (18%)</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>function show_or_hide_plot_1382695602201(){hydrophobicity_datapoints = [[2.5,-0.02],[3.5,0.36],[4.5,0.88],[5.5,0.50],[6.5,0.50],[7.5,1.00],[8.5,-0.46],[9.5,-0.46],[10.5,0.60],[11.5,-0.32],[12.5,0.16],[13.5,0.70],[14.5,0.70],[15.5,-0.36],[16.5,-0.42],[17.5,-0.42],[18.5,-0.42],[19.5,-1.06],[20.5,0.48],[21.5,1.46],[22.5,-0.08],[23.5,-0.62],[24.5,0.64],[25.5,-0.36],[26.5,-1.84],[27.5,-0.30],[28.5,0.24],[29.5,0.24],[30.5,-0.38],[31.5,0.12],[32.5,-1.62],[33.5,-2.16],[34.5,-3.30],[35.5,-1.68],[36.5,-2.24],[37.5,-0.98],[38.5,0.08],[39.5,1.24],[40.5,0.76],[41.5,0.76],[42.5,1.16],[43.5,0.10],[44.5,-0.54],[45.5,0.00],[46.5,0.38],[47.5,-1.08],[48.5,-1.28],[49.5,-0.18],[50.5,-0.72],[51.5,-1.10],[52.5,-1.10],[53.5,0.56],[54.5,0.08],[55.5,-0.36],[56.5,-0.44],[57.5,-0.44],[58.5,-1.36],[59.5,-0.96],[60.5,-0.12],[61.5,1.56],[62.5,2.18],[63.5,3.18],[64.5,2.78],[65.5,1.88],[66.5,0.82],[67.5,0.74],[68.5,0.66],[69.5,0.66],[70.5,1.56],[71.5,1.08],[72.5,1.60],[73.5,0.52],[74.5,0.00],[75.5,-1.46],[76.5,0.08],[77.5,0.56],[78.5,1.24],[79.5,1.76],[80.5,3.36],[81.5,1.68],[82.5,0.68],[83.5,-0.58],[84.5,-0.58],[85.5,-2.18],[86.5,-2.10],[87.5,-1.18],[88.5,-0.36],[89.5,-0.36],[90.5,0.18],[91.5,1.72],[92.5,1.80],[93.5,2.72],[94.5,2.20],[95.5,2.74],[96.5,2.74],[97.5,1.20],[98.5,-0.54],[99.5,-0.54],[100.5,-1.00],[101.5,-1.00],[102.5,-1.00],[103.5,0.26],[104.5,0.92],[105.5,0.22],[106.5,-0.26],[107.5,0.80],[108.5,1.28],[109.5,0.14],[110.5,0.22],[111.5,0.62],[112.5,1.02],[113.5,0.54],[114.5,0.48],[115.5,0.28],[116.5,0.36],[117.5,-0.56],[118.5,-1.00],[119.5,0.46],[120.5,2.26],[121.5,2.32],[122.5,1.78],[123.5,1.60],[124.5,0.52],[125.5,0.38],[126.5,-1.22],[127.5,-1.22],[128.5,-1.66],[129.5,-2.04],[130.5,-2.44],[131.5,-0.84],[132.5,0.22],[133.5,1.76],[134.5,1.76],[135.5,1.76],[136.5,1.22],[137.5,1.36],[138.5,0.38],[139.5,0.38],[140.5,0.86],[141.5,0.18],[142.5,0.04],[143.5,0.94],[144.5,2.20],[145.5,2.12],[146.5,1.74],[147.5,2.22],[148.5,1.30],[149.5,0.04],[150.5,-1.42],[151.5,-0.86],[152.5,-2.02],[153.5,-0.96],[154.5,-0.96],[155.5,-0.42],[156.5,0.62],[157.5,1.84],[158.5,1.50],[159.5,2.04],[160.5,1.56],[161.5,-0.04],[162.5,-1.64],[163.5,-2.28],[164.5,-2.26],[165.5,-2.52],[166.5,-1.06],[167.5,-0.44],[168.5,0.48],[169.5,-0.08],[170.5,0.18],[171.5,0.18],[172.5,1.10],[173.5,0.62],[174.5,2.08],[175.5,2.64],[176.5,1.24],[177.5,-0.30],[178.5,-1.36],[179.5,-1.22],[180.5,-0.78],[181.5,0.62],[182.5,2.08],[183.5,3.14],[184.5,2.16],[185.5,1.48],[186.5,1.48],[187.5,0.56],[188.5,0.04],[189.5,0.96],[190.5,1.12],[191.5,0.72],[192.5,-0.02],[193.5,0.90],[194.5,-0.84],[195.5,0.08],[196.5,0.08],[197.5,0.90],[198.5,-0.04],[199.5,0.22],[200.5,-1.32],[201.5,-1.94],[202.5,-1.10],[203.5,-1.06],[204.5,-1.32],[205.5,-1.24],[206.5,-1.68],[207.5,-1.54],[208.5,-2.10],[209.5,-1.52],[210.5,0.08],[211.5,1.14],[212.5,-0.46],[213.5,-0.66],[214.5,-1.04],[215.5,-2.02],[216.5,-3.08],[217.5,-2.56],[218.5,-1.82],[219.5,-0.76],[220.5,-0.30],[221.5,0.24],[222.5,0.34],[223.5,1.06],[224.5,0.00],[225.5,-1.08],[226.5,-1.06],[227.5,-0.60],[228.5,-1.86],[229.5,-0.78],[230.5,0.68],[231.5,0.12],[232.5,-0.96],[233.5,-0.34],[234.5,0.18],[235.5,0.26],[236.5,0.64],[237.5,1.20],[238.5,1.64],[239.5,1.12],[240.5,1.04],[241.5,2.20],[242.5,2.70],[243.5,1.64],[244.5,0.56],[245.5,-0.90],[246.5,-1.36],[247.5,-1.36],[248.5,0.10],[249.5,0.72],[250.5,1.78],[251.5,1.78],[252.5,0.52],[253.5,0.12],[254.5,1.10],[255.5,0.60],[256.5,-0.48],[257.5,0.26],[258.5,-0.18],[259.5,-0.32],[260.5,-1.08],[261.5,0.46],[262.5,0.54],[263.5,0.98],[264.5,-0.48],[265.5,1.32],[266.5,0.32],[267.5,1.24],[268.5,1.72],[269.5,2.34],[270.5,1.18],[271.5,0.64],[272.5,-0.90],[273.5,-1.88],[274.5,-2.50],[275.5,-2.94],[276.5,-2.40],[277.5,-1.86],[278.5,-1.22],[279.5,-0.78],[280.5,0.82],[281.5,0.66],[282.5,0.50],[283.5,0.76],[284.5,0.88],[285.5,-0.16],[286.5,1.06],[287.5,0.60],[288.5,-0.86],[289.5,-1.42],[290.5,-0.72],[291.5,-2.52],[292.5,-0.98],[293.5,0.48],[294.5,1.10],[295.5,-0.16],[296.5,0.60],[297.5,-0.32],[298.5,-0.24],[299.5,-0.86],[300.5,-1.06],[301.5,-0.16],[302.5,0.76],[303.5,-0.78],[304.5,0.68],[305.5,1.42],[306.5,-0.04],[307.5,-0.88],[308.5,-0.88],[309.5,-1.28],[310.5,-0.28],[311.5,-0.36],[312.5,-0.36],[313.5,-0.36],[314.5,-1.42],[315.5,-1.50],[316.5,0.04],[317.5,-0.20],[318.5,1.34],[319.5,1.88],[320.5,1.88],[321.5,1.96],[322.5,1.50],[323.5,-0.24],[324.5,-0.86],[325.5,-1.76],[326.5,-2.74],[327.5,-1.20],[328.5,0.06],[329.5,0.52],[330.5,-0.04],[331.5,-0.04],[332.5,-1.50],[333.5,-2.00],[334.5,-1.32],[335.5,-0.78],[336.5,-0.96],[337.5,-1.16],[338.5,-0.66],[339.5,-0.26],[340.5,0.26],[341.5,-0.12],[342.5,0.62],[343.5,1.02],[344.5,0.64],[345.5,-0.42],[346.5,1.04],[347.5,1.56],[348.5,-0.10],[349.5,-1.18],[350.5,0.36],[351.5,-0.56],[352.5,-1.82],[353.5,-0.16],[354.5,-0.16],[355.5,-1.16],[356.5,-1.08],[357.5,-0.88]];charge_datapoints = [[2.5,0.20],[3.5,0.20],[4.5,0.00],[5.5,-0.20],[6.5,-0.20],[7.5,-0.20],[8.5,-0.40],[9.5,-0.40],[10.5,-0.20],[11.5,-0.20],[12.5,-0.20],[13.5,0.00],[14.5,0.00],[15.5,0.00],[16.5,0.00],[17.5,0.00],[18.5,0.00],[19.5,0.20],[20.5,0.20],[21.5,0.20],[22.5,0.20],[23.5,0.20],[24.5,0.00],[25.5,0.00],[26.5,0.10],[27.5,0.10],[28.5,0.10],[29.5,0.10],[30.5,0.30],[31.5,0.20],[32.5,0.40],[33.5,0.20],[34.5,0.40],[35.5,0.20],[36.5,0.00],[37.5,-0.20],[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],[46.5,0.00],[47.5,0.00],[48.5,0.20],[49.5,0.20],[50.5,0.20],[51.5,0.20],[52.5,0.20],[53.5,0.00],[54.5,0.00],[55.5,0.00],[56.5,0.20],[57.5,0.20],[58.5,0.20],[59.5,0.20],[60.5,0.20],[61.5,0.00],[62.5,0.00],[63.5,0.00],[64.5,0.00],[65.5,0.00],[66.5,0.00],[67.5,0.00],[68.5,0.00],[69.5,0.00],[70.5,0.00],[71.5,0.10],[72.5,0.10],[73.5,0.10],[74.5,0.10],[75.5,0.10],[76.5,0.00],[77.5,0.00],[78.5,0.00],[79.5,0.00],[80.5,0.00],[81.5,0.20],[82.5,0.20],[83.5,0.40],[84.5,0.40],[85.5,0.20],[86.5,0.00],[87.5,0.00],[88.5,-0.20],[89.5,-0.20],[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,-0.20],[98.5,0.00],[99.5,0.00],[100.5,0.00],[101.5,0.00],[102.5,0.00],[103.5,-0.20],[104.5,-0.20],[105.5,0.00],[106.5,0.00],[107.5,0.20],[108.5,0.20],[109.5,0.30],[110.5,0.10],[111.5,0.10],[112.5,0.10],[113.5,0.10],[114.5,0.00],[115.5,0.20],[116.5,0.20],[117.5,0.20],[118.5,0.20],[119.5,0.20],[120.5,0.00],[121.5,0.00],[122.5,0.00],[123.5,0.00],[124.5,0.00],[125.5,0.00],[126.5,-0.20],[127.5,-0.40],[128.5,-0.40],[129.5,-0.60],[130.5,-0.60],[131.5,-0.40],[132.5,-0.20],[133.5,-0.20],[134.5,-0.20],[135.5,-0.20],[136.5,-0.20],[137.5,-0.20],[138.5,-0.20],[139.5,-0.00],[140.5,-0.00],[141.5,-0.00],[142.5,-0.00],[143.5,-0.00],[144.5,-0.00],[145.5,-0.00],[146.5,-0.20],[147.5,-0.20],[148.5,-0.20],[149.5,-0.40],[150.5,-0.40],[151.5,-0.20],[152.5,-0.20],[153.5,-0.20],[154.5,-0.00],[155.5,-0.00],[156.5,-0.00],[157.5,-0.00],[158.5,-0.00],[159.5,-0.00],[160.5,0.10],[161.5,-0.10],[162.5,-0.30],[163.5,-0.30],[164.5,-0.30],[165.5,-0.20],[166.5,0.00],[167.5,0.20],[168.5,0.20],[169.5,0.00],[170.5,-0.10],[171.5,-0.10],[172.5,-0.10],[173.5,-0.10],[174.5,0.10],[175.5,0.00],[176.5,0.10],[177.5,0.10],[178.5,0.10],[179.5,0.10],[180.5,0.10],[181.5,0.00],[182.5,0.00],[183.5,0.00],[184.5,0.00],[185.5,0.00],[186.5,0.00],[187.5,0.00],[188.5,0.00],[189.5,0.00],[190.5,0.00],[191.5,0.00],[192.5,0.20],[193.5,0.20],[194.5,0.40],[195.5,0.40],[196.5,0.40],[197.5,0.20],[198.5,0.20],[199.5,0.10],[200.5,0.30],[201.5,0.30],[202.5,0.30],[203.5,0.30],[204.5,0.40],[205.5,0.20],[206.5,0.20],[207.5,0.20],[208.5,0.20],[209.5,0.00],[210.5,0.00],[211.5,0.00],[212.5,-0.20],[213.5,0.00],[214.5,-0.20],[215.5,-0.20],[216.5,-0.40],[217.5,-0.20],[218.5,-0.40],[219.5,-0.20],[220.5,-0.20],[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,-0.20],[233.5,-0.20],[234.5,-0.20],[235.5,-0.20],[236.5,-0.20],[237.5,0.00],[238.5,0.00],[239.5,0.00],[240.5,0.00],[241.5,0.00],[242.5,0.00],[243.5,0.00],[244.5,-0.20],[245.5,-0.20],[246.5,-0.20],[247.5,-0.20],[248.5,-0.20],[249.5,0.00],[250.5,0.00],[251.5,0.00],[252.5,0.20],[253.5,0.20],[254.5,0.20],[255.5,0.20],[256.5,0.00],[257.5,-0.20],[258.5,-0.20],[259.5,-0.20],[260.5,0.00],[261.5,0.20],[262.5,0.20],[263.5,0.20],[264.5,0.00],[265.5,-0.20],[266.5,-0.20],[267.5,-0.20],[268.5,-0.20],[269.5,0.00],[270.5,0.00],[271.5,-0.20],[272.5,-0.40],[273.5,-0.40],[274.5,-0.60],[275.5,-0.80],[276.5,-0.60],[277.5,-0.40],[278.5,-0.40],[279.5,-0.20],[280.5,-0.00],[281.5,-0.00],[282.5,-0.00],[283.5,-0.00],[284.5,-0.00],[285.5,-0.00],[286.5,-0.00],[287.5,0.20],[288.5,0.20],[289.5,-0.00],[290.5,-0.00],[291.5,0.20],[292.5,-0.00],[293.5,-0.00],[294.5,0.20],[295.5,0.20],[296.5,-0.00],[297.5,-0.00],[298.5,-0.00],[299.5,-0.20],[300.5,-0.00],[301.5,-0.00],[302.5,-0.00],[303.5,-0.00],[304.5,0.20],[305.5,-0.00],[306.5,-0.00],[307.5,-0.00],[308.5,-0.00],[309.5,-0.00],[310.5,-0.00],[311.5,0.20],[312.5,0.20],[313.5,0.20],[314.5,0.20],[315.5,0.20],[316.5,-0.00],[317.5,-0.00],[318.5,-0.00],[319.5,-0.00],[320.5,-0.00],[321.5,-0.00],[322.5,0.20],[323.5,0.40],[324.5,0.60],[325.5,0.60],[326.5,0.60],[327.5,0.40],[328.5,0.20],[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,-0.00],[336.5,-0.00],[337.5,0.20],[338.5,0.20],[339.5,0.20],[340.5,0.20],[341.5,-0.00],[342.5,-0.20],[343.5,-0.20],[344.5,-0.20],[345.5,-0.20],[346.5,-0.00],[347.5,-0.00],[348.5,0.20],[349.5,0.20],[350.5,0.20],[351.5,0.20],[352.5,0.40],[353.5,0.20],[354.5,-0.00],[355.5,-0.00],[356.5,-0.00],[357.5,-0.20]];dis_datapoints = [];trans_datapoints = [];sec_helix_datapoints = [[6,12],[17,23],[32,45],[50,57],[74,89],[104,116],[132,140],[164,177],[194,200],[201,207],[222,234],[247,259],[278,280],[293,308],[344,357]];sec_strand_datapoints = [[63,68],[93,98],[121,126],[145,149],[158,161],[181,186],[214,217],[241,245],[268,272],[287,289],[317,326]];acc_exposed_datapoints = [[1,3],[7,8],[11,12],[14,14],[25,29],[32,33],[36,36],[40,40],[43,44],[46,46],[54,54],[58,61],[72,72],[81,81],[85,85],[88,89],[91,91],[100,106],[109,109],[112,112],[116,117],[128,133],[136,136],[139,140],[142,142],[152,155],[165,165],[176,176],[190,190],[193,193],[199,199],[203,203],[206,207],[209,209],[211,212],[219,219],[221,221],[223,224],[227,227],[231,231],[234,238],[259,259],[261,261],[263,263],[277,277],[280,280],[285,285],[294,295],[306,306],[309,312],[314,316],[327,327],[329,329],[333,341],[344,345],[348,348],[351,352],[354,355],[357,360]];acc_buried_datapoints = [[6,6],[9,10],[13,13],[15,16],[18,21],[23,24],[30,30],[34,34],[38,38],[41,42],[49,50],[52,53],[56,56],[63,69],[71,71],[75,77],[79,80],[82,83],[87,87],[92,92],[94,99],[107,107],[110,111],[114,115],[119,126],[138,138],[143,148],[150,150],[159,161],[163,163],[166,167],[170,171],[174,175],[178,179],[181,187],[194,194],[197,198],[200,200],[201,201],[204,205],[210,210],[225,225],[228,230],[232,233],[239,239],[241,254],[256,257],[264,265],[268,273],[275,276],[278,279],[282,282],[284,284],[286,289],[293,293],[296,297],[300,301],[304,305],[308,308],[319,319],[321,321],[323,324],[328,328],[346,346],[350,350],[353,353],[356,356]];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] = $.extend(true, {} ,flot_plot_options[0]);flot_plot_options[plot_num].xaxes = [{min: plot_num200,max: (plot_num + 1)200,ticks: [ [plot_num200 + 0.5, (plot_num200 + 1).toString()], [plot_num200 + 24.5, (plot_num200 + 25).toString()], [plot_num200 + 49.5, (plot_num200 + 50).toString()], [plot_num200 + 74.5, (plot_num200 + 75).toString()], [plot_num200 + 99.5, (plot_num200 + 100).toString()], [plot_num200 + 124.5, (plot_num200 + 125).toString()], [plot_num200 + 149.5, (plot_num200 + 150).toString()], [plot_num200 + 174.5, (plot_num200 + 175).toString()], [plot_num200 + 199.5, (plot_num200 + 200).toString()] ],tickLength: -5}];};try {if( $('#AutoAnnotator_container_1382695602201 #hydrophobicity_charge_button').val() =='Show' ){$('#AutoAnnotator_container_1382695602201 #hydrophobicity_charge_container').css('display','block');$('#AutoAnnotator_container_1382695602201 #hydrophobicity_charge_button').val('Hide');var description_html = '<div id=\'AutoAnnotator_plot_selectors\'>';description_html = description_html + '<br> <input type=\'checkbox\' id=\'hydrophobicity_checkbox\' checked=\'checked\'> Moving average over 5 amino acids for hydrophobicity (<img src=\'https://static.igem.org/mediawiki/2013/e/e9/TUM13_hydrophobicity_icon.png\' alt=\'blue graph\' height=\'10\'></img>)';description_html = description_html + '<br> <input type=\'checkbox\' id=\'charge_checkbox\' checked=\'checked\'> Moving 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sec_helix_datapoints.length ; j++ ){$('#AutoAnnotator_container_1382695602201 #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)200tick_diff).toFixed(0)).toString() + 'px\'></div>');}for ( j = 0 ; j < sec_strand_datapoints.length ; j++ ){$('#AutoAnnotator_container_1382695602201 #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] - 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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_1382695602201'><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1382695602201 --><th id="AutoAnnotatorHeader" colspan="2">Protein data table for BioBrick <a href="https://parts.igem.org/wiki/index.php?title=Part:BBa_K1088018</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>ATGAAACCA ... AGCGGGCAG</u>TGA</span><br> <strong>ORF</strong> from nucleotide position 1 to 1080 (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">MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVE<br>RSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAG<br>WHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTS<br>VDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRLESGQ</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">44 (12.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Arg (R)</td><td class="AutoAnnotatorInnerAmino">19 (5.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asn (N)</td><td class="AutoAnnotatorInnerAmino">12 (3.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asp (D)</td><td class="AutoAnnotatorInnerAmino">17 (4.7%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Cys (C)</td><td class="AutoAnnotatorInnerAmino">3 (0.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gln (Q)</td><td class="AutoAnnotatorInnerAmino">28 (7.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Glu (E)</td><td class="AutoAnnotatorInnerAmino">15 (4.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gly (G)</td><td class="AutoAnnotatorInnerAmino">22 (6.1%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">His (H)</td><td class="AutoAnnotatorInnerAmino">7 (1.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ile (I)</td><td class="AutoAnnotatorInnerAmino">18 (5.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Leu (L)</td><td class="AutoAnnotatorInnerAmino">41 (11.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Lys (K)</td><td class="AutoAnnotatorInnerAmino">11 (3.1%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Met (M)</td><td class="AutoAnnotatorInnerAmino">10 (2.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Phe (F)</td><td class="AutoAnnotatorInnerAmino">4 (1.1%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Pro (P)</td><td class="AutoAnnotatorInnerAmino">14 (3.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ser (S)</td><td class="AutoAnnotatorInnerAmino">32 (8.9%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Thr (T)</td><td class="AutoAnnotatorInnerAmino">19 (5.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Trp (W)</td><td class="AutoAnnotatorInnerAmino">2 (0.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Tyr (Y)</td><td class="AutoAnnotatorInnerAmino">8 (2.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Val (V)</td><td class="AutoAnnotatorInnerAmino">34 (9.4%)</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">360</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Positively charged (Arg+Lys):</td><td class="AutoAnnotatorAminoCountingInner3">30 (8.3%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Negatively charged (Asp+Glu):</td><td class="AutoAnnotatorAminoCountingInner3">32 (8.9%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Aromatic (Phe+His+Try+Tyr):</td><td class="AutoAnnotatorAminoCountingInner3">21 (5.8%)</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>1684</sub>H<sub>2762</sub>N<sub>484</sub>O<sub>524</sub>S<sub>13</sub></td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Molecular mass [Da]:</td><td class="AutoAnnotatorBiochemParInner3">38590.2</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Theoretical pI:</td><td class="AutoAnnotatorBiochemParInner3">6.39</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">22920 / 23108 (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_1382695602201()' 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 (0.79)</td><td class="AutoAnnotatorCodonUsage3">good (0.78)</td><td class="AutoAnnotatorCodonUsage3">acceptable (0.55)</td><td class="AutoAnnotatorCodonUsage3">good (0.60)</td><td class="AutoAnnotatorCodonUsage3">good (0.78)</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>)<table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorAlignment1"></td><td class="AutoAnnotatorAlignment2">SwissProt:</td><td class="AutoAnnotatorAlignment3"><a href='http://www.uniprot.org/uniprot/P03023'>P03023</a> (100% identity on 360 AAs), <a href='http://www.uniprot.org/uniprot/Q9CN88'>Q9CN88</a> (32% identity on 325 AAs)</td></tr><tr><td class="AutoAnnotatorAlignment1"></td><td class="AutoAnnotatorAlignment2">TrEML:</td><td class="AutoAnnotatorAlignment3"><a href='http://www.uniprot.org/uniprot/D8E1B5'>D8E1B5</a> (100% identity on 359 AAs), <a href='http://www.uniprot.org/uniprot/E3PES2'>E3PES2</a> (100% identity on 360 AAs), <a href='http://www.uniprot.org/uniprot/C6EJI7'>C6EJI7</a> (100% identity on 359 AAs), <a href='http://www.uniprot.org/uniprot/Q3Z584'>Q3Z584</a> (100% identity on 360 AAs), <a href='http://www.uniprot.org/uniprot/C6UB29'>C6UB29</a> (100% identity on 360 AAs), <a href='http://www.uniprot.org/uniprot/C6ZCU4'>C6ZCU4</a> (100% identity on 360 AAs), <a href='http://www.uniprot.org/uniprot/C9QQT3'>C9QQT3</a> (100% identity on 359 AAs), <a href='http://www.uniprot.org/uniprot/G2F6I6'>G2F6I6</a> (100% identity on 360 AAs), <a href='http://www.uniprot.org/uniprot/G2CUK7'>G2CUK7</a> (100% identity on 360 AAs), <a href='http://www.uniprot.org/uniprot/G2CFY7'>G2CFY7</a> (100% identity on 360 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=1lbg'>1lbg</a> (99% identity on 357 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 (99%)</td></tr><tr><td class="AutoAnnotatorLocalization1"></td><td class="AutoAnnotatorLocalization2">Eukarya:</td><td class="AutoAnnotatorLocalization3">mitochondria (61%)</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=GO:0043565'>GO:0043565</a> (25%), <a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0003700'>GO:0003700</a> (29%)</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:0006355'>GO:0006355</a> (34%), <a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0045449'>GO:0045449</a> (18%)</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>function show_or_hide_plot_1382695602201(){hydrophobicity_datapoints = 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