Difference between revisions of "Part:BBa K1159106"

Latest revision as of 19:23, 8 October 2013

PhyB(2-908 AA)_36AALinker_C-TEV-Protease (First part for a light-switchable TEV-Protease) in RFC[25]

This parts encodes are fusion protein consisting the photosensitive core of PhyB (2-908 AA) at the N-terminus and the C-terminal half of TEV Protease at its C-terminus. Both parts are seperated by a 36 amino acids long flexible linker. This part is flanked by RFC[25] pre- and suffix to allow further protein fusions.

By expressing this part together with its interaction partner BBa_K1159107 or BBa_K1159108 that contains the part which interacts with PhyB (PIF3 or PIF6) and the N-terminal half of the splitted TEV Protease, they form together a light-switchable TEV Protease system which can be activated by red light and inactivated by far-red light.

Note: PhyB requires Phycocyanobilin or Phytochromobilin as a cofactor to fulfill its function as photoswitchable protein; you can reach it by adding exogenous Phycocyanobilin/Phytochromobilin in the medium or by inserting genes for the Phycocyanobilin/Phytochromobilin synthesis. See here for more information: [http://2012.igem.org/Team:TU_Munich/Project/Light_Switchable_Promoter#Biosynthesis_of_Phycocyanobilin Click here]

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
INCOMPATIBLE WITH RFC[21]
Illegal BglII site found at 487
Illegal BamHI site found at 569
Illegal XhoI site found at 520
Illegal XhoI site found at 539
Illegal XhoI site found at 2674
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
INCOMPATIBLE WITH RFC[1000]
Illegal BsaI site found at 2059
Illegal BsaI site found at 2465
Illegal SapI site found at 736
Illegal SapI.rc site found at 3151

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

Nucleotide sequence in RFC 25, so ATGGCCGGC and ACCGGT were added (in italics) to the 5' and 3' ends: (underlined part encodes the protein)
ATGGCCGGCGTTTCCGGA ... CTCATGAATACCGGT
ORF from nucleotide position -8 to 3201 (excluding stop-codon)

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

1
101
201
301
401
501
601
701
801
901
1001

MAGVSGVGGSGGGRGGGRGGEEEPSSSHTPNNRRGGEQAQSSGTKSLRPRSNTESMSKAIQQYTVDARLHAVFEQSGESGKSFDYSQSLKTTTYGSSVPE
QQITAYLSRIQRGGYIQPFGCMIAVDESSFRIIGYSENAREMLGIMPQSVPTLEKPEILAMGTDVRSLFTSSSSILLERAFVAREITLLNPVWIHSKNTG
KPFYAILHRIDVGVVIDLEPARTEDPALSIAGAVQSQKLAVRAISQLQALPGGDIKLLCDTVVESVRDLTGYDRVMVYKFHEDEHGEVVAESKRDDLEPY
IGLHYPATDIPQASRFLFKQNRVRMIVDCNATPVLVVQDDRLTQSMCLVGSTLRAPHGCHSQYMANMGSIASLAMAVIINGNEDDGSNVASGRSSMRLWG
LVVCHHTSSRCIPFPLRYACEFLMQAFGLQLNMELQLALQMSEKRVLRTQTLLCDMLLRDSPAGIVTQSPSIMDLVKCDGAAFLYHGKYYPLGVAPSEVQ
IKDVVEWLLANHADSTGLSTDSLGDAGYPGAAALGDAVCGMAVAYITKRDFLFWFRSHTAKEIKWGGAKHHPEDKDDGQRMHPRSSFQAFLEVVKSRSQP
WETAEMDAIHSLQLILRDSFKESEAAMNSKVVDGVVQPCRDMAGEQGIDELGAVAREMVRLIETATVPIFAVDAGGCINGWNAKIAELTGLSVEEAMGKS
LVSDLIYKENEATVNKLLSRALRGDEEKNVEVKLKTFSPELQGKAVFVVVNACSSKDYLNNIVGVCFVGQDVTSQKIVMDKFINIQGDYKAIVHSPNPLI
PPIFAADENTCCLEWNMAMEKLTGWSRSEVIGKMIVGEVFGSCCMLKGPDALTKFMIVLHNAIGGQDTDKFPFPFFDRNGKFVQALLTANKRVSLEGKVI
GAFCFLQIPSTGGGSAGGSGSGSSGGSSGASGTGTAGGTGSGSGTGSGTGKSMSSMVSDTSCTFPSSDGIFWKHWIQTKDGQCGSPLVSTRDGFIVGIHS
ASNFTNTNNYFTSVPKNFMELLTNQEAQQWVSGWRLNADSVLWGGHKVFMVKPEEPFQPVKEATQLMNTG*

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

RFC25 scar (shown in bold):

911 to 912, 949 to 950

Amino acid composition:

Ala (A)	81 (7.6%)
Arg (R)	48 (4.5%)
Asn (N)	38 (3.6%)
Asp (D)	55 (5.1%)

Cys (C)	22 (2.1%)
Gln (Q)	47 (4.4%)
Glu (E)	60 (5.6%)
Gly (G)	106 (9.9%)

His (H)	23 (2.1%)
Ile (I)	55 (5.1%)
Leu (L)	84 (7.9%)
Lys (K)	51 (4.8%)

Met (M)	36 (3.4%)
Phe (F)	43 (4.0%)
Pro (P)	45 (4.2%)
Ser (S)	102 (9.5%)

Thr (T)	56 (5.2%)
Trp (W)	14 (1.3%)
Tyr (Y)	22 (2.1%)
Val (V)	82 (7.7%)

Amino acid counting

	Total number:	1070
	Positively charged (Arg+Lys):	99 (9.3%)
	Negatively charged (Asp+Glu):	115 (10.7%)
	Aromatic (Phe+His+Try+Tyr):	102 (9.5%)

Biochemical parameters

	Atomic composition:	C₅₀₇₈H₈₀₁₆N₁₄₁₀O₁₅₆₆S₅₈
	Molecular mass [Da]:	115735.5
	Theoretical pI:	5.86
	Extinction coefficient at 280 nm [M^-1 cm^-1]:	109780 / 111155 (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 (0.74)	good (0.67)	good (0.75)	excellent (0.80)	good (0.66)

Alignments (obtained from PredictProtein.org)

	SwissProt:	P14713 (99% identity on 915 AAs), P42497 (83% identity on 898 AAs)
	TrEML:	B0FWJ8 (99% identity on 898 AAs), Q5G893 (99% identity on 895 AAs), Q5G894 (99% identity on 898 AAs), Q5G899 (99% identity on 898 AAs), Q5G8A1 (99% identity on 898 AAs), Q5G8A3 (99% identity on 913 AAs), Q5G8A4 (99% identity on 895 AAs), Q5G8A5 (99% identity on 913 AAs), B0FWI4 (98% identity on 898 AAs), B0FWI5 (98% identity on 898 AAs)
	PDB:	-

Predictions (obtained from PredictProtein.org)

Subcellular Localization (reliability in brackets)

	Archaea:	secreted (100%)
	Bacteria:	secreted (52%)
	Eukarya:	cytosol (39%)

Gene Ontology (reliability in brackets)

	Molecular Function Ontology:	GO:0009883 (70%), GO:0042802 (26%)
	Biological Process Ontology:	GO:0006350 (30%), GO:0006355 (29%)

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.

@@ Line 4: / Line 4: @@
 This parts encodes are fusion protein consisting the photosensitive core of PhyB (2-908 AA) at the N-terminus and the C-terminal half of TEV Protease at its C-terminus. Both parts are seperated by a 36 amino acids long flexible linker. This part is flanked by RFC[25] pre- and suffix to allow further protein fusions.
-By expressing this part together with the second essential protein [https://parts.igem.org/wiki/index.php?title=Part:BBa_K1159107 BBa_K1159107] or [https://parts.igem.org/wiki/index.php?title=Part:BBa_K1159108 BBa_K1159108] that contains the part which interacts with PhyB (PIF3 or PIF6) and the N-terminal half of the splitted TEV Protease, they form together a light-switchable TEV Protease system which can be activated by red light and inactivated by far-red light.
+By expressing this part together with its interaction partner [https://parts.igem.org/wiki/index.php?title=Part:BBa_K1159107 BBa_K1159107] or [https://parts.igem.org/wiki/index.php?title=Part:BBa_K1159108 BBa_K1159108] that contains the part which interacts with PhyB (PIF3 or PIF6) and the N-terminal half of the splitted TEV Protease, they form together a light-switchable TEV Protease system which can be activated by red light and inactivated by far-red light.
 '''''Note: PhyB requires Phycocyanobilin or Phytochromobilin as a cofactor to fulfill its function as photoswitchable protein; you can reach it by adding exogenous Phycocyanobilin/Phytochromobilin in the medium or by inserting genes for the Phycocyanobilin/Phytochromobilin synthesis. See here for more information: [http://2012.igem.org/Team:TU_Munich/Project/Light_Switchable_Promoter#Biosynthesis_of_Phycocyanobilin Click here] '''''
@@ Line 14: / Line 14: @@
 <span class='h3bb'>Sequence and Features</span>
 <partinfo>BBa_K1159106 SequenceAndFeatures</partinfo>
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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_1381260103944'><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1381260103944 --><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</strong>, so ATGGCCGGC and ACCGGT were added (in italics) to the 5' and 3' ends: (underlined part encodes the protein)<br><span class="AutoAnnotatorSequence">&nbsp;<u><i>ATGGCCGGC</i>GTTTCCGGA&nbsp;...&nbsp;CTCATGAAT<i>ACCGGT</i></u></span><br>&nbsp;<strong>ORF</strong> from nucleotide position -8 to 3201 (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;<br>401&nbsp;<br>501&nbsp;<br>601&nbsp;<br>701&nbsp;<br>801&nbsp;<br>901&nbsp;<br>1001&nbsp;</td><td class="AutoAnnotatorSeqSeq">MAGVSGVGGSGGGRGGGRGGEEEPSSSHTPNNRRGGEQAQSSGTKSLRPRSNTESMSKAIQQYTVDARLHAVFEQSGESGKSFDYSQSLKTTTYGSSVPE<br>QQITAYLSRIQRGGYIQPFGCMIAVDESSFRIIGYSENAREMLGIMPQSVPTLEKPEILAMGTDVRSLFTSSSSILLERAFVAREITLLNPVWIHSKNTG<br>KPFYAILHRIDVGVVIDLEPARTEDPALSIAGAVQSQKLAVRAISQLQALPGGDIKLLCDTVVESVRDLTGYDRVMVYKFHEDEHGEVVAESKRDDLEPY<br>IGLHYPATDIPQASRFLFKQNRVRMIVDCNATPVLVVQDDRLTQSMCLVGSTLRAPHGCHSQYMANMGSIASLAMAVIINGNEDDGSNVASGRSSMRLWG<br>LVVCHHTSSRCIPFPLRYACEFLMQAFGLQLNMELQLALQMSEKRVLRTQTLLCDMLLRDSPAGIVTQSPSIMDLVKCDGAAFLYHGKYYPLGVAPSEVQ<br>IKDVVEWLLANHADSTGLSTDSLGDAGYPGAAALGDAVCGMAVAYITKRDFLFWFRSHTAKEIKWGGAKHHPEDKDDGQRMHPRSSFQAFLEVVKSRSQP<br>WETAEMDAIHSLQLILRDSFKESEAAMNSKVVDGVVQPCRDMAGEQGIDELGAVAREMVRLIETATVPIFAVDAGGCINGWNAKIAELTGLSVEEAMGKS<br>LVSDLIYKENEATVNKLLSRALRGDEEKNVEVKLKTFSPELQGKAVFVVVNACSSKDYLNNIVGVCFVGQDVTSQKIVMDKFINIQGDYKAIVHSPNPLI<br>PPIFAADENTCCLEWNMAMEKLTGWSRSEVIGKMIVGEVFGSCCMLKGPDALTKFMIVLHNAIGGQDTDKFPFPFFDRNGKFVQALLTANKRVSLEGKVI<br>GAFCFLQIPS<b>TG</b>GGSAGGSGSGSSGGSSGASGTGTAGGTGSGSGTGSG<b>TG</b>KSMSSMVSDTSCTFPSSDGIFWKHWIQTKDGQCGSPLVSTRDGFIVGIHS<br>ASNFTNTNNYFTSVPKNFMELLTNQEAQQWVSGWRLNADSVLWGGHKVFMVKPEEPFQPVKEATQLMNTG*</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">911 to 912, 949 to 950</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">81 (7.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Arg (R)</td><td class="AutoAnnotatorInnerAmino">48 (4.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asn (N)</td><td class="AutoAnnotatorInnerAmino">38 (3.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asp (D)</td><td class="AutoAnnotatorInnerAmino">55 (5.1%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Cys (C)</td><td class="AutoAnnotatorInnerAmino">22 (2.1%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gln (Q)</td><td class="AutoAnnotatorInnerAmino">47 (4.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Glu (E)</td><td class="AutoAnnotatorInnerAmino">60 (5.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gly (G)</td><td class="AutoAnnotatorInnerAmino">106 (9.9%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">His (H)</td><td class="AutoAnnotatorInnerAmino">23 (2.1%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ile (I)</td><td class="AutoAnnotatorInnerAmino">55 (5.1%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Leu (L)</td><td class="AutoAnnotatorInnerAmino">84 (7.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Lys (K)</td><td class="AutoAnnotatorInnerAmino">51 (4.8%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Met (M)</td><td class="AutoAnnotatorInnerAmino">36 (3.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Phe (F)</td><td class="AutoAnnotatorInnerAmino">43 (4.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Pro (P)</td><td class="AutoAnnotatorInnerAmino">45 (4.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ser (S)</td><td class="AutoAnnotatorInnerAmino">102 (9.5%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Thr (T)</td><td class="AutoAnnotatorInnerAmino">56 (5.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Trp (W)</td><td class="AutoAnnotatorInnerAmino">14 (1.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Tyr (Y)</td><td class="AutoAnnotatorInnerAmino">22 (2.1%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Val (V)</td><td class="AutoAnnotatorInnerAmino">82 (7.7%)</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">1070</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Positively charged (Arg+Lys):</td><td class="AutoAnnotatorAminoCountingInner3">99 (9.3%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Negatively charged (Asp+Glu):</td><td class="AutoAnnotatorAminoCountingInner3">115 (10.7%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Aromatic (Phe+His+Try+Tyr):</td><td class="AutoAnnotatorAminoCountingInner3">102 (9.5%)</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>5078</sub>H<sub>8016</sub>N<sub>1410</sub>O<sub>1566</sub>S<sub>58</sub></td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Molecular mass [Da]:</td><td class="AutoAnnotatorBiochemParInner3">115735.5</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Theoretical pI:</td><td class="AutoAnnotatorBiochemParInner3">5.86</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">109780 / 111155 (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_1381260103944()' 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 id="hydrophobicity_charge_placeholder2" style="width:100%;height:150px"></div><div id="hydrophobicity_charge_placeholder3" style="width:100%;height:150px"></div><div id="hydrophobicity_charge_placeholder4" style="width:100%;height:150px"></div><div id="hydrophobicity_charge_placeholder5" 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 (0.74)</td><td class="AutoAnnotatorCodonUsage3">good (0.67)</td><td class="AutoAnnotatorCodonUsage3">good (0.75)</td><td class="AutoAnnotatorCodonUsage3">excellent (0.80)</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/P14713'>P14713</a> (99% identity on 915 AAs), <a href='http://www.uniprot.org/uniprot/P42497'>P42497</a> (83% identity on 898 AAs)</td></tr><tr><td class="AutoAnnotatorAlignment1"></td><td class="AutoAnnotatorAlignment2">TrEML:</td><td class="AutoAnnotatorAlignment3"><a href='http://www.uniprot.org/uniprot/B0FWJ8'>B0FWJ8</a> (99% identity on 898 AAs), <a href='http://www.uniprot.org/uniprot/Q5G893'>Q5G893</a> (99% identity on 895 AAs), <a href='http://www.uniprot.org/uniprot/Q5G894'>Q5G894</a> (99% identity on 898 AAs), <a href='http://www.uniprot.org/uniprot/Q5G899'>Q5G899</a> (99% identity on 898 AAs), <a href='http://www.uniprot.org/uniprot/Q5G8A1'>Q5G8A1</a> (99% identity on 898 AAs), <a href='http://www.uniprot.org/uniprot/Q5G8A3'>Q5G8A3</a> (99% identity on 913 AAs), <a href='http://www.uniprot.org/uniprot/Q5G8A4'>Q5G8A4</a> (99% identity on 895 AAs), <a href='http://www.uniprot.org/uniprot/Q5G8A5'>Q5G8A5</a> (99% identity on 913 AAs), <a href='http://www.uniprot.org/uniprot/B0FWI4'>B0FWI4</a> (98% identity on 898 AAs), <a href='http://www.uniprot.org/uniprot/B0FWI5'>B0FWI5</a> (98% identity on 898 AAs)</td></tr><tr><td class="AutoAnnotatorAlignment1"></td><td class="AutoAnnotatorAlignment2">PDB:</td><td class="AutoAnnotatorAlignment3">&nbsp;- </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">secreted (100%)</td></tr><tr><td class="AutoAnnotatorLocalization1"></td><td class="AutoAnnotatorLocalization2">Bacteria:</td><td class="AutoAnnotatorLocalization3">secreted (52%)</td></tr><tr><td class="AutoAnnotatorLocalization1"></td><td class="AutoAnnotatorLocalization2">Eukarya:</td><td class="AutoAnnotatorLocalization3">cytosol (39%)</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:0009883'>GO:0009883</a> (70%), <a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0042802'>GO:0042802</a> (26%)</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:0006350'>GO:0006350</a> (30%), <a href='http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0006355'>GO:0006355</a> (29%)</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_1381260103944(){hydrophobicity_datapoints = 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= [];trans_datapoints = [];sec_helix_datapoints = [[139,143],[147,150],[165,168],[172,182],[230,248],[255,269],[311,320],[358,366],[414,459],[463,465],[470,476],[498,510],[531,537],[586,596],[605,609],[640,664],[684,688],[693,696],[711,723],[774,796],[818,822],[827,831],[851,864],[911,931],[935,939],[943,957],[1016,1024],[1060,1067]];sec_strand_datapoints = [[60,63],[69,73],[121,126],[131,135],[192,196],[202,209],[213,219],[274,281],[287,292],[323,328],[335,336],[370,380],[398,400],[401,405],[481,486],[488,492],[517,519],[540,546],[551,556],[560,565],[614,625],[631,639],[668,672],[677,681],[731,740],[745,756],[762,770],[802,806],[811,815],[871,877],[882,893],[899,907],[971,977],[987,989],[994,999],[1030,1035],[1041,1043],[1046,1049]];acc_exposed_datapoints = 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= 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= []; 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 = 6;for ( plot_num = 1 ; plot_num < number_of_plots ; plot_num ++){flot_plot_options[plot_num] = $.extend(true, {} 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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_1381260103944 #hydrophobicity_charge_explanation').html(description_html);plot_according_to_selectors_1381260103944();$('#AutoAnnotator_container_1381260103944 #AutoAnnotator_plot_selectors').find('input').click(plot_according_to_selectors_1381260103944);}else{$('#AutoAnnotator_container_1381260103944 #hydrophobicity_charge_container').css('display','none');$('#AutoAnnotator_container_1381260103944 #hydrophobicity_charge_button').val('Show');$('#AutoAnnotator_container_1381260103944 #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_1381260103944(){try{var plot_datasets = [[],[]];if($('#AutoAnnotator_container_1381260103944 #hydrophobicity_checkbox').prop('checked') == true){plot_datasets[0] = { color: 'rgba(100,149,237,1)',data: hydrophobicity_datapoints,label: 'Hydrophobicity',lines: { show: true, fill: true, fillColor: 'rgba(100,149,237,0.1)' },yaxis: 1};}if($('#AutoAnnotator_container_1381260103944 #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 ++){$.plot('#AutoAnnotator_container_1381260103944 #hydrophobicity_charge_placeholder'+ plot_num.toString(), plot_datasets, flot_plot_options[plot_num] );}var screen_width = $('canvas.flot-base').width(); var pos_of_first_tick = 46;var pos_of_last_tick = screen_width - 51;var tick_diff = (screen_width - 97)/199;if($('#AutoAnnotator_container_1381260103944 #dis_checkbox').prop('checked') == 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 <!-- Uncomment this to enable Functional Parameter display