Difference between revisions of "Part:BBa K1159105"

Revision as of 09:30, 20 October 2021

Mature Nuclease NucA from Staphylococcus aureus (Thermonuclease) in RFC[25]

Thermonuclease is a endo-exonuclease from Staphylococcus aureus that degrades dsDNA, ssDNA, dsRNA and ssRNA. This part is coding the mature form of the nuclease, also called NucA. This part is flanked by RFC[25] pre- and suffix for further protein fusions.

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, so ATGGCCGGC and ACCGGT were added (in italics) to the 5' and 3' ends: (underlined part encodes the protein)
ATGGCCGGCGCAACTTCA ... TCAGGTCAAACCGGT
ORF from nucleotide position -8 to 453 (excluding stop-codon)

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

1
101

MAGATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQRTDKYGRGLAYIYADGK
MVNEALVRQGLAKVAYVYKPNNTHEQHLRKSEAQAKKEKLNIWSEDNADSGQTG*

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)	15 (9.7%)
Arg (R)	5 (3.2%)
Asn (N)	6 (3.9%)
Asp (D)	8 (5.2%)

Cys (C)	0 (0.0%)
Gln (Q)	6 (3.9%)
Glu (E)	12 (7.8%)
Gly (G)	12 (7.8%)

His (H)	4 (2.6%)
Ile (I)	5 (3.2%)
Leu (L)	11 (7.1%)
Lys (K)	23 (14.9%)

Met (M)	5 (3.2%)
Phe (F)	3 (1.9%)
Pro (P)	6 (3.9%)
Ser (S)	5 (3.2%)

Thr (T)	11 (7.1%)
Trp (W)	1 (0.6%)
Tyr (Y)	7 (4.5%)
Val (V)	9 (5.8%)

Amino acid counting

	Total number:	154
	Positively charged (Arg+Lys):	28 (18.2%)
	Negatively charged (Asp+Glu):	20 (13.0%)
	Aromatic (Phe+His+Try+Tyr):	15 (9.7%)

Biochemical parameters

	Atomic composition:	C₇₆₃H₁₂₃₁N₂₁₃O₂₃₀S₅
	Molecular mass [Da]:	17228.8
	Theoretical pI:	9.48
	Extinction coefficient at 280 nm [M^-1 cm^-1]:	15930 / 15930 (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)	excellent (0.83)	excellent (0.82)	excellent (0.81)	good (0.72)	acceptable (0.60)

Alignments (obtained from PredictProtein.org)

	SwissProt:	P00644 (99% identity on 150 AAs), Q5HHM4 (98% identity on 150 AAs), Q6GB41 (98% identity on 150 AAs), Q6GIK1 (98% identity on 150 AAs), Q7A6P2 (98% identity on 150 AAs), Q8NXI6 (98% identity on 150 AAs), Q99VJ0 (98% identity on 150 AAs)
	TrEML:	A3QSR2 (98% identity on 140 AAs), A3QSR3 (98% identity on 140 AAs), A3QSR6 (98% identity on 140 AAs), A5A513 (98% identity on 148 AAs), A5A520 (98% identity on 148 AAs), A5A523 (98% identity on 148 AAs), A5IQZ5 (98% identity on 150 AAs), A6QFA0 (98% identity on 150 AAs), A6TZS0 (98% identity on 150 AAs), A7WZZ3 (98% identity on 150 AAs)
	PDB:	1ey0 (100% identity on 136 AAs), 1eyd (100% identity on 136 AAs), 1nsn (100% identity on 138 AAs), 1snc (100% identity on 135 AAs), 1sta (100% identity on 135 AAs), 1stb (100% identity on 136 AAs), 1stg (100% identity on 136 AAs), 1sth (100% identity on 136 AAs), 1stn (100% identity on 136 AAs), 1sty (100% identity on 136 AAs)

Predictions (obtained from PredictProtein.org)

Subcellular Localization (reliability in brackets)

	Archaea:	cytosol (100%)
	Bacteria:	secreted (55%)
	Eukarya:	cytosol (24%)

Gene Ontology (reliability in brackets)

	Molecular Function Ontology:	-
	Biological Process Ontology:	GO:0030541 (28%)

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.

Part Contributions<h2>

NUS Singapore 2021

Authors:
Tania Santosh Nair, Chew Chin Wei, Linus Tan
Contribution Summary:
NUS Singapore 2021 has successfully cloned part into S. cerevisiae and tested part by placing nuclease downstream of the galactose inducible promoter Gal1 (Figure 1). Kill switch efficacy was not optimal and post-induction of NucA yielded a 82% survival rate in S. cerevisiae.

Figure 1: Construct schematic of part assembled with a Gal1 promoter upstream to trigger galactose dependent endonuclease activity

It was postulated that part of the poor activity was due to a lack of a nuclear localization sequence (NLS), hence the inability for NucA translated in the cytosol from accessing the genomic DNA within the nucleus in S. cerevisiae chassis.
In order to improve the efficacy of the nuclease, a NLS sequence was added to the N-terminus of the part, as this was expected to increase the amount of NucA that is translocated to the nucleus to digest the genome and DNA, which in turn will increase the mortality rate of the cell culture.
Attempted to perform part improvement by adding a nuclear localization signal tag to the 5' end of the part sequence to improve the kill switch efficacy in part BBa_K3927015. Addition of NLS improved reduced overall overall survival rate post induction (figure 2).

Figure 2: CFU assay results from pGNucA-H(BY4741) and pGNLSNucA-H(BY4741), ratio of colonies counted from plates with the nuclease induced to the colonies counted from the plates with nuclease uninduced. Nuclease with the NLS attached reduces the total number of live colonies on the plate.

Additional Information Please visit the part registry page for our improved part BBa_K3927015 for more information on the part improvement.

@@ Line 12: / Line 12: @@
 <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_1381259770036'><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1381259770036 --><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>GCAACTTCA&nbsp;...&nbsp;TCAGGTCAA<i>ACCGGT</i></u></span><br>&nbsp;<strong>ORF</strong> from nucleotide position -8 to 453 (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;</td><td class="AutoAnnotatorSeqSeq">MAGATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQRTDKYGRGLAYIYADGK<br>MVNEALVRQGLAKVAYVYKPNNTHEQHLRKSEAQAKKEKLNIWSEDNADSGQTG*</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">15 (9.7%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Arg (R)</td><td class="AutoAnnotatorInnerAmino">5 (3.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asn (N)</td><td class="AutoAnnotatorInnerAmino">6 (3.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asp (D)</td><td class="AutoAnnotatorInnerAmino">8 (5.2%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Cys (C)</td><td class="AutoAnnotatorInnerAmino">0 (0.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gln (Q)</td><td class="AutoAnnotatorInnerAmino">6 (3.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Glu (E)</td><td class="AutoAnnotatorInnerAmino">12 (7.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gly (G)</td><td class="AutoAnnotatorInnerAmino">12 (7.8%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">His (H)</td><td class="AutoAnnotatorInnerAmino">4 (2.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ile (I)</td><td class="AutoAnnotatorInnerAmino">5 (3.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Leu (L)</td><td class="AutoAnnotatorInnerAmino">11 (7.1%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Lys (K)</td><td class="AutoAnnotatorInnerAmino">23 (14.9%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Met (M)</td><td class="AutoAnnotatorInnerAmino">5 (3.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Phe (F)</td><td class="AutoAnnotatorInnerAmino">3 (1.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Pro (P)</td><td class="AutoAnnotatorInnerAmino">6 (3.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ser (S)</td><td class="AutoAnnotatorInnerAmino">5 (3.2%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Thr (T)</td><td class="AutoAnnotatorInnerAmino">11 (7.1%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Trp (W)</td><td class="AutoAnnotatorInnerAmino">1 (0.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Tyr (Y)</td><td class="AutoAnnotatorInnerAmino">7 (4.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Val (V)</td><td class="AutoAnnotatorInnerAmino">9 (5.8%)</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">154</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Positively charged (Arg+Lys):</td><td class="AutoAnnotatorAminoCountingInner3">28 (18.2%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Negatively charged (Asp+Glu):</td><td class="AutoAnnotatorAminoCountingInner3">20 (13.0%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Aromatic (Phe+His+Try+Tyr):</td><td class="AutoAnnotatorAminoCountingInner3">15 (9.7%)</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>763</sub>H<sub>1231</sub>N<sub>213</sub>O<sub>230</sub>S<sub>5</sub></td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Molecular mass [Da]:</td><td class="AutoAnnotatorBiochemParInner3">17228.8</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Theoretical pI:</td><td class="AutoAnnotatorBiochemParInner3">9.48</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">15930 / 15930 (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_1381259770036()' 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></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">excellent (0.83)</td><td class="AutoAnnotatorCodonUsage3">excellent (0.82)</td><td class="AutoAnnotatorCodonUsage3">excellent (0.81)</td><td class="AutoAnnotatorCodonUsage3">good (0.72)</td><td class="AutoAnnotatorCodonUsage3">acceptable (0.60)</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/P00644'>P00644</a> (99% identity on 150 AAs), <a href='http://www.uniprot.org/uniprot/Q5HHM4'>Q5HHM4</a> (98% identity on 150 AAs), <a href='http://www.uniprot.org/uniprot/Q6GB41'>Q6GB41</a> (98% identity on 150 AAs), <a href='http://www.uniprot.org/uniprot/Q6GIK1'>Q6GIK1</a> (98% identity on 150 AAs), <a href='http://www.uniprot.org/uniprot/Q7A6P2'>Q7A6P2</a> (98% identity on 150 AAs), <a href='http://www.uniprot.org/uniprot/Q8NXI6'>Q8NXI6</a> (98% identity on 150 AAs), <a href='http://www.uniprot.org/uniprot/Q99VJ0'>Q99VJ0</a> (98% identity on 150 AAs)</td></tr><tr><td class="AutoAnnotatorAlignment1"></td><td class="AutoAnnotatorAlignment2">TrEML:</td><td class="AutoAnnotatorAlignment3"><a href='http://www.uniprot.org/uniprot/A3QSR2'>A3QSR2</a> (98% identity on 140 AAs), <a href='http://www.uniprot.org/uniprot/A3QSR3'>A3QSR3</a> (98% identity on 140 AAs), <a href='http://www.uniprot.org/uniprot/A3QSR6'>A3QSR6</a> (98% identity on 140 AAs), <a href='http://www.uniprot.org/uniprot/A5A513'>A5A513</a> (98% identity on 148 AAs), <a href='http://www.uniprot.org/uniprot/A5A520'>A5A520</a> (98% identity on 148 AAs), <a href='http://www.uniprot.org/uniprot/A5A523'>A5A523</a> (98% identity on 148 AAs), <a href='http://www.uniprot.org/uniprot/A5IQZ5'>A5IQZ5</a> (98% identity on 150 AAs), <a href='http://www.uniprot.org/uniprot/A6QFA0'>A6QFA0</a> (98% identity on 150 AAs), <a href='http://www.uniprot.org/uniprot/A6TZS0'>A6TZS0</a> (98% identity on 150 AAs), <a href='http://www.uniprot.org/uniprot/A7WZZ3'>A7WZZ3</a> (98% identity on 150 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=1ey0'>1ey0</a> (100% identity on 136 AAs), <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1eyd'>1eyd</a> (100% identity on 136 AAs), <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1nsn'>1nsn</a> (100% identity on 138 AAs), <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1snc'>1snc</a> (100% identity on 135 AAs), <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1sta'>1sta</a> (100% identity on 135 AAs), <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1stb'>1stb</a> (100% identity on 136 AAs), <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1stg'>1stg</a> (100% identity on 136 AAs), <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1sth'>1sth</a> (100% identity on 136 AAs), <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1stn'>1stn</a> (100% identity on 136 AAs), <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=1sty'>1sty</a> (100% identity on 136 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">secreted (55%)</td></tr><tr><td class="AutoAnnotatorLocalization1"></td><td class="AutoAnnotatorLocalization2">Eukarya:</td><td class="AutoAnnotatorLocalization3">cytosol (24%)</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:0030541'>GO:0030541</a> (28%)</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_1381259770036(){hydrophobicity_datapoints = [[2.5,0.88],[3.5,0.34],[4.5,-0.16],[5.5,-0.86],[6.5,-2.00],[7.5,-1.10],[8.5,-1.58],[9.5,-2.22],[10.5,-2.14],[11.5,-1.68],[12.5,-2.08],[13.5,-1.58],[14.5,-0.04],[15.5,1.56],[16.5,1.10],[17.5,1.10],[18.5,2.14],[19.5,0.68],[20.5,-0.30],[21.5,-0.22],[22.5,-0.72],[23.5,-0.78],[24.5,-0.86],[25.5,-0.02],[26.5,1.06],[27.5,0.94],[28.5,-0.68],[29.5,0.02],[30.5,-1.44],[31.5,-2.14],[32.5,-1.50],[33.5,-0.86],[34.5,-0.22],[35.5,-0.42],[36.5,0.66],[37.5,1.04],[38.5,1.94],[39.5,2.22],[40.5,2.42],[41.5,1.52],[42.5,0.44],[43.5,-1.02],[44.5,-2.00],[45.5,-2.08],[46.5,-2.58],[47.5,-2.58],[48.5,-2.66],[49.5,-3.30],[50.5,-2.60],[51.5,-1.12],[52.5,-1.50],[53.5,-1.50],[54.5,-0.98],[55.5,-0.98],[56.5,-2.14],[57.5,-2.14],[58.5,-1.00],[59.5,-0.90],[60.5,-0.46],[61.5,0.42],[62.5,0.98],[63.5,-0.16],[64.5,-0.78],[65.5,-0.76],[66.5,-0.48],[67.5,-1.04],[68.5,-0.96],[69.5,0.18],[70.5,-0.98],[71.5,-2.60],[72.5,-1.00],[73.5,-1.00],[74.5,-0.52],[75.5,-0.44],[76.5,0.90],[77.5,-0.70],[78.5,-0.78],[79.5,-1.70],[80.5,-1.70],[81.5,-3.16],[82.5,-2.60],[83.5,-2.52],[84.5,-3.22],[85.5,-2.78],[86.5,-1.96],[87.5,-2.72],[88.5,-2.10],[89.5,-0.56],[90.5,0.06],[91.5,-0.12],[92.5,1.68],[93.5,1.50],[94.5,1.10],[95.5,0.04],[96.5,0.22],[97.5,-1.46],[98.5,-0.82],[99.5,-0.34],[100.5,-0.34],[101.5,-0.96],[102.5,0.18],[103.5,0.56],[104.5,0.56],[105.5,0.36],[106.5,0.36],[107.5,-0.08],[108.5,-0.08],[109.5,-0.56],[110.5,-0.44],[111.5,1.10],[112.5,1.54],[113.5,0.52],[114.5,1.00],[115.5,1.52],[116.5,-0.10],[117.5,-0.78],[118.5,-1.22],[119.5,-2.76],[120.5,-2.64],[121.5,-2.50],[122.5,-2.88],[123.5,-2.88],[124.5,-2.82],[125.5,-1.92],[126.5,-2.18],[127.5,-2.26],[128.5,-1.72],[129.5,-1.78],[130.5,-2.18],[131.5,-1.98],[132.5,-0.84],[133.5,-1.46],[134.5,-1.54],[135.5,-2.60],[136.5,-2.68],[137.5,-2.28],[138.5,-2.20],[139.5,-0.52],[140.5,0.00],[141.5,0.62],[142.5,-0.84],[143.5,-0.84],[144.5,-2.44],[145.5,-1.90],[146.5,-2.44],[147.5,-1.90],[148.5,-1.28],[149.5,-1.28],[150.5,-1.78],[151.5,-1.16]];charge_datapoints = [[2.5,0.00],[3.5,0.00],[4.5,0.00],[5.5,0.20],[6.5,0.40],[7.5,0.40],[8.5,0.50],[9.5,0.70],[10.5,0.30],[11.5,0.10],[12.5,0.10],[13.5,-0.00],[14.5,-0.20],[15.5,-0.00],[16.5,0.20],[17.5,0.20],[18.5,0.20],[19.5,-0.00],[20.5,-0.00],[21.5,-0.40],[22.5,-0.40],[23.5,-0.40],[24.5,-0.00],[25.5,-0.00],[26.5,0.20],[27.5,0.20],[28.5,0.40],[29.5,0.20],[30.5,0.20],[31.5,0.20],[32.5,0.20],[33.5,-0.00],[34.5,-0.00],[35.5,0.20],[36.5,0.20],[37.5,0.20],[38.5,0.20],[39.5,0.20],[40.5,-0.20],[41.5,-0.20],[42.5,-0.20],[43.5,-0.40],[44.5,-0.40],[45.5,-0.00],[46.5,0.10],[47.5,0.10],[48.5,0.50],[49.5,0.70],[50.5,0.50],[51.5,0.40],[52.5,0.20],[53.5,0.20],[54.5,-0.00],[55.5,-0.00],[56.5,-0.00],[57.5,-0.00],[58.5,-0.20],[59.5,-0.20],[60.5,-0.20],[61.5,-0.20],[62.5,-0.00],[63.5,0.20],[64.5,0.40],[65.5,0.40],[66.5,0.40],[67.5,0.20],[68.5,-0.00],[69.5,-0.20],[70.5,-0.00],[71.5,0.20],[72.5,0.40],[73.5,0.20],[74.5,0.20],[75.5,-0.20],[76.5,-0.40],[77.5,-0.60],[78.5,-0.20],[79.5,-0.20],[80.5,-0.00],[81.5,0.20],[82.5,0.40],[83.5,-0.00],[84.5,0.20],[85.5,0.20],[86.5,-0.00],[87.5,0.20],[88.5,0.40],[89.5,0.20],[90.5,0.20],[91.5,0.20],[92.5,-0.00],[93.5,-0.00],[94.5,-0.00],[95.5,-0.20],[96.5,-0.20],[97.5,-0.00],[98.5,-0.00],[99.5,-0.00],[100.5,0.20],[101.5,-0.00],[102.5,-0.20],[103.5,-0.20],[104.5,-0.20],[105.5,-0.00],[106.5,0.20],[107.5,0.20],[108.5,0.20],[109.5,0.20],[110.5,0.20],[111.5,0.20],[112.5,0.20],[113.5,0.20],[114.5,0.20],[115.5,-0.00],[116.5,0.20],[117.5,0.20],[118.5,0.20],[119.5,0.20],[120.5,0.20],[121.5,0.10],[122.5,-0.10],[123.5,-0.10],[124.5,-0.00],[125.5,-0.00],[126.5,0.10],[127.5,0.50],[128.5,0.50],[129.5,0.20],[130.5,0.20],[131.5,-0.00],[132.5,-0.20],[133.5,-0.00],[134.5,0.40],[135.5,0.20],[136.5,0.40],[137.5,0.40],[138.5,0.20],[139.5,-0.00],[140.5,0.20],[141.5,-0.00],[142.5,-0.20],[143.5,-0.40],[144.5,-0.40],[145.5,-0.40],[146.5,-0.60],[147.5,-0.40],[148.5,-0.20],[149.5,-0.20],[150.5,-0.20],[151.5,-0.00]];dis_datapoints = [];trans_datapoints = [];sec_helix_datapoints = [[58,70],[101,109],[125,139]];sec_strand_datapoints = [[15,21],[25,30],[35,42],[74,79],[90,97],[113,117]];acc_exposed_datapoints = [[1,3],[5,6],[8,14],[22,22],[24,24],[31,34],[46,46],[48,53],[55,56],[59,59],[63,63],[66,67],[70,74],[81,84],[87,87],[98,98],[100,100],[108,109],[119,123],[126,126],[130,130],[133,133],[136,139],[141,141],[144,144],[146,154]];acc_buried_datapoints = [[15,15],[17,18],[20,21],[23,23],[25,26],[28,28],[35,35],[37,37],[39,42],[44,45],[58,58],[61,61],[64,65],[68,69],[75,75],[77,77],[88,93],[95,97],[102,103],[106,107],[110,112],[114,114],[128,128],[131,131],[135,135],[142,143]];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 = 1;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( $('#AutoAnnotator_container_1381259770036 #hydrophobicity_charge_button').val() =='Show' ){$('#AutoAnnotator_container_1381259770036 #hydrophobicity_charge_container').css('display','block');$('#AutoAnnotator_container_1381259770036 #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_1381259770036 #hydrophobicity_charge_explanation').html(description_html);plot_according_to_selectors_1381259770036();$('#AutoAnnotator_container_1381259770036 #AutoAnnotator_plot_selectors').find('input').click(plot_according_to_selectors_1381259770036);}else{$('#AutoAnnotator_container_1381259770036 #hydrophobicity_charge_container').css('display','none');$('#AutoAnnotator_container_1381259770036 #hydrophobicity_charge_button').val('Show');$('#AutoAnnotator_container_1381259770036 #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_1381259770036(){try{var plot_datasets = [[],[]];if($('#AutoAnnotator_container_1381259770036 #hydrophobicity_checkbox').prop('checked') == true){plot_datasets[0] = { color: 'rgba(100,149,237,1)',data: hydrophobicity_datapoints,label: 'Hydrophobicity',lines: { show: true, fill: true, fillColor: 'rgba(100,149,237,0.1)' },yaxis: 1};}if($('#AutoAnnotator_container_1381259770036 #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_1381259770036 #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_1381259770036 #dis_checkbox').prop('checked') == true){for ( j = 0 ; j < dis_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381259770036 #hydrophobicity_charge_placeholder' + Math.floor((dis_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_dis\' style=\'left:' + ((pos_of_first_tick - 8 + (dis_datapoints[j][0] - 1)*tick_diff - Math.floor((dis_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px;\'><b>' + (j+1) + '</b></div>');$('#AutoAnnotator_container_1381259770036 #hydrophobicity_charge_placeholder' + Math.floor((dis_datapoints[j][1] - 1)/200) ).append('<div class=\'AutoAnnotator_dis\' style=\'left:' + ((pos_of_first_tick - 8 + (dis_datapoints[j][1] - 1)*tick_diff - Math.floor((dis_datapoints[j][1] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px;\'><b>' + (j+1) + '</b></div>');}}if($('#AutoAnnotator_container_1381259770036 #trans_checkbox').prop('checked') == true){for ( j = 0 ; j < trans_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381259770036 #hydrophobicity_charge_placeholder' + Math.floor((trans_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_trans\' style=\'width:' + (((trans_datapoints[j][1] - trans_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px ;left:' + ((pos_of_first_tick + (trans_datapoints[j][0] - 1.5)*tick_diff - Math.floor((trans_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px\'></div>');}}if($('#AutoAnnotator_container_1381259770036 #sec_checkbox').prop('checked') == true){for ( j = 0 ; j < sec_helix_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381259770036 #hydrophobicity_charge_placeholder' + Math.floor((sec_helix_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_sec_helix\' style=\'width:' + (((sec_helix_datapoints[j][1] - sec_helix_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px; left:' + ((pos_of_first_tick + (sec_helix_datapoints[j][0] - 1.5)*tick_diff - Math.floor((sec_helix_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px\'></div>');}for ( j = 0 ; j < sec_strand_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381259770036 #hydrophobicity_charge_placeholder' + Math.floor((sec_strand_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_sec_strand\' style=\'width:' + (((sec_strand_datapoints[j][1] - sec_strand_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px; left:' + ((pos_of_first_tick + (sec_strand_datapoints[j][0] - 1.5)*tick_diff - Math.floor((sec_strand_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px\'></div>');}}if($('#AutoAnnotator_container_1381259770036 #acc_checkbox').prop('checked') == true){for ( j = 0 ; j < acc_buried_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381259770036 #hydrophobicity_charge_placeholder' + Math.floor((acc_buried_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_acc_buried\' style=\'width:' + (((acc_buried_datapoints[j][1] - acc_buried_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px; left:' + ((pos_of_first_tick + (acc_buried_datapoints[j][0] - 1.5)*tick_diff - Math.floor((acc_buried_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px\'></div>');}for ( j = 0 ; j < acc_exposed_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381259770036 #hydrophobicity_charge_placeholder' + Math.floor((acc_exposed_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_acc_exposed\' style=\'width:' + (((acc_exposed_datapoints[j][1] - acc_exposed_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px; left:' + ((pos_of_first_tick + (acc_exposed_datapoints[j][0] - 1.5)*tick_diff - Math.floor((acc_exposed_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px\'></div>');}}}catch(err){txt='There was an error while drawing the selected elements for the plot.\n';txt=txt+'The originating error is:\n' + err + '\n\n';throw(txt);}}</script></html>
-=== Part Contributions ===
+=== <h2>Part Contributions<h2> ===
-<h2>NUS Singapore 2021</h2>
+<h4>NUS Singapore 2021</h4>
 '''Authors:'''