| - | Percentage of amino acids: * * +--------------+--------+--------+--------+--------+--------+ * * | AA: | G | L | S | P | A | * * | % of AA: | 11.5 | 10.6 | 7.7 | 7.7 | 7.3 | * * +--------------+--------+--------+--------+--------+--------+ * * | AA: | R | E | V | K | C | * * | % of AA: | 7.0 | 5.6 | 5.2 | 4.7 | 4.5 | * * +--------------+--------+--------+--------+--------+--------+ * * | AA: | D | Q | T | F | Y | * * | % of AA: | 4.2 | 4.0 | 3.5 | 3.3 | 3.1 | * * +--------------+--------+--------+--------+--------+--------+ * * | AA: | H | N | I | W | M | * * | % of AA: | 2.8 | 2.3 | 2.3 | 1.9 | 0.7 | * * +--------------+--------+--------+--------+--------+--------+ * * * * Percentage of helical trans-membrane predicted: * * +--------------+--------+--------+ * * | SecStr: | H | L | * * | % Predicted: | 0.0 | 100.0 | * * +--------------+--------+--------+ * * * **************************************************************************** * * * PHD output for your protein * * 10:17, 4 September 2013 (CDT)10:17, 4 September 2013 (CDT)10:17, 4 September 2013 (CDT)10:17, 4 September 2013 (CDT)10:17, 4 September 2013 (CDT)~~ * * * * Jury on: 4 different architectures (version 8.94_69 ). * * Note: differently trained architectures, i.e., different versions can * * result in different predictions. * * * **************************************************************************** * * * About the protein * * 10:17, 4 September 2013 (CDT)10:17, 4 September 2013 (CDT)10:17, 4 September 2013 (CDT)~~ * * * * HEADER * * COMPND * * SOURCE * * AUTHOR * * SEQLENGTH 426 * * NCHAIN 1 chain(s) in query data set * * NALIGN 55 * * (=number of aligned sequences in HSSP file) * * * * * * protein: query length 426 * * * --- --- PhdTopology REFINEMENT AND TOPOLOGY PREDICTION: SYMBOLS --- AA : amino acid in one-letter code --- PHD htm : HTM's predicted by the PHD neural network --- system (H=HTM, ' '=not HTM) --- Rel htm : Reliability index of prediction (0-9, 0 is low) --- detail : Neural network output in detail --- prH htm : 'Probability' for assigning a helical trans- --- membrane region (HTM) --- prL htm : 'Probability' for assigning a non-HTM region --- note: 'Probabilites' are scaled to the interval --- 0-9, e.g., prH=5 means, that the first --- output node is 0.5-0.6 --- subset : Subset of more reliable predictions --- SUB htm : All residues for which the expected average --- accuracy is > 82% (tables in header). --- note: for this subset the following symbols are used: --- L: is loop (for which above ' ' is used) --- '.': means that no prediction is made for this, --- residue as the reliability is: Rel < 5 --- other : predictions derived based on PHDhtm --- PHDFhtm : filtered prediction, i.e., too long HTM's are --- split, too short ones are deleted --- PHDRhtm : refinement of neural network output --- PHDThtm : topology prediction based on refined model --- symbols used: --- i: intra-cytoplasmic --- T: transmembrane region --- o: extra-cytoplasmic --- --- PhdTopology REFINEMENT AND TOPOLOGY PREDICTION ....,....1....,....2....,....3....,....4....,....5....,....6 AA |MFRTKRSALVRRLWRSRAPGGEDEEEGAGGGGGGGELRGEGATDSRAHGAGGGGPGRAGC| PHD htm | | detail: prH htm |000000000000000000000000000000000000000000000000000000000000| prL htm |999999999999999999999999999999999999999999999999999999999999| subset: SUB htm |............................................................| ....,....7....,....8....,....9....,....10...,....11...,....12 AA |CLGKAVRGAKGHHHPHPPAAGAGAAGGAEADLKALTHSVLKKLKERQLELLLQAVESRGG| PHD htm | | detail: prH htm |000000000000000000000000000000000000000000000000000000000000| prL htm |999999999999999999999999999999999999999999999999999999999999| subset: SUB htm |............................................................| ....,....13...,....14...,....15...,....16...,....17...,....18 AA |TRTACLLLPGRLDCRLGPGAPAGAQPAQPPSSYSLPLLLCKVFRWPDLRHSSEVKRLCCC| PHD htm | | detail: prH htm |000000000000000000000000000000000000000000000000000000000000| prL htm |999999999999999999999999999999999999999999999999999999999999| subset: SUB htm |............................................................| ....,....19...,....20...,....21...,....22...,....23...,....24 AA |ESYGKINPELVCCNPHHLSRLCELESPPPPYSRYPMDFLKPTADCPDAVPSSAETGGTNY| PHD htm | | detail: prH htm |000000000000000000000000000000000000000000000000000000000000| prL htm |999999999999999999999999999999999999999999999999999999999999| subset: SUB htm |............................................................| ....,....25...,....26...,....27...,....28...,....29...,....30 AA |LAPGGLSDSQLLLEPGDRSHWCVVAYWEEKTRVGRLYCVQEPSLDIFYDLPQGNGFCLGQ| PHD htm | | detail: prH htm |000000000000000000000000000000000000000000000000000000000000| prL htm |999999999999999999999999999999999999999999999999999999999999| subset: SUB htm |............................................................| ....,....31...,....32...,....33...,....34...,....35...,....36 AA |LNSDNKSQLVQKVRSKIGCGIQLTREVDGVWVYNRSSYPIFIKSATLDNPDSRTLLVHKV| PHD htm | | detail: prH htm |000000000000000000000000000000000000000000000000000000000000| prL htm |999999999999999999999999999999999999999999999999999999999999| subset: SUB htm |............................................................| ....,....37...,....38...,....39...,....40...,....41...,....42 AA |FPGFSIKAFDYEKAYSLQRPNDHEFMQQPWTGFTVQISFVKGWGQCYTRQFISSCPCWLE| PHD htm | | detail: prH htm |000000000000000000000000000000000000000000000000000000000000| prL htm |999999999999999999999999999999999999999999999999999999999999| subset: SUB htm |............................................................| ....,....43...,....44...,....45...,....46...,....47...,....48 AA |VIFNSR| PHD htm | | detail: prH htm |000000| prL htm |999999| subset: SUB htm |......| --- --- PhdTopology REFINEMENT AND TOPOLOGY PREDICTION END ---
| + | <html><!--- Please copy this table containing parameters for BBa_K801060 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% } </style><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1378565906220 --><th id="AutoAnnotatorHeader" colspan="2">Protein data table for BioBrick <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K801060">BBa_K801060</a> automatically created by the <a href="https://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"> GTACACA<u>ATGCGTCGT ... TTCGAAAAA</u>TAA</span><br> <strong>ORF</strong> from nucleotide position 8 to 1705 (excluding stop-codon)</td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Amino acid sequence:</strong> (RFC25 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 <br>401 <br>501 </td><td class="AutoAnnotatorSeqSeq">MRRSANYQPSIWDHDFLQSLNSNYTDEAYKRRAEELRGKVKIAIKDVIEPLDQLDLIDNLQRLGLAHRFETEIRNILNNIYNNNKDYNWRKENLYATSLE<br>FRLLRQHGYPVSQEVFNGFKDDQGGFICDDFKGILSLHEASYYSLEGESIMEEAWQFTSKHLKEVMISKNMEEDVFVAEQAKRALELPLHWKVPMLEARW<br>FIHIYERREDKNHLLLELAKMEFNTLQAIYQEELKEISGWWKDTGLGEKLSFARNRLVASFLWSMGIAFEPQFAYCRRVLTISIALITVIDDIYDVYGTL<br>DELEIFTDAVERWDINYALKHLPGYMKMCFLALYNFVNEFAYYVLKQQDFDLLLSIKNAWLGLIQAYLVEAKWYHSKYTPKLEEYLENGLVSITGPLIIT<br>ISYLSGTNPIIKKELEFLESNPDIVHWSSKIFRLQDDLGTSSDEIQRGDVPKSIQCYMHETGASEEVARQHIKDMMRQMWKKVNAYTADKDSPLTGTTTE<br>FLLNLVRMSHFMYLHGDGHGVQNQETIDVGFTLLFQPIPLEDKHMAFTASPGTKG<b>TG</b>A<u>WSHPQFEK</u>*</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="https://2013.igem.org/Team:TU-Munich/Results/Software/FeatureList">list of supported features</a>)<table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorSeqFeat1"></td><td class="AutoAnnotatorSeqFeat2a">RFC25 scar (shown in bold): </td><td class="AutoAnnotatorSeqFeat3">556 to 557</td></tr><tr><td class="AutoAnnotatorSeqFeat1"></td><td class="AutoAnnotatorSeqFeat2a"><i>Strep</i>-tag II: </td><td class="AutoAnnotatorSeqFeat3">559 to 566</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">33 (5.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Arg (R)</td><td class="AutoAnnotatorInnerAmino">25 (4.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asn (N)</td><td class="AutoAnnotatorInnerAmino">27 (4.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asp (D)</td><td class="AutoAnnotatorInnerAmino">34 (6.0%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Cys (C)</td><td class="AutoAnnotatorInnerAmino">4 (0.7%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gln (Q)</td><td class="AutoAnnotatorInnerAmino">24 (4.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Glu (E)</td><td class="AutoAnnotatorInnerAmino">48 (8.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gly (G)</td><td class="AutoAnnotatorInnerAmino">29 (5.1%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">His (H)</td><td class="AutoAnnotatorInnerAmino">18 (3.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ile (I)</td><td class="AutoAnnotatorInnerAmino">39 (6.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Leu (L)</td><td class="AutoAnnotatorInnerAmino">64 (11.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Lys (K)</td><td class="AutoAnnotatorInnerAmino">36 (6.4%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Met (M)</td><td class="AutoAnnotatorInnerAmino">16 (2.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Phe (F)</td><td class="AutoAnnotatorInnerAmino">28 (4.9%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Pro (P)</td><td class="AutoAnnotatorInnerAmino">17 (3.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ser (S)</td><td class="AutoAnnotatorInnerAmino">33 (5.8%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Thr (T)</td><td class="AutoAnnotatorInnerAmino">26 (4.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Trp (W)</td><td class="AutoAnnotatorInnerAmino">14 (2.5%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Tyr (Y)</td><td class="AutoAnnotatorInnerAmino">27 (4.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Val (V)</td><td class="AutoAnnotatorInnerAmino">24 (4.2%)</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">566</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Positively charged (Arg+Lys):</td><td class="AutoAnnotatorAminoCountingInner3">61 (10.8%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Negatively charged (Asp+Glu):</td><td class="AutoAnnotatorAminoCountingInner3">82 (14.5%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Aromatic (Phe+His+Try+Tyr):</td><td class="AutoAnnotatorAminoCountingInner3">87 (15.4%)</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>3002</sub>H<sub>4586</sub>N<sub>778</sub>O<sub>868</sub>S<sub>20</sub></td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Molecular mass [Da]:</td><td class="AutoAnnotatorBiochemParInner3">66105.3</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Theoretical pI:</td><td class="AutoAnnotatorBiochemParInner3">5.38</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">117230 / 117480 (all Cys red/ox)</td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Hydrophobicity and charge plot</strong><br><div id="hydrophobicity_charge_placeholder" style="width:600px;height:300px"></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 (0.71)</td><td class="AutoAnnotatorCodonUsage3">good (0.75)</td><td class="AutoAnnotatorCodonUsage3">good (0.69)</td><td class="AutoAnnotatorCodonUsage3">good (0.78)</td><td class="AutoAnnotatorCodonUsage3">excellent (0.80)</td><td class="AutoAnnotatorCodonUsage3">good (0.68)</td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"> The BioBrick-AutoAnnotator was created by <a href="https://2013.igem.org/Team:TU-Munich">TU-Munich 2013</a> iGEM team. For more information please see the <a href="https://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="https://2013.igem.org/Team:TU-Munich/Results/AutoAnnotator">comment</a>.</td></tr></table><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='Flot.js'></script><script>$(document).ready(function() {var d1 = [[0.5, 0.3], [1.5, 2.8], [2.5, -1.5], [3.5, -3]];var d2 = [[0.5, 0.3], [1.5, 0.8], [2.5, -0.5], [3.5, -1]];var options = { grid: { //backgroundColor: { colors: [ '#fff', '#eee' ] }, borderWidth: { top: 0, right: 0, bottom: 0, left: 0 } }, xaxes: [{ min: 0, max: 3, ticks: [[0.5, 'M'], [1.5, 'F'], [2.5, 'A']], tickLength: -2 }], yaxes: [{ ticks: [[0, '0'], [4.5,'hydrophobic'], [-4.5,'hydrohilic']], min: -4.5, max: +4.5 }, { ticks: [[0, '0'], [1,'positively charged'], [-1,'negatively charged']], position: 'right', min: -1, max: 1 }]};$.plot('#hydrophobicity_charge_placeholder',[{ color: 'rgba(151,187,205,1)', data: d1, label: 'Hydrophobicity', lines: { show: true, fill: true }, yaxis: 1}, { color: 'rgba(220,220,220,1)', data: d2, label: 'Charge', lines: { show: true, fill: true }, yaxis: 2}],options );}</script></html> |
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