User:ChristopherW

From 2013.igem.org

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 ---