****************************************************************************
* *
* PHD: Profile fed neural network systems from HeiDelberg *
* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ *
* *
* Prediction of: *
* helical transmembrane regions, by PHDhtm *
* *
* Author: *
* Burkhard Rost *
* EMBL, 69012 Heidelberg, Germany *
* Internet: Rost@EMBL-Heidelberg.DE *
* *
* All rights reserved. *
* *
****************************************************************************
* *
* Percentage of helical trans-membrane predicted: *
* +--------------+--------+--------+ *
* | SecStr: | H | L | *
* | % Predicted: | 0.0 | 100.0 | *
* +--------------+--------+--------+ *
* *
****************************************************************************
---
--- 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 |............................................................|
PHD htm | |
Rel htm |999999999999999999999999999999999999999999999999999999999999|
detail: | |
prH htm |000000000000000000000000000000000000000000000000000000000000|
prL htm |999999999999999999999999999999999999999999999999999999999999|
subset: | |
SUB htm |LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL|
....,....7....,....8....,....9....,....10...,....11...,....12
AA |....................................................MRQTKTGI|
PHD htm | |
Rel htm |999999999999999999999999999999999999999999999999999999999999|
detail: | |
prH htm |000000000000000000000000000000000000000000000000000000000000|
prL htm |999999999999999999999999999999999999999999999999999999999999|
subset: | |
SUB htm |LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL|
....,....13...,....14...,....15...,....16...,....17...,....18
AA |LLANLGTPDAPTPEAVKRYLKQFLSDRRVVDTSRLLWWPLLRGVIFPLRSPRVAKLYASV|
PHD htm | |
Rel htm |999999999999999999999999999999999999999999999999999999999999|
detail: | |
prH htm |000000000000000000000000000000000000000000000000000000000000|
prL htm |999999999999999999999999999999999999999999999999999999999999|
subset: | |
SUB htm |LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL|
....,....19...,....20...,....21...,....22...,....23...,....24
AA |WMEG..GSPLMVYSRQQQQALAQRLP....EMPVA...LGMSYGSPSLESAVDELLAEHV|
PHD htm | |
Rel htm |999999999999999999999999999999999999999999999999999999999999|
detail: | |
prH htm |000000000000000000000000000000000000000000000000000000000000|
prL htm |999999999999999999999999999999999999999999999999999999999999|
subset: | |
SUB htm |LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL|
....,....25...,....26...,....27...,....28...,....29...,....30
AA |DHIVVLPLYPQFSCSTVGAVWDELARILARKRSIPGISF..IRDYADNHDYINALANSVR|
PHD htm | |
Rel htm |999999999999999999999999999999999999999999999999999999999999|
detail: | |
prH htm |000000000000000000000000000000000000000000000000000000000000|
prL htm |999999999999999999999999999999999999999999999999999999999999|
subset: | |
SUB htm |LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL|
....,....31...,....32...,....33...,....34...,....35...,....36
AA |ASFAKHG.EPD...LLLLSYHGIPQRYA.DEGDDYPQRCRTTTRELASALGMAP..EKVM|
PHD htm | |
Rel htm |999999999999999999999999999999999999999999999999999999999999|
detail: | |
prH htm |000000000000000000000000000000000000000000000000000000000000|
prL htm |999999999999999999999999999999999999999999999999999999999999|
subset: | |
SUB htm |LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL|
....,....37...,....38...,....39...,....40...,....41...,....42
AA |MTFQSRF.GREPWLMPYTDETLKML.GEKGVGHIQVMCPGFAADCLETLEEIAEQNREVF|
PHD htm | |
Rel htm |999999999999999999999999999999999999999999999999999999999999|
detail: | |
prH htm |000000000000000000000000000000000000000000000000000000000000|
prL htm |999999999999999999999999999999999999999999999999999999999999|
subset: | |
SUB htm |LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL|
....,....43...,....44...,....45...,....46...,....47...,....48
AA |.LGAGGKKYEYIPALNATPEHIEMMANLVAAYR...........................|
PHD htm | |
Rel htm |999999999999999999999999999999999999999999999999999999999999|
detail: | |
prH htm |000000000000000000000000000000000000000000000000000000000000|
prL htm |999999999999999999999999999999999999999999999999999999999999|
subset: | |
SUB htm |LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL|
....,....49...,....50...,....51...,....52...,....53...,....54
AA |....................................................|
PHD htm | |
Rel htm |9999888998887889999999999999999999999999999999999999|
detail: | |
prH htm |0000000000001000000000000000000000000000000000000000|
prL htm |9999999999998999999999999999999999999999999999999999|
subset: | |
SUB htm |LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL|
---
--- PhdTopology REFINEMENT AND TOPOLOGY PREDICTION END
---