****************************************************************************
* *
* 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: | 4.1 | 95.9 | *
* +--------------+--------+--------+ *
* *
****************************************************************************
---
--- ------------------------------------------------------------
--- PhdTopology prediction of transmembrane helices and topology
--- ------------------------------------------------------------
---
--- PhdTopology REFINEMENT AND TOPOLOGY HEADER: ABBREVIATIONS
---
--- NHTM_BEST : number of transmembrane helices best model
--- NHTM_2ND_BEST: number of transmembrane helices 2nd best model
--- REL_BEST : reliability of best model (0 is low, 9 high)
--- HTMTOP_PRD : topology predicted ('in': intra-cytoplasmic)
--- HTMTOP_RID : difference between positive charges
--- HTMTOP_RIP : reliability of topology prediction (0-9)
--- MOD_NHTM : number of transmembrane helices of model
--- MOD_STOT : score for all residues
--- MOD_SHTM : score for HTM added at current iteration step
--- MOD_N-C : N - C term of HTM added at current step
---
--- ALGORITHM REF: The refinement is performed by a dynamic pro-
--- ALGORITHM : gramming-like procedure: iteratively the best
--- ALGORITHM : transmembrane helix (HTM) compatible with the
--- ALGORITHM : network output is added (starting from the 0
--- ALGORITHM : assumption, i.e., no HTM's in the protein).
--- ALGORITHM TOP: Topology is predicted by the positive-inside
--- ALGORITHM : rule, i.e., the positive charges are compiled
--- ALGORITHM : separately for all even and all odd non-HTM
--- ALGORITHM : regions. If the difference (charge even-odd)
--- ALGORITHM : is < 0, topology is predicted as 'in'. That
--- ALGORITHM : means, the protein N-term starts on the intra
--- ALGORITHM : cytoplasmic side.
---
--- PhdTopology REFINEMENT HEADER: SUMMARY
MOD_NHTM MOD_STOT MOD_SHTM MOD_N-C
1 0.972 0.854 457 - 474
---
--- PhdTopology REFINEMENT AND TOPOLOGY HEADER: SUMMARY
--- NHTM_BEST : 1
--- NHTM_2ND_BEST: 0
--- REL_BEST : 2
--- HTMTOP_PRD : out
--- HTMTOP_RID : 1.720
--- HTMTOP_RIP : 1
---
--- 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 |MECVRSGALDLGRSGNFLGKSGSTTSCGKVRCSTNLAGSTKCEQNLHGKAKPLLLSASGK|
PHD htm | |
Rel htm |999999999999999999999999999999999999999999999999999999999999|
detail: | |
prH htm |000000000000000000000000000000000000000000000000000000000000|
prL htm |999999999999999999999999999999999999999999999999999999999999|
subset: | |
SUB htm |LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL|
other: | |
PHDFhtm | |
PHDRhtm | |
PHDThtm |oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo|
....,....7....,....8....,....9....,....10...,....11...,....12
AA |ARGTSGLVHRSPVLKHQHHLSVRSTSTDVCTTFDEDVKGVSSHAVEEKVGVLLLNLGGPE|
PHD htm | |
Rel htm |999999999999999999999999999999999999999999999999999999999999|
detail: | |
prH htm |000000000000000000000000000000000000000000000000000000000000|
prL htm |999999999999999999999999999999999999999999999999999999999999|
subset: | |
SUB htm |LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL|
other: | |
PHDFhtm | |
PHDRhtm | |
PHDThtm |oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo|
....,....13...,....14...,....15...,....16...,....17...,....18
AA |TLNDVQPFLFNLFADPDIIRLPRLFRFLQRPLAKLISTFRAPKSNEGYASIGGGSPLRKI|
PHD htm | |
Rel htm |999999999999999999999999999999998889999999999999999999999999|
detail: | |
prH htm |000000000000000000000000000000000000000000000000000000000000|
prL htm |999999999999999999999999999999999999999999999999999999999999|
subset: | |
SUB htm |LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL|
other: | |
PHDFhtm | |
PHDRhtm | |
PHDThtm |oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo|
....,....19...,....20...,....21...,....22...,....23...,....24
AA |TDEQANALKVALKSKNLEADIYVGMRYWYPFTEEAIDQIKKDKITKLVVLPLYPQYSIST|
PHD htm | |
Rel htm |999999999999999999999999999999999999999999999999988888888899|
detail: | |
prH htm |000000000000000000000000000000000000000000000000000000000000|
prL htm |999999999999999999999999999999999999999999999999999999999999|
subset: | |
SUB htm |LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL|
other: | |
PHDFhtm | |
PHDRhtm | |
PHDThtm |oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo|
....,....25...,....26...,....27...,....28...,....29...,....30
AA |SGSSIRVLQNIVKEDPYFAGLPISIIESWYQREGYVKSMADLIEKELSVFSNPEEVMIFF|
PHD htm | |
Rel htm |999999999999999999999999999999999999999999999999999999999877|
detail: | |
prH htm |000000000000000000000000000000000000000000000000000000000011|
prL htm |999999999999999999999999999999999999999999999999999999999988|
subset: | |
SUB htm |LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL|
other: | |
PHDFhtm | |
PHDRhtm | |
PHDThtm |oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo|
....,....31...,....32...,....33...,....34...,....35...,....36
AA |SAHGVPLTYVKDAGDPYRDQMEDCIALIMEELKSRGTLNDHTLAYQSRVGPVQWLKPYTD|
PHD htm | |
Rel htm |788999999999999999999999999999999999999999999999999999999999|
detail: | |
prH htm |100000000000000000000000000000000000000000000000000000000000|
prL htm |899999999999999999999999999999999999999999999999999999999999|
subset: | |
SUB htm |LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL|
other: | |
PHDFhtm | |
PHDRhtm | |
PHDThtm |oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo|
....,....37...,....38...,....39...,....40...,....41...,....42
AA |EVLVELGQKGVKSLLAVPVSFVSEHIETLEEIDMEYRELALESGIENWGRVPALGCTSSF|
PHD htm | |
Rel htm |999999999999988777667789999999999999999999999999999999999999|
detail: | |
prH htm |000000000000000111111100000000000000000000000000000000000000|
prL htm |999999999999999888888899999999999999999999999999999999999999|
subset: | |
SUB htm |LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL|
other: | |
PHDFhtm | |
PHDRhtm | |
PHDThtm |oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo|
....,....43...,....44...,....45...,....46...,....47...,....48
AA |ISDLADAVVEALPSASAMATRKVKDTDSDMDMMHYLTKMFLGSVLAFFLLLSPRLVSAFR|
PHD htm | HHHHHHHHHHHHHHHHHHHH |
Rel htm |988899999999999999999999999999987752036788888888887763200256|
detail: | |
prH htm |000000000000000000000000000000001123568899999999998886654321|
prL htm |999999999999999999999999999999998876431100000000001113345678|
subset: | |
SUB htm |LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL...HHHHHHHHHHHHHHH.....LL|
other: | |
PHDFhtm | HHHHHHHHHHHHHHHHHHHH |
PHDRhtm | HHHHHHHHHHHHHHHHHH |
PHDThtm |ooooooooooooooooooooooooooooooooooooTTTTTTTTTTTTTTTTTTiiiiii|
....,....49...,....50...,....51...,....52...,....53...,....54
AA |NTLQ|
PHD htm | |
Rel htm |7788|
detail: | |
prH htm |1100|
prL htm |8899|
subset: | |
SUB htm |LLLL|
other: | |
PHDFhtm | |
PHDRhtm | |
PHDThtm |iiii|
---
--- PhdTopology REFINEMENT AND TOPOLOGY PREDICTION END
---