Note: comments marked by "## COMMENT: "
The following information has been received by the server:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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rost@embl-heidelberg.de
pred htm top
return concise
# imm1_ecoli, IMMUNITY PROTEIN FOR COLICIN E1
MSLRYYIKNILFGLYCTLIYIYLITKNSEGYYFLVSDKMLYAIVISTILCPYSKYAIEYI
AFNFIKKDFFERRKNLNNAPVAKLNLFMLYNLLCLVLAIPFGLLELFISIKNN
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The sequence had been interpreted as being:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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>P1; t2
(#) imm1_ecoli, immunity protein for colicin e1
MSLRYYIKNILFGLYCTLIYIYLITKNSEGYYFLVSDKMLYAIVISTILCPYSKYAIEYI
AFNFIKKDFFERRKNLNNAPVAKLNLFMLYNLLCLVLAIPFGLLELFISIKNN
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The alignment that has been used as input to the network is:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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--- ------------------------------------------------------------
--- MAXHOM multiple sequence alignment
--- ------------------------------------------------------------
---
--- MAXHOM ALIGNMENT HEADER: ABBREVIATIONS FOR SUMMARY
--- ID : identifier of aligned (homologous) protein
--- STRID : PDB identifier (only for known structures)
--- PIDE : percentage of pairwise sequence identity
--- WSIM : percentage of weighted similarity
--- LALI : number of residues aligned
--- NGAP : number of insertions and deletions (indels)
--- LGAP : number of residues in all indels
--- LSEQ2 : length of aligned sequence
--- ACCNUM : SwissProt accession number
--- NAME : one-line description of aligned protein
---
--- MAXHOM ALIGNMENT HEADER: SUMMARY
ID STRID IDE WSIM LALI NGAP LGAP LEN2 ACCNUM NAME
imm1_ecoli 100 100 113 0 0 113 P02985 IMMUNITY PROTEIN FOR COLI
imm0_ecoli 96 97 113 0 0 113 P33637 IMMUNITY PROTEIN FOR COLI
imm1_shiso 79 90 112 1 1 113 P22558 IMMUNITY PROTEIN FOR COLI
---
--- MAXHOM ALIGNMENT: IN MSF FORMAT
MSF of: /home/phd/tmp/t2_20824.hssp from: 1 to: 113
/home/phd/tmp/t2_20824.ret_msf MSF: 113 Type: P 11-Mar-96 21:41:4 Check: 3736 ..
Name: t2_20824 Len: 113 Check: 8698 Weight: 1.00
Name: imm1_ecoli Len: 113 Check: 8698 Weight: 1.00
Name: imm0_ecoli Len: 113 Check: 8780 Weight: 1.00
Name: imm1_shiso Len: 113 Check: 7560 Weight: 1.00
//
1 50
t2_20824 MSLRYYIKNI LFGLYCTLIY IYLITKNSEG YYFLVSDKML YAIVISTILC
imm1_ecoli MSLRYYIKNI LFGLYCTLIY IYLITKNSEG YYFLVSDKML YAIVISTILC
imm0_ecoli MSLRYYIKNI LFGLYCTLIY IYLITKNSEE YYFLVTDKML YAIVISTILC
imm1_shiso MSLRYYIKNI LFGLYCALIY IYLITKNNEG YYFLASDKML YAIVISTILC
51 100
t2_20824 PYSKYAIEYI AFNFIKKDFF ERRKNLNNAP VAKLNLFMLY NLLCLVLAIP
imm1_ecoli PYSKYAIEYI AFNFIKKDFF ERRKNLNNAP VAKLNLFMLY NLLCLVLAIP
imm0_ecoli PYSKYAIEHI AFNFIKKHFF ERRKNLNNAP VAKLNLFMLY NLLCLVLAIP
imm1_shiso PYSKYAIEHI FFKFIKKDFF RKRKNLNKCP RGKIKPYlvY NLLCLVLAIP
101 113
t2_20824 FGLLELFISI KNN
imm1_ecoli FGLLELFISI KNN
imm0_ecoli FGLLGLFISI KNN
imm1_shiso FGLLGLVYIN KE.
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The resulting network (PHD) prediction is:
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PredictProtein@EMBL-Heidelberg.DE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PHD: Profile fed neural network systems from HeiDelberg
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Prediction of:
- secondary structure, by PHDsec
- solvent accessibility, by PHDacc
- and helical transmembrane regions, by PHDhtm
Author: Burkhard Rost
EMBL, Heidelberg, FRG
Meyerhofstrasse 1, 69 117 Heidelberg
Internet: Predict-Help@EMBL-Heidelberg.DE
All rights reserved.
The network systems are described in:
PHDsec: B Rost & C Sander: JMB, 1993, 232, 584-599.
B Rost & C Sander: Proteins, 1994, 19, 55-72.
PHDacc: B Rost & C Sander: Proteins, 1994, 20, 216-226.
PHDhtm: B Rost, R Casadio, P Fariselli & C Sander,
Prot. Science, 4, 521-533.
Some statistics
~~~~~~~~~~~~~~~
Percentage of amino acids:
+--------------+--------+--------+--------+--------+--------+
| AA: | L | I | Y | N | K |
| % of AA: | 16.8 | 12.4 | 10.6 | 8.8 | 8.0 |
+--------------+--------+--------+--------+--------+--------+
| AA: | F | S | A | V | E |
| % of AA: | 8.0 | 5.3 | 5.3 | 3.5 | 3.5 |
+--------------+--------+--------+--------+--------+--------+
| AA: | T | R | P | M | G |
| % of AA: | 2.7 | 2.7 | 2.7 | 2.7 | 2.7 |
+--------------+--------+--------+--------+--------+--------+
| AA: | C | D |
| % of AA: | 2.7 | 1.8 |
+--------------+--------+--------+
Percentage of helical trans-membrane predicted:
+--------------+--------+--------+
| SecStr: | H | L |
| % Predicted: | 54.9 | 45.1 |
+--------------+--------+--------+
PHD output for your protein
~~~~~~~~~~~~~~~~~~~~~~~~~~~
Mon Mar 11 21:41:53 1996
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
~~~~~~~~~~~~~~~~~
HEADER /home/phd/tmp/t2_20824.seq
COMPND
SOURCE
AUTHOR
SEQLENGTH 113
NCHAIN 1 chain(s) in t2_20824 data set
NALIGN 3
(=number of aligned sequences in HSSP file)
WARNING
~~~~~~~
Expected accuracy is about 94% if, and only if, the alignment contain
sufficient information. For your sequence there were not many
homologues in the current version of Swissprot detected. This
implies that the expected accuracy is some percentage points lower !
protein: t2_2082 length 113
---
--- ------------------------------------------------------------
--- 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
## COMMENT: most strongly predicted transmembrane helix (HTM)
1 0.618 0.911 88 - 105
## COMMENT: second best HTM
2 0.737 0.854 40 - 58
## COMMENT: third best HTM
3 0.789 0.662 9 - 26
---
--- PHDtopology REFINEMENT AND TOPOLOGY HEADER: SUMMARY
## COMMENT: best model predicted 3 HTM's
--- NHTM_BEST : 3
## COMMENT: second best model predicted 2 HTM's
--- NHTM_2ND_BEST: 2
## COMMENT: reliability of the prediction that there are 3 HTM's (0=low, 9=high)
--- REL_BEST : 5
## COMMENT: predicted topology in=> N-term intra-cytoplasmic
--- HTMTOP_PRD : in
--- HTMTOP_RID : -16.557
## COMMENT: reliability of topology prediction (0=low, 9=high)
--- HTMTOP_RIP : 9
---
--- 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
--- i: extra-cytoplasmic
---
--- PHDtopology REFINEMENT AND TOPOLOGY PREDICTION
....,....1....,....2....,....3....,....4....,....5....,....6
AA |MSLRYYIKNILFGLYCTLIYIYLITKNSEGYYFLVSDKMLYAIVISTILCPYSKYAIEYI|
PHD htm | HHHHHHHHHHHHHH HHHHHHHHHHHHHHHHHHHHHH|
Rel htm |999988887621356666677764025667765443313567777777777665666653|
detail: | |
prH htm |000000001135678888888887532111112223346788888888888887888876|
prL htm |999999998864321111111112467888887776653211111111111112111123|
subset: | |
SUB htm |LLLLLLLLLL...HHHHHHHHHH...LLLLLLL......HHHHHHHHHHHHHHHHHHHH.|
other: | |
PHDFhtm | HHHHHHHHHHHHHH HHHHHHHHHHHHHHHHHHHHHH|
PHDRhtm | HHHHHHHHHHHHHHHHHH HHHHHHHHHHHHHHHHHHH |
PHDThtm |iiiiiiiiTTTTTTTTTTTTTTTTTToooooooooooooTTTTTTTTTTTTTTTTTTTii|
....,....7....,....8....,....9....,....10...,....11...,....12
AA |AFNFIKKDFFERRKNLNNAPVAKLNLFMLYNLLCLVLAIPFGLLELFISIKNN|
PHD htm |HH HHHHHHHHHHHHHHHHHHHHHHHH |
Rel htm |20236899999999999999987404677888888888888887654114677|
detail: | |
prH htm |65331000000000000000001257888999999999999998877542111|
prL htm |34668999999999999999998742111000000000000001122457888|
subset: | |
SUB htm |....LLLLLLLLLLLLLLLLLLL...HHHHHHHHHHHHHHHHHHHH....LLL|
other: | |
PHDFhtm |HH HHHHHHHHHHHHHHHHHHHHHHHH |
PHDRhtm | HHHHHHHHHHHHHHHHHH |
PHDThtm |iiiiiiiiiiiiiiiiiiiiiiiiiiiTTTTTTTTTTTTTTTTTToooooooo|
---
--- PHDtopology REFINEMENT AND TOPOLOGY PREDICTION END
---
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