Here is an example of output from the PredictProtein (PHD) server
at EMBL. I have deleted the bulk of the HSSP lines and the lines
of text following them, but you should note: it is not necessary
to delete these lines or reformat the file in any way.
<![CDATA[
From phd@EMBL-Heidelberg.de Thu Mar 26 12:58:18 1998
Date: Thu, 26 Mar 1998 20:46:08 GMT
From: phd@EMBL-Heidelberg.de
To: bystroff@elina.bchem.washington.edu
Subject: Predict-Protein
The following information has been received by the server:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
________________________________________________________________________________
reference predict_h28087 (Thu Mar 26 21:43:25 MET 1998)
from bystroff@elina.bchem.washington.edu
password(###)
resp MAIL
orig HTML
prediction of: -secondary structure-
return hssp format
# 1hddC.2
RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS
________________________________________________________________________________
The sequence was interpreted to be:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
________________________________________________________________________________
>P1; /home/phd/server/work/predict_h28087
(#) 1hddc.2
RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS
________________________________________________________________________________
The HSSP file that has been used as input to the network is:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
________________________________________________________________________________
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 1.0 1991
PDBID predict_h28087_26825
DATE file generated on 26-Mar-98
SEQBASE RELEASE 34.0 OF EMBL/SWISS-PROT WITH 59021 SEQUENCES
PARAMETER SMIN: -0.5 SMAX: 1.0
PARAMETER gap-open: 3.0 gap-elongation: 0.1
PARAMETER conservation weights: YES
PARAMETER InDels in secondary structure allowed: YES
PARAMETER alignments sorted according to :DISTANCE
THRESHOLD according to: t(L)=(290.15 * L ** -0.562) + 5
REFERENCE Sander C., Schneider R. : Database of homology-derived protein structures. Proteins, 9:56-68 (1991).
CONTACT e-mail (INTERNET) Schneider@EMBL-Heidelberg.DE or Sander@EMBL-Heidelberg.DE / fax +49-6221-387306
AVAILABLE Free academic use. Commercial users must apply for license.
AVAILABLE No inclusion in other databanks without permission.
HEADER /home/phd/server/work/predict_h28087_268
COMPND
SOURCE
AUTHOR
SEQLENGTH 57
NCHAIN 1 chain(s) in predict_h28087_26825 data set
NALIGN 414
NOTATION : ID: EMBL/SWISSPROT identifier of the aligned (homologous) protein
NOTATION : STRID: if the 3-D structure of the aligned protein is known, then STRID is the Protein Data Bank identifier as taken
NOTATION : from the database reference or DR-line of the EMBL/SWISSPROT entry
## PROTEINS : EMBL/SWISSPROT identifier and alignment statistics
NR. ID STRID %IDE %WSIM IFIR ILAS JFIR JLAS LALI NGAP LGAP LSEQ2 ACCNUM PROTEIN
1 : hmen_drovi 1.00 1.00 1 57 488 544 57 0 0 584 P09145 SEGMENTATION POLARITY PROTEIN ENGRAILED.
2 : hmen_drome 1ENH 1.00 1.00 1 57 456 512 57 0 0 552 P02836 SEGMENTATION POLARITY PROTEIN ENGRAILED.
=========== 410 PROTEINS lines removed ===========
412 : hm08_caeel 0.35 0.54 1 57 132 188 57 0 0 346 Q94398 HOMEOBOX PROTEIN CEH-8.
413 : lh2_rat 0.35 0.48 1 57 266 322 57 0 0 426 P36198 HOMEOBOX PROTEIN LH-2.
414 : lh2_human 0.35 0.48 1 57 266 322 57 0 0 423 P50458 HOMEOBOX PROTEIN LH-2.
## ALIGNMENTS 1 - 70
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 R U 0 0 0 364 15 RRRRRRRRRRRRRRRRRRRRRRR R RRRRRRRRRRRRRRRRRRKRRRRRRRRRRKRRRRKRRKKRRR
2 P U 0 0 0 374 47 PPPPPPPPPPPPPPPPPPPPPPP P PSCCAQSQAASSASSSAAPAAAVQASAVSPSSSAPAGPPSSA
======== 54 ALINGMENT lines removed =========
56 K U 0 0 0 398 14 KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKRKKKKKKKKKKKKKKKRKKKKKKKKKKKKKKKKKK
57 S U 0 0 0 199 37 SSASASAAASSAAAASASAAAAAAAAAAASEE
## ALIGNMENTS 71 - 140
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....8....:....9....:....0....:....1....:....2....:....3....:....4
1 R U 0 0 0 364 15 RRRRRR KRRRRRRRRRRRKRRRRRRS KKKRKK RRKKKKKKKKKK RRRRRRSRRRRRRRR
2 P U 0 0 0 374 47 SGGMAM PASSSRRRSSSQPGGGGQGG PPPTPPATAPPPPPPPPPP AYGAGGIGAGGGGIG
3 R U 0 0 0 403 3 RRRRRR RRRRRRRRRRRRRRRRRRRR RRRRRRRRRRRRRRRRRRRRRRRR RRRRRRRRRRRRRRR
======== 54 ALINGMENT lines removed =========
56 K U 0 0 0 398 14 KKKKKKKKKKKKKRRRKKKKKKKKKKKKKKKKKKKKRKKKKKKKKKKKKKKKKKKKRKKKKKKKKKKKRK
57 S U 0 0 0 199 37 EEEEE EQEEEEEER RRRRR R QQEQEEREQEEEEQE
## ALIGNMENTS 141 - 210
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....5....:....6....:....7....:....8....:....9....:....0....:....1
1 R U 0 0 0 364 15 RRRRRRRRRRRRRRR RRKKKRKKKKKKKKKKKKKKKKKKKKKRRRRRRRRRRRRRSRRRRRRRRRR
2 P U 0 0 0 374 47 GGGGIGGPAGGGGGG ATPPPGPPPPPPPPPPPPPPPPPPPPPYGYIGYYGTTIGTGTTGGGGGGYT
======== 54 ALINGMENT lines removed =========
56 K U 0 0 0 398 14 KKKKRKKRKKKKKKKKKKKKKKKKKKKKRRRRRRRRRRRRRKRKRRRKRRKRRKKKRKKKKKKKKKKKRK
57 S U 0 0 0 199 37 EEEEQEESQEEEEEERRRR QEQQEQQEEEQREEEEEEEEEEQE
## ALIGNMENTS 211 - 280
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....2....:....3....:....4....:....5....:....6....:....7....:....8
1 R U 0 0 0 364 15 SRRRS RKKKKKKRKRKRKSRKKKKKRKKKKKKRKKKKKRKRRRRRRR KKKRKKKRKKKKRRKKKKKK
2 P U 0 0 0 374 47 GGGGG TPYPPPEPEQPYPLGPYKYYIYEYEEESKYYKYKSLLLLLLL KKKPKKKPKKYKPPKKKKKK
======== 54 ALINGMENT lines removed =========
56 K U 0 0 0 398 14 KKKKKKK RKKRKRKRKRRKKRRKKKKRKRKRRRRKKKRKRSRRRRRRRSKKKRKKKRKKRKRRKKKKKK
57 S U 0 0 0 199 37 EEEEE R EQQQREQ QQQQQQQQS
========= remainder of alignments removed ============
//
=========== text from PHD server removed ==========
protein: predict length 57
....,....1....,....2....,....3....,....4....,....5....,....6
AA |RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS|
PHD sec | HHHHHHHHHHHHHH HHHHHHHHHH HHHHEHHHHHHHH |
Rel sec |999666869999999999762431177999999972999203420222345543489|
detail:
prH sec |000012179999999998875334487999999884000445554354466666200|
prE sec |000110000000000000000000000000000000000001234533210000000|
prL sec |999777820000000000124655511000000015998543100112222223689|
subset: SUB sec |LLLLLLLHHHHHHHHHHHHH.....HHHHHHHHHH.LLL...........HH...LL|
========= trailing text removed ===========
]]></plaintext></div>