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.


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 ===========