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reference predict_h25944 (Jan 23, 2001 05:04:04) reference pred_h25944 (Jan 23, 2001 05:04:13) PPhdr from: pagomez@cnb.uam.es PPhdr resp: MAIL PPhdr orig: HTML PPhdr want: HTML PPhdr password(###) prediction of: - secondary structure (PHDsec)- return no alignment ret html ret html perline=60 # default: single protein sequence description=curso1 RLSWYDPDFQARLTRSNSKCQGQLEVYLKDGWHMVCS QSWGRSSKQWEDPSQASKVCQRLNCGVPLSLGPFLVT YTPQSSIICYGQLGSFSNCSHSRNDMCHSLGLTCLE
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Pattern-ID: ASN_GLYCOSYLATION PS00001 PDOC00001
Pattern-DE: N-glycosylation site
Pattern: N[^P][ST][^P]
92 NCSH
Pattern-ID: PKC_PHOSPHO_SITE PS00005 PDOC00005
Pattern-DE: Protein kinase C phosphorylation site
Pattern: [ST].[RK]
43 SSK
Pattern-ID: CK2_PHOSPHO_SITE PS00006 PDOC00006
Pattern-DE: Casein kinase II phosphorylation site
Pattern: [ST].{2}[DE]
3 SWYD
96 SRND
107 TCLE
Pattern-ID: MYRISTYL PS00008 PDOC00008
Pattern-DE: N-myristoylation site
Pattern: G[^EDRKHPFYW].{2}[STAGCN][^P]
63 GVPLSL
85 GQLGSF
Identities computed with respect to: (query) prot Colored by: consensus/70% and property
HSP processing: ranked
1 [ . . . . : . 60
prot RLSWYDPDFQARLTRSNSKCQGQLEVYLKDGWHMVCSQSWGRSSKQWEDPSQASKVCQRL
1 PD012755 QLSWEDPGLQMRLSGSGCRCQGQLEVQMSSRWHPVCSQSWGGVSPYWKNPRQAGKVCQQL
2 PD002499 ------PKGQIRLVGGSSPCEGRVEVHMRGQWGTVCDSNWTRSEAQWE--AQWEVVCREL
consensus/100% ......PthQhRLstuss.CpGplEV.hpstWt.VCspsWstsp..Wc..tQhthVCppL
consensus/90% ......PthQhRLstuss.CpGplEV.hpstWt.VCspsWstsp..Wc..tQhthVCppL
consensus/80% ......PthQhRLstuss.CpGplEV.hpstWt.VCspsWstsp..Wc..tQhthVCppL
consensus/70% ......PthQhRLstuss.CpGplEV.hpstWt.VCspsWstsp..Wc..tQhthVCppL
61 . . . 1 ] 110
prot NCGVPLSLGPFLVTYTPQSSIICYGQXXSFSNCSHSRNDMCHSLGLTCLE
1 PD012755 GCRPPLKLGSAPPDYEPQWAIICHGQ--SFSNCNHSRNDQCHSLGLICLE
2 PD002499 GCGDAVSV------------------------------------------
consensus/100% sCtsslpl.................. ......................
consensus/90% sCtsslpl.................. ......................
consensus/80% sCtsslpl.................. ......................
consensus/70% sCtsslpl.................. ......................
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--- ------------------------------------------------------------ --- --- Again: these results were obtained based on the domain data- --- base collected by Daniel Kahn and his coworkers in Toulouse. --- --- PLEASE quote: --- F Corpet, J Gouzy, D Kahn (1998). The ProDom database --- of protein domain families. Nucleic Ac Res 26:323-326. --- --- The general WWW page is on: ---- --------------------------------------- --- http://www.toulouse.inra.fr/prodom.html ---- --------------------------------------- --- --- For WWW graphic interfaces to PRODOM, in particular for your --- protein family, follow the following links (each line is ONE --- single link for your protein!!): --- http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD012755 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD012755 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD012755 ==> graphical output of all proteins having domain PD012755 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD002499 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD002499 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD002499 ==> graphical output of all proteins having domain PD002499 --- --- NOTE: if you want to use the link, make sure the entire line --- is pasted as URL into your browser! --- --- END of PRODOM --- ------------------------------------------------------------
**************************************************************************** * * * 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, 69012 Heidelberg, Germany * * Internet: Rost@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 et al.: Prot. Science, 1995, 4, 521-533. * * * ****************************************************************************
| %H: 14.6 | %E: 33.6 | %L: 51.8 |
| %A: 1.8 | %C: 7.3 | %D: 4.5 | %E: 2.7 | %F: 2.7 |
| %G: 7.3 | %H: 2.7 | %I: 1.8 | %K: 3.6 | %L: 10.9 |
| %M: 1.8 | %N: 3.6 | %P: 4.5 | %Q: 8.2 | %R: 5.5 |
| %S: 15.4 | %T: 3.6 | %V: 4.5 | %W: 3.6 | %Y: 3.6 |
| AA : | amino acid sequence | |
| PHD_sec: | PHD predicted secondary structure: H=helix, E=extended (sheet), blank=other (loop) PHD = PHD: Profile network prediction HeiDelberg | |
| Rel_sec: | reliability index for PHDsec prediction (0=low to 9=high) Note: for the brief presentation strong predictions marked by '*' | |
| SUB_sec: | subset of the PHDsec prediction, for all residues with an expected average accuracy > 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 | |
| pH_sec: | 'probability' for assigning helix (1=high, 0=low) | |
| pE_sec: | 'probability' for assigning strand (1=high, 0=low) | |
| pL_sec: | 'probability' for assigning neither helix, nor strand (1=high, 0=low) |
PHD results (brief)....,....1....,....2....,....3....,....4....,....5....,....6 AA RLSWYDPDFQARLTRSNSKCQGQLEVYLKDGWHMVCSQSWGRSSKQWEDPSQASKVCQRL PHD_sec EEEEE EEEE EEEEEEE EEEEEE HHHHHH HHHHHHHHHH Rel_sec * *** ** **** ******* ****** * ***** *** * ******* ....,....11...,....12...,....13...,....14...,....15 AA NCGVPLSLGPFLVTYTPQSSIICYGQLGSFSNCSHSRNDMCHSLGLTCLE PHD_sec EEE EEEEEE EE EEEE Rel_sec **** *** *** ***** **** *********** ** *
PHD results (normal) ....,....1....,....2....,....3....,....4....,....5....,....6 AA RLSWYDPDFQARLTRSNSKCQGQLEVYLKDGWHMVCSQSWGRSSKQWEDPSQASKVCQRL PHD_sec EEEEE EEEE EEEEEEE EEEEEE HHHHHH HHHHHHHHHH Rel_sec 905673682798616998786289999517477897423121347860614699998543 SUB_sec L.EEE.LL.EEEE.LLLLLLL.EEEEEE.L.EEEEE........HHH.L..HHHHHHH.. ....,....11...,....12...,....13...,....14...,....15 AA NCGVPLSLGPFLVTYTPQSSIICYGQLGSFSNCSHSRNDMCHSLGLTCLE PHD_sec EEE EEEEEE EE EEEE Rel_sec 77883432586334598459998165553113788899875774145639 SUB_sec LLLL....LLL...LLL.EEEEE.LLLL....LLLLLLLLLLL...EE.L
END of results for file predict_h25944
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