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Results from PredictProtein for predict_h22624

TOC for file /home/ppuser/server/work/predict_h22624

1. The following information has been received by the server (TOC)
2. PROSITE motif search (A Bairoch; P Bucher and K Hofmann) (TOC)
3. SEG low-complexity regions (J C Wootton & S Federhen) (TOC)
4. ProDom domain search (E Sonnhammer, Corpet, Gouzy, D Kahn) (TOC)
5. PSI-BLAST alignment header (TOC)
6. MAXHOM alignment header (TOC)
7. MAXHOM alignment (TOC)
8. DISULFIND (A. Vullo and P. Frasconi) (TOC)
9. PHD information about accuracy (TOC)
10. PHD predictions (TOC)
11. PROF predictions (TOC)
12. GLOBE prediction of globularity (TOC)
13. Ambivalent Sequence Predictor(Malin Young, Kent Kirshenbaum, Stefan Highsmith) (TOC)

BEG of results for file /home/ppuser/server/work/predict_h22624

The following information has been received by the server

reference predict_h22624 (Oct 8, 2004 04:43:59)
reference pred_h22624 (Oct 8, 2004 05:21:42)
PPhdr from: drose@web.de
PPhdr resp: MAIL
PPhdr orig: HTML
PPhdr want: HTML
PPhdr password(###)
prediction of: - default prediction of: - ProSite SEG ProDom
return msf format
ret html
ret store
# default: single protein sequence resfilename=if2759ht
MAVDMFIKIGDVKGESKDKTHAEEIDVLAWSWGMSQSGSMHMGGGGGAGKVNVQDLSFTK
YIDKSTPNLMMACSSGKHYPQAKLTIRKAGGENQVEYLIITLKEVLVSSVSTGGSGGEDR
LTENVTLNFAQVQVDYQPQKADGAKDGGPVKYGWNIRQNVQA

PROSITE motif search (A Bairoch; P Bucher and K Hofmann)

-------------------------------------------------------------
Pattern-ID: ASN_GLYCOSYLATION PS00001 PDOC00001
Pattern-DE: N-glycosylation site
Pattern:    N[^P][ST][^P]
   124      NVTL

Pattern-ID: PKC_PHOSPHO_SITE PS00005 PDOC00005
Pattern-DE: Protein kinase C phosphorylation site
Pattern:    [ST].[RK]
   75       SGK
   85       TIR
   101      TLK

Pattern-ID: CK2_PHOSPHO_SITE PS00006 PDOC00006
Pattern-DE: Casein kinase II phosphorylation site
Pattern:    [ST].{2}[DE]
   20       THAE
   101      TLKE
   115      SGGE

Pattern-ID: MYRISTYL PS00008 PDOC00008
Pattern-DE: N-myristoylation site
Pattern:    G[^EDRKHPFYW].{2}[STAGCN][^P]
   33       GMSQSG
   43       GGGGGA
   113      GGSGGE
   143      GAKDGG

SEG low-complexity regions (J C Wootton & S Federhen)

prot (#) default: single protein sequence resfilename=if2759ht /home/ppuser/server/work/predict_h22624  from:     1 to:  162

prot (#) default: single protein sequence resfilename=if2759ht /home/ppuser/server/work/predict_h22624 
 /home/ppuser/server/work/predict_h22624.segNormGcg Length:  162   11-Jul-99 Check: 2818 ..

       1  MAVDMFIKIG DVKGESKDKT HAEEIDVLAW SWxxxxxxxx xxxxxxxxxK

      51  VNVQDLSFTK YIDKSTPNLM MACSSGKHYP QAKLTIRKAG GENQVEYLII

     101  TLKEVLxxxx xxxxxxxEDR LTENVTLNFA QVQVDYQPQK ADGAKDGGPV

     151  KYGWNIRQNV QA

ProDom domain search (E Sonnhammer, Corpet, Gouzy, D Kahn)

Identities computed with respect to: (query) prot
Colored by: consensus/70% and property

HSP processing: ranked

                                                                            1 [        .         .         .         .         :         .         .         .         .         1         .         .         .         .         :        ] 159
  prot           (#) default: single protein... score      P(N)  N 100.0%     MAVDMFIKIGDVKGESKDKTHAEEIDVLAWSWGMSQSGSMHMGGGGGAGKVNVQDLSFTKYIDKSTPNLMMACSSGKHYPQAKLTIRKAGGENQVEYLIITLKEVLVSSVSTGGSGGEDRLTENVTLNFAQVQVDYQPQKADGAKDGGPVKYGWNIRQN    
1 PD095647       p2000.1 (1) O52405_BBBBB //...   210   2.0e-17  1  32.1%     MAFDTYIKLDKVDGESTDAKHKKWIEVLGFAWGAGNECSMESGTQgnTGKATMSVFRITKWMDCASVKLASAAVQGQNFPSLEVEICTQAGD-KFAFCIYKFTNVAISSYdsGASGGSDRPQETIDFAYKEVTWEYIPQDQSG-KAGSKipEGWSLITN    
  consensus/100%                                                              MAhDhaIKlscVcGESpDtpHtc.I-VLuauWGhuppsSMc.GstGssGKsshpshphTKahDpuospLh.AsspGppaPphclpIpptuG-.phtahIhphppVhlSShsoGuSGGpDR.pEslshsatpVph-Y.PQctsG.KsGu.l..GWslhpN    
  consensus/90%                                                               MAhDhaIKlscVcGESpDtpHtc.I-VLuauWGhuppsSMc.GstGssGKsshpshphTKahDpuospLh.AsspGppaPphclpIpptuG-.phtahIhphppVhlSShsoGuSGGpDR.pEslshsatpVph-Y.PQctsG.KsGu.l..GWslhpN    
  consensus/80%                                                               MAhDhaIKlscVcGESpDtpHtc.I-VLuauWGhuppsSMc.GstGssGKsshpshphTKahDpuospLh.AsspGppaPphclpIpptuG-.phtahIhphppVhlSShsoGuSGGpDR.pEslshsatpVph-Y.PQctsG.KsGu.l..GWslhpN    
  consensus/70%                                                               MAhDhaIKlscVcGESpDtpHtc.I-VLuauWGhuppsSMc.GstGssGKsshpshphTKahDpuospLh.AsspGppaPphclpIpptuG-.phtahIhphppVhlSShsoGuSGGpDR.pEslshsatpVph-Y.PQctsG.KsGu.l..GWslhpN    

--- ------------------------------------------------------------
--- 
--- 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=PD095647 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD095647
http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD095647 ==> graphical output of all proteins having domain PD095647
--- 
--- NOTE: if you want to use the link, make sure the entire line
---       is pasted as URL into your browser!
--- 
--- END of PRODOM
--- ------------------------------------------------------------

PSI-BLAST alignment header

--- ------------------------------------------------------------
--- PSI-BLAST multiple sequence alignment
--- ------------------------------------------------------------
--- 
--- PSI-BLAST ALIGNMENT HEADER: ABBREVIATIONS FOR SUMMARY
--- SEQLENGTH    : 162
--- ID           : identifier of aligned (homologous) protein
--- LSEQ2        : length of aligned sequence
--- IDE          : percentage of pairwise sequence identity
--- SIM          : percentage of similarity
--- LALI         : number of residues aligned
--- LGAP         : number of residues in all indels
--- BSCORE       : blast score (bits)
--- BEXPECT      : blast expectation value
--- OMIM         : OMIM (Online Mendelian Inheritance in Man) ID
--- PROTEIN      : one-line description of aligned protein
--- '!'          : indicates lower scoring alignment that is combined
---                with the higher scoring adjacent one
--- 
--- PSI-BLAST ALIGNMENT HEADER: SUMMARY

ID                          LSEQ2  IDE  SIM LALI LGAP BSCORE BEXPECT PROTEIN                  
Q9I747                        162   82   82  162    0    194   4e-49 (Q9I747) Hypothetical pro
Q7NR08                        165   25   46  158    4    190   1e-47 (Q7NR08) Hypothetical pro
Q89P91                        161   44   61  157    2    174   5e-43 (Q89P91) Bll3592 protein 
Q7AXZ0                        161   36   51  157    3    172   2e-42 (Q7AXZ0) SciK protein    
Q93IS5                        161   36   51  157    3    172   2e-42 (Q93IS5) Hypothetical pro
Q7CR58                        161   36   51  157    3    172   2e-42 (Q7CR58) Putative cytopla
Q7AXY8                        161   36   53  157    3    171   5e-42 (Q7AXY8) SciM protein    
Q93IS3                        161   36   53  157    3    171   5e-42 (Q93IS3) Putative cytopla
Q8CLE0                        189   34   50  160    3    169   1e-41 (Q8CLE0) Hypothetical    
Q8ZCP1                        161   34   50  160    3    169   1e-41 (Q8ZCP1) Hypothetical pro
Q88CE3                        162   24   47  156    5    168   3e-41 (Q88CE3) Hypothetical pro
Q88IB0                        180   26   44  158   11    168   3e-41 (Q88IB0) Hypothetical pro
Q88DE1                        181   25   47  156    5    168   4e-41 (Q88DE1) Hypothetical pro
O52405                        163   23   39  158    3    158   4e-38 (O52405) Putative 17.8 kD
Q7N4M6                        164   20   38  156    8    154   5e-37 (Q7N4M6) Similar to unkno
Q8ZM26                        161   23   46  153    3    153   9e-37 (Q8ZM26) Putative cytopla
Q6EE19                        163   25   41  158    3    152   2e-36 (Q6EE19) EvpC            
Q8Z3S0                        161   22   46  152    3    150   7e-36 (Q8Z3S0) Hypothetical pro
Q8ZIJ6                        172   29   49  157   14    147   5e-35 (Q8ZIJ6) Hypothetical pro
Q7W1H3                        161   34   49  157    2    147   6e-35 (Q7W1H3) Hypothetical pro
Q8XRT6                        167   27   45  154    7    137   6e-32 (Q8XRT6) Hypothetical pro
Q8FED4                        163   19   34  135   14    136   9e-32 (Q8FED4) Secreted protein
Q6B365                        174   26   47  155   12    136   1e-31 (Q6B365) Hypothetical pro
Q9I1B2                        165   26   47  147    6    136   2e-31 (Q9I1B2) Hypothetical pro
Q7WP83                        155   32   47  151    2    135   3e-31 (Q7WP83) Hypothetical pro
Q8PF41                        167   36   50  156    7    133   1e-30 (Q8PF41) Hypothetical pro
Q87U73                        172   15   33  142   23    132   3e-30 (Q87U73) Secreted protein
Q7CUP6                        158   17   37  152    6    131   4e-30 (Q7CUP6) AGR_L_1037p     
Q8U7V4                        158   17   37  152    6    131   4e-30 (Q8U7V4) Hypothetical pro
Q9HI36                        172   14   34  142   23    130   9e-30 (Q9HI36) Secreted protein
Q7N244                        163   19   36  135   14    130   1e-29 (Q7N244) Similar to Hcp p
Q6B388                        163   19   36  135   14    129   2e-29 (Q6B388) Hemolysin-coregu
Q8XGB3                        163   18   36  135   14    127   6e-29 (Q8XGB3) Hypothetical pro
Q7MZR6                        163   20   34  135   14    126   1e-28 (Q7MZR6) Similar to Hcp p
Q747U1                        161   16   32  136   14    124   7e-28 (Q747U1) Hcp protein     
trembl|AAR36565|AAR36565      161   16   32  136   14    124   7e-28 Hcp protein.             
Q7VJK0                        169   16   31  142   23    122   2e-27 (Q7VJK0) Hypothetical pro
Q8ZAT2                        172   15   28  142   23    119   2e-26 (Q8ZAT2) Hypothetical pro
Q6F922                        167   26   44  157    7    119   2e-26 (Q6F922) Hypothetical pro
Q87HD8                        159   24   43  150    7    119   2e-26 (Q87HD8) Hypothetical pro
Q93C89                        176   21   41  125    7    117   5e-26 (Q93C89) Hyperinvasive lo
Q7CP76                        176   21   41  125    7    117   5e-26 (Q7CP76) Putative cytopla
Q88FK8                        171   16   34  142   23    117   6e-26 (Q88FK8) Hcp protein     
P72350                        172   15   30  142   23    116   1e-25 (P72350) Hcp (Haemolysin 
Q7N9G3                        172   15   29  142   23    116   1e-25 (Q7N9G3) Similar to Hcp p
Q88JN4                        171   16   34  142   23    116   1e-25 (Q88JN4) Hcp protein     
Q98IM3                        160   23   41  139    3    116   2e-25 (Q98IM3) Mlr2339 protein 
Q8D6U6                        159   23   43  150    7    116   2e-25 (Q8D6U6) Hemolysin-coregu
Q7MDQ7                        159   23   43  150    7    116   2e-25 (Q7MDQ7) Uncharacterized 
Q8Z0X8                        176   20   41  125    7    114   4e-25 (Q8Z0X8) Hypothetical pro
Q7UL70                        159   21   39  149    6    112   2e-24 (Q7UL70) Hypothetical pro
Q6TKV2                        172   16   29  142   23    110   9e-24 (Q6TKV2) Aec16           
trembl|AAQ96710|AAQ96710      172   16   29  142   23    110   9e-24 Aec16.                   
Q7N6J8                        152   17   36  125    9    108   3e-23 (Q7N6J8) Similar to Hcp p
Q6D378                        172   15   29  142   23    108   3e-23 (Q6D378) Hypothetical pro
Q6TP03                        172   14   30  142   23    106   1e-22 (Q6TP03) Putative hemolys
trembl|AAQ95772|AAQ95772      172   14   30  142   23    106   1e-22 Putative hemolysin co-reg
Q6CZ78                        172   15   29  142   23    106   1e-22 (Q6CZ78) Hypothetical pro
Q6D1L7                        172   15   29  142   23    106   1e-22 (Q6D1L7) Hypothetical pro
Q882T3                        171   15   29  141   24    106   2e-22 (Q882T3) Secreted protein
Q7AHI2                        172   15   29  142   23    104   4e-22 (Q7AHI2) Hypothetical pro
O52671                        172   15   29  142   23    104   4e-22 (O52671) Hcp             
Q7DC35                        172   15   29  142   23    104   4e-22 (Q7DC35) Z0266 protein   
Q7QMP3                        169   15   33  129    9    104   6e-22 (Q7QMP3) EbiP1623 (Fragme
Q7BU96                        154   15   31  129    9    103   1e-21 (Q7BU96) Hcp (Fragment)  
Q8ZD06                        190   18   31  118   17    102   2e-21 (Q8ZD06) Putative membran
Q6LUD0                        159   20   40  146    6     99   1e-20 (Q6LUD0) Hypothetical pro
Q8ZCU5                        159   17   33  131   31     95   2e-19 (Q8ZCU5) Hypothetical pro
Q6D0X7                        159   17   32  122   18     91   5e-18 (Q6D0X7) Hypothetical pro
Q88Q43                        108   21   45   82    2     90   1e-17 (Q88Q43) Fimbrial protein
Q7N9D7                        159   18   32  121   18     88   5e-17 (Q7N9D7) Similar to Hcp p
Q8ZCM0                        161   17   34  122   18     82   2e-15 (Q8ZCM0) Hypothetical pro
Q938W4                        172   16   30  142   23     81   4e-15 (Q938W4) BfdA            
Q6DA07                        159   19   35  131   31     80   8e-15 (Q6DA07) Hypothetical pro
Q7NAC9                        159   16   30  131   31     73   2e-12 (Q7NAC9) Similar to Hcp p
Q6DAS7                        159   15   32  131   31     71   5e-12 (Q6DAS7) Hypothetical pro
Q6D8A5                        159   15   31  130   31     71   6e-12 (Q6D8A5) Hypothetical pro
Q8FDJ5                        159   17   31  111   17     71   6e-12 (Q8FDJ5) Hypothetical pro
Q6TKT6                        159   14   30  129   33     70   8e-12 (Q6TKT6) Aec32           
trembl|AAQ96726|AAQ96726      159   14   30  129   33     70   8e-12 Aec32.                   
Q7N2U6                        159   17   30  131   29     69   2e-11 (Q7N2U6) Similar to Hcp p
Q7N2D1                        159   17   29  123   16     65   3e-10 (Q7N2D1) Similar to Hcp p
Q7AHJ9                        159   13   28  117   17     64   4e-10 (Q7AHJ9) Hcp-like protein
Q8X7X3                        159   13   28  117   17     64   4e-10 (Q8X7X3) Z0248 protein   
Q7N3Y9                        159   17   33  122   18     63   1e-09 (Q7N3Y9) Similar to unkno
Q87X44                         71   24   45   60    2     54   8e-07 (Q87X44) Conserved domain
Q8ZF46                        114   16   33   91   27     50   9e-06 (Q8ZF46) Hypothetical pro
Q8GFB2                        159   14   24  110   15     48   6e-05 (Q8GFB2) Orf23           
Q6EB93                         64   10   35   50    6     41   0.005 (Q6EB93) Tgh034 (Fragment
Q7N6E5                         89   18   37   57   12     37   0.074 (Q7N6E5) Similarities wit
---
--- PSI-BLAST ALIGNMENT 

MAXHOM alignment header

--- ------------------------------------------------------------
--- MAXHOM multiple sequence alignment
--- ------------------------------------------------------------
--- 
--- MAXHOM ALIGNMENT HEADER: ABBREVIATIONS FOR SUMMARY
--- ID           : identifier of aligned (homologous) protein
--- STRID        : PDB identifier (only for known structures)
--- IDE          : 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
--- OMIM         : OMIM (Online Mendelian Inheritance in Man) ID
--- NAME         : one-line description of aligned protein
--- 
--- MAXHOM ALIGNMENT HEADER: SUMMARY
ID         STRID  IDE WSIM LALI NGAP LGAP LSEQ2 ACCNUM NAME                     
predict_h226        83   83  162    0    0   162   prot (#) default: single prote
--- 
--- MAXHOM ALIGNMENT: IN MSF FORMAT

--- 
--- Version of database searched for alignment:
--- SWISS-PROT release 41 (02/2003) with 122 564 proteins
--- 

MAXHOM alignment

Identities computed with respect to: (1) predict_h2260
Colored by: consensus/70% and property

                          1 [        .         .         .         .         :         .         .         .         .         1         .         .         .         .         :         . ] 162
1 predict_h2260  100.0%     MAVDMFIKIGDVKGESKDKTHAEEIDVLAWSWGMSQSGSMHMGGGGGAGKVNVQDLSFTKYIDKSTPNLMMACSSGKHYPQAKLTIRKAGGENQVEYLIITLKEVLVSSVSTGGSGGEDRLTENVTLNFAQVQVDYQPQKADGAKDGGPVKYGWNIRQNVQA    
2 predict_h226    82.7%     MAVDMFIKIGDVKGESKDKTHAEEIDVLAWSWXXXXXXXXXXXXXXXXXKVNVQDLSFTKYIDKSTPNLMMACSSGKHYPQAKLTIRKAGGENQVEYLIITLKEVLXXXXXXXXXXXEDRLTENVTLNFAQVQVDYQPQKADGAKDGGPVKYGWNIRQNVQA    
  consensus/100%            MAVDMFIKIGDVKGESKDKTHAEEIDVLAWSW.................KVNVQDLSFTKYIDKSTPNLMMACSSGKHYPQAKLTIRKAGGENQVEYLIITLKEVL...........EDRLTENVTLNFAQVQVDYQPQKADGAKDGGPVKYGWNIRQNVQA    
  consensus/90%             MAVDMFIKIGDVKGESKDKTHAEEIDVLAWSW.................KVNVQDLSFTKYIDKSTPNLMMACSSGKHYPQAKLTIRKAGGENQVEYLIITLKEVL...........EDRLTENVTLNFAQVQVDYQPQKADGAKDGGPVKYGWNIRQNVQA    
  consensus/80%             MAVDMFIKIGDVKGESKDKTHAEEIDVLAWSW.................KVNVQDLSFTKYIDKSTPNLMMACSSGKHYPQAKLTIRKAGGENQVEYLIITLKEVL...........EDRLTENVTLNFAQVQVDYQPQKADGAKDGGPVKYGWNIRQNVQA    
  consensus/70%             MAVDMFIKIGDVKGESKDKTHAEEIDVLAWSW.................KVNVQDLSFTKYIDKSTPNLMMACSSGKHYPQAKLTIRKAGGENQVEYLIITLKEVL...........EDRLTENVTLNFAQVQVDYQPQKADGAKDGGPVKYGWNIRQNVQA    

DISULFIND (A. Vullo and P. Frasconi)

-------------------------------------------------------------------------------
              Cysteines Bonding State and Connectivity Predictor               
-------------------------------------------------------------------------------


0 = Not Bonded
1 = Bonded


Chain identifier: predict_h22624.fasta


.........10........20........30........40........50........60........70........
MAVDMFIKIGDVKGESKDKTHAEEIDVLAWSWXXXXXXXXXXXXXXXXXKVNVQDLSFTKYIDKSTPNLMMACSSGKHY
                                                                        0      

80........90........100.......110.......120.......130.......140.......150......
PQAKLTIRKAGGENQVEYLIITLKEVLXXXXXXXXXXXEDRLTENVTLNFAQVQVDYQPQKADGAKDGGPVKYGWNIRQ
                                                                               

.160
NVQA
    

-------------------------------------------------------------------------------
Please cite:

P. Frasconi, A. Passerini, and A. Vullo.
"A Two-Stage SVM Architecture for Predicting the Disulfide Bonding State of Cysteines"
Proc. IEEE Workshop on Neural Networks for Signal Processing, pp. 25-34, 2002.

A.Ceroni, P.Frasconi, A.Passerini and A.Vullo.
"Predicting the Disulfide Bonding State of Cysteines with Combinations of Kernel Machines"
Journal of VLSI Signal Processing, 35, 287-295, 2003.

A. Vullo and P. Frasconi.
"Disulfide Connectivity Prediction using Recursive Neural Networks and Evolutionary Information"
Bioinformatics, 20, 653-659, 2004.

Questions and comments are very appreciated.
Please, send email to: cystein@dsi.unifi.it

Created by members of the Machine Learning and
Neural Network Group, Universita' di Firenze

The server is hosted at the Department of Systems and
Computer Science (DSI), Faculty of Engineering,
Universita' di Firenze, Italy
-------------------------------------------------------------------------------

PHD information about accuracy

****************************************************************************
*                                                                          *
*    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.	   *
*                                                                          *
****************************************************************************

PHD predictions

PHD predictions for predict_h22624

SYNOPSIS of prediction

HEADER information

• About your protein:

• About the alignment used:

• Residue composition for your protein:

  %A: 6.8	%C: 0.6	%D: 6.2	%E: 4.9	%F: 1.9
  %G: 13.0	%H: 1.9	%I: 4.9	%K: 8.6	%L: 5.6
  %M: 4.3	%N: 4.3	%P: 2.5	%Q: 6.2	%R: 1.9
  %S: 8.0	%T: 4.9	%V: 8.6	%W: 1.9	%Y: 3.1

• About the PHD methods used:

• Please quote:
  1. PHD: B Rost (1996) Methods in Enzymology, 266:525-539

• Copyright & Contact:
  
  • Burkhard Rost, CUBIC NYC / LION Heidelberg
  • Email: rost@columbia.edu
  • WWW: http://cubic.bioc.columbia.edu
  • Fax: +1-212-305 3773

• ABBREVIATIONS used:

  AA :	amino acid sequence
  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)
  pL_sec:	'probability' for assigning neither helix, nor strand (1=high, 0=low)
  PHD_htm:	PHD predicted membrane helix: M=helical transmembrane region, blank=non-membrane PHD = PHD: Profile network prediction HeiDelberg
  pT_htm:	'probability' for assigning transmembrane helix
  pN_htm:	'probability' for assigning globular region
  phd_skip:	note: sequence stretches with less than 9 are not predicted, the symbol '*' is used!

BODY with predictions

PHD results (brief)

           ....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8....,....9....,....1
AA         MAVDMFIKIGDVKGESKDKTHAEEIDVLAWSWGMSQSGSMHMGGGGGAGKVNVQDLSFTKYIDKSTPNLMMACSSGKHYPQAKLTIRKAGGENQVEYLII
Rel_sec    ****************************************************************************************************

PHD_htm                                                                                                        

           ....,....15...,....16...,....17...,....18...,....19...,....20...,....21
AA         TLKEVLVSSVSTGGSGGEDRLTENVTLNFAQVQVDYQPQKADGAKDGGPVKYGWNIRQNVQA
Rel_sec    **************************************************************

PHD_htm                                                                  




PHD results (normal)

           ....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8....,....9....,....1
AA         MAVDMFIKIGDVKGESKDKTHAEEIDVLAWSWGMSQSGSMHMGGGGGAGKVNVQDLSFTKYIDKSTPNLMMACSSGKHYPQAKLTIRKAGGENQVEYLII
Rel_sec    9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
SUB_sec    

PHD_htm                                                                                                        

           ....,....15...,....16...,....17...,....18...,....19...,....20...,....21
AA         TLKEVLVSSVSTGGSGGEDRLTENVTLNFAQVQVDYQPQKADGAKDGGPVKYGWNIRQNVQA
Rel_sec    99999999999999999999999999999999999999999999999999999999999999
SUB_sec    

PHD_htm                                                                  

PROF predictions

• PROFsec summary overall your protein can be classified as:
  mixed given the following classes:
  
  • 'all-alpha': %H > 45% AND %E < 5%
  • 'all-beta': %H < 5% AND %E > 45%
  • 'alpha-beta': %H > 30% AND %E > 20%
  • 'mixed': all others

• Predicted secondary structure composition for your protein:

  sec str type	H	E	L
  % in protein	4.94	48.77	46.30

• Predicted solvent accessibility composition (core/surface ratio) for your protein:
  Classes used:
  • e: residues exposed with more than 16% of their surface
  • b: all other residues.

  accessib type	b	e
  % in protein	27.16	72.84

• About your protein:

  prot_id	query
  prot_nres	162
  prot_nali	54
  prot_nchn	1
  prot_nfar	52

• About the alignment used:

  ali_orig

  /home/ppuser/server/work/predict_h22624.hsspPsiFil

• Residue composition for your protein:

  %A: 6.8	%C: 0.6	%D: 6.2	%E: 4.9	%F: 1.9
  %G: 13.0	%H: 1.9	%I: 4.9	%K: 8.6	%L: 5.6
  %M: 4.3	%N: 4.3	%P: 2.5	%Q: 6.2	%R: 1.9
  %S: 8.0	%T: 4.9	%V: 8.6	%W: 1.9	%Y: 3.1

• About the PROF methods used:

  prof_fpar	acc=/home/ppuser/server/pub/prof/net/PROFboth_best.par
  prof_nnet	acc=6

• Please quote:
  1. PROF: B Rost & C Sander (1993) J Mol Biol, 232:584-599
  2. PROFhtm: B Rost, P Fariselli & R Casadio (1996) Prot Science, 7:1704-1718

• Copyright & Contact:
  
  • Burkhard Rost, CUBIC NYC / LION Heidelberg
  • Email: rost@columbia.edu
  • WWW: http://cubic.bioc.columbia.edu
  • Fax: +1-212-305 3773

• ABBREVIATIONS used:

  AA :	amino acid sequence
  OBS_sec:	observed secondary structure: H=helix, E=extended (sheet), blank=other (loop)
  PROF_sec:	PROF predicted secondary structure: H=helix, E=extended (sheet), blank=other (loop) PROF = PROF: Profile network prediction HeiDelberg
  Rel_sec:	reliability index for PROFsec prediction (0=low to 9=high) Note: for the brief presentation strong predictions marked by '*'
  SUB_sec:	subset of the PROFsec 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)
  O_2_acc:	observerd relative solvent accessibility (acc) in 2 states: b = 0-16%, e = 16-100%.
  P_2_acc:	PROF predicted relative solvent accessibility (acc) in 2 states: b = 0-16%, e = 16-100%.
  O_3_acc:	observerd relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%.
  P_3_acc:	PROF predicted relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%.
  OBS_acc:	observed relative solvent accessibility (acc) in 10 states: a value of n (=0-9) corresponds to a relative acc. of between n*n % and (n+1)*(n+1) % (e.g. for n=5: 16-25%).
  PROF_acc:	PROF predicted relative solvent accessibility (acc) in 10 states: a value of n (=0-9) corresponds to a relative acc. of between n*n % and (n+1)*(n+1) % (e.g. for n=5: 16-25%).
  Rel_acc:	reliability index for PROFacc prediction (0=low to 9=high) Note: for the brief presentation strong predictions marked by '*'
  SUB_acc:	subset of the PROFacc prediction, for all residues with an expected average correlation > 0.69 (tables in header) NOTE: for this subset the following symbols are used: I: is intermediate (for which above ' ' is used) .: means that no prediction is made for this residue, as the reliability is: Rel < 4
  ali_orig:	input file
  prof_fpar:	name of parameter file, used [w]
  prof_nnet:	number of networks used for prediction [d]
  prof_skip:	note: sequence stretches with less than 9 are not predicted, the symbol '*' is used!

BODY with predictions for query

PROF results (normal)

           ....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8....,....9....,....10.1.,....11.1.,....12.1.,....13.1.,....14.1.,....15.1.,....16.
AA         MAVDMFIKIGDVKGESKDKTHAEEIDVLAWSWGMSQSGSMHMGGGGGAGKVNVQDLSFTKYIDKSTPNLMMACSSGKHYPQAKLTIRKAGGENQVEYLIITLKEVLVSSVSTGGSGGEDRLTENVTLNFAQVQVDYQPQKADGAKDGGPVKYGWNIRQNVQA
OBS_sec                                                                                                                                                                      
PROF_sec       EEEEE              EEEEEEEEE  EE             EEEEEEEEEEEEE    HHHHHHHH      EEEEEEEEE     EEEEEEEEEEEEEEEE           EEEEEEEEEEEEEEEEE           EEEEEEEE     
Rel_sec    964226774042355333444234789874310000133455576665402210037765303455034443204653430478998735776056778875204676520223576655303588876666677642035676467501111231003028
SUB_sec    LL...EEE.....LL.........EEEEE...........LLLLLLLL........EEEE....LL.........LL.....EEEEEE.LLLL.EEEEEEEE...EEEE.....LLLLLL...EEEEEEEEEEEEE....LLLL.LLL.............L

O_3_acc    bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb
P_3_acc    ee ebbb b e e eeeeee ee b bbbb  e ee ee eeeeeeeeeebe  ebeb   bee    bb bbbeeeebe b b b    eeee  bb b b  bbbb b    eeeeee  e b b b ebebe   eeeeeeeee e e e ebee eee
Rel_acc    432331843211503120322214859022312022011012232222030213323343202300235120202123021346454120452313123445421222201101102422221333551422303221020411242030221130210048
SUB_acc    e.....bi....e..........ibib...............................i.........b.............ibibi...ee.......bibi..............e........bi.i...........e...e..............ee





PROF results (detail)

           ....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8....,....9....,....10.1.,....11.1.,....12.1.,....13.1.,....14.1.,....15.1.,....16.
AA         MAVDMFIKIGDVKGESKDKTHAEEIDVLAWSWGMSQSGSMHMGGGGGAGKVNVQDLSFTKYIDKSTPNLMMACSSGKHYPQAKLTIRKAGGENQVEYLIITLKEVLVSSVSTGGSGGEDRLTENVTLNFAQVQVDYQPQKADGAKDGGPVKYGWNIRQNVQA
 pH_sec                                                                                                                                                                       1.0 
 pH_sec                                                                                                                                                                       0.9 
 pH_sec                                                                                                                                                                       0.8 
 pH_sec                                                                      .....                                                                                            0.7 
 pH_sec                                                                     .......                                                                                           0.6 
 pH_sec                                                                     ........                                                                                          0.5 
 pH_sec                                                                     ........                                                                                          0.4 
 pH_sec                  ...                                             .  .........                                                                                  .      0.3 
 pH_sec                  .......         ............  ...              ..............                                  ...   ..                         ...      .  .....    0.2 
          ------------------------------------------------------------------------------------------------------------------------------------------------------------------
 pE_sec                            ...                                                       ....          ...                         .                                      1.0 
 pE_sec        ...                .....                           ..                        ......        .....    ...                ...... .....                            0.9 
 pE_sec        ...                ......                          ....                      ......      ........   ....              ..............                           0.8 
 pE_sec       .....              ........                   .    ......                    ........     ........  .....             ...............                 .         0.7 
 pE_sec       .....              .........                 .... ........                  .........     ......... ......            ................           .......        0.6 
 pE_sec       ......             ......... ...             .............                  .........    ..................          ..................         .........       0.5 
 pE_sec      ....... ..         ...............            .............               .  .........    ....................       ...................         .......... ..   0.4 
 pE_sec     ............ .    ....................        ...............     . ....   .............   .....................     ......................      ..............   0.3 
 pE_sec    .......................................... .....................  ........ ..............  .......................   ........................ ..................   0.2 
          ------------------------------------------------------------------------------------------------------------------------------------------------------------------
 pL_sec   .                                                                                                                                                                .  1.0 
 pL_sec   .                                          .                               .              ..                       ..                         .   .              .  0.9 
 pL_sec   ..        .  ..                           .....                  .         .. .          ....                     ......                    .... ...             .  0.8 
 pL_sec   ....      . ... ..... .               ...........             ....        ......         ....                    ........                  .........             .  0.7 
 pL_sec   ....      .............              ............             ....        ......         .....                 ..........                  .........          . ..  0.6 
 pL_sec   ....     ..............         ... ..............   ..      ......       .......        .....         .      ............                ............      . ....  0.5 
 pL_sec   .....    ..............        ........................      ......      ........       ......        ..     ..............              .........................  0.4 
 pL_sec   .....   ................     ...........................   .........     .........      .......      ....    ...............            ..........................  0.3 
 pL_sec   ....... .................   ......................................................     ..........   ...... .................   ...................................  0.2 
          ------------------------------------------------------------------------------------------------------------------------------------------------------------------
OBS_acc                                                                                                                                                                       100% 
OBS_acc                                                                                                                                                                        81% 
OBS_acc                                                                                                                                                                        64% 
OBS_acc                                                                                                                                                                        49% 
OBS_acc                                                                                                                                                                        36% 
OBS_acc                                                                                                                                                                        25% 
OBS_acc                                                                                                                                                                        16% 
OBS_acc                                                                                                                                                                         9% 
OBS_acc                                                                                                                                                                         4% 
          ------------------------------------------------------------------------------------------------------------------------------------------------------------------
PROF_acc  ..                .                     ........                           ..             ..                        ...                      ......             ..  100% 
PROF_acc  ..        . .  .  ..                 .. ........                           ..             ..                      .....                    . ......             ..   81% 
PROF_acc  ..        . . ... .. .          .    .. ........      .        .          ....            ...                     ......                   . ...... .           ..   64% 
PROF_acc  .. .      . . ...... ..         . .. .. .......... .  . .     ..          .... .          ....                    ......  .       . . .   ......... . . . . .. ...   49% 
PROF_acc  ....   . ........... ...      . . ................ . .. . ... ..  ..  .   .... .. .   ........ .    . ..    . .............. . . .. . . ............. ... . ......   36% 
PROF_acc  ....   . ........... ... .    . . ................ .... . ... ..  ..  .   .... .. . . ..........  . . ..    . .............. . . .. . ............... ... . ......   25% 
PROF_acc  ....   . ............... .    .................... .... . ... ......  .   .... .. . . ..........  . . ..    . .............. . . .. . ..................... ......   16% 
PROF_acc  ....   . ............... .    .................... .... . ... ......  .   .... .. . . ..........  . . ..    . .............. . . .. . ..................... ......    9% 
PROF_acc  ....   . ............... .    ......................... . ... ......  .   .... .. . . ..........  . . ..    . .............. . . .. . ..................... ......    4% 
          ------------------------------------------------------------------------------------------------------------------------------------------------------------------

GLOBE prediction of globularity

--- 
--- GLOBE: prediction of protein globularity
--- 
--- nexp =   118    (number of predicted exposed residues)
--- nfit =    76    (number of expected exposed residues
--- diff =    42.00 (difference nexp-nfit)
--- =====> your protein appears not to be globular
--- 
--- 
--- GLOBE: further explanations preliminaryily in:
---        http://cubic.bioc.columbia.edu/papers/1999_globe/paper.html
--- 
--- END of GLOBE

Ambivalent Sequence Predictor(Malin Young, Kent Kirshenbaum, Stefan Highsmith)

Ambivalent Sequence Predictor (ASP v1.0) mmy


Parameters:
	Window size	:	5
	Min mu dPr	:	9
	Z-score cutoff	:	-1.75

	Mean dPr score=12.309, Standard deviation=2.616


Please note: ASP was designed to identify the location of conformational 
switches in amino acid sequences. It is NOT designed to predict whether 
a given sequence does or does not contain a switch.  For best results,
ASP should be used on sequences of length >150 amino acids with >10 
sequence homologues in the SWISS-PROT data bank. 
ASP has been validated against a set of globular proteins and may not 
be generally applicable. Please see Young et al., Protein Science 
8(9):1852-64. 1999. for details and for how best to interpret this 
output.  We consider ASP to be experimental at this time, and would 
appreciate any feedback from our users.

END of results for file predict_h22624

Quotes for methods

1. PredictProtein: B Rost and J Liu (2003) The PredictProtein Server. Nucleic Acids Research 31(13): 3300-3304.
   • Author: B Rost
   • Contact: liu@maple.bioc.columbia.edu
   • URL: http://cubic.bioc.columbia.edu
   • Version: 1.99.08
   • Description: PredictProtein is the acronym for all prediction programs run.
2. PROSITE: A Bairoch, P Bucher & K Hofmann (1997) Nucleic Acids Research, 25:217-221
   • Author: A Bairoch, bairoch@cmu.unige.ch P Bucher & K Hofmann
   • Contact: bairoch@cmu.unige.ch
   • URL: http://www.expasy.ch/prosite
   • Version: 99.07
   • Description: PROSITE is a database of functional motifs. ScanProsite, finds all functional motifs in your sequence that are annotated in the ProSite db.
3. SEG: J C Wootton & S Federhen (1996) Methods in Enzymology, 266:554-571
   • Author: J C Wootton & S Federhen, wootton@ncbi.nlm.nih.gov
   • Contact: rost@columbia.edu
   • URL: wootton@ncbi.nlm.nih.gov
   • Version: 1994
   • Description: SEG divides sequences into regions of low-, and high-complexity. Low-complexity regions typically correspond to 'simple sequences' or 'compositionally-biased' regions.
4. ProDom: ELL Sonnhammer & D Kahn (1994) Protein Science, 3:482-492
   • Author: LL Sonnhammer; J Gouzy, F Corpet, F Servant, D Kahn, dkahn@zyx.toulouse.inra.fr
   • Contact: dkahn@zyx.toulouse.inra.fr
   • URL: http://protein.toulouse.inra.fr/prodom.html
   • Version: 2000.1
   • Description: ProDom is a database of putative protein domains. The database is searched with BLAST for domains corresponding to your protein.
5. MaxHom: MaxHom: C Sander R Schneider (1991) Proteins, 9:56-68
   • Author: C Sander & R Schneider, schneider@lion-ag.de
   • Contact: schneider@lion-ag.de
   • Version: 1.99.04
   • Description: MaxHom is a dynamic multiple sequence alignment program which finds similar sequences in a database.
6. MView: MView: N P Brown, C Leroy & C Sander (1998) Bioinformatics, 14:380-381
   • Author: N Brown, nbrown@nimr.mrc.ac.uk
   • URL: http://mathbio.nimr.mrc.ac.uk/~nbrown/mview/
   • Copyright: Copyright (C) Nigel P. Brown, 1997-1998. All rights reserved.
   • Version: 1.40.2
   • Description: MView is a program converting multiple sequence alignments into fancy HTML formatted output.
7. PHD: B Rost (1996) Methods in Enzymology, 266:525-539
   • Author: B Rost
   • Contact: rost@columbia.edu
   • URL: http://cubic.bioc.columbia.edu
   • Version: 1.96
   • Description: PHD is a suite of programs predicting 1D structure (secondary structure, solvent accessibility) from multiple sequence alignments.
8. PHDsec: B Rost & C Sander (1993) J. of Molecular Biology, 232:584-599
   • Author: B Rost
   • Contact: rost@columbia.edu
   • URL: http://cubic.bioc.columbia.edu
   • Version: 1.96
   • Description: PHDsec predicts secondary structure from multiple sequence alignments.
9. PHDacc: B Rost & C Sander (1994) Proteins, 20:216-226
   • Author: B Rost
   • Contact: rost@columbia.edu
   • Version: 1.96
   • Description: PHDacc predicts per residue solvent accessibility from multiple sequence alignments.
10. PHDhtm: B Rost, P Fariselli & R Casadio (1996) Protein Science, 7:1704-1718
    • Author: B Rost
    • Contact: rost@columbia.edu
    • URL: http://cubic.bioc.columbia.edu
    • Version: 1.96
    • Description: PHDhtm predicts the location and topology of transmembrane helices from multiple sequence alignments.
11. PROF: B Rost (2004) Meth. Mol. Biol., submitted.
    • Author: B Rost
    • Contact: rost@columbia.edu
    • Version: 2000_04
    • Description: PROF is a suite of programs predicting 1D structure (secondary structure, solvent accessibility) from multiple sequence alignments.
12. PROFsec: B Rost (2004) Meth. Mol. Biol., submitted.
    • Author: B Rost
    • Contact: rost@columbia.edu
    • URL: http://cubic.bioc.columbia.edu
    • Version: 2000_04
    • Description: PROFsec predicts secondary structure from multiple sequence alignments.
13. PROFACC: B Rost (2004) Meth. Mol. Biol., submitted.
    • Author: B Rost
    • Contact: rost@columbia.edu
    • URL: http://cubic.bioc.columbia.edu
    • Version: 2000_04
    • Description: PROFacc predicts per residue solvent accessibility from multiple sequence alignments.
14. GLOBE: B Rost (1998) unpublished
    • Author: B Rost
    • Contact: rost@columbia.edu
    • URL: http://cubic.bioc.columbia.edu/papers/1999_globe/paper.html
    • Version: 1.98.05
    • Description: GLOBE predicts the globularity of a protein
15. DISULFIND: A.Ceroni, P.Frasconi, A.Passerini and A.Vullo (2004) Bioinformatics, 20, 653-659, 2004
    • Author: A.Ceroni, P.Frasconi, A.Passerini and A.Vullo
    • Contact: cystein@dsi.unifi.it
    • URL: http://cassandra.dsi.unifi.it/cysteines/index.html
    • Version: 2.0
    • Description: DISULFIND is a disulphide bridges predictor based on a two steps process. First, the bonding state of each cysteine in the sequence is predicted as either reduced or oxidized. Such prediction is based on a local Support Vector Machines predictor using the context of the cysteine in the form of multiple alignment profiles, and a global refinement using Bidirectional Recurrent Neural Networks. Second, the connectivity pattern for the subset of oxidized cysteines, if any, is predicted with Recursive Neural Networks, pairing each oxidized cysteine with its predicted partner. Experimental assessment on a non redundant subset of the PDB reports state of the art performance for both steps of prediction.
16. A conformational switch prediction program: Young et al. Protein Science(1999) 8:1752-64.
    • Author: Young M, Kirshenbaum K, Dill KA and Highsmith S.
    • Contact: mmyoung@sandia.gov, kent@cheme.caltech.edu, shighsmith@sf.uop.edu
    • Version: 1.0
    • Description: ASP finds regions that are most likely to behave as switches in proteins known to exhibit this behavior
17. HMMPFAM: Bateman et al. Nucleic Acids Research 2004 32:D138-D141.
    • Author: Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR.
    • Contact: agb@sanger.ac.uk
    • Version: 2.2g
    • Description: Search one or more sequences against HMM database

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