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Results from PredictProtein for predict_h29929

TOC for file /home/ppuser/server/work/predict_h29929

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_h29929

The following information has been received by the server

reference predict_h29929 (Oct 11, 2004 06:57:26)
reference pred_h29929 (Oct 11, 2004 07:35:56)
PPhdr from: mai01duu@studserv.uni-leipzig.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=kk1982fj
MEWEMGLQEEFLELIKLRKKKIEGRLYDEKRRQIKPGDVISFEGGKLKVRVKAIRVYNSF
REMLEKEGLENVLPGVKSIEEGIQVYRRFYDEEKEKKYGVVAIEIEPLEY

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

-------------------------------------------------------------
Pattern-ID: PKC_PHOSPHO_SITE PS00005 PDOC00005
Pattern-DE: Protein kinase C phosphorylation site
Pattern:    [ST].[RK]
   59       SFR

Pattern-ID: CK2_PHOSPHO_SITE PS00006 PDOC00006
Pattern-DE: Casein kinase II phosphorylation site
Pattern:    [ST].{2}[DE]
   59       SFRE
   78       SIEE

Pattern-ID: TYR_PHOSPHO_SITE PS00007 PDOC00007
Pattern-DE: Tyrosine kinase phosphorylation site
Pattern:    [RK].{2,3}[DE].{2,3}Y
   19       KKKIEGRLY

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

prot (#) default: single protein sequence resfilename=kk1982fj /home/ppuser/server/work/predict_h29929  from:     1 to:  110

prot (#) default: single protein sequence resfilename=kk1982fj /home/ppuser/server/work/predict_h29929 
 /home/ppuser/server/work/predict_h29929.segNormGcg Length:  110   11-Jul-99 Check: 2818 ..

       1  MEWEMGLQxx xxxxxxxxxx xxxxxxYDEK RRQIKPGDVI SFEGGKLKVR

      51  VKAIRVYNSF REMLEKEGLE NVLPGVKSIE EGIQVYRRFY DEEKEKKYGV

     101  VAIEIEPLEY

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

                                                                            3 [      .         .         .         .         :         .         .         .         .         1     ] 106
  prot           (#) default: single protein... score      P(N)  N 100.0%     WEMGLQEEFLELIKLRKKKIEGRLYDEKRRQIKPGDVISFEGGKLKVRVKAIRVYNSFREMLEKEGLENVLPGVKSIEEGIQVYRRFYDEEKEKKYGVVAIEIE    
1 PD020487       p2000.1 (3) O22861(1) O5809...   285   2.2e-25  1  51.9%     WRMYLRDEYIEMIKAGKKRIEGRLYYPQRRGMKPGDKIIFNDGELPAEVNEIHQYASFYELLKAESIEKVFPGTKTIEEGMQMFRKLYDTDQENFYGVVAIHLE    
  consensus/100%                                                              WcMhLp-EalEhIKhtKK+IEGRLY..pRRthKPGDhI.FpsGcL.scVptI+.YsSFhEhLctEulEpVhPGsKoIEEGhQhaR+hYDp-pEphYGVVAIclE    
  consensus/90%                                                               WcMhLp-EalEhIKhtKK+IEGRLY..pRRthKPGDhI.FpsGcL.scVptI+.YsSFhEhLctEulEpVhPGsKoIEEGhQhaR+hYDp-pEphYGVVAIclE    
  consensus/80%                                                               WcMhLp-EalEhIKhtKK+IEGRLY..pRRthKPGDhI.FpsGcL.scVptI+.YsSFhEhLctEulEpVhPGsKoIEEGhQhaR+hYDp-pEphYGVVAIclE    
  consensus/70%                                                               WcMhLp-EalEhIKhtKK+IEGRLY..pRRthKPGDhI.FpsGcL.scVptI+.YsSFhEhLctEulEpVhPGsKoIEEGhQhaR+hYDp-pEphYGVVAIclE    

--- ------------------------------------------------------------
--- 
--- 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=PD020487 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD020487
http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD020487 ==> graphical output of all proteins having domain PD020487
--- 
--- 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    : 110
--- 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                  
Q8TY14                        350   50   64  103    1    132   1e-30 (Q8TY14) Archaea-specific
Q8U3L1                        110   83   83  110    0    129   8e-30 (Q8U3L1) Hypothetical pro
O58093                        109   71   81  109    0    127   4e-29 (O58093) Hypothetical pro
Q9UY95                        111   69   80  109    0    125   1e-28 (Q9UY95) Hypothetical pro
Q6HFQ1                        113   30   48  109    4    118   2e-26 (Q6HFQ1) Hypothetical pro
Q81YF0                        113   30   48  109    4    118   2e-26 (Q81YF0) Hypothetical pro
Q813A1                        113   29   47  109    4    116   1e-25 (Q813A1) Hypothetical Cyt
Q733V0                        113   30   49  109    4    114   3e-25 (Q733V0) Hypothetical pro
Q9SRN6                        244   54   68   72    1    110   3e-24 (Q9SRN6) T21P5.26 protein
Q8LGK4                        244   53   67   72    1    107   6e-23 (Q8LGK4) Hypothetical pro
O22861                        483   38   63   73    3    104   3e-22 (O22861) Hypothetical pro
Q9UYC1                        113   34   56   72    1    103   8e-22 (Q9UYC1) Hypothetical pro
O58178                        114   30   57   72    1     99   1e-20 (O58178) Hypothetical pro
Q8U3J6                        113   31   55   76    1     99   1e-20 (Q8U3J6) Hypothetical pro
Q9KEN6                        113   26   40  106    5     69   9e-12 (Q9KEN6) BH0816 protein  
Q88TE9                        115   26   49   80    7     43   6e-04 (Q88TE9) Hypothetical pro
---
--- 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_h299        84   85  110    0    0   110   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_h2990
Colored by: consensus/70% and property

                          1 [        .         .         .         .         :         .         .         .         .         1         ] 110
1 predict_h2990  100.0%     MEWEMGLQEEFLELIKLRKKKIEGRLYDEKRRQIKPGDVISFEGGKLKVRVKAIRVYNSFREMLEKEGLENVLPGVKSIEEGIQVYRRFYDEEKEKKYGVVAIEIEPLEY    
2 predict_h299    83.6%     MEWEMGLQXXXXXXXXXXXXXXXXXXYDEKRRQIKPGDVISFEGGKLKVRVKAIRVYNSFREMLEKEGLENVLPGVKSIEEGIQVYRRFYDEEKEKKYGVVAIEIEPLEY    
  consensus/100%            MEWEMGLQ..................YDEKRRQIKPGDVISFEGGKLKVRVKAIRVYNSFREMLEKEGLENVLPGVKSIEEGIQVYRRFYDEEKEKKYGVVAIEIEPLEY    
  consensus/90%             MEWEMGLQ..................YDEKRRQIKPGDVISFEGGKLKVRVKAIRVYNSFREMLEKEGLENVLPGVKSIEEGIQVYRRFYDEEKEKKYGVVAIEIEPLEY    
  consensus/80%             MEWEMGLQ..................YDEKRRQIKPGDVISFEGGKLKVRVKAIRVYNSFREMLEKEGLENVLPGVKSIEEGIQVYRRFYDEEKEKKYGVVAIEIEPLEY    
  consensus/70%             MEWEMGLQ..................YDEKRRQIKPGDVISFEGGKLKVRVKAIRVYNSFREMLEKEGLENVLPGVKSIEEGIQVYRRFYDEEKEKKYGVVAIEIEPLEY    

DISULFIND (A. Vullo and P. Frasconi)

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


Chain identifier: 


MEWEMGLQXXXXXXXXXXXXXXXXXXYDEKRRQIKPGDVISFEGGKLKVRVKAIRVYNSFREMLEKEGLENVLPGVKSIEEGIQVYRRFYDEEKEKKYGVVAIEIEPLEY

The sequence contains no cysteine !!

-------------------------------------------------------------------------------
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. 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_h29929

SYNOPSIS of prediction

HEADER information

• About your protein:

• About the alignment used:

• Residue composition for your protein:

  %A: 1.8	%C: 0.0	%D: 2.7	%E: 18.2	%F: 3.6
  %G: 8.2	%H: 0.0	%I: 8.2	%K: 12.7	%L: 9.1
  %M: 2.7	%N: 1.8	%P: 2.7	%Q: 2.7	%R: 8.2
  %S: 2.7	%T: 0.0	%V: 8.2	%W: 0.9	%Y: 5.5

• 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         MEWEMGLQEEFLELIKLRKKKIEGRLYDEKRRQIKPGDVISFEGGKLKVRVKAIRVYNSFREMLEKEGLENVLPGVKSIEEGIQVYRRFYDEEKEKKYGV
Rel_sec    ****************************************************************************************************

PHD_htm                                                                                                        

           ....,....1
AA         VAIEIEPLEY
Rel_sec    **********

PHD_htm              




PHD results (normal)

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

PHD_htm                                                                                                        

           ....,....1
AA         VAIEIEPLEY
Rel_sec    9999999999
SUB_sec    

PHD_htm              

PROF predictions

• PROFsec summary overall your protein can be classified as:
  alpha-beta 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	30.91	30.00	39.09

• 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.
• The subsets are for the fractions of residues predicted at higher levels of reliability, i.e. accuracy. This set covers 32% of all residues.

accessib type	b	e		sub...:	accessib type	b	e
% in protein	30.91	69.09		...set:	% in subset	16.67	83.33

• About your protein:

  prot_id	query
  prot_nres	110
  prot_nali	7
  prot_nchn	1
  prot_nfar	6

• About the alignment used:

  ali_orig

  /home/ppuser/server/work/predict_h29929.hsspPsiFil

• Residue composition for your protein:

  %A: 1.8	%C: 0.0	%D: 2.7	%E: 18.2	%F: 3.6
  %G: 8.2	%H: 0.0	%I: 8.2	%K: 12.7	%L: 9.1
  %M: 2.7	%N: 1.8	%P: 2.7	%Q: 2.7	%R: 8.2
  %S: 2.7	%T: 0.0	%V: 8.2	%W: 0.9	%Y: 5.5

• 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.,....1
AA         MEWEMGLQEEFLELIKLRKKKIEGRLYDEKRRQIKPGDVISFEGGKLKVRVKAIRVYNSFREMLEKEGLENVLPGVKSIEEGIQVYRRFYDEEKEKKYGVVAIEIEPLEY
OBS_sec                                                                                                                  
PROF_sec            HHHHHHH    EEEEEEHHHHH       EEEE   EEEEEEEEEEEE  HHHHHHH            HHHHHHHHHHH  HHHHEE  EEEEEEEEE  
Rel_sec    92002467117777523871577440025312347898688438445788765311012678763156200267865478888887641450120012315578775118
SUB_sec    L.....LL..HHHHH..LL.EEE.....H.....LLLLEEE..L..EEEEEEE......HHHHH..LL....LLLLL.HHHHHHHHH...L.........EEEEEEE..L

O_3_acc    bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb
P_3_acc    ee e ebeee  e beeeeee eb b eeeeee eee  b beeeeb b beebe    beebbeeee ee  ee e beebbe b e beeeeeee bbbbb b e ee
Rel_acc    26331134331174156332314242310223424422253351033344332033013445236633254125404314431333331223411151225594242166
SUB_acc    .e.....e....ei.ee.....e.i.......e.ee...b..e.....bi.........bee..ee...ee..ee.e..ee...........e...e...bbbi.i..ee





PROF results (detail)

           ....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8....,....9....,....10.1.,....1
AA         MEWEMGLQEEFLELIKLRKKKIEGRLYDEKRRQIKPGDVISFEGGKLKVRVKAIRVYNSFREMLEKEGLENVLPGVKSIEEGIQVYRRFYDEEKEKKYGVVAIEIEPLEY
 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 =    76    (number of predicted exposed residues)
--- nfit =    55    (number of expected exposed residues
--- diff =    21.00 (difference nexp-nfit)
--- =====> your protein may be globular, but it is not as compact as a domain
--- 
--- 
--- 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=12.656, Standard deviation=3.194


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_h29929

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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