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Results from PredictProtein for predict_h10434

TOC for file /home/ppuser/server/work/predict_h10434

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_h10434

The following information has been received by the server

reference predict_h10434 (Jun 20, 2006 18:18:20)
reference pred_h10434 (Jun 20, 2006 18:18:06)
PPhdr from: sanchez@cnb.uam.es
PPhdr resp: MAIL
PPhdr orig: HTML
PPhdr want: HTML
PPhdr password(###)
prediction of: - transmembrane helices (PHDhtm)-
return msf format
ret html
ret store
# default: single protein sequence resfilename=sl9718ji
MPVTVTRTTI TTTTTSSSGL GSPMIVGSPR ALTQPLGLLR LLQLVSTCVA FSLVASVGAW
TGSMGNWSMF TWCFCFSVTL IILIVELCGL QARFPLSWRN FPITFACYAA LFCLSASIIY
PTTYVQFLSH GRSRDHAIAA TFFSCIACVA YATEVAWTRA RPGEITGYMA TVPGLLKVLE
TFVACIIFAF ISDPNLYQHQ PALEWCVAVY AICFILAAIA ILLNLGECTN VLPIPFPSFL
SGLALLSVLL YATALVLWPL YQFDEKYGGQ PRRSRDVSCS RSHAYYVCAW DRRLAVAILT
AINLLAYVAD LVHSAHLVFV KV

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]
   66       NWSM

Pattern-ID: GLYCOSAMINOGLYCAN PS00002 PDOC00002
Pattern-DE: Glycosaminoglycan attachment site
Pattern:    SG.G
   18       SGLG

Pattern-ID: PKC_PHOSPHO_SITE PS00005 PDOC00005
Pattern-DE: Protein kinase C phosphorylation site
Pattern:    [ST].[RK]
   28       SPR
   97       SWR

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

Pattern-ID: MYRISTYL PS00008 PDOC00008
Pattern-DE: N-myristoylation site
Pattern:    G[^EDRKHPFYW].{2}[STAGCN][^P]
   27       GSPRAL
   58       GAWTGS

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

prot (#) default: single protein sequence resfilename=sl9718ji /home/ppuser/server/work/predict_h10434  from:     1 to:  322

prot (#) default: single protein sequence resfilename=sl9718ji /home/ppuser/server/work/predict_h10434 
 /home/ppuser/server/work/predict_h10434.segNormGcg Length:  322   11-Jul-99 Check: 2818 ..

       1  MPVxxxxxxx xxxxxxxxGL GSPMIVGSPR Axxxxxxxxx xxxxVSTCVA

      51  FSLVASVGAW TGSMGNWSMF TWCFCFSVTL IILIVELCGL QARFPLSWRN

     101  FPITFACYAA LFCLSASIIY PTTYVQFLSH GRSRDHAIAA TFFSCIACVA

     151  YATEVAWTRA RPGEITGYMA TVPGLLKVLE TFVACIIFAF ISDPNLYQHQ

     201  PALEWCVAVY xxxxxxxxxx xxxxxGECTN VLPIPFPSFx xxxxxxxxxx

     251  xxxxxxxWPL YQFDEKYGGQ PRRSRDVSCS RSHAYYVCAW DRRLAVAILT

     301  AINLLAYVAD LVHSAHLVFV KV

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

                                                                           27 [  .         .         :         .         .         .         .         1         .         .         .         .         :         .         .         .         .         2         .         .         .         .   ] 244
  prot           (#) default: single protein... score      P(N)  N 100.0%     GSPRALTQPLGLLRLLQLVSTCVAFSLVASVGAWTGSMGNWSMFTWCFCFSVTLIILIVELCGLQARFPLSWRNFPITFACYAALFCLSASIIYPTTYVQFLSHGRSRDHAIAATFFSCIACVAYATEVAWTRARPGEITGYMATVPGLLKVLETFVACIIFAFISDPNLYQHQPALEWCVAVYAICFILAAIAILLNLGECTNVLPIPFPSFLSGLA    
1 PD091083       p2000.1 (1) MUG_MOUSE // MY...   434   3.6e-41  1  87.1%     -----------------------------------------------------------------------------------------------------------------------------ATEVAWTRARPGEITGYMATVPGLLKVFETFVACIIFAFIGEPLLYNQKPALEWCVAVYAICFILAGVTILLNLGDCTNVLPIPFPTFLSGLA    
2 PD009373       p2000.1 (7) MAL(4) PLLP(1) ...   185   1.9e-14  1  44.4%     --------------------------LIASTGVPYYPAQGWVMFVSVFCFLVTTSLLILYLFGLHGgyEISwtRLDIVFFCYAALFYLSASVLYATACVQMVAGSTYRHYhiAATFFACVAMLAY---------------------------------------------------------------------------------------------    
3 PD081596       p2000.1 (1) MUG_MOUSE // MY...   118   5.3e-07  1  92.3%     GSARALTQPLGLLRLLQLISTCVAFS------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------    
  consensus/100%                                                              ..........................................................................................................................................................................................................................    
  consensus/90%                                                               ..........................................................................................................................................................................................................................    
  consensus/80%                                                               ..........................................................................................................................................................................................................................    
  consensus/70%                                                               ..........................................................................................................................................................................................................................    

--- ------------------------------------------------------------
--- 
--- 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=PD091083 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD091083
http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD091083 ==> graphical output of all proteins having domain PD091083
http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD009373 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD009373
http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD009373 ==> graphical output of all proteins having domain PD009373
http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD081596 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD081596
http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD081596 ==> graphical output of all proteins having domain PD081596
--- 
--- 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    : 322
--- 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 OMIM    PROTEIN                  
swiss|Q96S97|MYADM_HUMAN      322   81   81  322    0    420   e-116         Myeloid-associated differ
trembl|Q542Z1_HUMAN|Q542Z1_HUMAN  322   81   81  322    0    420   e-116         CDNA FLJ90795 fis, clone 
trembl|Q5R6H1_PONPY|Q5R6H1_PONPY  322   79   79  322    0    413   e-114         Hypothetical protein     
trembl|Q63ZU3_XENLA|Q63ZU3_XENLA  307   50   64  278    1    389   e-107         LOC494734 protein        
trembl|Q6VBQ5_RAT|Q6VBQ5_RAT  318   70   76  301    2    389   e-107         Myeloid-associated differ
trembl|Q8BGS9_MOUSE|Q8BGS9_MOUSE  320   70   76  301    4    387   e-106         13 days embryo heart cDNA
trembl|Q6DFR5_XENTR|Q6DFR5_XENTR  307   49   63  278    1    387   e-106         Myeloid-associated       
trembl|Q8N9R4_HUMAN|Q8N9R4_HUMAN  304   75   75  304   18    385   e-106         CDNA FLJ36680 fis, clone 
trembl|Q4T7U8_TETNG|Q4T7U8_TETNG  284   45   62  271    6    345   1e-93         Chromosome undetermined S
trembl|Q5BKP1_MOUSE|Q5BKP1_MOUSE  303   36   48  268   12    340   3e-92         1110012N22Rik protein    
trembl|Q4SGM4_TETNG|Q4SGM4_TETNG  303   35   50  269   10    340   3e-92         Chromosome 3 SCAF14593, w
trembl|Q8BPS8_MOUSE|Q8BPS8_MOUSE  282   70   76  264    0    332   1e-89         0 day neonate eyeball cDN
trembl|Q96M12_HUMAN|Q96M12_HUMAN  245   68   75  245    0    323   4e-87         CDNA FLJ32908 fis, clone 
trembl|Q5XGR0_XENLA|Q5XGR0_XENLA  302   34   49  269   11    323   6e-87         LOC495162 protein        
trembl|Q53R84_HUMAN|Q53R84_HUMAN  245   68   75  245    0    319   6e-86         Hypothetical protein tmp_
trembl|Q6P5K9_BRARE|Q6P5K9_BRARE  288   39   53  264   13    305   1e-81         Hypothetical protein zgc:
trembl|Q4S007_TETNG|Q4S007_TETNG  305   32   49  267   12    303   7e-81         Chromosome 18 SCAF14786, 
swiss|O35682|MYADM_MOUSE      296   75   81  218    0    298   2e-79         Myeloid-associated differ
trembl|Q7Z507_HUMAN|Q7Z507_HUMAN  298   86   86  210    0    297   3e-79         Myeloid upregulated prote
trembl|Q4SZQ1_TETNG|Q4SZQ1_TETNG  281   36   52  259   16    281   1e-74         Chromosome 3 SCAF11549, w
trembl|Q96SK9_HUMAN|Q96SK9_HUMAN  154   78   78  154    0    206   9e-52         CDNA FLJ14787 fis, clone 
trembl|Q4T362_TETNG|Q4T362_TETNG  264   26   38  141    8    142   1e-32         Chromosome undetermined  
trembl|Q9D1F1_MOUSE|Q9D1F1_MOUSE  153   34   50   88    0    135   2e-30         18-day embryo whole body 
trembl|Q567J3_BRARE|Q567J3_BRARE  152   29   43  111    9    122   2e-26         Hypothetical protein zgc:
swiss|P21145|MAL_HUMAN        153   31   42  111    8    113   1e-23 188860  Myelin and lymphocyte pro
trembl|Q6FH77_HUMAN|Q6FH77_HUMAN  153   31   42  111    8    113   1e-23         Hypothetical protein MAL 
trembl|Q66ID0_BRARE|Q66ID0_BRARE  159   26   39  111   15    101   3e-20         Zgc:101772               
swiss|Q28296|MAL_CANFA        153   27   41  111    8     98   2e-19         Myelin and lymphocyte pro
swiss|Q64349|MAL_RAT          153   27   41  111    8     98   3e-19         Myelin and lymphocyte pro
swiss|O09198|MAL_MOUSE        153   26   41  111    8     96   1e-18         Myelin and lymphocyte pro
trembl|Q545Q7_MOUSE|Q545Q7_MOUSE  153   26   41  111    8     96   1e-18         Adult male lung cDNA, RIK
trembl|Q3ZBY0_BOVIN|Q3ZBY0_BOVIN  153   24   38  111    8     88   2e-16         Hypothetical protein     
trembl|Q6DER3_XENTR|Q6DER3_XENTR  159   21   41  111    8     70   7e-11         Mal, T-cell differentiati
trembl|Q6PBB5_XENLA|Q6PBB5_XENLA  159   22   37  111    8     66   9e-10         MGC68692 protein         
swiss|Q91X49|MALL_MOUSE       154   24   42  106    7     56   2e-06         MAL-like protein (Protein
trembl|Q3TQ65_MOUSE|Q3TQ65_MOUSE  154   24   42  106    7     56   2e-06         16 days embryo head cDNA,
trembl|Q4SQP2_TETNG|Q4SQP2_TETNG  163   25   39   68    3     55   2e-06         Chromosome 17 SCAF14532, 
trembl|Q4SH88_TETNG|Q4SH88_TETNG  184   20   32  112   31     54   4e-06         Chromosome 8 SCAF14587, w
trembl|Q9D2R2_MOUSE|Q9D2R2_MOUSE   97   21   38   91   22     54   4e-06         Adult male stomach cDNA, 
trembl|Q3KTJ8_SCHJA|Q3KTJ8_SCHJA   58   36   52   36    0     54   5e-06         SJCHGC04081 protein (Frag
swiss|Q13021|MALL_HUMAN       153   24   41  106    8     52   2e-05 602022  MAL-like protein (Protein
trembl|Q2HJI7_BOVIN|Q2HJI7_BOVIN  152   21   42  105    9     49   2e-04         Hypothetical protein     
trembl|Q5EB48_RAT|Q5EB48_RAT  154   22   42  106    7     49   2e-04         Mal, T-cell differentiati
swiss|Q969L2|MAL2_HUMAN       176   19   32  113   19     47   6e-04         Protein MAL2             
trembl|Q4T196_TETNG|Q4T196_TETNG  221   34   42   42    5     47   6e-04         Chromosome undetermined  
swiss|Q9DCU2|PLLP_MOUSE       182   21   41  112    2     45   0.002         Plasmolipin (Plasma membr
trembl|Q544Q5_MOUSE|Q544Q5_MOUSE  182   21   41  112    2     45   0.002         Adult male olfactory brai
swiss|Q9Y342|PLLP_HUMAN       182   21   41  114    2     45   0.003 600340  Plasmolipin (Plasma membr
swiss|Q8CJ61|CKLF4_MOUSE      208   25   38   81    8     45   0.003         CKLF-like MARVEL transmem
swiss|P47987|PLLP_RAT         182   21   41  114    2     44   0.004         Plasmolipin (Plasma membr
swiss|Q8IZV2|CKLF8_HUMAN      173   22   44  107    2     43   0.009 607891  CKLF-like MARVEL transmem
swiss|Q8IZR5|CKLF4_HUMAN      234   25   38   81    8     42   0.015 607887  CKLF-like MARVEL transmem
trembl|Q52M40_HUMAN|Q52M40_HUMAN  208   25   38   81    8     42   0.015         Chemokine-like factor sup
swiss|Q9CZR4|CKLF8_MOUSE      173   23   44  107    2     42   0.022         CKLF-like MARVEL transmem
trembl|Q71B06_RAT|Q71B06_RAT  173   23   44  107    2     41   0.035         Chemokine-like related pr
trembl|Q5F3S0_CHICK|Q5F3S0_CHICK  178   22   35  107   20     40   0.057         Hypothetical protein     
trembl|Q66KX7_XENLA|Q66KX7_XENLA  174   25   38   75    5     39    0.15         MGC85344 protein         
trembl|Q6DGM6_BRARE|Q6DGM6_BRARE  208   21   35   81    8     39    0.19         Hypothetical protein zgc:
trembl|Q4SI17_TETNG|Q4SI17_TETNG  207   16   33  100   14     38    0.21         Chromosome 5 SCAF14581, w
trembl|Q6GPN9_XENLA|Q6GPN9_XENLA  170   18   42  113    1     38    0.37         MGC82744 protein         
---
--- 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                     
myadm_human       100  100  322    0    0   322 Q96S97 Myeloid-associated differ
myadm_ponpy        98   97  322    0    0   322 Q5R6H1 Myeloid-associated differ
myadm_mouse        88   84  238    1    6   296 O35682 protein).                
myadm_rat          86   79  316    2    8   318 Q6VBQ5 protein).                
--- 
--- 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_h1040
Colored by: consensus/70% and property

                          1 [        .         .         .         .         :         .         .         .         .         1         .         .         .         .         :         .         .         .         .         2         .         .         .         .         :         .         .         .         .         3         .         . ] 322
1 predict_h1040  100.0%     MPVTVTRTTITTTTTSSSGLGSPMIVGSPRALTQPLGLLRLLQLVSTCVAFSLVASVGAWTGSMGNWSMFTWCFCFSVTLIILIVELCGLQARFPLSWRNFPITFACYAALFCLSASIIYPTTYVQFLSHGRSRDHAIAATFFSCIACVAYATEVAWTRARPGEITGYMATVPGLLKVLETFVACIIFAFISDPNLYQHQPALEWCVAVYAICFILAAIAILLNLGECTNVLPIPFPSFLSGLALLSVLLYATALVLWPLYQFDEKYGGQPRRSRDVSCSRSHAYYVCAWDRRLAVAILTAINLLAYVADLVHSAHLVFVKV    
2 myadm_human    100.0%     MPVTVTRTTITTTTTSSSGLGSPMIVGSPRALTQPLGLLRLLQLVSTCVAFSLVASVGAWTGSMGNWSMFTWCFCFSVTLIILIVELCGLQARFPLSWRNFPITFACYAALFCLSASIIYPTTYVQFLSHGRSRDHAIAATFFSCIACVAYATEVAWTRARPGEITGYMATVPGLLKVLETFVACIIFAFISDPNLYQHQPALEWCVAVYAICFILAAIAILLNLGECTNVLPIPFPSFLSGLALLSVLLYATALVLWPLYQFDEKYGGQPRRSRDVSCSRSHAYYVCAWDRRLAVAILTAINLLAYVADLVHSAHLVFVKV    
3 myadm_ponpy     98.1%     MPVTVTRTTITTTTTSSSGQGSPTIVGSPRALTQPLGLLRLLQLVSTCVAFSLVASVGAWTGPMGNWSMFTWCFCFSVTLIILIVELCGLQARFPLSWRNFPITFACYAALFCLSASIIYPTTYVQFLSHGRSRDHAIAATFFSCIACVAYATEVAWTRARPGEITGYMATVPGLLKVLETFVACIIFAFISDTYLYQHQPALEWCVAVYAICFILAAIAILLNLGECTNVLPIPFPSFLSGLALLSVLLYATALVLWPLYQFDEKYGGQPRRSRDVSCSRSHAYYVCGWDRRLAVAILTAINLLAYVADLVHSAHLVFVKV    
4 myadm_mouse     86.1%     MPVTVTRTTITTTTSSST------TVGSARALTQPLGLLRLLQLISTCVAFSLVASVGAWTGPMGNWAMFTWCFCFAVTLIILIVELGGLQAHFPLSWRNFPITFACYAALFCLSSSIIYPTTYVQFLAHGRTRDHAIAATTFSCVACLAYATEVAWTRARPGEITGYMATVPGLLKVFETFVACIIFAFIGEPLLYNQKPALEWCVAVYAICFILAGVTILLNLGDCTNVLPIPFPTFLSGLA------------------------------------------------------------------------------    
5 myadm_rat       84.2%     MPVTVTRTTITTTSSSST------TVGSARALTQPLGLLRLLQLVSTCVAFSLVASVGAWTGPMGNWAMFTWCFCFAVTLIILIEELGGFQARFPLSWRNFPITFACYAALFCLSSSIIYPTTYVQFLPHGRSRDHAIAATTFSCVACLAYATEVAWTRARPGEITGYMATVPGLLKVFETFVACIIFAFISEPSLYQQRPALEWCVAVYAICFILAAVTVLLNLGDCTNMLPIPFPTFLSGLALLSVLLYATAIVLWPLYQFDQRYNSQPRRSMDPSCSRSYVqeVCNWDRRLAVSILTGINLLAYVSDLVYSTRLVFVKV    
  consensus/100%            MPVTVTRTTITTTooSSo......hVGSsRALTQPLGLLRLLQLlSTCVAFSLVASVGAWTGsMGNWuMFTWCFCFuVTLIILI.ELsGhQA+FPLSWRNFPITFACYAALFCLSuSIIYPTTYVQFLsHGRoRDHAIAAThFSClAClAYATEVAWTRARPGEITGYMATVPGLLKVhETFVACIIFAFIu-s.LYpppPALEWCVAVYAICFILAulslLLNLG-CTNhLPIPFPoFLSGLA..............................................................................    
  consensus/90%             MPVTVTRTTITTTooSSo......hVGSsRALTQPLGLLRLLQLlSTCVAFSLVASVGAWTGsMGNWuMFTWCFCFuVTLIILI.ELsGhQA+FPLSWRNFPITFACYAALFCLSuSIIYPTTYVQFLsHGRoRDHAIAAThFSClAClAYATEVAWTRARPGEITGYMATVPGLLKVhETFVACIIFAFIu-s.LYpppPALEWCVAVYAICFILAulslLLNLG-CTNhLPIPFPoFLSGLA..............................................................................    
  consensus/80%             MPVTVTRTTITTTToSSo......hVGSsRALTQPLGLLRLLQLVSTCVAFSLVASVGAWTGsMGNWuMFTWCFCFuVTLIILIVELsGLQARFPLSWRNFPITFACYAALFCLSuSIIYPTTYVQFLuHGRSRDHAIAAThFSClAClAYATEVAWTRARPGEITGYMATVPGLLKVhETFVACIIFAFIS-P.LYQppPALEWCVAVYAICFILAAlsILLNLG-CTNVLPIPFPoFLSGLALLSVLLYATAlVLWPLYQFDp+YsuQPRRShDsSCSRSas..VCsWDRRLAVuILTuINLLAYVuDLVaSs+LVFVKV    
  consensus/70%             MPVTVTRTTITTTToSSo......hVGSsRALTQPLGLLRLLQLVSTCVAFSLVASVGAWTGsMGNWuMFTWCFCFuVTLIILIVELsGLQARFPLSWRNFPITFACYAALFCLSuSIIYPTTYVQFLuHGRSRDHAIAAThFSClAClAYATEVAWTRARPGEITGYMATVPGLLKVhETFVACIIFAFIS-P.LYQppPALEWCVAVYAICFILAAlsILLNLG-CTNVLPIPFPoFLSGLALLSVLLYATAlVLWPLYQFDp+YsuQPRRShDsSCSRSas..VCsWDRRLAVuILTuINLLAYVuDLVaSs+LVFVKV    

DISULFIND (A. Vullo and P. Frasconi)

Results for predict_h10434.fasta

         .........10........20........30........40........50........60........70........
AA       MPVXXXXXXXXXXXXXXXGLGSPMIVGSPRAXXXXXXXXXXXXXVSTCVAFSLVASVGAWTGSMGNWSMFTWCFCFSVT
DB_state                                                                             

         80........90........100.......110.......120.......130.......140.......150......
AA       LIILIVELCGLQARFPLSWRNFPITFACYAALFCLSASIIYPTTYVQFLSHGRSRDHAIAATFFSCIACVAYATEVAWT
DB_state                                                                           

         .160.......170.......180.......190.......200.......210.......220.......230.....
AA       RARPGEITGYMATVPGLLKVLETFVACIIFAFISDPNLYQHQPALEWCVAVYXXXXXXXXXXXXXXXGECTNVLPIPFP
DB_state                                                                             

         ..240.......250.......260.......270.......280.......290.......300.......310....
AA       SFXXXXXXXXXXXXXXXXXXWPLYQFDEKYGGQPRRSRDVSCSRSHAYYVCAWDRRLAVAILTAINLLAYVADLVHSAH
DB_state                                                                              

         ...320
AA       LVFVKV
DB_state       


Please cite:

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

Contact information:

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

Abbreviations used:

AA
amino acid sequence
DB_state
predicted disulfide bonding state (1=disulfide bonded, 0=not disulfide bonded)

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_h10434

SYNOPSIS of prediction

• PHDhtm summary
  • NHTM=8
    PHDhtm detected 8 membrane helices for the best model.The second best model contained 7 helices.
  • TOP=out
    PHDhtm predicted the topology out, i.e. the first loop region is out (Note: this prediction may be problematic when the sequence you sent starts or ends with a region predicted in a membrane helix!)
  • Reliability of best model=3 (0 is low, 9 is high)
  • Zscore for best model=1.382
  • Difference of positive charges (K+R) inside - outside=0.095 (the higher the value, the more reliable)
  • Reliability of topology prediction =0 (0 is low, 9 is high)
  • Details of the strength of each predicted membrane helix:
    (sorted by strength, strongest first)
    

    N HTM	Total score	Best HTM	c-N
    1	0.4647	0.9010	294 - 313
    2	0.5108	0.8905	68 - 86
    3	0.5570	0.8915	207 - 225
    4	0.6030	0.8900	239 - 257
    5	0.6468	0.8911	102 - 119
    6	0.6928	0.8702	173 - 192
    7	0.7331	0.8608	138 - 155
    8	0.7724	0.8513	39 - 56

  • Overview over transmembrane segments:
    

    Positions	Segments	Explain
    1- 38	o1	outside region 1
    39- 56	T1	?=error 1
    57- 67	i1	inside region 1
    68- 86	T2	?=error 2
    87- 101	o2	outside region 2
    102- 119	T3	?=error 3
    120- 137	i2	inside region 2
    138- 155	T4	?=error 4
    156- 172	o3	outside region 3
    173- 192	T5	?=error 5
    193- 206	i3	inside region 3
    207- 225	T6	?=error 6
    226- 238	o4	outside region 4
    239- 257	T7	?=error 7
    258- 293	i4	inside region 4
    294- 313	T8	?=error 8
    314- 322	o5	outside region 5

HEADER information

• About your protein:

• About the alignment used:

• Residue composition for your protein:

  %A: 11.5	%C: 4.3	%D: 1.9	%E: 2.2	%F: 5.9
  %G: 5.0	%H: 1.9	%I: 6.5	%K: 0.9	%L: 13.0
  %M: 1.6	%N: 1.9	%P: 5.0	%Q: 2.5	%R: 4.7
  %S: 8.1	%T: 8.1	%V: 8.7	%W: 2.5	%Y: 4.0

• About the PHD methods used:

• Please quote:
  1. PHD: B Rost (1996) Methods in Enzymology, 266:525-539
  2. PHDhtm: 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
  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
  Rel_htm:	reliability index for PHDhtm prediction (0=low to 9=high) Note: for the brief presentation strong predictions marked by '*'
  SUB_htm:	subset of the PHDhtm prediction, for all residues with an expected average accuracy > 98% (tables in header) NOTE: for this subset the following symbols are used: N: is non-membrane region (for which above ' ' is used) .: means that no prediction is made for this residue, as the reliability is: Rel < 7
  PHDrhtm:	refined PHD prediction: M=helical transmembrane region, blank=non-membrane
  PiMohtm:	PHD prediction of membrane topology: T=helical transmembrane region, i=inside of membrane, o=outside of membrane
  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         MPVTVTRTTITTTTTSSSGLGSPMIVGSPRALTQPLGLLRLLQLVSTCVAFSLVASVGAWTGSMGNWSMFTWCFCFSVTLIILIVELCGLQARFPLSWRN
PHD_htm                                        MMMMMMMMMMMMMMMMMMMMMMMM   MMMMMMMMMMMMMMMMMMMMMMMMMM          M
Rel_htm    *********************************        ************               ******************              

PiMohtm    ooooooooooooooooooooooooooooooooooooooTTTTTTTTTTTTTTTTTTiiiiiiiiiiiTTTTTTTTTTTTTTTTTTToooooooooooooo

           ....,....11...,....12...,....13...,....14...,....15...,....16...,....17...,....18...,....19...,....20
AA         FPITFACYAALFCLSASIIYPTTYVQFLSHGRSRDHAIAATFFSCIACVAYATEVAWTRARPGEITGYMATVPGLLKVLETFVACIIFAFISDPNLYQHQ
PHD_htm    MMMMMMMMMMMMMMMMMMMMMMM             MMMMMMMMMMMMMMMMMMMM            MMMMMMMMMMMMMMMMMMMMMMMMMM      
Rel_htm      ******************       *******     *************        ****          *  *************          

PiMohtm    oTTTTTTTTTTTTTTTTTTiiiiiiiiiiiiiiiiiiTTTTTTTTTTTTTTTTTToooooooooooooooooTTTTTTTTTTTTTTTTTTTTiiiiiiii

           ....,....21...,....22...,....23...,....24...,....25...,....26...,....27...,....28...,....29...,....30
AA         PALEWCVAVYAICFILAAIAILLNLGECTNVLPIPFPSFLSGLALLSVLLYATALVLWPLYQFDEKYGGQPRRSRDVSCSRSHAYYVCAWDRRLAVAILT
PHD_htm        MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM                           MMMMMMMMMMMM
Rel_htm          ********************             ******************       **********************       *******

PiMohtm    iiiiiiTTTTTTTTTTTTTTTTTTToooooooooooooTTTTTTTTTTTTTTTTTTTiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiTTTTTTT

           ....,....31...,....32...,....33
AA         AINLLAYVADLVHSAHLVFVKV
PHD_htm    MMMMMMMMMMMMMMMM      
Rel_htm    ************          

PiMohtm    TTTTTTTTTTTTTooooooooo




PHD results (normal)

           ....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8....,....9....,....1
AA         MPVTVTRTTITTTTTSSSGLGSPMIVGSPRALTQPLGLLRLLQLVSTCVAFSLVASVGAWTGSMGNWSMFTWCFCFSVTLIILIVELCGLQARFPLSWRN
PHD_htm                                        MMMMMMMMMMMMMMMMMMMMMMMM   MMMMMMMMMMMMMMMMMMMMMMMMMM          M
Rel_htm    9999999999999999999999999999887775211344677777777777765421000010245677778777777777877764102344542212
SUB_htm    NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN........MMMMMMMMMMMM...............MMMMMMMMMMMMMMMMMM..............

PHDrhtm                                          MMMMMMMMMMMMMMMMMM           MMMMMMMMMMMMMMMMMMM              
PiMohtm    ooooooooooooooooooooooooooooooooooooooTTTTTTTTTTTTTTTTTTiiiiiiiiiiiTTTTTTTTTTTTTTTTTTToooooooooooooo

           ....,....11...,....12...,....13...,....14...,....15...,....16...,....17...,....18...,....19...,....20
AA         FPITFACYAALFCLSASIIYPTTYVQFLSHGRSRDHAIAATFFSCIACVAYATEVAWTRARPGEITGYMATVPGLLKVLETFVACIIFAFISDPNLYQHQ
PHD_htm    MMMMMMMMMMMMMMMMMMMMMMM             MMMMMMMMMMMMMMMMMMMM            MMMMMMMMMMMMMMMMMMMMMMMMMM      
Rel_htm    4677777777777778887764204567777777521467788877777777653114667777653023456676677777777778776530234555
SUB_htm    ..MMMMMMMMMMMMMMMMMM.......NNNNNNN.....MMMMMMMMMMMMM........NNNN..........M..MMMMMMMMMMMMM..........

PHDrhtm     MMMMMMMMMMMMMMMMMM                  MMMMMMMMMMMMMMMMMM                 MMMMMMMMMMMMMMMMMMMM        
PiMohtm    oTTTTTTTTTTTTTTTTTTiiiiiiiiiiiiiiiiiiTTTTTTTTTTTTTTTTTToooooooooooooooooTTTTTTTTTTTTTTTTTTTTiiiiiiii

           ....,....21...,....22...,....23...,....24...,....25...,....26...,....27...,....28...,....29...,....30
AA         PALEWCVAVYAICFILAAIAILLNLGECTNVLPIPFPSFLSGLALLSVLLYATALVLWPLYQFDEKYGGQPRRSRDVSCSRSHAYYVCAWDRRLAVAILT
PHD_htm        MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM                           MMMMMMMMMMMM
Rel_htm    4320467788887777777777777765433211245667777777777777778776531146889999999999999999999731123457777788
SUB_htm    ......MMMMMMMMMMMMMMMMMMMM.............MMMMMMMMMMMMMMMMMM.......NNNNNNNNNNNNNNNNNNNNNN.......MMMMMMM

PHDrhtm          MMMMMMMMMMMMMMMMMMM             MMMMMMMMMMMMMMMMMMM                                    MMMMMMM
PiMohtm    iiiiiiTTTTTTTTTTTTTTTTTTToooooooooooooTTTTTTTTTTTTTTTTTTTiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiTTTTTTT

           ....,....31...,....32...,....33
AA         AINLLAYVADLVHSAHLVFVKV
PHD_htm    MMMMMMMMMMMMMMMM      
Rel_htm    8888888888776530123566
SUB_htm    MMMMMMMMMMMM..........

PHDrhtm    MMMMMMMMMMMMM         
PiMohtm    TTTTTTTTTTTTTooooooooo

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	53.42	12.11	34.47

• 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 44% of all residues.

accessib type	b	e		sub...:	accessib type	b	e
% in protein	67.08	32.92		...set:	% in subset	95.07	4.93

• About your protein:

  prot_id	query
  prot_nres	322
  prot_nali	29
  prot_nchn	1
  prot_nfar	24

• About the alignment used:

  ali_orig

  /home/ppuser/server/work/predict_h10434.hsspPsiFil

• Residue composition for your protein:

  %A: 11.5	%C: 4.3	%D: 1.9	%E: 2.2	%F: 5.9
  %G: 5.0	%H: 1.9	%I: 6.5	%K: 0.9	%L: 13.0
  %M: 1.6	%N: 1.9	%P: 5.0	%Q: 2.5	%R: 4.7
  %S: 8.1	%T: 8.1	%V: 8.7	%W: 2.5	%Y: 4.0

• 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.,....16.1.,....17.1.,....18.1.,....19.1.,....20.1.,....21.1.,....22.1.,....23.1.,....24.1.,....25.1.,....26.1.,....27.1.,....28.1.,....29.1.,....30.1.,....31.1.,....32.
AA         MPVTVTRTTITTTTTSSSGLGSPMIVGSPRALTQPLGLLRLLQLVSTCVAFSLVASVGAWTGSMGNWSMFTWCFCFSVTLIILIVELCGLQARFPLSWRNFPITFACYAALFCLSASIIYPTTYVQFLSHGRSRDHAIAATFFSCIACVAYATEVAWTRARPGEITGYMATVPGLLKVLETFVACIIFAFISDPNLYQHQPALEWCVAVYAICFILAAIAILLNLGECTNVLPIPFPSFLSGLALLSVLLYATALVLWPLYQFDEKYGGQPRRSRDVSCSRSHAYYVCAWDRRLAVAILTAINLLAYVADLVHSAHLVFVKV
OBS_sec                                                                                                                                                                                                                                                                                                                                      
PROF_sec      EEE   EEEE           EEE HHH   HHHHHHHHHHHHHHHHHHH             EEEEHHHHHHHHHHHHHHHHHHH        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH        HHHHHHHHHHHHHHHHHHHHHHHH        HHHHHHHHHHHHHHHHHEEEEEE          HHHHHHHHHHHHHHHHHHHHHHHH            HHHHHHHHHHHHHHHHHH EEEEEEEE                      EEEE  HHHHHHHHHHHHHHHHHH     EEEEEEE 
Rel_sec    9711220201110003467777415416213114014788888888887653102446644443643542134678888888889884022334324003468899999888766767778877520145333431356778989988888886322212755321023313458998886322022100058750343423345567787888887653110002000566676103565888998888753000101133243347776767775466656400100010244457767668887760001302578636
SUB_sec    LL...............LLLLL..E..L.........HHHHHHHHHHHHHH......LL.....L..E.....HHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHHHHHHHH....L.......HHHHHHHHHHHHHHHHH......LLL..........HHHHHHHH..........LLLL.........HHHHHHHHHHHHHHH..........LLLLLL...HHHHHHHHHHHHHH...............LLLLLLLLLL.LLLLL.............HHHHHHHHHHHHH.......EEEE.L

O_3_acc    bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb
P_3_acc    ee ebeeee eeeeeeeee ebebbbbb eebeebbbbb bb bbbbbbbbbbbbeeee e     bbbbbbbbbbbbbbbbbbb bbe  eebeb be b bbbbbbbbbbbbbbbbbbbbbbbe  eeeee  bbbbbbbbbbbbbbbbbb bbb  b eeebbbbbbbb bbb bbe bbbbbbbbbb  ee  e   bb bbbbbbbbbbbbbbbbbbbbbbe be  e eb  bbbbbbbbbbbbbbbbbbbbbbb b ee eeeeeee e ebeee e bbb b   bbbbbbbbbbbbbbbbbbbbbbbbbbbee
Rel_acc    1415233342332222102112111231040103000524882293455735040203121110013488865556789996997271221233332032503654779889398969729323322221321222059969897998972851043130310100414448049245620659999875301131121113223989969998987999999272100321121112353748999999594936755331120211102003300231420120251002248668666859672942340300523210
SUB_acc    .e.e....e....................e.......b.ibb..b.bbbb.b.b.............bbbbbbbbbbbbbbbbbb.b.............b..bbbbbbbbb.bbbbbb.b................bbbbbbbbbbbbb.bb..b..........b.bbbb.bb.ibb..bbbbbbbbb...............bbbbbbbbbbbbbbbbbb.b..............b.bbbbbbbbbbbbb.bbbb.....................e......b.....bbbbbbbbbbbbb.bb..b....b.....





PROF results (detail)

           ....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8....,....9....,....10.1.,....11.1.,....12.1.,....13.1.,....14.1.,....15.1.,....16.1.,....17.1.,....18.1.,....19.1.,....20.1.,....21.1.,....22.1.,....23.1.,....24.1.,....25.1.,....26.1.,....27.1.,....28.1.,....29.1.,....30.1.,....31.1.,....32.
AA         MPVTVTRTTITTTTTSSSGLGSPMIVGSPRALTQPLGLLRLLQLVSTCVAFSLVASVGAWTGSMGNWSMFTWCFCFSVTLIILIVELCGLQARFPLSWRNFPITFACYAALFCLSASIIYPTTYVQFLSHGRSRDHAIAATFFSCIACVAYATEVAWTRARPGEITGYMATVPGLLKVLETFVACIIFAFISDPNLYQHQPALEWCVAVYAICFILAAIAILLNLGECTNVLPIPFPSFLSGLALLSVLLYATALVLWPLYQFDEKYGGQPRRSRDVSCSRSHAYYVCAWDRRLAVAILTAINLLAYVADLVHSAHLVFVKV
 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 =   106    (number of predicted exposed residues)
--- nfit =   133    (number of expected exposed residues
--- diff =   -27.00 (difference nexp-nfit)
--- =====> your protein appears not as globular, 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=12.541, Standard deviation=3.781


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_h10434

Quotes for methods

1. PredictProtein: B Rost,G Yachdav and J Liu (2004) The PredictProtein Server. Nucleic Acids Research 32(Web Server issue):W321-W326.
   • Author: B Rost
   • Contact: yachdav@maple.bioc.columbia.edu
   • URL: http://cubic.bioc.columbia.edu
   • Version: 10.20.04
   • 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.
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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