Links: BOTTOM PredictProtein Burkhard Rost




Results from PredictProtein for predict_h348

TOC for file /home/ppuser/server/work/predict_h348

  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. CYSPRED prediction(P Fariselli,P Riccobelli & R Casadio) (TOC)
  9. PHD information about accuracy (TOC)
  10. PHD predictions (TOC)
  11. GLOBE prediction of globularity (TOC)
  12. Ambivalent Sequence Predictor(Malin Young, Kent Kirshenbaum, Stefan Highsmith) (TOC)
  13. PROF predictions (TOC)
  14. GLOBE prediction of globularity (TOC)

END of TOC




BEG of results for file /home/ppuser/server/work/predict_h348


The following information has been received by the server


reference predict_h348 (Feb 18, 2004 09:49:26)
reference pred_h348 (Feb 18, 2004 09:50:02)
PPhdr from: arojas@cnb.uam.es
PPhdr resp: MAIL
PPhdr orig: HTML
PPhdr want: HTML
PPhdr password(###)
prediction of: - default prediction of: - PHDsec PHDacc PHDhtm ProSite SEG ProDom
return msf format
ret html
ret store
# default: single protein sequence description=target-thr
MLKNTSSNLDAPVARSCDFAMKKMDLRKAFTLIEPGPVTLVTTSAGGTNNVMTISWTMAV
DFTPKLAITTGPWNFSYKALTKSRECVIAIPTVDLLDKVVGVGTCSGKDTDKFDTFRLTP
IKGKYVEAPLIKECVANIECKVVDIIKKHDIVVLEGVAAYFDTSRKEKRTLHAVGDGTFV
VDGRTLDRKKQMRSKLLGIF


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


TOP - BOTTOM - PROSITE
-------------------------------------------------------------
Pattern-ID: ASN_GLYCOSYLATION PS00001 PDOC00001
Pattern-DE: N-glycosylation site
Pattern:    N[^P][ST][^P]
   4        NTSS
   74       NFSY

Pattern-ID: PKC_PHOSPHO_SITE PS00005 PDOC00005
Pattern-DE: Protein kinase C phosphorylation site
Pattern:    [ST].[RK]
   63       TPK
   76       SYK
   106      SGK
   110      TDK
   115      TFR
   163      TSR

Pattern-ID: CK2_PHOSPHO_SITE PS00006 PDOC00006
Pattern-DE: Casein kinase II phosphorylation site
Pattern:    [ST].{2}[DE]
   7        SNLD
   31       TLIE
   106      SGKD
   164      SRKE

Pattern-ID: MYRISTYL PS00008 PDOC00008
Pattern-DE: N-myristoylation site
Pattern:    G[^EDRKHPFYW].{2}[STAGCN][^P]
   46       GGTNNV
   101      GVGTCS



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


TOP - BOTTOM - SEG

prot (#) default: single protein sequence description=target-thr /home/ppuser/server/work/predict_h348 from: 1 to: 200 prot (#) default: single protein sequence description=target-thr /home/ppuser/server/work/predict_h348 /home/ppuser/server/work/predict_h348.segNormGcg Length: 200 11-Jul-99 Check: 2818 .. 1 MLKNTSSNLD APVARSCDFA MKKMDLRKAF TLIEPGPVTL VTTSAGGTNN 51 VMTISWTMAV DFTPKLAITT GPWNFSYKAL TKSRECVIAI PTVDLLDKVV 101 GVGTCSGKDT DKFDTFRLTP IKGKYVEAPL IKECVANIEC xxxxxxxxxx 151 xxxLEGVAAY FDTSRKEKRT LHAVGDGTFV VDGRTLDRKK QMRSKLLGIF


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


TOP - BOTTOM - ProDom - MView
Identities computed with respect to: (query) prot
Colored by: consensus/70% and property
HSP processing: ranked
                                                                           35 [    .         :         .         .         .         .         1         .         .         .         .         :         .         .    ] 175
  prot           (#) default: single protein... score      P(N)  N 100.0%     PGPVTLVTTSAGGTNNVMTISWTMAVDFTPKLAITTGPWNFSYKALTKSRECVIAIPTVDLLDKVVGVGTCSGKDTDKFDTFRLTPIKGKYVEAPLIKECVANIECKVVDIIKKHDIVVLEGVAAYFDTSRKEKRTLHAVG    
1 PD002643       p2000.1 (34) // PROTEIN MON...   118   9.2e-07  1  24.8%     PTGVTVVTTEegGRPHGMTASWFTSVSFEPPLVMVCINKSSSTHSLIksGKFAVNVLSAEQQEEVAKFFSMTRKEGDKFFGMSWWQVTSKKTGAPVLEeaLAWLECRVESVVEahTIFIGEVVSVSVEEEGKPAPLLYRRG    
2 PD110067       p2000.1 (1) P96682_BACSU //...   105   0.00029  1  30.3%     -----LTTLNEDGTTNISPMSSSWALGHYIILGVGLG--GKAIDNLERHKECVINLPGPDLWENVERISSYSGKKseKYEAAGLTPLQSKTVSPTRIKECPIQIEAEVKHilPEYefAIVETQALHF--------------    
  consensus/100%                                                              .....lsThptsGpsph.shS..hulsa...Lshshh..s.uhcsL.+ptchslsl.ss-..-pV.th.ohotKcs-Ka.shthh.lpuKhstsshlcEs.h.lEscV.pll.taphhlhEs.uh.h..............    
  consensus/90%                                                               .....lsThptsGpsph.shS..hulsa...Lshshh..s.uhcsL.+ptchslsl.ss-..-pV.th.ohotKcs-Ka.shthh.lpuKhstsshlcEs.h.lEscV.pll.taphhlhEs.uh.h..............    
  consensus/80%                                                               .....lsThptsGpsph.shS..hulsa...Lshshh..s.uhcsL.+ptchslsl.ss-..-pV.th.ohotKcs-Ka.shthh.lpuKhstsshlcEs.h.lEscV.pll.taphhlhEs.uh.h..............    
  consensus/70%                                                               .....lsThptsGpsph.shS..hulsa...Lshshh..s.uhcsL.+ptchslsl.ss-..-pV.th.ohotKcs-Ka.shthh.lpuKhstsshlcEs.h.lEscV.pll.taphhlhEs.uh.h..............    
--- ------------------------------------------------------------
--- 
--- 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=PD002643 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD002643
http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD002643 ==> graphical output of all proteins having domain PD002643
http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD110067 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD110067
http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD110067 ==> graphical output of all proteins having domain PD110067
--- 
--- 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    : 200
--- 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                  
trembl|Q930M1|Q930M1          182   41   58  172    3    197   7e-50 Hypothetical protein RA01
trembl|CAE27709|CAE27709      186   38   52  168    3    196   1e-49 Flavin reductase-like.   
trembl|Q8P5Y0|Q8P5Y0          193   33   52  170    3    185   4e-46 Hypothetical protein XCC3
trembl|Q7NTI1|Q7NTI1          184   30   46  160   15    172   3e-42 Hypothetical protein.    
trembl|Q8PYB7|Q8PYB7          222   27   48  137    6    162   2e-39 Putative NADPH-flavin oxi
swiss|P76121|YDDH_ECOLI       189   27   45  164   17    157   1e-37 Hypothetical protein yddH
trembl|Q8FHI7|Q8FHI7          189   25   45  167   17    156   2e-37 Hypothetical protein yddH
trembl|Q882G9|Q882G9          194   27   42  166   17    150   1e-35 NAD(P)H-flavin oxidoreduc
trembl|Q8RDP3|Q8RDP3          197   26   42  156    4    147   7e-35 Flavoredoxin.            
trembl|CAE29853|CAE29853      205   21   43  109    2    142   4e-33 Hypothetical protein.    
trembl|Q89SH5|Q89SH5          236   22   43  109    2    141   6e-33 Blr2425 protein.         
trembl|Q8TNJ0|Q8TNJ0          188   28   48  112    2    141   7e-33 Flavoredoxin Flr.        
trembl|Q92YH5|Q92YH5          241   21   38  123   11    138   5e-32 Hypothetical protein RA09
trembl|Q7MX56|Q7MX56          195   28   42  136    4    135   3e-31 Flavin reductase domain p
trembl|Q8PT07|Q8PT07          188   28   49  112    2    135   4e-31 Flavoredoxin.            
swiss|Q9UZA8|YC46_PYRAB       172   30   49  111    3    134   6e-31 Hypothetical protein PYRA
trembl|Q8UJR1|Q8UJR1          235   20   41  121   13    134   9e-31 Hypothetical protein Atu5
trembl|Q8U370|Q8U370          172   34   49  111    3    132   2e-30 Hypothetical protein PF06
trembl|Q97GD1|Q97GD1          199   31   46  119    3    132   3e-30 Uncharacterized conserved
pdb|pdb|1eje_A                192   23   41  122    7    132   3e-30                          
swiss|O58586|Y856_PYRHO       172   32   49  111    3    132   3e-30 Hypothetical protein PH08
trembl|Q8TR43|Q8TR43          217   27   44  115    3    131   7e-30 Fmn-binding protein.     
trembl|Q8XYD8|Q8XYD8          207   22   43  109    2    130   1e-29 Hypothetical protein RSc1
trembl|Q8EJH3|Q8EJH3          209   24   42  106    2    129   2e-29 Conserved hypothetical pr
swiss|O26255|P152_METTH       186   23   41  120    7    129   2e-29 Protein MTH152.          
trembl|Q8PQ49|Q8PQ49          210   19   37  106    2    129   3e-29 Hypothetical protein XAC0
trembl|Q8PS00|Q8PS00          195   24   41  116    5    129   3e-29 Conserved protein.       
trembl|Q8TJ24|Q8TJ24          202   29   49  110    3    129   4e-29 Flavoredoxin.            
swiss|O67071|Y928_AQUAE       196   23   47  123   11    129   4e-29 Hypothetical protein AQ_9
trembl|Q8PD72|Q8PD72          210   16   38  106    2    129   4e-29 Hypothetical protein XCC0
swiss|O26674|Y574_METTH       212   27   45  115    3    128   4e-29 Hypothetical protein MTH5
trembl|Q8U6V3|Q8U6V3          212   20   40  123   11    128   4e-29 Hypothetical protein Atu4
trembl|Q87X90|Q87X90          207   22   41  106    2    128   6e-29 Conserved hypothetical pr
trembl|Q92ML2|Q92ML2          208   18   41  123   11    128   7e-29 Hypothetical protein R026
trembl|Q88N18|Q88N18          201   18   38  106    2    127   7e-29 Conserved hypothetical pr
trembl|Q8TKS4|Q8TKS4          200   26   43  116    5    127   8e-29 Hypothetical protein MA33
trembl|Q8A9S5|Q8A9S5          179   28   43  133    4    127   1e-28 Flavoredoxin.            
swiss|O28488|YH86_ARCFU       177   33   54  107    2    127   1e-28 Hypothetical protein AF17
trembl|Q89PT2|Q89PT2          205   16   32  144   16    126   2e-28 Blr3398 protein.         
trembl|Q7NZL0|Q7NZL0          201   18   38  123   11    125   3e-28 Hypothetical protein.    
trembl|CAE29606|CAE29606      231   16   30  155   17    125   4e-28 Hypothetical protein.    
swiss|Q9KIT1|FLR_DESGI        194   28   46  112    2    125   5e-28 Flavoredoxin.            
trembl|AAR33593|AAR33593      189   28   48  112    2    125   5e-28 Flavoredoxin.            
trembl|Q8ZVY7|Q8ZVY7          180   26   46  112    2    123   2e-27 Hypothetical protein PAE2
trembl|Q7WND0|Q7WND0          200   23   37  113   11    123   2e-27 Hypothetical protein.    
trembl|Q8UEL4|Q8UEL4          205   21   45  112    2    123   2e-27 Hypothetical protein Atu1
trembl|Q8X9X9|Q8X9X9          147   25   44  129   15    122   4e-27 Hypothetical protein z225
swiss|O05220|YWRF_BACSU       205   22   40  122   10    120   9e-27 Hypothetical protein ywrF
trembl|Q89PZ9|Q89PZ9          225   18   33  117   13    118   4e-26 Blr3331 protein.         
trembl|Q92QA7|Q92QA7          200   23   45  112    2    117   8e-26 Hypothetical protein R014
trembl|Q8TTU7|Q8TTU7          190   28   47  107    3    117   1e-25 Flavoredoxin.            
trembl|Q8YH85|Q8YH85          203   22   43  112    2    115   4e-25 Nitrilotriacetate monooxy
trembl|Q8G0M1|Q8G0M1          203   22   43  112    2    115   4e-25 Conserved hypothetical pr
trembl|Q8CRD3|Q8CRD3          203   22   37  120   15    114   6e-25 Conserved hypothetical pr
swiss|Q9Y8Q3|YP80_AERPE       263   26   43  119    2    114   7e-25 Hypothetical protein APE2
trembl|Q9CJB9|Q9CJB9          196   19   40  120    6    113   1e-24 Hypothetical protein yaiB
swiss|Q9KAK9|YM78_BACHD       209   18   36  114   11    113   2e-24 Hypothetical protein BH22
trembl|Q7UYR8|Q7UYR8          216   23   38  109    7    112   3e-24 Hypothetical protein.    
trembl|Q814U7|Q814U7          203   18   38  119   10    112   3e-24 Nitrilotriacetate monooxy
trembl|Q89V20|Q89V20          206   19   35  118   10    112   4e-24 Blr1238 protein.         
trembl|Q99QX9|Q99QX9          203   18   37  122   10    112   5e-24 Hypothetical protein SAV2
trembl|Q8NUJ0|Q8NUJ0          203   18   37  122   10    110   1e-23 Hypothetical protein MW25
trembl|Q896G0|Q896G0          164   28   44  114    4    109   3e-23 Conserved protein.       
trembl|Q81JX8|Q81JX8          203   18   38  119   10    108   4e-23 Hypothetical protein.    
trembl|Q9HI97|Q9HI97          214   23   43  106   16    107   2e-22 Hypothetical protein Ta14
trembl|Q9I381|Q9I381          202   14   33  121   11    104   6e-22 Hypothetical protein PA16
trembl|Q99QY3|Q99QY3          230   20   37  105   13    104   9e-22 Hypothetical protein SAV2
trembl|Q9K5V3|Q9K5V3          208   22   42  109   17    103   2e-21 Hypothetical protein BH39
trembl|Q9WY04|Q9WY04          149   25   49  100    4    102   2e-21 Actinorhodin polyketide d
trembl|Q8NUJ2|Q8NUJ2          230   21   38  105   13    102   2e-21 Hypothetical protein MW25
trembl|Q8RGH5|Q8RGH5          180   28   39  102    3    102   4e-21 Hypothetical cytosolic pr
trembl|Q9KFT5|Q9KFT5          202   28   43  110   17    101   9e-21 Hypothetical protein BH03
trembl|Q7P288|Q7P288          180   28   39  102    3    100   1e-20 Hypothetical cytosolic pr
trembl|P96682|P96682          207   27   43  118   22    100   2e-20 YDFE protein.            
trembl|Q8ZXG6|Q8ZXG6          256   20   38  120    2     97   8e-20 Hypothetical protein PAE1
trembl|Q838S6|Q838S6          206   21   37  118   11     97   1e-19 Hypothetical protein.    
trembl|Q98LR6|Q98LR6          202   17   34  129   11     97   1e-19 Hypothetical protein mll0
trembl|Q7RZX5|Q7RZX5          315   25   42  111   15     95   3e-19 Hypothetical protein.    
trembl|Q7V7L8|Q7V7L8          168   15   30  142   10     93   2e-18 Hypothetical protein.    
swiss|P74373|DFA3_SYNY3       597   18   30  135    5     90   1e-17 Putative diflavin flavopr
trembl|Q55660|Q55660          160   21   34  142   10     90   2e-17 Hypothetical protein slr0
trembl|Q9WZ34|Q9WZ34          159   24   42  101    3     88   4e-17 Hypothetical protein TM05
trembl|Q7P4J3|Q7P4J3           88   26   44   86    1     88   7e-17 FLAVOREDOXIN.            
trembl|Q8UK94|Q8UK94          323   24   38  113   11     86   2e-16 Nitrilotriacetate monooxy
trembl|Q83VC4|Q83VC4          174   20   37  111    9     85   3e-16 Putative oxidoreductase M
trembl|Q89PP1|Q89PP1          194   19   39  118   10     85   4e-16 Bll3439 protein.         
trembl|Q9JN75|Q9JN75          174   20   37  111    9     85   4e-16 Hypothetical protein (Put
trembl|Q8AA80|Q8AA80          169   26   39   82    2     85   5e-16 Conserved hypothetical pr
trembl|Q92CX9|Q92CX9          183   25   39  113    7     85   6e-16 Hypothetical protein lin1
trembl|Q92DQ8|Q92DQ8          206   17   35  120   11     85   6e-16 Hypothetical protein lin0
swiss|Q9RRA9|YP85_DEIRA       227   15   32  121   17     84   9e-16 Hypothetical protein DR25
trembl|Q7WT19|Q7WT19          167   18   32  109    8     84   1e-15 NADH:FMN oxidoreductase. 
trembl|Q8Y8Y1|Q8Y8Y1          206   17   36  112   11     82   4e-15 Hypothetical protein lmo0
trembl|Q8Y867|Q8Y867          184   16   33  112   10     82   5e-15 Hypothetical protein lmo1
trembl|Q7P2F4|Q7P2F4          186   24   42  107    9     81   9e-15 Hypothetical cytosolic pr
trembl|Q89ER5|Q89ER5          193   21   39  113    8     79   2e-14 Bll7007 protein.         
swiss|Q9FDN6|HRB_MOOTH        229   19   39  111    8     77   2e-13 High molecular weight rub
trembl|Q7U6T9|Q7U6T9          160   17   29  147   11     75   4e-13 Hypothetical protein.    
trembl|Q7V1I8|Q7V1I8          162   16   28  141   14     74   8e-13 Hypothetical protein.    
trembl|Q7VBY9|Q7VBY9          160   14   29  145    8     72   3e-12 DIM6/NTAB family protein.
trembl|Q07948|Q07948          160   23   36  116    8     72   3e-12 ORF1.                    
pdb|pdb|1usc_A                178   20   35  103    5     72   3e-12                          
pdb|pdb|1usf_A                178   20   35  103    5     72   3e-12                          
trembl|Q8CQX0|Q8CQX0          177   17   32   78    7     71   7e-12 Conserved hypothetical pr
trembl|O69360|O69360          194   16   40  111    9     71   8e-12 Orf61 protein.           
trembl|P96849|P96849          187   17   37  112    9     68   6e-11 Hypothetical protein (Oxi
trembl|Q7TW67|Q7TW67          187   17   37  112    9     68   6e-11 Possible oxidoreductase (
trembl|Q7NJQ6|Q7NJQ6          579   18   29  138    6     68   7e-11 Glr1776 protein.         
swiss|Q8YQD8|DFA3_ANASP       574   14   29  142    6     67   2e-10 Putative diflavin flavopr
trembl|O68914|O68914          171   19   35  111    6     66   2e-10 ActVB homolog.           
trembl|Q7TUJ5|Q7TUJ5          591   16   29  159   12     66   2e-10 Metallo-beta-lactamase su
trembl|Q8XKI9|Q8XKI9           68   28   46   61    3     66   2e-10 Hypothetical protein CPE1
trembl|Q7U3R2|Q7U3R2          582   14   28  143    9     66   3e-10 Flavoprotein.            
trembl|Q92ZM6|Q92ZM6          320   18   33  114    7     66   3e-10 Hypothetical protein RA04
trembl|Q7V3N2|Q7V3N2          600   13   27  133    6     65   3e-10 Flavoprotein.            
trembl|Q7VEG8|Q7VEG8          590   15   32  143    9     65   4e-10 Diflavin flavoprotein.   
trembl|Q82GR7|Q82GR7          199   15   33  118    8     65   4e-10 Hypothetical protein.    
swiss|Q8YQE2|DFA6_ANASP       570   14   29  138    6     65   7e-10 Putative diflavin flavopr
trembl|Q7WG76|Q7WG76          172   17   33  101    5     64   1e-09 Putative monooxygenase co
trembl|Q7W4Q0|Q7W4Q0          172   17   33  101    5     64   1e-09 Putative monooxygenase co
swiss|Q55393|DFA1_SYNY3       573   12   24  141    8     64   1e-09 Diflavin flavoprotein A 1
trembl|Q83VZ7|Q83VZ7          325   19   33  119    7     64   1e-09 TesA protein.            
swiss|P54994|SNAC_STRPR       175   14   29  116    6     63   1e-09 NADH:riboflavin 5'-phosph
swiss|Q8Z0C1|DFA5_ANASP       570   14   26  166   24     63   2e-09 Putative diflavin flavopr
trembl|Q8XKI8|Q8XKI8          117   23   32   82    3     62   3e-09 Hypothetical protein CPE1
trembl|Q8UAE9|Q8UAE9          181   19   38  125   11     62   3e-09 Hypothetical protein Atu3
trembl|Q82KT4|Q82KT4          184   15   28  117    4     62   4e-09 Putative NADPH-flavin oxi
trembl|Q7VF70|Q7VF70          208   14   34  113   11     62   4e-09 Hypothetical protein.    
trembl|Q8U860|Q8U860          312   19   29  151    9     62   5e-09 Flavoprotein oxidoreducta
trembl|Q7VU71|Q7VU71          172   17   33  101    5     62   5e-09 Putative monooxygenase co
trembl|Q92ZP7|Q92ZP7          230   16   28  114    7     61   7e-09 Hypothetical protein RA04
swiss|P72723|DFA2_SYNY3       578   17   32   99    5     61   7e-09 Putative diflavin flavopr
trembl|Q7U3R1|Q7U3R1          600   18   32   97    5     61   8e-09 Putative flavoprotein.   
trembl|Q7TUJ4|Q7TUJ4          615   14   27  124    6     61   8e-09 Flavodoxin:flavin reducta
trembl|Q93LZ6|Q93LZ6          167   19   31  114   10     61   1e-08 Oxygenase-like protein.  
swiss|P54990|NTAB_CHEHE       322   22   34  110    9     60   1e-08 Nitrilotriacetate monooxy
trembl|Q8Y1C7|Q8Y1C7          191   21   35  110   14     60   2e-08 Putative monooxygenase ox
trembl|Q7NJQ7|Q7NJQ7          584   12   27  142    6     60   2e-08 Glr1775 protein.         
swiss|Q8DJY2|DFA1_SYNEL       571   14   28  156   11     60   2e-08 Putative diflavin flavopr
trembl|Q92ZP5|Q92ZP5          200   15   28   97    7     60   2e-08 Hypothetical protein RA04
swiss|Q8YNW5|DFA1_ANASP       576   13   25  138    8     59   2e-08 Putative diflavin flavopr
trembl|Q9LAG2|Q9LAG2          161   22   41   98   11     59   3e-08 Phenol 2-hydroxylase comp
trembl|Q9ZE13|Q9ZE13          161   20   36  102    6     59   3e-08 Hypothetical protein RP14
trembl|Q8RLG2|Q8RLG2          204   17   34  117    6     58   4e-08 HpaC.                    
swiss|Q02058|DIM6_STRCO       177   23   36  101    8     58   4e-08 Actinorhodin polyketide d
trembl|O06835|O06835          170   14   36   99   12     58   4e-08 StyB protein.            
trembl|Q8F271|Q8F271          159   20   36  116    6     58   4e-08 Flavin reductase like pro
trembl|Q8U773|Q8U773          187   16   32  124    6     58   5e-08 Hypothetical protein Atu4
trembl|O34138|O34138          194   15   35  113    5     58   5e-08 NADPH-flavin oxidoreducta
trembl|Q7PAU0|Q7PAU0          159   24   37  102    6     58   5e-08 Hypothetical protein.    
trembl|Q88GS1|Q88GS1          161   20   34  101    7     58   6e-08 Oxidoreductase, putative.
trembl|Q89DZ7|Q89DZ7          184   19   34  113    5     58   7e-08 HpaC protein.            
trembl|AAQ87163|AAQ87163      310   15   31  113    7     57   9e-08 Nitrilotriacetate monooxy
trembl|CAE28050|CAE28050      189   20   36  114    6     57   1e-07 Possible monooxygenase.  
pdb|pdb|1i0r_A                160   16   37  112   14     57   1e-07                          
pdb|pdb|1i0r_B                168   16   37  112   14     57   1e-07                          
pdb|pdb|1i0s_A                160   16   37  112   14     57   1e-07                          
pdb|pdb|1i0s_B                168   16   37  112   14     57   1e-07                          
trembl|O29428|O29428          169   16   37  112   14     57   1e-07 Hypothetical protein AF08
trembl|Q845S6|Q845S6          155   20   36  109   11     57   1e-07 Flavin reductase.        
trembl|O50215|O50215          170   17   35  112   11     57   2e-07 Styrene monooxygenase sma
trembl|O33495|O33495          170   17   35  112   11     57   2e-07 Styrene monooxygenase com
trembl|Q9A620|Q9A620          174   21   38   99    7     56   2e-07 NADH:riboflavin 5'-phosph
swiss|Q8Z0C0|DFA2_ANASP       579   13   26  139    6     56   2e-07 Putative diflavin flavopr
trembl|Q92J78|Q92J78          159   19   30  134    8     56   3e-07 Hypothetical protein RC01
trembl|Q88JF2|Q88JF2          193   13   36  114    8     55   4e-07 Flavin reductase domain p
trembl|Q8GME2|Q8GME2          182   24   38  104    5     55   5e-07 Oxidoreductase.          
trembl|Q89H99|Q89H99          187   19   32  150   14     55   6e-07 Nitrilotriacetate monooxy
trembl|Q88GS5|Q88GS5          161   17   32  101    7     54   9e-07 Oxidoreductase, putative.
trembl|AAQ17112|AAQ17112      183   20   32  119    7     54   1e-06 Putative oxidoreductase. 
trembl|Q9KXW1|Q9KXW1          202   17   35  114   14     53   1e-06 Putative reductase.      
trembl|Q8YHT7|Q8YHT7          173   15   28  112    2     53   2e-06 4-HYDROXYPHENYLACETATE 3-
trembl|Q8G024|Q8G024          173   15   28  112    2     53   2e-06 Monooxygenase, putative. 
trembl|Q7VEG9|Q7VEG9          614   13   26  130    6     52   3e-06 Diflavin flavoprotein.   
trembl|Q7V3N1|Q7V3N1          591   15   29  154   27     52   4e-06 Flavoprotein.            
trembl|Q882F6|Q882F6          161   19   34  101    7     52   5e-06 NAD(P)H-flavin oxidoreduc
trembl|Q9K3F9|Q9K3F9          192   12   32  103    6     51   6e-06 Putative oxidoreductase. 
trembl|Q84HA3|Q84HA3          182   19   38  104    5     51   7e-06 Monooxygenase.           
trembl|Q98G86|Q98G86          167   16   36  118    8     51   8e-06 Hypothetical protein mll3
trembl|O53254|O53254          236   14   33   99    4     50   2e-05 Hypothetical protein (Oxi
trembl|Q7TXG4|Q7TXG4          204   14   33   99    4     50   2e-05 Possible oxidoreductase (
trembl|AAQ62382|AAQ62382      144   14   32   96    7     49   2e-05 'Potential flavoprotein o
trembl|Q82N21|Q82N21          168   16   36   98    6     49   3e-05 Putative flavin-dependent
trembl|Q974C9|Q974C9          156   17   35   99    8     48   4e-05 Putative NADH-dependent F
trembl|Q89Q06|Q89Q06          180   14   31  117    4     48   5e-05 Flavoprotein oxidoreducta
trembl|Q97WR2|Q97WR2          155   13   32   99   10     48   7e-05 Hypothetical protein SSO2
trembl|Q8EMH3|Q8EMH3          157   19   39  108   13     48   8e-05 Phenol 2-hydroxylase comp
trembl|Q98NL6|Q98NL6          175   14   28  120    2     48   9e-05 Monooxygenase.           
trembl|Q93NA5|Q93NA5          177   14   31  111   10     47   9e-05 Putative NADH:FMN oxidore
trembl|Q7TZ93|Q7TZ93          244   15   30  119   14     47   9e-05 Probable oxidoreductase (
trembl|P95275|P95275          171   15   30  119   14     47   1e-04 Hypothetical protein (Dim
trembl|Q92PJ7|Q92PJ7          175   18   33   98    5     47   2e-04 Putative monooxygenase pr
trembl|Q97S48|Q97S48          149    9   36   72    4     47   2e-04 Conserved domain protein.
trembl|Q52976|Q52976          183   16   29   73    6     47   2e-04 Belongs to stac operon (F
trembl|Q9RRM9|Q9RRM9          186   15   32   95   11     47   2e-04 Oxidoreductase, putative.
trembl|O53667|O53667          162   16   30  100    7     47   2e-04 Hypothetical protein (Oxi
trembl|Q7U2G9|Q7U2G9          162   16   30  100    7     47   2e-04 Putative oxidoreductase (
trembl|Q9K416|Q9K416          169   16   37   98    6     46   3e-04 Putative flavin-dependent
trembl|Q8NQZ1|Q8NQZ1          162   16   43   99    7     46   3e-04 Conserved protein/domain 
trembl|Q7VMJ0|Q7VMJ0          169   10   30  112    4     46   3e-04 4-hydroxyphenylacetic aci
trembl|Q8CZ39|Q8CZ39          149    9   36   72    4     46   3e-04 Hypothetical protein.    
trembl|Q9ZA25|Q9ZA25          179   20   36  113   10     45   4e-04 Putative FMN:NADH oxidore
trembl|Q82GF2|Q82GF2          192   16   37  114   11     45   7e-04 Putative reductase.      
trembl|Q9EWU5|Q9EWU5          162   17   35   96    4     44   0.001 Putative oxidoreductase. 
swiss|P72721|DFA4_SYNY3       594   15   28  137    6     44   0.001 Putative diflavin flavopr
trembl|Q8VQV3|Q8VQV3          195   19   35  112   11     43   0.001 NimA protein.            
trembl|Q8XYC2|Q8XYC2          183   19   29  102    7     43   0.002 Hypothetical protein RSc1
trembl|Q8RQP9|Q8RQP9          176   17   37   94   14     43   0.002 4-nitrophenol hydroxylase
trembl|Q9UTQ4|Q9UTQ4          244   18   37   75    6     43   0.002 Puatative oxidoreductase.
trembl|Q7ML53|Q7ML53          168   15   36  114    4     43   0.002 Putative 4-hydroxyphenyla
trembl|Q887X7|Q887X7          180   11   27  114    4     43   0.002 NAD(P)H-flavin oxidoreduc
trembl|Q8FPW6|Q8FPW6          166   21   37   99    7     42   0.004 Putative oxidoreductase. 
trembl|Q8KL32|Q8KL32          208   14   33  109   13     42   0.004 Probable                 
swiss|Q48441|HPAC_KLEOX       170   14   34  112   10     42   0.004 4-hydroxyphenylacetate 3-
trembl|Q8NRN7|Q8NRN7          163   16   34   99   10     41   0.006 Conserved protein/domain 
trembl|Q8ZVT5|Q8ZVT5          140   12   31   96    8     41   0.006 Hypothetical protein PAE2
trembl|Q8UCF6|Q8UCF6          179   13   30  113    6     41   0.007 Actinorhodin polyketide d
trembl|Q8KI76|Q8KI76          170   15   30   95    8     41   0.008 Flavin dependent oxidored
trembl|Q8UCI9|Q8UCI9          174   13   32   97    5     41   0.010 Flavoprotein oxidoreducta
trembl|Q8FJ45|Q8FJ45          184   13   30  115    6     40   0.015 Putative flavin:NADH redu
trembl|O68503|O68503          192   16   32   98    8     40   0.016 NADH-dependent FMN OXYDOR
swiss|P75893|YCDH_ECOLI       164   14   31  115    6     40   0.018 Putative flavin:NADH redu
trembl|Q8F2D6|Q8F2D6          134   24   49   60    1     39   0.033 Hypothetical protein.    
trembl|Q9CKT4|Q9CKT4          168   13   31  113    0     39   0.036 Hypothetical protein PM15
trembl|Q83LK9|Q83LK9          184   13   30  115    6     38   0.044 4-hydroxyphenylacetate 3-
swiss|Q8YNW7|DFA4_ANASP       575   12   25  149   28     38   0.047 Putative diflavin flavopr
swiss|Q8XAV0|YCDH_ECO57       164   13   30  115    6     38   0.049 Putative flavin:NADH redu
trembl|O87008|O87008          179   14   30  102    5     38   0.067 Chlorophenol-4-monooxygen
trembl|Q8CQW9|Q8CQW9           57   25   43   31    1     38   0.073 Conserved hypothetical pr
trembl|Q9HWT6|Q9HWT6          170    9   28  115    2     38   0.081 4-hydroxyphenylacetate 3-
trembl|Q7UD00|Q7UD00          152   13   31   97    5     37   0.091 Hypothetical protein.    
trembl|Q9R594|Q9R594           38   34   43   31    1     36    0.17 FLAVOREDOXIN (Fragment). 
trembl|Q8UAU0|Q8UAU0          175   17   35   97    9     36    0.17 Nitrilotriacetate monooxy
swiss|Q8DJ55|DFA2_SYNEL       578   15   31   82    6     36    0.21 Putative diflavin flavopr
trembl|Q9C2E6|Q9C2E6          248   23   39   49    2     35    0.43 (AL513463) conserved hypo
trembl|Q7N7X7|Q7N7X7          172   14   32   98    3     35    0.63 4-hydroxyphenylacetic aci
trembl|Q8PVV4|Q8PVV4          212   14   32   83   13     34    0.84 Conserved protein.       
trembl|Q8TSV0|Q8TSV0          212   16   31   90   14     34    0.98 Hypothetical protein MA06
---
--- 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                     
yh86_arcfu         31   44  150    2   13   177 O28488 Hypothetical protein AF17
yddh_ecoli         30   39  161    5   21   205 P76121 HYPOTHETICAL 22.8 KDA PRO
y856_pyrho         28   31  161    4   12   172 O58586 Hypothetical protein PH08
yc46_pyrab         28   31  151    3   12   172 Q9UZA8 Hypothetical protein PYRA
--- 
--- MAXHOM ALIGNMENT: IN MSF FORMAT


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

MAXHOM alignment


TOP - BOTTOM - MaxHom - MView
Identities computed with respect to: (1) predict_h3480
Colored by: consensus/70% and property
                          1 [        .         .         .         .         :         .         .         .         .         1         .         .         .         .         :         .         .         .         .         ] 200
1 predict_h3480  100.0%     MLKNTSSNLDAPVARSCDFAMKKMDLRKAFTLIEPGPVTLVTTSAGGTNNVMTISWTMAVDFTPKLAITTGPWNFSYKALTKSRECVIAIPTVDLLDKVVGVGTCSGKDTDKFDTFRLTPIKGKYVEAPLIKECVANIECKVVDIIKKHDIVVLEGVAAYFDTSRKEKRTLHAVGDGTFVVDGRTLDRKKQMRSKLLGIF    
2 yh86_arcfu      28.4%     --------------------------------------TYLIVSGVEKPNVMTADWVVPLSFSPqlGVAIGHSRYTHSLIKECGEFVVAVPTIELLKDVWKAGTLSGAKENKMEKLSLTLVESKKVKVPSIKECQANLECRVVKEVETGDHTLFVGE------------ILHVTHGDAFKDGKPDINYKFVMHASFGKNF    
3 yddh_ecoli      28.2%     -----------------------IELHHASRLLNHGPTVLITSFDEQsrNIMAAAWSMPVEFepRVAIVVDKSTWTRELIEHNGKFGIVIPGVAATNWTWAVGSVSGRDEDKFNCYGIPVVRGPVFGLPLVEecLAWMECRLLPATSaaDARVFVEGRWQFDDDKLN--TLHHLGAGTFVTSGKRV--------------    
4 y856_pyrho      28.2%     ---------------------------EGYRLLYPMRTYLIVSGHGEETNVMAADWVTVVSFDPfvGVAVAPKRTTHKLIKKYGEFVISVPSLDVLRDVWIAGTKKGP--SKLKEMSVTLIPSKKVKVPSIEEALANIECRVIDARSYGDHTFFVGEVvaFEKGKPNlkFLAHVSWSEFVTFSEKVHKAE----------    
5 yc46_pyrab      28.1%     ---------------------------EGYRLLYPMRTYLVVSGHGDEANVMAADWVTVLSFDPFMVGviAPKRTTHKLIKKYNEFVISVPSLEMLRDVWIAGTKKGP--SKLKDMGITLVPSRKVKVPSIKEALANIECEVYDTKDYGDHTLFVGKVLAYTYKEEAfnFLAHVSWSEFV--------------------    
  consensus/100%            ......................................hhlhs.t.tp.NlMshsWshslpFpP.hshshs..phohphlpc.tchslslPslthhp.shhsGohpG...sKhpphtls.l.u.hhthP.lcEs.A.hECclh..hphtDhhhh.t.............hLthht.stFh....................    
  consensus/90%             ......................................hhlhs.t.tp.NlMshsWshslpFpP.hshshs..phohphlpc.tchslslPslthhp.shhsGohpG...sKhpphtls.l.u.hhthP.lcEs.A.hECclh..hphtDhhhh.t.............hLthht.stFh....................    
  consensus/80%                                    ....cu.pLl..h.shLlsoutsppsNVMsAsWshslsFsPhlulslu.pphT+cLIc+.sEFVIulPol-hLccVWhsGThpG...sKhcphulTll.u+hVclP.IcEslANlEC+VlcthphuDtslFVGthh.ap.tc.t..hLttluhupFVs.t.pl..............    
  consensus/70%                                    ....cu.pLl..h.shLlsoutsppsNVMsAsWshslsFsPhlulslu.pphT+cLIc+.sEFVIulPol-hLccVWhsGThpG...sKhcphulTll.u+hVclP.IcEslANlEC+VlcthphuDtslFVGthh.ap.tc.t..hLttluhupFVs.t.pl..............    


CYSPRED prediction(P Fariselli,P Riccobelli & R Casadio)


TOP - BOTTOM - CYSPRED
PREDICTION OF BONDING STATE OF CYSTEINES
Network N. 1  Conservation+ Entropy
N.cys	Prob.SS		Prob.SH
17	0.063152	0.936849
86	0.172651	0.827348
105	0.139590	0.860410
134	0.013818	0.986182
140	0.589704	0.410297
###################
Network N. 2  Conservation+ Entropy + Charges
N.cys	Prob.SS		Prob.SH
17	0.056250	0.603368
86	0.140452	0.364905
105	0.084989	0.615075
134	0.035703	0.775042
140	0.569967	0.097433
###################
Network N. 3  Charge
N.cys	Prob.SS		Prob.SH
17	0.182775	0.817209
86	0.077382	0.922617
105	0.031596	0.968402
134	0.041876	0.958124
###################
Network N. 4   Conservation+ Entropy+Hydrophobicity
N.cys	Prob.SS		Prob.SH
17	0.032125	0.967874
86	0.095396	0.904606
105	0.060646	0.939354
134	0.021265	0.978734
140	0.554396	0.445600
###################
Network N. 5   Conservation+ Entropy + Charges + Hydrophobicity
N.cys	Prob.SS		Prob.SH
17	0.056526	0.943477
86	0.113916	0.886084
105	0.075339	0.924661
134	0.037543	0.962456
140	0.609607	0.390399
###################
JURY AMONG THE DIFFERENT NETWORKS
	Prob.SS	Prob.SH
N.cys	BONDED	NON-BONDED	DISULFIDE
17	0.078	0.854		NO 
86	0.120	0.781		NO 
105	0.078	0.862		NO 
134	0.030	0.932		NO 
140	0.465	0.269		YES
#==============================================#


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


TOP - BOTTOM - PHD

PHD predictions for predict_h348

Contents:






SYNOPSIS of prediction








HEADER information






BODY with predictions

PHD results (brief)

....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8....,....9....,....1 AA MLKNTSSNLDAPVARSCDFAMKKMDLRKAFTLIEPGPVTLVTTSAGGTNNVMTISWTMAVDFTPKLAITTGPWNFSYKALTKSRECVIAIPTVDLLDKVV PHD_sec HHHHHHHH HHHH HHHHHHHH EEEEEE EEEEEEEE EEEEEE HHHHHHH EEEEEE HHHHHHHH Rel_sec **** **** * ****** **** **** ******* * ********* *** **** ** **** ** ****** P_3_acc ebeeb ebbe bbe bb bbeeb beebb bbbb bbbbbbb eee bbbbbbbbbbbe bbbbbbbbeeeeb ebbeebe bbbbbbbeebeebb Rel_acc * * ***** * ***** * *** ** * ....,....11...,....12...,....13...,....14...,....15...,....16...,....17...,....18...,....19...,....20 AA GVGTCSGKDTDKFDTFRLTPIKGKYVEAPLIKECVANIECKVVDIIKKHDIVVLEGVAAYFDTSRKEKRTLHAVGDGTFVVDGRTLDRKKQMRSKLLGIF PHD_sec HHH HHH HHH EEEEEEEEEEE EEEEEEEE EEEEEE EEEE EE Rel_sec ** **** * ** **** ********* *** ******* ***** * ** ** *** ** * P_3_acc bbee eeb b ebbb b ebeebbbbbbeebbb b b b b bebb bbbbbbbb bee eeebbbbbb ebb bbbbbe b eeb b bbbbb Rel_acc * * * * * * * ** ** ** * * **


PHD results (normal)

....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8....,....9....,....1 AA MLKNTSSNLDAPVARSCDFAMKKMDLRKAFTLIEPGPVTLVTTSAGGTNNVMTISWTMAVDFTPKLAITTGPWNFSYKALTKSRECVIAIPTVDLLDKVV PHD_sec HHHHHHHH HHHH HHHHHHHH EEEEEE EEEEEEEE EEEEEE HHHHHHH EEEEEE HHHHHHHH Rel_sec 9867222314577642045211322678875226996499983689977622464433213986699998267523566641571788625523589999 SUB_sec LLLL......HHHH....H......HHHHHH..LLLL.EEEE.LLLLLLL...E.......LLLEEEEEE.LLL..HHHH..LL.EEEE.LL..HHHHHH P_3_acc ebeeb ebbe bbe bb bbeeb beebb bbbb bbbbbbb eee bbbbbbbbbbbe bbbbbbbbeeeeb ebbeebe bbbbbbbeebeebb Rel_acc 1222102042022113210021101011201250003458651112010022232340220001165754021010011511001678274010001241 SUB_acc ........b.......................b....bbbbb..............b........bbbbb.........b.....bbb.bb.......b. ....,....11...,....12...,....13...,....14...,....15...,....16...,....17...,....18...,....19...,....20 AA GVGTCSGKDTDKFDTFRLTPIKGKYVEAPLIKECVANIECKVVDIIKKHDIVVLEGVAAYFDTSRKEKRTLHAVGDGTFVVDGRTLDRKKQMRSKLLGIF PHD_sec HHH HHH HHH EEEEEEEEEEE EEEEEEEE EEEEEE EEEE EE Rel_sec 9744379751122114522136646897422113337899986652269736999986202247899535466337748871761014334342303429 SUB_sec HH...LLLL.......L....LL.LLLL........EEEEEEEEE..LLL.EEEEEEE.....LLLLL.E.EE..LL.EEE.LL...............L P_3_acc bbee eeb b ebbb b ebeebbbbbbeebbb b b b b bebb bbbbbbbb bee eeebbbbbb ebb bbbbbe b eeb b bbbbb Rel_acc 0231100210125001121000011012216005150909161002100002680752101111230005404010313030412200121311274100 SUB_acc ............b.................b..b.b.b.b.b..........bb.bb............bb.b.........b............bb...



GLOBE prediction of globularity


--- 
--- GLOBE: prediction of protein globularity
--- 
--- nexp =    87    (number of predicted exposed residues)
--- nfit =    90    (number of expected exposed residues
--- diff =    -3.00 (difference nexp-nfit)
--- =====> your protein appears as compact, as a globular domain
--- 
--- 
--- GLOBE: further explanations preliminaryily in:
---        http://www.columbia.edu/~rost/Papers/98globe.html
--- 
--- END of GLOBE


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


TOP - BOTTOM - A conformational switch prediction program


Ambivalent Sequence Predictor (ASP v1.0) mmy


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

	Mean dPr score=12.145, Standard deviation=2.741

                  ....,....1....,....2....,....3....,....4....,....5....,....6
         AA      |MLKNTSSNLDAPVARSCDFAMKKMDLRKAFTLIEPGPVTLVTTSAGGTNNVMTISWTMAV|
         prH sec |001134434677776546654434577887642100000000000001000000000000|
         prE sec |000000000000011100000000000000122100268998610000113567665554|
         prL sec |987755554321112342234565321111234799730001378887775432223345|
         ASP sec |............................................................|

                  ....,....7....,....8....,....9....,....10...,....11...,....12
         AA      |DFTPKLAITTGPWNFSYKALTKSRECVIAIPTVDLLDKVVGVGTCSGKDTDKFDTFRLTP|
         prH sec |000000000000124667765420010001125568999987633101244544321111|
         prE sec |301179898842100001111111478875100000000000000001000011112334|
         prL sec |698720000157775321112467410013664321000001366887644333466444|
         ASP sec |....................................................S.....SS|

                  ....,....13...,....14...,....15...,....16...,....17...,....18
         AA      |IKGKYVEAPLIKECVANIECKVVDIIKKHDIVVLEGVAAYFDTSRKEKRTLHAVGDGTFV|
         prH sec |111210012344432110000000000000000000001100000001000000000000|
         prE sec |210000001211112578888877654201379999875443310002566775311688|
         prL sec |567678985434455210000112245798510000113455678986322223587311|
         ASP sec |..........SSSS..............................................|

                  ....,....19...,....20...,....21...,....22...,....23...,....24
         AA      |VDGRTLDRKKQMRSKLLGIF|
         prH sec |00000012222325542110|
         prE sec |84114442221001001230|
         prL sec |15774445455563345559|
         ASP sec |......SSSS..........|


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.


PROF predictions


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PROF predictions for query

Contents:






SYNOPSIS of prediction for query









HEADER information








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.,....2 AA MLKNTSSNLDAPVARSCDFAMKKMDLRKAFTLIEPGPVTLVTTSAGGTNNVMTISWTMAVDFTPKLAITTGPWNFSYKALTKSRECVIAIPTVDLLDKVVGVGTCSGKDTDKFDTFRLTPIKGKYVEAPLIKECVANIECKVVDIIKKHDIVVLEGVAAYFDTSRKEKRTLHAVGDGTFVVDGRTLDRKKQMRSKLLGIF OBS_sec PROF_sec HHHHHHH HHHHHHH EEEEEE EEEEEEEEE EEEEEE HHHHH EEEEE HHHHHHHHHH HHH EEEEEEEEEEEE EEEEEEEEEEE EEEEEE EEEEE EEE Rel_sec 96555344340233100011342453353321268864888615677531135544432256541678734544221233205807887325226778876325678763300001120013644565301111035675776441047616888876532046765135563024416762426401213340003668 SUB_sec LLLLL...................L..H.....LLLL.EEEE.LLLLL....EE......LLL..EEEE..L..........LL.EEEE..L..HHHHHHH..LLLLLL.............L..LLL........EEEEEEE.....LL.EEEEEEEE....LLLL..EEE......EEE...E............LLL O_3_acc bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb P_3_acc e ee eeebeebbe bbe e ee ebeeb e b eebbbbbbb eeeee bbbbbbbb be eb bbbbb eee b e beee bbbbbb ebbe b ebbe eeee eebee ebe e ee e b beebbb b b b bee ebbbbbbbb e eeee bb b ee eb b b ebe eee eeb e e Rel_acc 61220132333012230311045220534232212214598622021011233432102021112648531102201526231124794622240243713013101640333132331123042120004111033517433231230211680630030101243222210020031332123112021042210406 SUB_acc e....................ee...e.b........bbbbb...........b...........bbbb........e.b.....bbbbb...e..e.b........ee..............e......b......b.bi...........bb.b.........e..........................i....e.e


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.,....2 AA MLKNTSSNLDAPVARSCDFAMKKMDLRKAFTLIEPGPVTLVTTSAGGTNNVMTISWTMAVDFTPKLAITTGPWNFSYKALTKSRECVIAIPTVDLLDKVVGVGTCSGKDTDKFDTFRLTPIKGKYVEAPLIKECVANIECKVVDIIKKHDIVVLEGVAAYFDTSRKEKRTLHAVGDGTFVVDGRTLDRKKQMRSKLLGIF 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% --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------


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GLOBE prediction of globularity


--- 
--- GLOBE: prediction of protein globularity
--- 
--- nexp =   118    (number of predicted exposed residues)
--- nfit =    90    (number of expected exposed residues
--- diff =    28.00 (difference nexp-nfit)
--- =====> your protein appears as compact, as a globular domain
--- 
--- 
--- GLOBE: further explanations preliminaryily in:
---        http://www.columbia.edu/~rost/Papers/98globe.html
--- 
--- END of GLOBE


END of results for file predict_h348




Quotes for methods

  1. PredictProtein: B Rost and J Liu (2003) The PredictProtein Server. Nucleic Acids Research 31(13): 3300-3304.
  2. PROSITE: A Bairoch, P Bucher & K Hofmann (1997) Nucleic Acids Research, 25:217-221
  3. SEG: J C Wootton & S Federhen (1996) Methods in Enzymology, 266:554-571
  4. ProDom: ELL Sonnhammer & D Kahn (1994) Protein Science, 3:482-492
  5. MaxHom: MaxHom: C Sander R Schneider (1991) Proteins, 9:56-68
  6. MView: MView: N P Brown, C Leroy & C Sander (1998) Bioinformatics, 14:380-381
  7. PHD: B Rost (1996) Methods in Enzymology, 266:525-539
  8. PHDsec: B Rost & C Sander (1993) J. of Molecular Biology, 232:584-599
  9. PHDacc: B Rost & C Sander (1994) Proteins, 20:216-226
  10. PHDhtm: B Rost, P Fariselli & R Casadio (1996) Protein Science, 7:1704-1718
  11. PROF: B Rost (2004) Meth. Mol. Biol., submitted.
  12. PROFsec: B Rost (2004) Meth. Mol. Biol., submitted.
  13. PROFACC: B Rost (2004) Meth. Mol. Biol., submitted.
  14. GLOBE: B Rost (1998) unpublished
  15. CYSPRED: Fariselli P, Riccobelli P & Casadio R (1999) PROTEINS 36:340-346
  16. A conformational switch prediction program: Young et al. Protein Science(1999) 8:1752-64.



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