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<TITLE>Dali: PF04479</TITLE><A name=s001A>
<h1>Results: PF04479</h1>
<h2>Query: <a name="s001A">s001A</a></h2>
                                                                      
<P><A NAME="summary">
Select neighbours (check boxes) for viewing as multiple structural alignment or 3D superimposition. 
The list of neighbours is sorted by Z-score. Similarities with a Z-score lower than 2 are spurious.
Each neighbour has links to pairwise structural alignment with the query structure, 
 and to the PDB format coordinate file where the neighbour
is superimposed onto the query structure. 

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<input TYPE="hidden" NAME="title" VALUE="PF04479">
<input TYPE="hidden" NAME="jobid" VALUE=PF04479>
<input TYPE="hidden" NAME="query_sequence" VALUE="PIIGTIGELAGWACRLDASYNPDDYNAFLGQIIALIIAPVFYSAQAYVLFHHIVLLYGPRFSVLSPKLYGGIFITFDIIALILQAAGGGVAGGADSGSQLQTQGSQIMLGGICFQLFTIVVFSILFSIFFIALYTHHPIRPSTGRREPDVPYTRVRTMSCNCLALATFAMVVRSVYRVIELAQGWEGAVITHEVWFDIFDFIPMIFTSALLIPSLYPAL"> 
<input TYPE="hidden" NAME="query_dssp" VALUE="LHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLHHHHHHHLHHHHHHHHHHHLHHHHHHL"> 
<input TYPE="hidden" NAME="cd1" VALUE=s001A>
<input TYPE="hidden" NAME="pdbresnos" VALUE="219   45    46    47    48    49    50    51    52    53    54    55    56    57    58    59    60    61    62    63    64    65    66    67    68    69    70    71    72    73    74    75    76    77    78    79    80    81    82    83    84    85    86    87    88    89    90    91    92    93    94    95    96    97    98    99   100   101   102   103   104   105   106   107   108   109   110   111   112   113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   161   162   163   164   165   166   167   168   169   170   171   172   173   174   175   176   177   178   179   180   181   182   183   184   185   186   187   188   189   190   191   192   193   194   195   196   197   198   199   200   201   202   203   204   205   206   207   208   209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   225   226   227   228   229   230   231   232   233   234   235   236   237   238   239   240   241   242   243   244   245   246   247   248   249   250   251   252   253   254   255   256   257   258   259   260   261   262   263 
">
<input TYPE="hidden" NAME="cd2list" VALUE="dummy">
<input TYPE="button" NAME="D1" VALUE="Structural Alignment" ONCLICK="return mview();"/> 
<INPUT TYPE="CHECKBOX" NAME="expand_gaps" VALUE=1 CHECKED /> Expand gaps 
<input TYPE="button" NAME="D3" VALUE="3D Superimposition (PV)" ONCLICK="return openViewer();"/> 
<input TYPE="button" NAME="D4" VALUE="SANS" ONCLICK="return sans();"/>
<input TYPE="button" NAME="D5" VALUE="PANZ" ONCLICK="return sanspanz();"/>
<input TYPE="button" NAME="D3" VALUE="Pfam" ONCLICK="return poppush();"/>
<input TYPE="reset" VALUE="Reset Selection"/>
<h2>Summary</h2>
<PRE>
    No:  Chain   Z    rmsd lali nres  %id PDB  Description
<INPUT TYPE="CHECKBOX" NAME="cd2list" VALUE="cd2=1x0k1 sequence=tgrpewiwlalgtalmglgtlyflvkgmgvsdpdakkfyaiTTLVPAIAFTMYLSMLLGYGLtmvpfggeqnpiYWARYADWLfTTPLLLLDLALLVDaDQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESmRPEVASTFKVLRNVTVVLWSAYPVVWLIgseGAGIVPLNIeTLLFMVLDVSAKVGFGLILLRsrAIFG dssp=lllllhhhhhhhhhhhhhhhhhhhhhhlllllhhhhhhhhhHHHHHHHHHHHHHHHHLLLLEeeeeelleeeeeELHHHHHHHhHHHHHHHHHHHHHLlLHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLlLHHHHHHHHHHHHHHHHHHLHHHHHHHHlllLLLLLLHHHhHHHHHHHHHHHHHHHHHHHHLlhHHLL qstarts=0,24,28,37,65,98,155,183,192,213 sstarts=41,58,74,84,99,124,159,190,200,223 lengths=17,4,9,14,25,34,28,9,21,4 u=-0.729958,0.183001,-0.658537,0.013318,-0.959499,-0.281398,-0.683362,-0.214179,0.697957 t=43,30,6 segments=46-62,63-66,79-87,89-102,104-128,129-162,164-191,195-203,205-225,228-231 compnd=_BACTERIORHODOPSIN;>"   <A HREF=#alignment-1>1</A>:  1x0k-1 13.0  3.0  165   227   10 <A HREF="http://ekhidna2.biocenter.helsinki.fi/cgi-bin/daliviewer/readpdb.cgi?html=1&jobid=pdb&pdbid=1x0k&u=-0.729958,0.183001,-0.658537,0.013318,-0.959499,-0.281398,-0.683362,-0.214179,0.697957&t=43,30,6">PDB</A>  MOLECULE: BACTERIORHODOPSIN;                                         

</form>
</PRE>
<A NAME="alignments">
<h2>Pairwise Structural Alignments </h2>
Notation: three-state secondary structure definitions by DSSP (reduced to H=helix, E=sheet, L=coil) are shown above the amino acid sequence. Structurally equivalent residues are in uppercase, structurally non-equivalent residues (e.g. in loops) are in lowercase. Amino acid identities are marked by vertical bars.
<a name=alignment-1><h3> No 1: Query=s001A Sbjct=1x0k1 Z-score=13.0</h3>

<A HREF="#s001A">back to top</A>
<PRE>
DSSP  -----------------------------------------LHHHHHHHHHHHHHHHHhh
Query -----------------------------------------PIIGTIGELAGWACRLDas   19
ident                                                         |   
Sbjct tgrpewiwlalgtalmglgtlyflvkgmgvsdpdakkfyaiTTLVPAIAFTMYLSMLL--   58
DSSP  lllllhhhhhhhhhhhhhhhhhhhhhhlllllhhhhhhhhhHHHHHHHHHHHHHHHHL--


DSSP  hllllHHHH------------HHHHHHHHH-HHHHHHHHHHHHHHhhhhhhlhhhllllH
Query ynpddYNAF------------LGQIIALII-APVFYSAQAYVLFHhivllygprfsvlsP   66
ident                           |               |                 
Sbjct -----GYGLtmvpfggeqnpiYWARYADWLfTTPLLLLDLALLVD-------------aD  100
DSSP  -----LLLEeeeeelleeeeeELHHHHHHHhHHHHHHHHHHHHHL-------------lL


DSSP  HHHHHHHHHHHHHHHHHHHHHHHHhhllllllHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Query KLYGGIFITFDIIALILQAAGGGVaggadsgsQLQTQGSQIMLGGICFQLFTIVVFSILF  126
ident           | |       |                            |    |    |
Sbjct QGTILALVGADGIMIGTGLVGALT--------KVYSYRFVWWAISTAAMLYILYVLFFGF  152
DSSP  HHHHHHHHHHHHHHHHHHHHHHHL--------LLHHHHHHHHHHHHHHHHHHHHHHHHHH


DSSP  HHHHHHhhlllllllllllllllllllhhHHHHHHHHHHHHHHHHHHHHHHHHHHHL---
Query SIFFIAlythhpirpstgrrepdvpytrvRTMSCNCLALATFAMVVRSVYRVIELAQ---  183
ident                              |              ||              
Sbjct TSKAES----------------------mRPEVASTFKVLRNVTVVLWSAYPVVWLIgse  190
DSSP  HHHHLL----------------------lLHHHHHHHHHHHHHHHHHHLHHHHHHHHlll


DSSP  LLLLLLLLL-HHHHHHHLHHHHHHHHHHHLH--HHHHhl
Query GWEGAVITH-EVWFDIFDFIPMIFTSALLIP--SLYPal  219
ident |            |   |          |          
Sbjct GAGIVPLNIeTLLFMVLDVSAKVGFGLILLRsrAIFG--  227
DSSP  LLLLLLHHHhHHHHHHHHHHHHHHHHHHHHLlhHHLL--


</PRE>
</PRE>
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<H1>PF04479</H1>
<TITLE>Dali logos </TITLE>
<H1>Dali logos </H1>
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