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<TITLE>Dali: PF04250</TITLE><A name=s001A>
<h1>Results: PF04250</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="query_sequence" VALUE="GVDLAWAGRNPTGVAAVDADGCLVGVGAARDDASVLAALRPYVVGDCLVAFDAPLVVANRTGQRPAEAALNRDFRQFEAGAYPANTEKPEFADVPRAARLARQLALDMDPLSSATRRAIEVYPHPATVALFRLPRALKYKAKPGRSVDLLKSELLRLMDGVEGLAQAGVRMQVAGQPDWVSLRRQVTVAQRKSDLRAAEDPIDAVVCAYVALYAQRRPADVTIYGDFTT"> 
<input TYPE="hidden" NAME="query_dssp" VALUE="LEELLLLLLLLEEEEEELLLLLEEEEEEELLHHHHHHHHHHHLLLLEEEEELLLLLLLLLLLLLHHHHHHHHHHHHHLLLLLLLLLLLHHHLLLLHHHHHHHHLLLLLLLLLLLLEEEEELLHHHHHHHHHLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHLHHHLLLLLLLLL"> 
<input TYPE="hidden" NAME="cd1" VALUE=s001A>
<input TYPE="hidden" NAME="pdbresnos" VALUE="229    5     6     7     8     9    10    11    12    13    14    15    16    17    18    19    20    21    22    23    24    25    26    27    28    29    30    31    32    33    34    35    36    37    38    39    40    41    42    43    44    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 
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<h2>Summary</h2>
<PRE>
    No:  Chain   Z    rmsd lali nres  %id PDB  Description
<INPUT TYPE="CHECKBOX" NAME="cd2list" VALUE="cd2=6s16B sequence=hmvvaGIDPGITHLGLGVVAVKgalkARLLHGEVVKtspqepakervgrIHARVLEVLHRFRpEAVAVEEqFFYRQNELAYkvgWALGAVLVAAFeagVPVYAYGPMQVKQALAGHGHAAKEEVALMVRGILGLKEAPRPSHLADALAIALTHAFYARMGTAKPL dssp=lleeeEEELLLLEEEEEEEELLllllLEEEEEEEEEllllllhhhhhhhHHHHHHHHHHHHLlLEEEEELlLLLLLHHHHHhhhHHHHHHHHHHHhhlLLEEEELHHHHHHHHLLLLLLLHHHHHHHHHHHHLLLLLLLLHHHHHHHHHHHHHHHHHHLLLLLLL qstarts=0,9,20,30,46,80,87,94,115,134,153,171,179,196,219 sstarts=5,11,26,49,63,71,76,84,98,116,120,130,134,138,159 lengths=6,11,10,13,7,5,5,11,18,4,10,4,4,21,4 u=-0.059123,0.607854,-0.791844,-0.874261,-0.414412,-0.252844,-0.481842,0.677330,0.555925 t=-21,-20,-74 segments=5-10,11-23,28-37,51-63,65-71,73-77,78-82,86-96,100-117,118-121,122-131,132-135,136-139,140-160,161-164 compnd=_CROSSOVER_JUNCTION_ENDODEOXYRIBONUCLEASE_RUVC;>"   <A HREF=#alignment-1>1</A>:  6s16-B  9.5  3.1  133   165   15 <A HREF="http://ekhidna2.biocenter.helsinki.fi/cgi-bin/daliviewer/readpdb.cgi?html=1&jobid=pdb&pdbid=6s16&u=-0.059123,0.607854,-0.791844,-0.874261,-0.414412,-0.252844,-0.481842,0.677330,0.555925&t=-21,-20,-74">PDB</A>  MOLECULE: CROSSOVER JUNCTION ENDODEOXYRIBONUCLEASE RUVC;             

</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=6s16B Z-score=9.5</h3>

<A HREF="#s001A">back to top</A>
<PRE>
DSSP  -----LEELLLlllLLEEEEEELLL----LLEEEEEEEL-------------LHHHHHHH
Query -----GVDLAWagrNPTGVAAVDAD----GCLVGVGAAR-------------DDASVLAA   38
ident      | |         |   |         |                      | ||  
Sbjct hmvvaGIDPGI---THLGLGVVAVKgalkARLLHGEVVKtspqepakervgrIHARVLEV   57
DSSP  lleeeEEELLL---LEEEEEEEELLllllLEEEEEEEEEllllllhhhhhhhHHHHHHHH


DSSP  HHHHLlllEEEEELLlllllllllllhhhhhhhhhhhhhlllLLLLLllLHHHL-llLHH
Query LRPYVvgdCLVAFDAplvvanrtgqrpaeaalnrdfrqfeagAYPANteKPEFA-dvPRA   97
ident |         ||                                                
Sbjct LHRFR--pEAVAVEE--------------------------qFFYRQ--NELAYkvgWAL   87
DSSP  HHHHL--lLEEEEEL--------------------------lLLLLL--HHHHHhhhHHH


DSSP  HHHHHHLLllllllllllEEEEELLHHHHHHHHHLLlLLLLllllllllhhhhhhhHHHH
Query ARLARQLAldmdplssatRRAIEVYPHPATVALFRLpRALKykakpgrsvdllkseLLRL  157
ident                          |     ||                           
Sbjct GAVLVAAF-------eagVPVYAYGPMQVKQALAGH-GHAA---------------KEEV  124
DSSP  HHHHHHHH-------hhlLLEEEELHHHHHHHHLLL-LLLL---------------HHHH


DSSP  HHHHHHhhhlllllLLLLlhhhHHHHhhhhhlllhhhhhHHHHHHHHHHHHHHHHHHHHL
Query MDGVEGlaqagvrmQVAGqpdwVSLRrqvtvaqrksdlrAAEDPIDAVVCAYVALYAQRR  217
ident    | |                                       ||   |       | 
Sbjct ALMVRG--------ILGL----KEAP-------------RPSHLADALAIALTHAFYARM  159
DSSP  HHHHHH--------HHLL----LLLL-------------LLHHHHHHHHHHHHHHHHHHL


DSSP  hhHLLLllllll
Query paDVTIygdftt  229
ident             
Sbjct --GTAK----pl  165
DSSP  --LLLL----ll


</PRE>
</PRE>
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<H1>PF04250</H1>
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