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<TITLE>Dali: PF17720</TITLE><A name=s001A>
<h1>Results: PF17720</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="PF17720">
<input TYPE="hidden" NAME="jobid" VALUE=PF17720>
<input TYPE="hidden" NAME="query_sequence" VALUE="MRRLGSVQQKIPCVFLTEVRDEPSRKRDCQQFQVVATENVSPAALASDVHCAAATEKVDGTCCYVTTFNGEPYLWARLDRKPTKQADKRFKKYQYSQKTCKGFVWNVNEDFREVPEFWMAAHRVQHENGHPVPDEHGHIPGWVPVDHTNKQYCWHSSVVNYGTGVALVLKTHGEDEGQLEIVSVPLADLMEQTLELIGTNVNGNPYGLGSKKHPVHVLVPHGVLRIRNPPAVEFQQICSWFQECQEGRVEGIVWHCDDGMLIKIHRHHLGLKWPVADTFLNTRPVVVHVDESDADPCASEKDLFKSFSSVNRQTFSSVRDIQFE"> 
<input TYPE="hidden" NAME="query_dssp" VALUE="LLLLLLLLLLLLLLEEEEEELLLLLLLLLLLLEEEEEEEELHHHHHLLHHHLEEEEELLLEEEEEEEELLEEEEEEELLLLLLHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLLLLEELLLLLEELLEELLLLLLLLLEEEELLLLLHHHHHHHLLEELLLLEEEEEEEELLEEEEEEEEEEEHHHHLLLEEEEEELLLLLLLLLLLLLLLLLEEEEELLLLLLLLLLLLLHHHHHHHHHHLLLLLLLEEEEELLLLLEEEEEHHHHLLLLLLLLLHHHHLLEEEELLHHHLLLLLLLLLHHHHHHHLLLLEELLHHHLLLL"> 
<input TYPE="hidden" NAME="cd1" VALUE=s001A>
<input TYPE="hidden" NAME="pdbresnos" VALUE="324    1     2     3     4     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   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   264   265   266   267   268   269   270   271   272   273   274   275   276   277   278   279   280   281   282   283   284   285   286   287   288   289   290   291   292   293   294   295   296   297   298   299   300   301   302   303   304   305   306   307   308   309   310   311   312   313   314   315   316   317   318   319   320   321   322   323   324 
">
<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=5cotA sequence=smgvrklatirtageitpiagaeaiecchvdgwtcvikkgefkqgdrgvyfeidsfikedndrypmlskqvidyegqrgtrlrtarlrgqlsqglflpmdrfpelasnqvgddvteilgitkweppistnlsgeilgefptfisKTDQERVQNLIPQIEENKgQKFEVTVKLDGSSMTVYRKDDHIGVCGRNWELRETATNAQWHAARrNKMIEGlqflnrnLALQGEIIGESIQGNLEKLKGQDFYLFdiydidkaqyltpierqslvkqlndngftvkhVPILDDLelnHTAEQILAMAdgpslnknvKREGLVFKRLDGkFSFKAISNayLEKHKDR dssp=llllllleeeeeeeeeeelllllleeeeeelleeeeeelllllllleeeeellleeeellllllhhhhhhleeelleeeeellleeelleeelleeeehhhlhhhlllllllllhhhhlleellllllhhhllleeeellllllLLLLLLHHHLHHHHHHLLlLEEEEEEELLLEEEEEEEELLEEEEELLLEEELLLLLLHHHHHHHhLLHHHHhhhhlllEEEEEEEEELLLLLLLLLLLLEEEEEEeeeelllleellhhhhhhhhhhhhhllllleeLLLLLLEellLLHHHHHHHHlllllllllLLLEEEEEELLLlLEEEEELHhhHHHLLLL qstarts=7,39,49,142,148,153,182,189,214,222,231,247,259,269 sstarts=144,153,163,192,197,201,209,222,242,281,291,310,323,333 lengths=9,9,29,5,4,7,6,20,7,7,10,12,8,4 u=-0.534291,-0.840591,0.089109,0.718320,-0.395931,0.572062,-0.445589,0.369657,0.815356 t=24,3,-54 segments=144-152,153-161,163-191,192-196,197-200,201-207,209-214,222-241,242-248,281-287,291-300,310-321,323-330,333-336 compnd=_NAEGLERIA_GRUBERI_RNA_LIGASE;>"   <A HREF=#alignment-1>1</A>:  5cot-A  7.3  2.9  137   340   18 <A HREF="http://ekhidna2.biocenter.helsinki.fi/cgi-bin/daliviewer/readpdb.cgi?html=1&jobid=pdb&pdbid=5cot&u=-0.534291,-0.840591,0.089109,0.718320,-0.395931,0.572062,-0.445589,0.369657,0.815356&t=24,3,-54">PDB</A>  MOLECULE: NAEGLERIA GRUBERI RNA LIGASE;                              

</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=5cotA Z-score=7.3</h3>

<A HREF="#s001A">back to top</A>
<PRE>
DSSP  ------------------------------------------------------------
Query ------------------------------------------------------------    0
ident                                                             
Sbjct smgvrklatirtageitpiagaeaiecchvdgwtcvikkgefkqgdrgvyfeidsfiked   60
DSSP  llllllleeeeeeeeeeelllllleeeeeelleeeeeelllllllleeeeellleeeell


DSSP  ------------------------------------------------------------
Query ------------------------------------------------------------    0
ident                                                             
Sbjct ndrypmlskqvidyegqrgtrlrtarlrgqlsqglflpmdrfpelasnqvgddvteilgi  120
DSSP  llllhhhhhhleeelleeeeellleeelleeelleeeehhhlhhhlllllllllhhhhll


DSSP  -----------------lllllllLLLLLLLEEeeeelllllllllllleeeeeeeELHH
Query -----------------mrrlgsvQQKIPCVFLtevrdepsrkrdcqqfqvvatenVSPA   43
ident                               |                           | 
Sbjct tkweppistnlsgeilgefptfisKTDQERVQN-----------------------LIPQ  157
DSSP  eellllllhhhllleeeellllllLLLLLLHHH-----------------------LHHH


DSSP  HHHLLhHHLEEEEELLLEEEEEEEELLEEEEEEELlllllhhhhhhhhhhhhhhllllll
Query ALASDvHCAAATEKVDGTCCYVTTFNGEPYLWARLdrkptkqadkrfkkyqysqktckgf  103
ident            | | ||    |           |                          
Sbjct IEENKgQKFEVTVKLDGSSMTVYRKDDHIGVCGRN-------------------------  192
DSSP  HHHLLlLEEEEEEELLLEEEEEEEELLEEEEELLL-------------------------


DSSP  llllllllllllllleellllleelleellllllllleeEELLLlLHHHhHHHLLEElll
Query vwnvnedfrevpefwmaahrvqhenghpvpdehghipgwVPVDHtNKQYcWHSSVVNygt  163
ident                                                             
Sbjct ---------------------------------------WELRE-TATN-AQWHAAR---  208
DSSP  ---------------------------------------EEELL-LLLL-HHHHHHH---


DSSP  leeeeeeeelleeeeeeeeEEEHHH------hLLLEEEEEELLLLLLLLLLLlllllLEE
Query gvalvlkthgedegqleivSVPLAD------lMEQTLELIGTNVNGNPYGLGskkhpVHV  217
ident                                      | ||    ||   |         
Sbjct ------------------rNKMIEGlqflnrnLALQGEIIGESIQGNLEKLK-----GQD  245
DSSP  ------------------hLLHHHHhhhhlllEEEEEEEEELLLLLLLLLLL-----LEE


DSSP  EEEL-------------------------------lLLLLLLL-llLLHHHHHHHH---h
Query LVPH-------------------------------gVLRIRNP-paVEFQQICSWF---q  242
ident                                     |             ||        
Sbjct FYLFdiydidkaqyltpierqslvkqlndngftvkhVPILDDLelnHTAEQILAMAdgps  305
DSSP  EEEEeeeelllleellhhhhhhhhhhhhhllllleeLLLLLLEellLLHHHHHHHHllll


DSSP  hllllLLLEEEEELLLL-LEEEEEHHhhLLLLlllllhhhhlleeeellhhhllllllll
Query ecqegRVEGIVWHCDDG-MLIKIHRHhlGLKWpvadtflntrpvvvhvdesdadpcasek  301
ident        || |    ||    |        |                             
Sbjct lnknvKREGLVFKRLDGkFSFKAISNayLEKH----------------------------  337
DSSP  lllllLLLEEEEEELLLlLEEEEELHhhHHHL----------------------------


DSSP  lhhhhhhhlllleellhhhllll
Query dlfksfssvnrqtfssvrdiqfe  324
ident                        
Sbjct --------------------kdr  340
DSSP  --------------------lll


</PRE>
</PRE>
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<H1>PF17720</H1>
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<H1>Dali logos </H1>
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