Content-type: text/html

<TITLE>Dali: PF06420</TITLE><A name=s001A>
<h1>Results: PF06420</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. 

<form NAME="optionform" METHOD="POST" TARGET="_blank"/>
<input TYPE="hidden" NAME="title" VALUE="PF06420">
<input TYPE="hidden" NAME="jobid" VALUE=PF06420>
<input TYPE="hidden" NAME="query_sequence" VALUE="DWYTSWYGLGMKPFEAKVQKDLIEPLDPKDIEIKPDGLIYLPEIKYRRILNKAFGAGGWGLVPRSQTIVTSKLVTREYGLICHGQLISVARGEQDYFNEAGIPTATEGCKSNALMRCCKDLGVGSELWDPVFIKKFKVDHCTEKFVEHVTTKRKKKIWLRKDRQVEYPYK"> 
<input TYPE="hidden" NAME="query_dssp" VALUE="LLLLLLLLLLLLLLLHHHHHHHLLLLLLLLLEELLLLLEELLHHHHHHHHHHHHLLLLEEEEELLLLEEELLEEEEEEEEEELLEEEEEEEEEEELLLHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHLHHHHHHHHHHLEEEEEEELLLLLLEEEEEEELLLLLLLLLL"> 
<input TYPE="hidden" NAME="cd1" VALUE=s001A>
<input TYPE="hidden" NAME="pdbresnos" VALUE="170  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 
">
<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=5xs0G sequence=cfgQCQYtaeEYQAIQKALRQRLGPEYISSRMagggQKVCYIEGHRVINLANEMFGYNGWAHSITQQNVDFVdlnngkfyVGVCAFVRVQLKDGSYHEDVGYGVSEglksKALSLEKARKEAVTDGLKRALRSFGnaLGNCILDKDYLRSLNKLPRQLPLEVDLTKAKRQDLEPSVEEARYNSC dssp=lllLLLLlhhHHHHHHHHHHLLLLLLLEEEEEllllLEEEEELHHHHHHHHHHHHLLLLEEEEEEEEEEEEEeeelleeeEEEEEEEEEEELLLLEEEEEEEEEEEeellHHHHHHHHHHHHHHHHHHHHHHLLLhhHLHHHHLHHHHHHHHLLLLLLLLLLLHHHLLLLLLLHHHHHHHHLLL qstarts=9,13,35,71,97,122,159 sstarts=3,10,36,80,110,137,155 lengths=4,22,36,26,25,18,4 u=-0.101599,0.570241,0.815170,0.910087,0.384204,-0.155335,-0.401770,0.726094,-0.558004 t=79,-6,30 segments=28-31,35-56,61-96,105-130,135-159,162-179,180-183 compnd=_DNA_REPAIR_PROTEIN_RAD52_HOMOLOG;>"   <A HREF=#alignment-1>1</A>:  5xs0-G 12.4  2.9  135   184   16 <A HREF="http://ekhidna2.biocenter.helsinki.fi/cgi-bin/daliviewer/readpdb.cgi?html=1&jobid=pdb&pdbid=5xs0&u=-0.101599,0.570241,0.815170,0.910087,0.384204,-0.155335,-0.401770,0.726094,-0.558004&t=79,-6,30">PDB</A>  MOLECULE: DNA REPAIR PROTEIN RAD52 HOMOLOG;                          

</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=5xs0G Z-score=12.4</h3>

<A HREF="#s001A">back to top</A>
<PRE>
DSSP  lllllllllLLLL---LLHHHHHHHLLLLLLLLLEELL----LLLEELLHHHHHHHHHHH
Query dwytswyglGMKP---FEAKVQKDLIEPLDPKDIEIKP----DGLIYLPEIKYRRILNKA   53
ident                      || |   | |  |            |          |  
Sbjct ------cfgQCQYtaeEYQAIQKALRQRLGPEYISSRMagggQKVCYIEGHRVINLANEM   54
DSSP  ------lllLLLLlhhHHHHHHHHHHLLLLLLLEEEEEllllLEEEEELHHHHHHHHHHH


DSSP  HLLLLEEEEELLLLEEEL--------LEEEEEEEEEELLEEEEEEEEEEELL----LHHH
Query FGAGGWGLVPRSQTIVTS--------KLVTREYGLICHGQLISVARGEQDYF----NEAG  101
ident ||  ||      |               |                 |             
Sbjct FGYNGWAHSITQQNVDFVdlnngkfyVGVCAFVRVQLKDGSYHEDVGYGVSEglksKALS  114
DSSP  HLLLLEEEEEEEEEEEEEeeelleeeEEEEEEEEEEELLLLEEEEEEEEEEEeellHHHH


DSSP  HHHHHHHHHHHHHHHHHHHLL--LLHHHHLHHHHHHHHHHLeeeeeeelllllleeeeee
Query IPTATEGCKSNALMRCCKDLG--VGSELWDPVFIKKFKVDHctekfvehvttkrkkkiwl  159
ident    |        | |     |   |    |                              
Sbjct LEKARKEAVTDGLKRALRSFGnaLGNCILDKDYLRSLNKLP-------------------  155
DSSP  HHHHHHHHHHHHHHHHHHLLLhhHLHHHHLHHHHHHHHLLL-------------------


DSSP  ELLL------------------lllllll
Query RKDR------------------qveypyk  170
ident |                            
Sbjct RQLPlevdltkakrqdlepsveearynsc  184
DSSP  LLLLllllhhhlllllllhhhhhhhhlll


</PRE>
</PRE>
<HR>
<script>

function openViewer() {
    document.optionform.action = "/cgi-bin/daliviewer/viewer.cgi";
    document.optionform.target = "_blank";
    document.optionform.submit();
    return true;
}

function poppush() {
        document.optionform.action = "/cgi-bin/daliviewer/test_poppush.cgi";
        document.optionform.target = "_blank";
        document.optionform.submit();
}

function mview() {
	document.optionform.action = "/cgi-bin/daliviewer/strali.cgi";
	document.optionform.target = "_blank";
	document.optionform.submit();
}

function sans() {
        document.optionform.action = "/cgi-bin/daliviewer/call_sans.cgi";
        document.optionform.target = "_blank";
        document.optionform.submit();
}

function sanspanz() {
        document.optionform.action = "/cgi-bin/daliviewer/call_sanspanz.cgi";
        document.optionform.target = "_blank";
        document.optionform.submit();
}

</script>


<H1>PF06420</H1>
<TITLE>Dali logos </TITLE>
<H1>Dali logos </H1>
<PRE>
</PRE>
<PRE><IMG SRC=1.png>
<PRE>
<PRE>
</PRE>
<PRE><IMG SRC=2.png>
<PRE>