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author matteoc
date Thu, 22 Dec 2016 04:45:31 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pfam_search/prova2	Thu Dec 22 04:45:31 2016 -0500
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+<html>
+<head></head>
+<body>
+Proteins with PFAM domains:
+<br><br>
+<div>
+<table cellpadding="0" width=650>
+<td>
+<HR SIZE=3 WIDTH=80%>
+<center><b>PROKKA_00001</b><br>
+</center>
+</td
+<tr></tr>
+<td bgcolor="#czb9dz">
+<pre> 
+MENNLENLTIGVFAKAAGVNVETIRFYQRKGLLREPDKPYGSIRRYGEADVVRVKFVKSA
+QRLGFSLDEIAELLRLDDGTHCEEASSLAEHKLKDVREKMADLARMETVLSELVCACHAR
+KGNVSCPLIASLQGEAGLARSAM
+
+ </pre>
+</td>
+<tr></tr>
+<td></td>
+<tr></tr>
+<td>
+<p align="left">
+<a href=http://pfam.xfam.org/family/PF09278> PF09278</a>
+<p align="justify">MerR, DNA binding<br>Members of this family of DNA-binding domains are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold  . </p>
+
+</p>
+</td>
+<tr></tr>
+<td></td>
+<tr></tr>
+<td bgcolor="#czb9dz">
+<p align="left">
+<a href=http://pfam.xfam.org/clan/CL0123> CL0123</a>
+ <p align="justify">This family contains a diverse range of mostly DNA-binding domains that contain a helix-turn-helix motif. </p>
+
+</p>
+</td>
+<tr></tr>
+<td></td>
+<tr></tr>
+<td>
+<HR SIZE=3 WIDTH=80%>
+<center><b>PROKKA_00009</b><br>
+</center>
+</td
+<tr></tr>
+<td bgcolor="#czb9dz">
+<pre> 
+MATDTPRIPEQGVATLPDEAWERARRRAEIISPLAQSETVGHEAADMAAQALGLSRRQVY
+VLIRRARQGSGLVTDLVPGQSGGGKGKGRLPEPVERVIHELLQKRFLTKQKRSLAAFHRE
+VTQVCKAQKLRVPARNTVALRIASLDPRKVIRRREGQDAARDLQGVGGEPPAVTAPLEQV
+QIDHTVIDLIVVDDRDRQPIGRPYLTLAIDVFTRCVLGMVVTLEAPSAVSVGLCLVHVAC
+DKRPWLEGLNVEMDWQMSGKPLLLYLDNAAEFKSEALRRGCEQHGIRLDYRPLGQPHYGG
+IVERIIGTAMQMIHDELPGTTFSNPDQRGDYDSENKAALTLRELERWLTLAVGTYHGSVH
+NGLLQPPAARWAEAVARVGVPAVVTRATSFLVDFLPILRRTLTRTGFVIDHIHYYADGHC
+C
+
+ </pre>
+</td>
+<tr></tr>
+<td></td>
+<tr></tr>
+<td>
+<p align="left">
+<a href=http://pfam.xfam.org/family/PF13518> PF13518</a>
+<p align="justify">Helix-turn-helix domain<br>This helix-turn-helix domain is often found in transposases and is likely to be DNA-binding. </p>
+
+</p>
+</td>
+<tr></tr>
+<td></td>
+<tr></tr>
+<td bgcolor="#czb9dz">
+<p align="left">
+<a href=http://pfam.xfam.org/clan/CL0123> CL0123</a>
+ <p align="justify">This family contains a diverse range of mostly DNA-binding domains that contain a helix-turn-helix motif. </p>
+
+</p>
+</td>
+<tr></tr>
+<td></td>
+<tr></tr>
+<td>
+<p align="left">
+<a href=http://pfam.xfam.org/family/PF00665> PF00665</a>
+<p align="justify">Integrase core domain<br>Integrase mediates integration of a DNA copy of the viral genome into the host chromosome.  Integrase is composed of three domains.  The amino-terminal domain is a zinc binding domain Pfam:PF02022.  This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain Pfam:PF00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyses the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site  . </p>
+
+</p>
+</td>
+<tr></tr>
+<td></td>
+<tr></tr>
+<td bgcolor="#czb9dz">
+<p align="left">
+<a href=http://pfam.xfam.org/clan/CL0219> CL0219</a>
+ <p align="justify">Ribonuclease H-like superfamily This clan includes a diverse set of nucleases that share a similar structure to Ribonuclease H. </p>
+
+</p>
+</td>
+<tr></tr>
+<td></td>
+<tr></tr>
+<td>
+<HR SIZE=3 WIDTH=80%>
+<center><b>PROKKA_00016</b><br>
+</center>
+</td
+<tr></tr>
+<td bgcolor="#czb9dz">
+<pre> 
+MSDISRVKILSALMDGRAWTATELSSVANISASTASSHLSKLLDCQLITVVAQGKHRYFR
+LAGKDIAELMESMMGISLNHGVHARVSTPVHLRKARTCYDHLAGEVAVKIYDSLCQQQWI
+TENGSMITLSGIQYFHEMGIDVPSKHSRKICCACLDWSERRFHLGGYVGAALFSLYESKG
+WLTRHLGYREVTITEKGYAAFKTHFH
+
+ </pre>
+</td>
+<tr></tr>
+<td></td>
+<tr></tr>
+<td>
+<p align="left">
+<a href=http://pfam.xfam.org/family/PF12840> PF12840</a>
+<p align="justify">Helix-turn-helix domain<br>This domain represents a DNA-binding Helix-turn-helix domain found in transcriptional regulatory proteins. </p>
+
+</p>
+</td>
+<tr></tr>
+<td></td>
+<tr></tr>
+<td bgcolor="#czb9dz">
+<p align="left">
+<a href=http://pfam.xfam.org/clan/CL0123> CL0123</a>
+ <p align="justify">This family contains a diverse range of mostly DNA-binding domains that contain a helix-turn-helix motif. </p>
+
+</p>
+</td>
+<tr></tr>
+<td></td>
+<tr></tr>
+</table>
+</div>
+</body>
+</html>