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This collection of related protein sequences (clusters) consists of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters. For release-specific information check the <a href="https://web.archive.org/web/20111216125007/http://www.ncbi.nlm.nih.gov/genomes/prkstats.html">stats page</a>. </p> <p> The Protein Clusters database provides easy access to annotation information, publications, domains, structures, and external links and analysis tools including multiple alignments, phylogenetic trees, and genomic neighborhoods (<a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/sutils/protmap.cgi">ProtMap</a>). </p> <p> Protein Clusters can be searched like any other Entrez database. For more information on how to use Entrez please examine the <a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/books/NBK3797/">Entrez Help</a> Document. </p> <p> A publication describing ProtClustDB is now available: <a href="https://web.archive.org/web/20111216125007/http://www.ncbi.nlm.nih.gov/pubmed/18940865">Klimke et al., 2009. The National Center for Biotechnology Information's Protein Clusters Database. Nucleic Acids Res. 2009 Jan;37(Database issue):D216-23. Epub 2008 Oct 21.</a> </p> <p> A specialized BLAST service is accessible (<a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/genomes/prokhits.cgi">Concise Protein BLAST</a>). </p> Data is available for download via <a href="https://web.archive.org/web/20111216125007/ftp://ftp.ncbi.nih.gov/genomes/CLUSTERS/">Protein Clusters FTP</a> </blockquote></font> </td> </tr> </table> <table width="533" cellpadding="2" cellspacing="0" border="0"> <td width="529" bgcolor="#ADD8E6" height="24"> <font face="Verdana" size="2"><b>聽Example Searches</b></font></td> <tr valign="top"> <td align="LEFT" width="529" class="medium2"><font size="2" face="Verdana"> <blockquote> <p> all clusters with ribosomal protein as the curated name <br></br> <a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/proteinclusters?term=ribosomal%20protein%5BProtein%20Name%5D&cmd=search">"ribosomal protein"[Protein Name]</a> <br></br> all clusters that are encoded by chloroplasts <br></br> <a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/proteinclusters?term=source%20chloroplast%5BAll%20Fields%5D">"source chloroplast"[All Fields]</a> </p> <p> Check the <a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/proteinclusters/limits">limits page</a> and the <a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/books/NBK3797/">help document</a> for more information. </p> </blockquote></font> </td> </tr> </table> </table> </div></div>    </div>   </div>  </div>  </div> </div>  <div id="LeftCol"> <div id="nav_column"> <table id="SideBar" style="margin-left:0.25em"><tr><td bgcolor="#336699"> <img src="/web/20111216125007im_/http://www.ncbi.nlm.nih.gov/corehtml/transparent.gif" width="120" height="1" border="0"/> <a href="https://web.archive.org/web/20111216125007/http://www.ncbi.nlm.nih.gov/" class="GUTTER2">NCBI</a> <img src="/web/20111216125007im_/http://www.ncbi.nlm.nih.gov/corehtml/transparent.gif" width="125" height="8" border="0"></img> <table border="0" width="125" cellspacing="0" cellpadding="0"> <tr valign="bottom"> <td width="120"><a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/Database/index.html" class="GUTTER2">About Entrez </a> <img src="/web/20111216125007im_/http://www.ncbi.nlm.nih.gov/corehtml/transparent.gif" width="1" height="4"></img></td> <td width="8" align="right"><img src="/web/20111216125007im_/http://www.ncbi.nlm.nih.gov/corehtml/GoUp1.gif" width="8" height="19"></img></td> </tr> <tr align="right"> <td colspan="2"><img src="/web/20111216125007im_/http://www.ncbi.nlm.nih.gov/corehtml/GoUp2.gif" width="125" height="12"></img></td> </tr> </table> <p> <span class="GUTTER1">Entrez Protein Clusters</span> <br/> <a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/sites/entrez?db=proteinclusters" class="GUTTER3">Home</a><br/> <a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/books/NBK3797/" class="GUTTER3">Help</a><br/> <a href="https://web.archive.org/web/20111216125007/ftp://ftp.ncbi.nih.gov/genomes/CLUSTERS/" class="GUTTER3"><font color="FFFFFF">FTP</font></a><br/> <a href="https://web.archive.org/web/20111216125007/http://www.ncbi.nlm.nih.gov/genomes/prkstats.html" class="GUTTER3"><font color="FFFFFF">Statistics</font></a> </p> <p> <span class="GUTTER1"><font color="FFCC66">NCBI Resources</font></span><br/> <a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/genomes/prokhits.cgi" class="GUTTER3"><font color="FFCC66">Concise BLAST</font></a><br/> <a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/genomes/prokhits.cgi" class="GUTTER3">search clusters sliced at genera with BLAST</a><br/><br/> <a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi" class="GUTTER3"><font color="FFCC66">CD-Search</font></a><br/> <a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi" class="GUTTER3"><font color="FFFFFF">search against PSSMs with RPS-BLAST</font></a> <br/><br/> <a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/genomes/MICROBES/microbial_taxtree.html" class="GUTTER3"><font color="FFCC66">Microbial Genomes</font></a> <br/> <a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/genomes/MICROBES/microbial_taxtree.html" class="GUTTER3"><font color="FFFFFF">browse microbial resources at NCBI</font></a> <br/><br/> <a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/genomes/static/o.html" class="GUTTER3"><font color="FFCC66">Plasmids</font></a> <br/> <a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/genomes/static/o.html" class="GUTTER3"><font color="FFFFFF">browse complete plasmids at NCBI</font></a> <br/><br/> <a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/genomes/ORGANELLES/organelles.html" class="GUTTER3"><font color="FFCC66">Organelles</font></a> <br/> <a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/genomes/ORGANELLES/organelles.html" class="GUTTER3"><font color="FFFFFF">browse organelle genome resources</font></a> <br/><br/> <a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/genomes/GenomesHome.cgi?taxid=10239" class="GUTTER3"><font color="FFCC66">Viruses</font></a> <br/> <a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/genomes/GenomesHome.cgi?taxid=10239" class="GUTTER3"><font color="FFFFFF">browse viral genome resources</font></a> <br/><br/> <a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/genomes/PLANTS/PlantList.html" class="GUTTER3"><font color="FFCC66">Plants</font></a> <br/> <a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/genomes/PLANTS/PlantList.html" class="GUTTER3"><font color="FFFFFF">browse plant genome resources</font></a> <br/><br/> <a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/sutils/protmap.cgi" class="GUTTER3"><font color="FFCC66">ProtMap</font></a> <br/> <a href="/web/20111216125007/http://www.ncbi.nlm.nih.gov/sutils/protmap.cgi" class="GUTTER3"><font color="FFFFFF">examine genome neighborhoods</font></a> </p> <p> <span class="GUTTER1"><font color="FFCC66">Related Resources</font></span> <br/> <a href="https://web.archive.org/web/20111216125007/http://aclame.ulb.ac.be/perl/Aclame/show_cluster.cgi?mode=list&cat=plasmids" class="GUTTER3"><font color="FFCC66">ACLAME</font></a> <br/> <a href="https://web.archive.org/web/20111216125007/http://aclame.ulb.ac.be/perl/Aclame/show_cluster.cgi?mode=list&cat=plasmids" class="GUTTER3"><font color="FFFFFF">A CLAssification of genetic Mobile Elements</font></a> <br/><br/> <a href="https://web.archive.org/web/20111216125007/http://hamap.expasy.org/" class="GUTTER3"><font color="FFCC66">HAMAP</font></a> <br/> <a href="https://web.archive.org/web/20111216125007/http://hamap.expasy.org/" class="GUTTER3"><font color="FFFFFF">High-quality Automated and Manual Annotation of microbial Proteomes</font></a> <br/><br/> <a href="https://web.archive.org/web/20111216125007/http://www.genome.jp/dbget-bin/get_htext?KO" class="GUTTER3"><font color="FFCC66">KEGG Orthology</font> </a> <br/> <a href="https://web.archive.org/web/20111216125007/http://www.genome.jp/dbget-bin/get_htext?KO" class="GUTTER3"><font color="FFFFFF">Kyoto Encyclopedia of Genes and Genomes Orthologs</font></a> <br/><br/> <a href="https://web.archive.org/web/20111216125007/http://www.ebi.ac.uk/interpro/" class="GUTTER3"><font color="FFCC66">InterPro</font></a> <br/> <a href="https://web.archive.org/web/20111216125007/http://www.ebi.ac.uk/interpro/" class="GUTTER3"><font color="FFFFFF">EMBL-EBI Database of Protein Families</font></a> <br/><br/> <a href="https://web.archive.org/web/20111216125007/http://cmr.tigr.org/tigr-scripts/CMR/CmrHomePage.cgi" class="GUTTER3"><font color="FFCC66">TIGR CMR</font></a> <br/> <a href="https://web.archive.org/web/20111216125007/http://cmr.tigr.org/tigr-scripts/CMR/CmrHomePage.cgi" class="GUTTER3"><font color="FFFFFF">TIGR Comprehensive Microbial Resource</font></a> </p> </td> <td><img 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