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<meta name="description" content="Search methods for the Conserved Domains Database (CDD), a resource of the National Center for Biotechnology Information (NCBI) Structure Group" />
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<meta name="keywords" content="Conserved Domain Database (CDD), CD-Search, RPS-BLAST, proteins, protein sequences, classification, families, superfamilies, superfamily, protein function, homologous, homologs, orthologs, multiple sequence alignment, protein sequence analysis and annotation, CDTree, CD Tree, Conserved Domain Architecture Retrieval Tool (CDART), Molecular Modeling Database (MMDB), Cn3D structure viewing software, 3-D, three-dimensional structures, macromolecular structures, x-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, nucleic acids, nucleotide sequences, DNA, RNA, ligands, bound chemicals, drugs, medicine, NCBI, National Center for Biotechnology Information" />
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<TD class="DocTitleText" align="left"> Conserved Domains and Protein Classification</TD>
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<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="//ftp.ncbi.nih.gov/pub/mmdb/cdd"> FTP </A></TD>
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<!-- ============ VERTICAL_SPACER_WITHIN_CONTENT_AREA ============= -->
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<!-- ============== BOX_SEARCH_CDD ================= -->
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<A NAME="Search"></A>
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<!-- ########## BLUE_HEADER ########## -->
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<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCellBlueEdgeTopAndSides">
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<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="CENTER">Search Methods:  Quick Start Guide</TD>
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<A HREF="#HowTo">  How To Use CDD (examples) </A></TD>
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<A HREF="../cdd_help.shtml">  Help Document </A></TD>
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<TD class="WhiteCell TOCText" ALIGN="LEFT" VALIGN="TOP">
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<P class="indent10 NormalText">Introductory/overview text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text.</P>
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</TD>
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</TR -->
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<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> </TD>
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<TR>
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<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP">
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<!-- ========== CDD_SEARCH_METHODS ========== -->
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<TABLE width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell">
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<TR>
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<TD colspan="3" class="WhiteCell MicroText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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</TR>
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<TR>
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<TD width="200" class="WhiteCell ThumbText" ALIGN="LEFT" VALIGN="TOP">
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<P class="indent20"><A HREF="/cdd/"><B>Text Term Search</B></A></P></TD>
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<TD class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">Retrieve <A HREF="../cdd_help.shtml#CDWhat">conserved domain</A> records that contain a term(s) of interest (e.g., chloride channel). Enter the terms in the query box at the top of this page <!--, in the text box below, --> or use the <A HREF="/cdd/"><B>Entrez Conserved Domains Database (CDD)</B></A> home page. See the <!-- A HREF="../cdd_help.shtml" -->help document for <A HREF="../cdd_help.shtml#SearchEntrezCDD">search tips</A>, including a list of available <A HREF="../cdd_help.shtml#CDD_Search_Fields">search fields</A> and examples of their use.
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<I>(Note: the "text term search" function also allows you to enter either unique identifiers (UIDs), in the form of an <A HREF="../cdd_help.shtml#CDSource_accession_prefix"><B>accession</B></A> (e.g., cd00400) or <A HREF="../cdd_help.shtml#CD_PSSM_ID"><B>PSSM ID</B></A> (e.g., 79359); it first searches the Entrez indices for the UID, then retrieves the record.)</I></TD>
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<TD width="5" class="WhiteCell TOCText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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</TR>
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<TR>
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<TD colspan="3" class="WhiteCell NormalText2" ALIGN="LEFT" VALIGN="TOP"> </TD>
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<TR>
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<TD width="200" class="WhiteCell ThumbText" ALIGN="LEFT" VALIGN="TOP">
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<P class="indent20"><A HREF="/Structure/cdd/wrpsb.cgi"><B>Protein or Nucleotide Query Sequence</B></A></P></TD>
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<TD class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">Enter a <A HREF="../cdd_help.shtml#QuerySequence">protein or nucleotide query</A> as an <A HREF="/Sitemap/samplerecord.html#AccessionB">accession or GI</A> number (e.g., AAC50285 or 463989), or as a sequence in <!-- A HREF="/BLAST/fasta.shtml" --><A HREF="https://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml">FASTA</A> format, <!-- (if the sequence already exists in the <A HREF="/protein/">Entrez Protein</A> database) -->to identify the protein's <!-- A HREF="../cdd_help.shtml#CDWhat" -->conserved domains and therefore its putative function via the <a href="/Structure/cdd/wrpsb.cgi"><b>CD-Search</b></a> interface
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<!-- The <A HREF="../cdd_help.shtml">CD-Search Help document</A> provides additional information about system <A HREF="../cdd_help.shtml#RPSBInput">input</A> and <A HREF="../cdd_help.shtml#RPSBResults">output</A>, including illustrations of the default <A HREF="../cdd_help.shtml#ConciseDisplay">concise display</A>, optional <A HREF="../cdd_help.shtml#FullDisplay">full display</A>, and <A HREF="../cdd_help.shtml#RPSBTriangles">small triangles</A> identifying amino acids involved in <A HREF="../cdd_help.shtml#ConservedFeatures">conserved features</A> such as catalytic and binding sites. -->
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</TD>
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<TD width="5" class="WhiteCell TOCText" ALIGN="LEFT" VALIGN="TOP">
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 </TD>
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</TR>
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<TR>
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<TD colspan="3" class="WhiteCell NormalText2" ALIGN="LEFT" VALIGN="TOP"> </TD>
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</TR>
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<TR>
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<TD width="200" class="WhiteCell ThumbText" ALIGN="LEFT" VALIGN="TOP">
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<P class="indent20"><A HREF="/Structure/bwrpsb/bwrpsb.cgi"><B>Batch of Protein Sequences</B></A></P></TD>
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<TD class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP"><A HREF="../cdd_help.shtml#BatchRPSBInput">Input up to 40,000 protein query sequences</A> as a list of sequence identifiers and/or raw sequence data into the <A HREF="/Structure/bwrpsb/bwrpsb.cgi"><B>Batch CD-Search</B></A> tool, which allows the computation and download of <!-- A HREF="../cdd_help.shtml#CDWhat" -->conserved domain annotation for large sets of protein queries. Then download <A HREF="../cdd_help.shtml#BatchRPSBOutput">output</A> in a variety of formats (including tab-delimited text files) or <A HREF="../cdd_help.shtml#BatchRPSBOutputGraphical">view the search results graphically</A>. See the <A HREF="../cdd_help.shtml#TOC_BatchCDSearch">help document</A> for additional details, including information on using Batch CD-Search for <A HREF="../cdd_help.shtml#BatchRPSBWebAPI">scripted data downloads</A>.</TD>
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<TD width="5" class="WhiteCell TOCText" ALIGN="LEFT" VALIGN="TOP">
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 </TD>
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</TR>
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<TD colspan="3" class="WhiteCell NormalText2" ALIGN="LEFT" VALIGN="TOP"> </TD>
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<TD width="200" class="WhiteCell ThumbText" ALIGN="LEFT" VALIGN="TOP">
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<A NAME="SearchCDART"></A>
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<P class="indent20"><A HREF="/Structure/lexington/lexington.cgi"><B>Find proteins with similar domain architectures</B></A></P></TD>
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<TD class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">Enter a <B>protein query</B> as an <A HREF="/Sitemap/samplerecord.html#AccessionB">accession or GI</A> number (e.g., AAC50285 or 463989), or as a sequence in <!-- A HREF="/BLAST/fasta.html" --><A HREF="https://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml">FASTA</A> format, <!-- (if the sequence already exists in the <A HREF="/protein/">Entrez Protein</A> database) --> on the <A HREF="/Structure/lexington/lexington.cgi"><B>Conserved Domain Architecture Retrieval Tool (CDART)</B></A> page to find other proteins with similar domain architectures. <I>(Note: If a sequence of interest is already in the <a HREF="/protein/">Entrez Protein</a> database, you can simply select "<B>Domain Relatives</B>" in that sequence record's "<B>Links</B>" menu to find proteins with similar architecture.)</I>
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</TD>
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<TD width="5" class="WhiteCell TOCText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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</TR>
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<TR>
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<TD colspan="3" class="WhiteCell MiniText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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</TR>
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</TABLE>
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</TD>
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<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> <BR><BR><BR></TD>
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</TR>
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</TABLE>
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<!-- ============== END_BOX_RESOURCE_GROUP_SUMMARY ================= -->
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<!-- ============ VERTICAL_SPACER_WITHIN_CONTENT_AREA ============= -->
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<!-- TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
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<!-- =================== RIGHT_SIDE_CONTENT_AREA ================ -->
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<TD WIDTH="300" class="Yellow1CellBlueEdge" ALIGN="LEFT" VALIGN="TOP">
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<!-- ============== BOX5_THUMBNAILS ================ -->
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<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0">
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<!-- ########## BLUE_HEADER ########## -->
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<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP">Step by step guides showing how to:</TD>
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<!-- ########## END_BLUE_HEADER ########## -->
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<TD class="Yellow1Cell NormalText" ALIGN="Center" VALIGN="TOP"> </TD>
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<!-- ============== THUMBNAILS ================= -->
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<TD class="Yellow1Cell NormalText" ALIGN="Center" VALIGN="TOP">
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<BR>
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<SPAN class="ThumbText2"><A HREF="cdd_how_to_protein_function.html"><B>  Identify putative function of protein query sequence with CD-Search tool  </B></A></SPAN><BR><BR>
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<A HREF="cdd_how_to_protein_function.html">
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<IMG src="images/1cyg_a_cdsearch_concise_display_thumbnail.png" width="240" height="80" border=0 align="center" alt="Thumbnail image of a CD-Search concise display, which shows only the top-scoring conserved domain hits for each region of the query sequence (1CYG_A, Cyclodextrin Glucanotransferase). Click on image to jump to a larger, annotated version in the CD-Search guide on: How to identify the putative function of a protein sequence with CD-Search."></A>
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<!-- IMG SRC="/Structure/cdd/1cyg_a_cdsearch_full_display_thumb.png" width="240" height="130" border=0 align="center" alt="Thumbnail image for RPS-BLAST full display, which shows all hits on each region of the query sequence. Click on image to jump to a larger, annotated version in the CD-Search help document." --><BR><BR>
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<!-- P class="pad20">Legend briefly summarizing what is shown in graphic and containing a <A HREF="#______">link to full size graphic and detailed description</A> in help document.</P -->
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</TD>
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<TD class="Yellow1Cell NormalText" ALIGN="Center" VALIGN="TOP">
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<BR><BR>
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<SPAN class="ThumbText2"><A HREF="cdd_how_to_conserved_features.html"><B>  Identify amino acids<BR>involved in binding and catalysis  </B></A></SPAN><BR><BR>
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<A HREF="cdd_how_to_conserved_features.html"><IMG src="images/np_081086_triangles_site_features_on_query_gi255958238_mouse_mutl1_thumbnail.png" width="240" height="125" border=0 align="center" alt="Thumbnail image of the small triangles displayed in CD-Search results. The triangles point to specific residues involved in conserved features, such as binding and catalytic sites, as mapped from a conserved domain to the query protein sequence (NP_081086, mouse DNA mismatch repair protein Mlh1). Click on image to jump to a larger, annotated version in the CD-Search help document."></A><BR><BR>
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<!-- P class="pad20">Legend briefly summarizing what is shown in graphic and containing a <A HREF="#______">link to full size graphic and detailed description</A> in help document.</P -->
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</TD>
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</TR>
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<TD class="Yellow1Cell NormalText" ALIGN="Center" VALIGN="TOP">
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<BR><BR>
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<SPAN class="ThumbText2"><A HREF="../../lexington/docs/cdart_about.html"><B>  Find proteins with similar domain architecture using CDART  </B></A></SPAN><BR><BR>
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<A HREF="../../lexington/docs/cdart_about.html"><IMG src="images/np_081086_cdart_thumbnail.png" width="240" height="185" border=0 align="center" alt="Thumbnail image showing the domain relatives for a protein query sequence (NP_081086, mouse DNA mismatch repair protein Mlh1). Domain relatives are protein sequences that contain one or more of the conserved domains found in the query sequence. Click on the image to open the CDART help document for more information about the tool."></A><BR>
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<!-- P class="pad20">Legend briefly summarizing what is shown in graphic and containing a <A HREF="#______">link to full size graphic and detailed description</A> in help document.</P -->
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</TD>
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</TR>
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<!-- TR>
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<TD class="Yellow1Cell NormalText" ALIGN="Center" VALIGN="TOP">
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<BR><BR><BR>
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<SPAN class="ThumbText2"><A HREF="../cdd_help.shtml#SpecificHit"><B>  CD-Search "specific hits" must meet or<BR>exceed a domain-specific threshold score  </B></A></SPAN><BR><BR>
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<A HREF="../cdd_help.shtml#SpecificHit"><IMG SRC="/Structure/cdd/cd03683_domain_specific_threshold_score_thumb.png" width="240" height="182" border=0 align="center" alt="Thumbnail image that shows the method for determining the domain-specific E-value threshold score for RPS-BLAST. A specific hit must meet or exceed the threshold score and represents a high confidence association between a protein query sequence and a conserved domain. Click on the image to jump to a larger, annotated version in the CD-Search help document."></A><BR>
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<!-- P class="pad20">Legend briefly summarizing what is shown in graphic and containing a <A HREF="#______">link to full size graphic and detailed description</A> in help document.</P -->
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</TR -->
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<!-- TR>
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<TD class="Yellow1Cell NormalText" ALIGN="Center" VALIGN="TOP">
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<BR><BR><BR>
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<SPAN class="ThumbText2"><A HREF="#______"><B>Thumbnail header/key concept</B></A></SPAN><BR><BR>
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<A HREF="#______"><IMG src="_________thumb.png" width="130" height="105" border=0 align="center" alt="Thumbnail image for example of ________________________. Click on image to jump to a larger, annotated version in this help document."></A><BR>
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<!-- P class="pad20">Legend briefly summarizing what is shown in graphic and containing a <A HREF="#______">link to full size graphic and detailed description</A> in help document.</P -->
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<!-- ======================== END_BOX5 =========================== -->
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<TD VALIGN="top" ALIGN="RIGHT"><SPAN CLASS="HELPBAR1" STYLE="color="#646464"">Revised 26 March 2020</SPAN></TD>
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<TD width="25"><IMG SRC="/coreweb/template1/pix/pixel.gif" width="1" height="1" alt="" border=0></TD>
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<!-- ##################### END_EDITABLE_CONTENT ##################### -->
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<script type="text/javascript">doc_tmp.getDocFtr('<A HREF="/research/">Computational Biology Branch</A> > <A HREF="/Structure/index.shtml">Structure Group</A> > <A HREF="/Structure/cdd/cdd.shtml">Conserved Domains and Protein Classification</A> > Search methods','other');</script>
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<!-- script type="text/javascript">doc_tmp.getDocFtr(' > <A HREF="______">__________</A> > <A HREF="______">__________</A> > <A HREF="______">__________</A> > ___currentpage_____', 'other');</script -->
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