Conserved Domains Database banner graphic
Structure Home 3D Macromolecular Structures Conserved Domains   PubChem    BioSystems 
 
[Clear]  Help
 
 
 Conserved Domains and Protein Classification
 
 
Search Methods
 
 

Text Term Search

Retrieve conserved domain 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 or use the Entrez Conserved Domains Database (CDD) search page  (search tips).  
 

Protein Query Sequence

Enter a protein query as an accession or GI number (e.g., AAC50285 or 463989), or as a sequence in FASTA format, to identify the protein's conserved domains and therefore its putative function:
Search Database
The CD-Search help document provides additional details on database selection and search results. Enter your query on the CD-Search page if you'd like to use advanced search options. (Note: If a sequence of interest is already in the Entrez Protein database, you can simply follow the "Conserved Domains" link for that sequence record to view its pre-computed CD-Search results.)
 
 

Direct fetch via UID

Retrieve a conserved domain record directly from the backend database by entering its unique identifier (UID), in the form of an accession (e.g., cd00400) or PSSM ID (e.g., 79359), in the text box below:
(Note: the "text term search" function also allows you to enter either of those unique identifiers (UIDs), but it first searches the Entrez indices for the UID, then retrieves the record. The "direct fetch via UID" option bypasses the Entrez indices and simply retrieves the specified record.)
 
 

Find proteins with similar domain architectures

Enter a protein query as an accession or GI number (e.g., AAC50285 or 463989), or as a sequence in FASTA format, on the Conserved Domain Architecture Retrieval Tool (CDART) page to find other proteins with similar domain architectures. (Note: If a sequence of interest is already in the Entrez Protein database, you can simply select "Domain Relatives" in that sequence record's "Links" menu to find proteins with similar architecture.)  
 
 


Step by step guides showing how to:
 

  Identify putative function of protein query sequence with CD-Search tool  

Thumbnail image for RPS-BLAST concise display (default), which shows only the top-scoring conserved domain hits for each region of the query sequence.  Click on image to jump to a larger, annotated version in the CD-Search help document.



  Identify amino acids
involved in binding and catalysis  


Thumbnail image showing 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_000240, human MutL protein homolog. Click on image to jump to a larger, annotated version in the CD-Search help document.



  Find proteins with similar domain architecture using CDART  

Thumbnail image showing the domain relatives for protein sequence NP_000240, human MutL protein homolog. 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.

 
 
 
 | Revised 01 October 2009 | | Help Desk | Disclaimer | Privacy statement | Accessibility |
NCBI Home NCBI Search NCBI SiteMap