Information Technology Reference
In-Depth Information
6.5 Viewing Multiple Alignments of a Query Protein with Members of a Conserved
Domain
These can be displayed by clicking a CD bar within a MMDB Structure Summary page
or from a hyperlinked CD name on a CD-Search results page.
6.6 Viewing CD Alignments in the Context of 3D Structure
If members of a CD have MMDB records, one of these records can be viewed as a 3D
image along with the sequence alignment using Cn3D (launched by selecting the pink dot
on a CD-Search results page). As in other alignment views, colored capital letters
indicate aligned residues, allowing the sequence of the protein sequence of interest to be
mapped onto the available 3D structure.
7. Finding and Viewing Proteins with Similar Domain Architectures
For an example query on finding and viewing proteins with similar domain architectures,
see Appendix 3.
7.1 Why Would I Want to Do This?
x To locate related functional domains in other protein families
x To gain insights into how a given CD is situated within a protein relative to other
CDs
x To explore functional links between different CDs
x To predict the function of a protein whose function is unknown
x To establish evolutionary relationships across protein families
7.2 How to Begin
Following the
Domain Relatives
link for any protein in Entrez, one can find other
proteins with similar domain architecture. The Conserved Domain Architecture Retrieval
Tool (CDART
15
) can take an Accession number or the FASTA sequence as a query to
find out the domain architecture of a protein sequence and list other proteins with related
domain architectures.
7.3 Alternative Points of Entry
x From a CD-Search results page, click
Show Domain Relatives
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[http://www.ncbi.nlm.nih.gov/Structure/lexington/lexington.cgi?cmd=rps]
