What are the shortcomings of the Conserved Domain Database (CDD)? When I'm doing bioinformatics work on a hypothetical protein, what should I be weary of when using this database?
The CDD database used for finding the conserved protein domains in your query sequences. If your protein is hypothetical, you can predict the functions of this protein by comparing with existing family domains. The databases you can use are CDD, Pfam and SMART.
Give it a few years in bioinformatics and you'll be "weary" of everything :)