The Conserved Domain Database (CDD) version 3.19 is now available. This version contains 3,148 new or updated NCBI-curated domains and now mirrors Pfam version 33.1 as well as models from the NCBIfam collection. We also included fine-grained classifications of the immunoglobulin, RRM, cytochrome P450, 7-transmembrane GPCRs, KH, calponin homology and C1 domain superfamilies.
With this CDD release, we introduce model-specific word-score thresholds for the RPS-BLAST heuristics. These are included in the position-specific score matrices (PSSMs) and are used by database formatting software when constructing word lookup tables for the BLAST heuristics stage. The current implementation results in a 3-fold speedup of RPS-BLAST searches and misses annotation for about 0.6% of query proteins, mostly at the borderline of significance.