CDD: a conserved domain database for interactive domain family analysis

Abstract

The conserved domain database (CDD) is part of NCBI's Entrez database system and serves as a primary resource for the annotation of conserved domain footprints on protein sequences in Entrez. Entrez's global query interface can be accessed at and will search CDD and many other databases. Domain annotation for proteins in Entrez has been pre-computed and is readily available in the form of ‘Conserved Domain’ links. Novel protein sequences can be scanned against CDD using the CD-Search service; this service searches databases of CDD-derived profile models with protein sequence queries using BLAST heuristics, at . Protein query sequences submitted to NCBI's protein BLAST search service are scanned for conserved domain signatures by default. The CDD collection contains models imported from Pfam, SMART and COG, as well as domain models curated at NCBI. NCBI curated models are organized into hierarchies of domains related by common descent. Here we report on the status of the curation effort and present a novel helper application, CDTree, which enables users of the CDD resource to examine curated hierarchies. More importantly, CDD and CDTree used in concert, serve as a powerful tool in protein classification, as they allow users to analyze protein sequences in the context of domain family hierarchies.

Genetic variation in sialidase and linkage to N-acetylneuraminate catabolism in Mycoplasma synoviae

“…P10481) were readily identified by inspection of local and global sequence alignments, and were conserved across strains, but no equivalent of the Arg 312 that is strictly conserved in many other bacterial and eukaryotic sialidases [31] could be recognized in any strain. All of the dissimilar amino acid substitutions of NanA, NanE, NagA, NagB, and NagC were in their broadly-defined functional domains [29]. Dissimilar amino acid changes were least common in NanA, representing just 4% of all mutations in nanA across strains.…”

“…They represented 26%, 28%, and 26% of all mutations in NanI, NagA, and NagB, respectively ( Figure 3). Approximately half of the dissimilar amino acid substitutions in NanI were in the functional domain defined by the Conserved Domain Database [29]. The signature Arg-Ile-Pro and two Ser-X-Asp-X-Gly-XThr-Trp "Asp box" motifs [30], plus Asp box variants Thr-X-Asp-X-Gly-X-Thr-Trp and Ser-X-Asp-X-Gly-X-Asn-Trp, were conserved in NanI.…”

Isolation and characterization of Argonaute 2: A key gene of the RNA interference pathway in the rare minnow, Gobiocypris rarus

“…It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3 0 -terminal nucleotides in single-stranded nucleic acids and buries the 3 0 OH group, and that it might recognize characteristic 3 0 overhangs in siRNAs within RISC and other complexes. The Piwi domain is the C-terminal portion of Argonaute and consists of two subdomains: one of which provides the 5 0 anchoring of the guide RNA and the other is the catalytic site for slicing exerted by RNase H activity [23]. All the aligned Ago2 contained all the conserved active sites (Fig.…”

Wider than Thought Phylogenetic Occurrence of Apicortin, A Characteristic Protein of Apicomplexan Parasites

“…Orthology was established if three criteria were fulfilled: the BLAST E-score was lower than 1e-5; the query and the hit were reciprocal best-hits and the new protein/nucleotide contained both the partial p25alpha and DCX domains. The European Bioinformatics Institute InterPro (http://www.ebi.ac.uk/interpro/) (Hunter et al 2009), the Pfam protein families (http://pfam.sanger.ac.uk/) (Finn et al 2008) and the CDD (http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml) (Marchler-Bauer et al 2007) databases were checked for proteins possessing both DCX and partial p25alpha domains not detected by BLAST.…”