CDD: a Conserved Domain Database for protein classification

Abstract

The Conserved Domain Database (CDD) is the protein classification component of NCBI's Entrez query and retrieval system. CDD is linked to other Entrez databases such as Proteins, Taxonomy and PubMed®, and can be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. CD-Search, which is available at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi, is a fast, interactive tool to identify conserved domains in new protein sequences. CD-Search results for protein sequences in Entrez are pre-computed to provide links between proteins and domain models, and computational annotation visible upon request. Protein–protein queries submitted to NCBI's BLAST search service at http://www.ncbi.nlm.nih.gov/BLAST are scanned for the presence of conserved domains by default. While CDD started out as essentially a mirror of publicly available domain alignment collections, such as SMART, Pfam and COG, we have continued an effort to update, and in some cases replace these models with domain hierarchies curated at the NCBI. Here, we report on the progress of the curation effort and associated improvements in the functionality of the CDD information retrieval system.

The direct route: a simplified pathway for protein import into the mitochondrion of trypanosomes

“…A single inner membrane translocase The Tim17-Tim22-Tim23 family of proteins (PFAM: PF02466) [22] are a set of highly-conserved proteins found in animals, plants, fungi and protists that range from Plasmodium to Trichomonas [2,23,24]. In all cases, the protein has four predicted transmembrane domains with specific amino acid signature motifs [23].…”

Characterization of an ATP-dependent DNA ligase from the acidophilic archaeon “Ferroplasma acidarmanus” Fer1

“…This is the only open reading frame in F. acidarmanus Fer1 predicted to be a functional DNA ligase so, for convenience, we refer to this gene as falig and its protein product as FaLig. Three regions of the predicted amino acid sequence have significant similarity to domains within the Conserved Domain Database (CDD) (Marchler-Bauer et al 2005) (Fig. 1a).…”

Structure of Arabidopsis thaliana At1g77540 Protein, a Minimal Acetyltransferase from the COG2388 Family,

“…Primary sequence analysis of At1g77540 revealed that it belongs to the biochemically uncharacterized COG2388 family, which shows sequence relationship to the GNAT family of histone acetyltransferases (HATs) (30). We investigated this relationship in more detail and established that At1g77540 is indeed capable of binding acetyl-CoA as well as acetylating histones H3 and H4.…”