CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 39:D225-D229

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA.
Nucleic Acids Research (Impact Factor: 9.11). 01/2011; 39(Database issue):D225-9. DOI: 10.1093/nar/gkq1189
Source: PubMed


NCBI’s Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with the location of conserved
domain footprints, and functional sites inferred from these footprints. CDD includes manually curated domain models that make
use of protein 3D structure to refine domain models and provide insights into sequence/structure/function relationships. Manually
curated models are organized hierarchically if they describe domain families that are clearly related by common descent. As
CDD also imports domain family models from a variety of external sources, it is a partially redundant collection. To simplify
protein annotation, redundant models and models describing homologous families are clustered into superfamilies. By default,
domain footprints are annotated with the corresponding superfamily designation, on top of which specific annotation may indicate
high-confidence assignment of family membership. Pre-computed domain annotation is available for proteins in the Entrez/Protein
dataset, and a novel interface, Batch CD-Search, allows the computation and download of annotation for large sets of protein
queries. CDD can be accessed via

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    • "The protein termed AadA6 belongs to the subclass of 3″-O-nucleotidyltransferases (ANT3″), it consists of 281 amino-acid residues (UniProt: Q9RGC2) and confers resistance to streptomycin and spectinomycin [16]. The sequence information collected from the Conserved Domain Database (CDD) [18] for this protein points to the conserved nucleotidyltransferase (NTase) domain lying between residues 10 and 110. This domain includes the nucleotide triphosphate binding site and one Mg 2 þ binding site [19] [20]. "
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    ABSTRACT: The gene coding for the aminoglycoside adenylyltransferase (aadA6) from a clinical isolate of Pseudo-monas aeruginosa was cloned and expressed in Escherichia coli strain BL21(DE3)pLysS. The overexpressed enzyme (AadA6, 281 amino-acid residues) and a carboxy-terminal truncated variant molecule ([1-264] AadA6) were purified to near homogeneity and characterized. Light scattering experiments conducted under low ionic strength supported equilibrium between monomeric and homodimeric arrangements of the enzyme subunits. Circular Dichroism spectropolarimetry indicated a close structural relation to adenylate kinases. Both forms modified covalently the aminoglycosides streptomycin and spectinomycin. The enzyme required at least 5 mM MgCl 2 for normal Michaelis–Menten kinetics. Streptomycin exhibited a strong substrate inhibition effect at 1 mM MgCl 2. The truncated 17 residues at the C-terminus have little influence on protein folding, whereas they have a positive effect on the enzymic activity and stabilize dimers at high protein concentrations (4 100 μM). Homology modelling and docking based on known crystal structures yielded models of the central ternary complex of monomeric AadA6 with ATP and streptomycin or spectinomycin.
    Full-text · Article · Oct 2015
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    • "Characteristic protein signatures in the RbFST sequence were predicted using the ExPASy-prosite server ( and the NCBI conserved domain database (CDD) (Marchler-Bauer et al., 2011). Some physicochemical properties of RbFST were determined using the ExPASy ProtParam tool (http://web.expasy "
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    ABSTRACT: The follistatin (FST) gene encodes a monomeric glycoprotein that plays a role in binding and inhibiting the functions of members of the transforming growth factor (TGF)-β superfamily. Thus, FST facilitates a wide variety of functions, ranging from muscle growth, to inflammation and immunity. In this study, we sought to characterize an FST counterpart, RbFST, which was identified from rock bream Oplegnathus fasciatus. The RbFST cDNA sequence (2,419 bp) contains a 933-bp open reading frame (ORF) that encodes a putative amino acid sequence for RbFST (35 kDa). The putative amino acid sequence contains a Kazal-type serine protease inhibitor domain (51-98 residues) and an EF-hand, calcium-binding domain (191-226 residues). Additionally , this sequence shares a high identity (98.7%) with the Siniperca chuatsi FST sequence, with which it also has the closest evolutionary relationship according to a phylogenetic study. Omnipresent distribution of RbFST transcripts were detected in the gill, liver, spleen, head kidney, kidney, skin, muscle, heart, brain, and intestine of healthy animals, with significantly higher expression levels in the heart, followed by the liver tissue. Under pathogenic stress caused by two bacterial pathogens, Streptococcus iniae and Edwardsiella tarda, RbFST transcription was found to be significantly up-regulated. Altogether, our findings suggest the putative role of RbFST in immune related responses against pathogenic infections, further prefiguring its significance in rock bream physiology.
    Full-text · Article · Sep 2015 · Fisheries and Aquatic Science
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    • "Conserved domain architecture retrieval tool (cDART) (Geer et al., 2002), reverse position-specific (RPS)-basic local sequence alignment tool (BLAST) (Altschul et al. 1997), the conserved domain database (Marchler-Bauer et al., 2011), accession # of the case-study viral glycoproteins of HIV "

    Full-text · Article · Aug 2015 · AFRICAN JOURNAL OF BIOTECHNOLOGY
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