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

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Nucleic Acids Research (Impact Factor: 9.11). 01/2011; 39(Database issue):D225-9. DOI: 10.1093/nar/gkq1189
Source: PubMed

ABSTRACT 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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    • "Motif Scan (, and webbased NCBI's Conserved Domain Database (CDD) (Marchler-Bauer et al., 2011). To place dorsal and dorsal-like genes on phylogenetic trees, we performed multiple alignments of these genes using Clustal X software (Ver. "
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    ABSTRACT: To date, knowledge of the immune system in aquatic invertebrates has been reported in only a few model organisms, even though all metazoans have an innate immune system. In particular, information on the copepod's immunity and the potential role of key genes in the innate immune systems is still unclear. In this study, we identified dorsal and dorsal-like genes in the cyclopoid copepod Paracyclopina nana. In silico analyses for identifying conserved domains and phylogenetic relationships supported their gene annotations. The transcriptional levels of both genes were slightly increased from the nauplius to copepodid stages, suggesting that these genes are putatively involved in copepodid development of P. nana. To examine the involvement of both genes in the innate immune response and under stressful conditions, the copepods were exposed to lipopolysaccharide (LPS), different culture densities, salinities, and temperatures. LPS significantly upregulated mRNA expressions of dorsal and dorsal-like genes, suggesting that both genes are transcriptionally sensitive in response to immune modulators. Exposure to unfavorable culture conditions also increased mRNA levels of dorsal and dorsal-like genes. These findings suggest that transcriptional regulation of the dorsal and dorsal-like genes would be associated with environmental changes in P. nana. Copyright © 2015 Elsevier B.V. All rights reserved.
    Marine Genomics 08/2015; DOI:10.1016/j.margen.2015.08.002 · 1.79 Impact Factor
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    • "Open reading frames (ORFs) were predicted using ORF Finder ( ). Conserved domains of predicted ORFs were detected using NCBI's Conserved Domain Database (NCBI) (Marchler-Bauer et al., 2011), TMHMM (Moller et al., 2001) and SMART softwares (Letunic et al., 2012). Importin ␣-dependent nuclear localization signals and DNA and RNA binding residues in the coat protein (CP) deduced amino acid (aa) sequence were scanned, respectively, using cNLS Mapper (Kosugi et al., 2009) and BindN softwares (Wang and Brown, 2006). "
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    ABSTRACT: Fruit trees of temperate and tropical climates are of great economical importance worldwide and several viruses have been reported affecting their productivity and longevity. Fruit trees of different Brazilian regions displaying virus-like symptoms were evaluated for infection by circular DNA viruses. Seventy-four fruit trees were sampled and a novel, highly divergent, monopartite circular ssDNA virus was cloned from apple, pear and grapevine trees. Forty-five complete viral genomes were sequenced, with a size of approx. 3.4kb and organized into five ORFs. Deduced amino acid sequences showed identities in the range of 38% with unclassified circular ssDNA viruses, nanoviruses and alphasatellites (putative Replication-associated protein, Rep), and begomo-, curto- and mastreviruses (putative coat protein, CP, and movement protein, MP). A large intergenic region contains a short palindromic sequence capable of forming a hairpin-like structure with the loop sequence TAGTATTAC, identical to the conserved nonanucleotide of circoviruses, nanoviruses and alphasatellites. Recombination events were not detected and phylogenetic analysis showed a relationship with circo-, nano- and geminiviruses. PCR confirmed the presence of this novel ssDNA virus in field plants. Infectivity tests using the cloned viral genome confirmed its ability to infect apple and pear tree seedlings, but not Nicotiana benthamiana. The name "Temperate fruit decay-associated virus" (TFDaV) is proposed for this novel virus. Copyright © 2015. Published by Elsevier B.V.
    Virus Research 07/2015; 210. DOI:10.1016/j.virusres.2015.07.005 · 2.32 Impact Factor
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    • "Then, the domain structure of these CBPs was determined by searching against the Conserved Domains Database (http://www.ncbi.nlm. (Marchler-Bauer et al., 2011). "
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    ABSTRACT: In insects, chitin is a major structural component of the cuticle and the peritrophic membrane (PM). In nature, chitin is always associated with proteins among which chitin-binding proteins (CBPs) are the most important for forming, maintaining and regulating the functions of these extracellular structures. In this study, a genome-wide search for genes encoding proteins with ChtBD2-type (peritrophin A-type) chitin-binding domains (CBDs) was conducted. A total of 53 genes encoding 56 CBPs were identified, including 15 CPAP1s (cuticular proteins analogous to peritrophins with 1 CBD), 11 CPAP3s (CPAPs with 3 CBDs) and 17 PMPs (PM proteins) with a variable number of CBDs, which are structural components of cuticle or of the PM. CBDs were also identified in enzymes of chitin metabolism including 6 chitinases and 7 chitin deacetylases encoded by 6 and 5 genes, respectively. RNA-seq analysis confirmed that PMP and CPAP genes have differential spatial expression patterns. The expression of PMP genes is midgut-specific, while CPAP genes are widely expressed in different cuticle forming tissues. Phylogenetic analysis of CBDs of proteins in insects belonging to different orders revealed that CPAP1s from different species constitute a separate family with 16 different groups, including 6 new groups identified in this study. The CPAP3s are clustered into a separate family of 7 groups present in all insect orders. Altogether, they reveal that duplication events of CBDs in CPAP1s and CPAP3s occurred prior to the evolutionary radiation of insect species. In contrast to the CPAPs, all CBDs from individual PMPs are generally clustered and distinct from other PMPs in the same species in phylogenetic analyses, indicating that the duplication of CBDs in each of these PMPs occurred after divergence of insect species. Phylogenetic analysis of these three CBP families showed that the CBDs in CPAP1s form a clearly separate family, while those found in PMPs and CPAP3s were clustered together in the phylogenetic tree. For chitinases and chitin deacetylases, most of phylogenetic analysis performed with the CBD sequences resulted in similar clustering to the one obtained by using catalytic domain sequences alone, suggesting that CBDs were incorporated into these enzymes and evolved in tandem with the catalytic domains before the diversification of different insect orders. Based on these results, the evolution of CBDs in insect CBPs is discussed to provide a new insight into the CBD sequence structure and diversity, and their evolution and expression in insects.
    Insect Biochemistry and Molecular Biology 06/2015; 62:127-141. DOI:10.1016/j.ibmb.2014.12.002 · 3.45 Impact Factor
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