Article

CDD: a Conserved Domain Database for the functional annotation of proteins.

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: 8.81). 01/2011; 39(Database issue):D225-9.
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 http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.

0 Bookmarks
 · 
351 Views
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Flavonoids are secondary metabolites that are present at high levels in the Polugonum minus. In recent years, flavonoids have attracted the interest of researchers because of their antioxidant properties .Flavonoids are synthesised via the condensation of 4 coumaryl-CoA and 3 malonyl-CoA by the action of Chalcone synthase. A cDNA encoding a chalcone synthase was isolated from the leaves of Polygonum minus by rapid amplification of cDNA ends (RACE) and designated pmCHS (GenBank accession no. JQ801338). The full-length cDNA of P. minus pmCHS was 1472 bp with a 1179 bp open reading frame (ORF) that corresponded to a predicted protein of 392 amino acid deduced protein. In silico analysis showed that the calculated molecular weight and theoretical isoelectric point (pI) of pmCHS were 43.1 kDa and 5.78, respectively. Several important motifs, such as the product binding site, active site and dimer interface, were also successfully identified from the deduced amino acid sequence. Multiple sequence alignment indicated that the pmCHS sequence was highly conserved and shared high sequence identity (>90%) with chalcone synthases from other plants. Gene expression analysis via qRT-PCR showed that pmCHS was most highly expressed in the roots, showing a 10-fold increase compared to leaves and a 15-fold increase compared to stems . The specific mechanism underlying the high expression of pmCHS in the roots requires further investigation.
    Australian Journal of Crop Science 01/2013; 7(6):777-783. · 1.63 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Transglutaminases (E.C. 2.3.2.13) catalyze the post-translational modification of proteins by establishing ε-(γ-glutamyl) lysine isopeptide bonds and by the covalent conjugation of polyamines to endo-glutamyl residues of proteins. In light of the confirmed role of transglutaminases in animal cell apoptosis and only limited information on the role of these enzymes in plant senescence, we decided to investigate the activity of chloroplast transglutaminases (ChlTGases) and the fate of chloroplast-associated polyamines in Hordeum vulgare L. 'Nagrad' leaves, where the senescence process was induced by darkness (day 0) and continued until chloroplast degradation (day 12). Using an anti-TGase antibody, we detected on a subcellular level, the ChlTGases that were associated with destacked/degraded thylakoid membranes, and beginning on day 5, were also found in the stroma. Colorimetric and radiometric assays revealed during senescence an increase in ChlTGases enzymatic activity. The MS/MS identification of plastid proteins conjugated with exogenous polyamines had shown that the ChlTGases are engaged in the post-translational modification of proteins involved in photosystem organization, stress response, and oxidation processes. We also computationally identified the cDNA of Hv-Png1-like, a barley homologue of the Arabidopsis AtPng1 gene. Its mRNA level was raised from days 3 to 10, indicating that transcriptional regulation controls the activity of barley ChlTGases. Together, the presented results deepen our knowledge of the mechanisms of the events happened in dark-induced senescence of barley leaves that might be activation of plastid transglutaminases.
    Amino Acids 01/2015; · 3.65 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Citrobacter freundii is an opportunistic pathogen responsible for many urinary tract infections acquired in hospitals and is thus a concern for public health. C. freundii phage Stevie might prove beneficial as a treatment against these infections. The complete genome of Stevie and its key features are described here. FOOTNOTES Address correspondence to Gabriel F. Kuty Everett, gabbyeverett{at}tamu.edu. J.P.S., C.A.A.M., and Y.C. are co-first authors. Citation Shaw JP, Aviles Medina CA, Chen Y, Luna AJ, Hernandez AC, Kuty Everett GF. 2015. Complete genome of Citrobacter freundii siphophage Stevie. Genome Announc 3(1):e01434-14. doi:10.1128/genomeA.01434-14. Received 2 December 2014. Accepted 18 December 2014. Published 5 February 2015. Copyright © 2015 Shaw et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
    Genome Announcements 02/2015; 3(1).

Full-text (2 Sources)

Download
63 Downloads
Available from
May 28, 2014