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Plant-PrAS (Plant-Protein Annotation Suite) is a database of physicochemical and structural properties, and novel functional region in plant proteomes.
Motivation

The amount of annotation information such as gene-coding regions and structures is steadily growing in the field of plant research. In contrast to the genomics resource of animals and microorganisms, there are still some difficulties with characterization of some gene functions in the plant genomics studies. Acquisition of information on protein structure can help to elucidate the corresponding gene function because proteins encoded in the genome possess highly specific structures and functions. Thus, we calculated multiple physicochemical and secondary structural parameters of protein sequences, using protein sequences from the genomes of six representative plant species.

Resources

The target plant species in the Plant-PrAS database are Arabidopsis[link] (dicotyledoneae:brassicaceae Arabidopsis thaliana), soybean[link] (dicotyledoneae:leguminosae Glycine max), poplar[link] (dicotyledoneae:poplar Populus trichocarpa), rice (MSU)[link], rice (RAP)[link] (monocotyledoneae:rice Oryza sativa), moss[link] (moss Physcomitrella patens) and algae[link](algae Cyanidioschyzon merolae). Their filtered proteomes contained 26,326; 34,972; 35,791; 40,087; 35,908; 30,654 and 4,595 non-redundant amino acid sequences, correspondingly. The mouse[link] (Mus musculus) and yeast[link] (Saccharomyces cerevisiae) datasets, containing 20,572 and 6,216 sequences, respectively, were used as the reference proteomes.

Calculation data

We carried out the calculation and prediction of physicochemical parameters (Length, Charged, Nonpolar, Acidic, Basic, Low complexity, GRAVY and pI), secondary structural properties (Solvent accessibility, β sheet, Intrinsically disordered regions, Signal peptide cleavage sites, Transmembrane helices, S-S bond and Domain linker), functional annotation (Pfam, Uniprot-plant, Uniprot-sprot, EC number, PDB and KOG), functional region (PASS and Rosetta stone proteins) and others (Ubiquitylation site, N-glycosylation site, O-glycosylation and Subcellular location, Protein solubility).

Related Papers

Kurotani A. et al. Plant-PrAS: A database of physicochemical and structural properties and novel functional regions in plant proteomes. Plant and Cell Physiology 56(1):e11(1–9) doi: 10.1093/pcp/pcu176 (2015) [PubMed][Link]

Kurotani A. et al. Alga-PrAS (Algal Protein Annotation Suite): A Database of Comprehensive Annotation in Algal Proteomes. Plant and Cell Physiology 0(0):e6(1–13). doi: 10.1093/pcp/pcw212 (2017) [PubMed][Link]

Kurotani A. and Sakurai T. In silico analysis of correlations between protein disorder and post-translational modifications in algae. Int J Mol Sci. 20;16(8):19812-35. doi: 10.3390/ijms160819812. (2015) [PubMed][Link]

Kurotani A. et al. Correlations between predicted protein disorder and post-translational modifications in plants. Bioinformatics 30(8):1095-1103. doi: 10.1093/bioinformatics/btt762 (2014) [PubMed][Link]

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