Arabidopsis thaliana, L.

Costa, Laura S. M., Allan, Pires, S., Damaceno, Neila B., Rigueiras, Pietra O., Maximiano, Mariana R., Franco, Octavio L. & Porto, William F., 2020, In silico characterization of class II plant defensins from Arabidopsis thaliana, Phytochemistry (112511) 179, pp. 1-8 : 2

publication ID

https://doi.org/ 10.1016/j.phytochem.2020.112511

DOI

https://doi.org/10.5281/zenodo.8301829

persistent identifier

https://treatment.plazi.org/id/442187AF-FFCC-FFD2-2869-F8D5FA520388

treatment provided by

Felipe

scientific name

Arabidopsis thaliana
status

 

2.1. The majority of A. thaliana View in CoL View at ENA defensins belongs to class I defensins

In order to identify class II defensin sequences, we designed a semiautomatic pipeline ( Fig. 1 View Fig ). For that, initially all proteins from the A. thaliana Uniprot database were downloaded. The dataset consisted of 86,486 sequences (March 2017). From this dataset, 387 sequences were retrieved by using regular expression (RegEx) search (step 2, Fig. 1 View Fig ). From these, 285 had up to 130 amino acid residues (step 3, Fig. 1 View Fig ). This criterion allows eventual larger C-terminal prodomains to be identified. Then, we used a PERL script to select the sequences with the following flags: hypothetical, unknown, unnamed and/or uncharacterized (step 4, Fig. 1 View Fig ), resulting in 15 sequences. From 15 sequences, seven were incomplete and therefore were discarded, (step 5, Fig. 1 View Fig ). From the remaining sequences, two sequences without signal peptide or with transmembrane domains were discarded (step 6, Fig. 1 View Fig ). Finally, from six remaining sequences, two sequences with a potential C-Terminal prodomain were selected, with accession codes A7 REG2 About REG and A7 REG4 About REG .

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