Computational protocol: Time-Resolved Investigation of Molecular Components Involved in the Induction of NO3– High Affinity Transport System in Maize Roots

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Protocol publication

[…] Putative maize PM H+-ATPases were primarily identified on the basis of amino acid sequence similarity with the PM H+-ATPase of Nicotiana plumbaginifolia Viv., Oryza sativa L., Arabidopsis thaliana (L.) Heynh. (), Vitis vinifera (), and Fragaria vesca (). The amino acid sequences were obtained from public databases1,, (The Arabidopsis Information Resource (TAIR), MSU) and the relative accession numbers were reported in Supplementary Table . Putative maize PM H+-ATPases were identified through BLASTP () research using the MaizeSequence.org. BLASTP analysis was carried out using each known protein and selecting the putative maize proteins on the basis of the highest sequence homology value (≥80%). A phylogenetic analysis was carried out using the selected maize proteins encoding for putative members of PM H+-ATPase family. Protein sequences of the previously mentioned dicot and monocot plant species were aligned by the ClustalW ver. 2.1 algorithm. Phylogenetic tree was produced using the Phylogenetic Interference Package program (PHYLIP; University of Washington) and visualized by the FigTree ver. 1.4.2 software. […]

Pipeline specifications

Software tools BLASTP, Clustal W, PHYLIP, FigTree
Databases TAIR
Application Phylogenetics