Abstract
A combination of multiple protein classification methods is described and used to identify a minimum set of 54 candidate seven transmembrane receptors in Arabidopsis thaliana.
Highlights
Seven-transmembrane (7TM)-region containing proteins constitute the largest receptor superfamily in vertebrates and other metazoans
Generating robust multiple alignments is difficult or impossible when extremely diverged sequences are included in the analysis; 7TM receptors (7TMRs) are one such protein family whose sequence similarities between subgroups can be lower than 25%
To reduce the number of false positives as well as false negatives (7TMRs predicted as non-7TMRs) and to obtain a set of 7TM putative receptors (7TMpRs) candidates with higher confidence, we examined combinations of the prediction results by the remaining six alignment-free methods (LDA, QDA, KNN with K = 20, support vector machines (SVMs)-AA, SVM-di, and partial least squares (PLS)-auto/cross covariance (ACC))
Summary
Seven-transmembrane (7TM)-region containing proteins constitute the largest receptor superfamily in vertebrates and other metazoans. These cell-surface receptors are activated by a diverse array of ligands, and are involved in various signaling processes, such as cell proliferation, neurotransmission, metabolism, smell, taste, and vision. They are the central players in eukaryotic signal transduction. They are commonly referred to as G protein-coupled receptors (GPCRs) because most transduce extracellular signals into cellular physiological responses through the activation of heterotrimeric guanine nucleotide binding proteins (G proteins) [1]. For precision and clarity, we refer to these proteins as 7TM receptors (7TMRs), and candidate proteins in organisms greatly divergent to humans are designated here as 7TM putative receptors (7TMpRs)
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