Plant LRR-RLKs structure
In plants, the leucine-rich repeat receptor-like protein kinases (LRR-RLKs) are composed of an extracellular LRR domain (ECD) responsible for ligand binding, a single membrane-spanning helix (TM), and a cytoplasmic kinase domain (KD). The extracellular LRR motifs share canonical plant specific LRR consensus sequences (CS): LxxLxLxxNxL(s/t)GxLPxxLGxLxx (x represents any amino acid), where the LxxLxLxxNxL(s/t)GxLP segments are the plant-specific LRR highly conserved segment (HCS).
The Phyto-LRR prediction program
Since the program is based on the position specific scoring matrix (PSSM) algorithm and its training dataset are 4000 LRR motifs HCSs from LRR-RLKs of 17 land plant species (Tab. 1), this plant LRR prediction program could identify plant LRRs effectively, especially for LRR motifs in plant LRR-RLKs. The program also has an offline version in the form of a python package, which has been published on PyPI: https://pypi.org/project/predict-phytolrr/.
The database of the plant LRR repeats
In this database, a total of 55457 LRR motifs were identified from 3987 LRR-RLK genes in 17 represented land plants (Tab. 1) using the "Phyto-LRR-predict" program, which is freely accessible at the Predict LRRs page. The sequence second structure and the soluble accessibility were obtained from the SSpro and ACCpro20 programs in the SCRATCH suite (Magnan CN & Baldi P., 2014). Moreover, since the ectodomains are heavily asparagine-linked (N-) glycosylated, the database also integrated with the predicted canonical N-glycosylation sites (Asn-x-Ser/Thr (x ≠ Pro)).
Table 1: Number of LRR-RLK genes in 17 represented land plants
|Species||Five Digit Code||Number of LRR-RLKs|
|Oryza sativa ssp. Indica||ORYSI||287|
|Oryza sativa ssp. Japonica||ORYSJ||281|