The kinase gatekeepers were determined by performing a multiple sequence alignment on the kinases using MEGA version 5 [54], using the default parameters (Protein Weight Matrix: Gonnet, Gap Open penalty: 10, Gap Extension penalty: 0.20 and Gap Distances: 5).
The default parameters for gap open penalty, gap extension penalty, and perform fft were used (1.53, 0.12, "localpair").
The standard parameters (Protein Gap open penalty: 10.0; Gap Extension penalty: 0.2; Protein matrix: Gonnet; Protein ENDGAP: -1 and GAPDIST: 4) were used for the entire analysis.
Current sequence alignment methods typically score pairwise alignments with an affine gap scoring scheme consisting of a gap open penalty and a gap extend penalty.
HCEs were aligned against genomes using BLASTn with non-stringent parameters (mismatch penalty −1, gap open penalty 1, word size 9, and soft masking).
Phylograms were first built with a default parameter (DNA Gap Open Penalty = 15.0, DNA Gap Extension Penalty = 6.66, DNA Matrix = Identity, Protein Gap Open Penalty = 10.0, Protein Gap Extension Penalty = 0.2, Protein Matrix = Gonnet, Protein/DNA ENDGAP = −1, Protein/DNA GAPDIST = 4).
In the first method, we first aligned P with the promoter region of G's ortholog in species S (rhesus or mouse) using the Needleman-Wunsch algorithm (gap open penalty = 10 and gap extension penalty = 0.5).
The selected sequences were analyzed using the ClustalW program (with DNA identity matrix, gap open penalty of 15, gap extension penalty of 6.66, gap separation penalty of 4 with no end gaps).
A gap open penalty of 6 and a gap extension penalty of 0.2 were used.
Amino acid sequences were aligned with ClustalW [ 39] (gap open penalty: 100; gap extension penalty: 0.2).
Gap open penalty: 12. Gap extension penalty: 3. Alignment type: Global alignment with free end gaps.
