Here, by sequence alignment analyses of the human KCNQ1 channel and scorpion potassium channel MmKv2, which is completely insensitive to scorpion toxins, we proposed that the insensitivity mechanism of KCNQ1 toward natural scorpion toxins might involve two functional regions, the turret and filter regions.
For the Zygnematophyceaen alignment analyses, the TrN + I + G model was chosen; for the Spirogyra alignment the GTR + I + G was chosen by Modeltest.
If needed, identified peptides were subjected to a protein similarity search performed by alignment analyses against the NCBI-nr database using the FASTS algorithm http://fasta.bioch.virginia.edu/fasta_www2/[ 55].edu/fasta_www2/[
If needed, identified peptides were used in protein similarity search performed by alignment analyses against the NCBI-nr database using the FASTS algorithm [ 98].
The conservative motifs among AP2/ERF proteins in plants were clarified by performing multiple alignment analyses using amino acid sequences of the AP2/ERF domain.
The conservative motifs among AP2/ERF proteins in plants were clarified by conducting multiple alignment analyses using amino acid sequences of the AP2/ERF domain.
Gaps introduced by the alignment were excluded from phylogenetic analyses.
DNA alignment analyses were conducted by using ClustalW version 1.83 (www.ebi.ac.uk/clustalw), and nucleotide substitutions were identified by using BioEdit version 7.0.1 (Isis Pharmaceuticals, Inc., Carlsbad, CA, USA) (7 ).
To exclude the potential alignment ambiguity from the analyses, nucleotide positions that contained one or more gaps introduced by the alignment were omitted from the matrix.
If analyses start generating an alignment (phylogenetic footprinting), the result, i.e. statements about homology on the sequence level, given by the alignment, may be of low quality.
