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Here I propose four requirements for establishing adaptive parallel evolution at the protein sequence level and use these criteria to demonstrate such a case.
Early comparative bioinformatics analysis has suggested a limited role for AS in plants in terms of functional expansion of the proteome35,36,37; only a small number of AS events have conserved effects at the protein sequence level in Arabidopsis and rice37.
Phylogenetic analysis of ComA homologues at the protein sequence level again separated these into three main groups (Fig. 2).
In this study we have identified nine nucleotide sequences in the genome of A. fumigatus Af293 that contain all sequence hallmarks that, at the protein sequence level, are typical for Type I BVMOs.
However, instances of convergent evolution at the protein sequence level are rare.
As they become established in the molecular repertoire, do duplicated genes adaptively differentiate at the protein sequence level, or are differences primarily regulatory?
At the protein sequence level it is apparent that there has been conservation of amino acids at many sites within each ortholog [4].
For variants at the UniProt protein sequence level, we looked up BLOSUM62 [32] to get the substitution score for a corresponding variant.
These long ORFs were then pairwise aligned to assess for possible homology at the protein sequence level using BlastP program of BLAST package [29].
Humans and chimpanzees are almost identical at the protein sequence level; hence, it has been hypothesized that most of the phenotypic differences are caused by the regulation of gene expression [4].
Thus, despite differences at the protein sequence level, HSF4 and HSF1 are strongly conserved at the DNA-binding domain level and are therefore likely to bind to similar regulatory sequences on the DNA [9].
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