Significant Segment Alignment of Pairs of Protein Sequences from Animals, Plants and Fungi

Abstract

A new method for scoring pairwise similarities between protein sequences (SSPA, Significant Segment Pair Alignment) is applied to assess similarities between groups of animals, plants, and fungi for a large number of protein families. At variance with the recent view that animals are closer to fungi than to plants, SSPA similarities between these groups produce variant associations with respect to different proteins. A case in point concerns calmodulin, where different species of fungi do not consistently cluster with animals or plants. The Transcription Factor IID provides an example of a protein where clustering of plants with fungi is predominant Ambiguities in species evolutionary relationships based on protein sequence comparisons are discussed.