Database of Supergene Family

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(1) For each of three protein families involved in cell adhesion, six protein families involved in signal transduction, ras-related GTP binding protein family, and other six protein families, the amino acid sequences were aligned among members, and the consensus sequence and weighted motifs of highly conserved segments were determined based on the alignment. phylogenetic trees representing branching orders of family members in evolution were also inferred. These data were included in our database of supergene family.(2) A new method was developed to search sequences in database that show significant similarities with motifs of known family members : In this method a score system was introduced representing the frequency of occurrence of an amino acid on each amino acid position of the motif. On the basis of the score system, a statistical test was carried out for the observed sequence similarity.(3) Applying the above method to three protein families involved in cell adhesion, we found sequence similarities between trk and immunoglobulin family members, between ret and cadherin family members, and between several tyrosine kinases and fibronectin type III family members.(4) From the above results, we showed that known receptor type protein tyrosine kinases are classified into at least four groups, based on the structural differences of the extracellular domains. This classification in almost parallel to that based on a phylogenetic tree inferred from a sequence comparison of the kinase domains.