Trial to Determine Identity of Proteins by Motifs.

Seto, Y.[1]
Ikeuchi, Y.[1]
Kawakita, S.[2]
Nishikawa, K.[2]
Kanehisa, M.[3]

[1]Protein Res. Found.
[2]Protein Eng. Res. Inst.
[3]Kyoto Univ.


We propose a semi-automatic method to classify protein seqeunces into superfamilies. The method is a combination of the global sequence homology search and the local sequence identifier. The former is performed by a pairwise homology search method developed by Nishikawa et al(2), which jointed five different measures to improve sensitivity for detecting seqeunce similarity. The latter is done by applying the fragment peptide library(FRAP) compiled by Seto et al(3). We evaluate our method by applying it to 89 superfamilies in the PIR database.

Out of 89 superfamilies, 65 superfamilies are classified by the combination method. We find that 20 superfamilies are multi-superfamilies: Different superfamilies belong to a same group by our criteria. We find difficulty to classify 4 superfamilies.