Detection of weak sequence homology of proteins for tertiary structure prediction

Multiple measures of similarity were employed to detect weak homologies among protein sequences (e.g., below 30% residue identity). A set of thresholds was empirically determined, by using sample proteins of known structure, so as to select only correct pairs of sequences; correct or incorrect alignment of sequences was judged by direct comparison of corresponding conformations. The empirical criterion thus set up is applicable to the prediction of a protein structure when the structure of the other protein in the pair is known. We searched all the combinations between 84 proteins of known structure and 4610 proteins stored in a sequence database, and found about 4000 pairs of sequences which satisfied the criterion. However, after excluding such pairs of proteins that belong to the same family or superfamily, the number of pairs remaining was reduced to only 19. The reliability of these data for structural prediction is discussed.