Recognition of different nucleotide-binding sites in primary structures using a property-pattern approach.

Consensus sequence patterns for beta-alpha-beta folds binding FAD, NAD and GTP were constructed on the basis of 11 steric and physicochemical properties. These property patterns permit detection and distinction of the respective nucleotide-binding sites on the basis of amino acid sequence analysis alone. The SWISS-PROT database (release 9) was screened with the three calculated patterns, and nucleotide-binding sites identified are presented. They correspond to existing structure data (if known). For the detected sequence segments we are able to predict the beta-alpha-beta motif as well as the respective binding sites. For some of the proteins so detected a nucleotide-binding capacity has not previously been reported.