The success of genome sequencing has resulted in many protein sequences without functional annotation. We present ConFunc, an automated Gene Ontology (GO)-based protein function prediction approach, which uses conserved residues to generate sequence profiles to infer function. ConFunc split sets of sequences identified by PSI-BLAST into sub-alignments according to their GO annotations. Conserved residues are identified for each GO term sub-alignment for which a position specific scoring matrix is generated. This combination of steps produces a set of feature (GO annotation) derived profiles from which protein function is predicted.