Over-annotation of hypothetical ORFs is a common phenomenon in bacte-rial genomes, which necessitates confirming the coding reliability of hypo-thetical ORFs and then predicting their functions. The important plant pathogenErwinia carotovorasubsp. atrosepticaSCRI1043 (Eca1043) is a typical case because more than a quarter of its annotated ORFs are hypo-thetical.