Example of annotation of a hypothetical protein using GeneOrder4.0. A row displaying computed paired similar proteins from the tabular output of GeneOrder4.0. The first column shows a protein belonging to Rhodococcus opacus and the second column shows a protein belonging to Methylobacterium nodulans. This match is a function of the default or user-entered threshold discrimination score, reflected in the third column, which shows the BLAT score. The fourth column indicates, by the presence of a "*", whether either of the proteins are annotated as hypothetical. Numbers in front of the links are the protein numbers, designated in numerical order from its Genbank entry, in the genome. By clicking the (underlined) links, GenBank files are displayed showing that the Rhodococcus opacus protein in the first column is annotated as hypothetical, while the Methylobacterium nodulans protein in the second column is annotated as a beta-lactamase domain protein.