Sequencing of several genomes has resulted in numerous predicted open reading frames to which functions cannot be readily assigned.
The real evidences for the hypothetical protein functioning in the metabolism of the organism can be predicted by comparing its sequence or structure homology by considering the conserved domain analysis.
Hypothetical proteins are created by gene prediction software during genome analysis.
When the bioinformatic tool used for the gene identification finds a large open reading frame without a characterised homologue in the protein database, it returns "hypothetical protein" as an annotation remark.
The function of a hypothetical protein can be predicted by domain homology searches with various confidence levels.