In biochemistry, a hypothetical protein is a protein whose existence has been predicted, but for which there is no experimental evidence that it is expressed in vivo. Nowadays, most protein sequences are inferred from computational analysis of genomic DNA sequence. 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. Conserved domains are available in the hypothetical proteins which need to be compared with the known family domains by which hypothetical protein could be classified into particular protein families even though they have not been in vivo investigated.
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