hypothetical proteins

Genes are either (i) homologous to genes of unknown function, and are typically referred to as “conserved hypothetical” genes, or (ii) do not have any known homologs termed“hypothetical” or “non characterized” or “unknown” because it is unclear whether they encode actual proteins. Since it is often unclear whether they encode actual proteins, the latter genes are commonly referred to as“hypothetical”, “uncharacterized”, or “unknown” proteins.

approaches developed for predicting protein function:
sequence similarity
phylogenetic profiles
protein-protein interactions
protein complexes
gene expression profiles

Classical way to infer function is based on sequence similarity using sequence database searching programs such as FASTA and PSI-BLAST.

Lack of sequence similarity in the database to the protein of interest creates difficulties for functional predictions. However, examples of dissimilar function for similar proteins are also available.

Approaches to predict protein fucntion by in silico methods are discussed HERE

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891709/