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How does sequence similarity provide clues about the function of an unknown gene?

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Computer-generated model of anthrax toxin showing seven differently colored protein units, with a small gold molecule representing a drug bound to the protein structure. — bioinformatics This computerized image of anthrax shows the various structural relationships of seven units within the protein and demonstrates the interaction of a drug (shown in yellow) bound to the protein to block the so-called lethal factor unit. Bioinformatics plays an important role in enabling scientists to predict where a drug molecule will bind within a protein, given the individual structures of the molecules.

In bioinformatics, sequence similarity serves as a primary method for inferring the function of an unknown gene by comparing its sequence to those of genes with known functions.12

When a researcher identifies a new gene—often by locating an open reading frame (ORF) within a genome—they compare its sequence against databases of previously characterized genes from various organisms. If the unknown gene shares significant sequence similarity with a known gene, researchers can assign a putative function to the unknown gene based on this homology.2

This process is further refined by identifying specific functional domains within the sequence. For example:3
* Conserved Domains: Certain amino acid sequences are consistently associated with specific biological roles. If an unknown gene contains a sequence known to be a transmembrane domain, it suggests the encoded protein is likely located in the cell membrane.3
* Functional Motifs: Other sequences may characterize specific activities, such as DNA-binding, allowing scientists to predict the protein's behavior even if the entire gene has not been previously studied.3

By leveraging these patterns of conservation, bioinformatics tools help bridge the gap between raw genomic data and biological understanding.12