Page "Protein structure prediction" Paragraph 16

In considering protein classification schemes, it is important to keep several observations in mind.

First, two entirely different protein sequences from different evolutionary origins may fold into a similar structure.

Conversely, the sequence of an ancient gene for a given structure may have diverged considerably in different species while at the same time maintaining the same basic structural features.

Recognizing any remaining sequence similarity in such cases may be a very difficult task.

Second, two proteins that share a significant degree of sequence similarity either with each other or with a third sequence also share an evolutionary origin and should share some structural features also.

However, gene duplication and genetic rearrangements during evolution may give rise to new gene copies, which can then evolve into proteins with new function and structure.