From Bioinformatics.Org Wiki
"Homology" is a much-misused term and existed in biology long before the notion of protein sequences. Strictly homology cannot be qualified; it is not correct to state that two proteins are "30% homologous" with each other, for example. If we could look back far enough in the evolutionary histories of any two molecules under comparison, we would be guaranteed to find a common ancestor eventually, but this is not true homology. An example of this would be the relationship between two variants of a single ancestral enzyme resulting from a gene duplication event.As a rule-of-thumb, true homology should be assigned only when the feature which leads us to suspect a relationship between molecules is one we consider likely to have derived from the molecules' common ancestor. To quote Page and Holmes [Molecular Evolution: A Phylogenetic Approac, Roderick D. M. Page and Edward C. Holmes; Blackwell Scientific; ISBN 0865428891]:
"The classic molecular example is the parallel evolution of amino acid sequences in the lysozyme enzyme in leaf-eating langur monkeys and in cows. Both animals have independently evolved foregut fermentation using bacteria, and in both cases lysozyme has been recruited to degrade these bacteria. Therefore, langur and cow lysozymes are homologous as genes; however, as digestive enzymes they are not homologous because this functionality was not present in the ancestral lysozyme"Although sequence determines structure, it is possible for two proteins to have very different sequences and functions and share a common fold. In fact, most gene products with similar three-dimensional structures are insufficiently similar at the sequence level for true homology or analogy (non-homologous similarity) to be distinguished.