Hi Ruan Qi,
Homology of two proteins can tell you a number of things which may help you with your research. For example, you are interested in a protein which nobody studied yet, comparing it with other proteins (i.e. on the amino acid level) will allow you to predict the function (in case if there is a close homology with a studied protein). There are many other applications which use homologues, from structural modelling to the use of Nested Primer PCR and so on...- please let me know if you need any further specific information. Good luck with your project!
It means the two proteins evolved from a common ancestor. Usually such proteins have recognizable similarity on sequence and structural levels, so similarity can be used as partial evidence for homology. Homologous proteins tend to carry out identical or similar functions, especially if they are orthologs - homologs resulting from a speciation event (as opposed to paralogs resulting from gene/genome duplication).
Dear Qi,
The question you asked it is not simple as it looks. When you aligns two sequences, you are facing a lot of challenges. To avoid bias, you have to check sequence of the protein against set of sequences, which is done by BLAST server. This alignment gives better results.
So, the answer of any question depends on the properly stated question. What was the purpose of the alignment? Are you looking for similarities or differences? Are you looking for possible function of your protein? Are you looking for possible 3D structure reconstruction using results of the alignment?
In general, if sequences match 75% and higher, then proteins have the same function. They belong to the same protein family but from different species. Usually, with this level of match in sequences (> 75%), one should expect similar 3D structures.
If sequences match 50%-75%, we are talking about similar function, but not necessary identical.
If sequences are less than 30% identical, we are talking about unrelated proteins. Not similar at all.
But one has to be careful with assumptions. It highly depends on each case. Just one example from my experience. I solved structure of protein using a model with only 26% of identity. And it worked because the protein belongs to antigen-like proteins. These proteins have very similar fold, but purely could be aligned by sequence. Which means, just alignment of sequences would not work in this case.
In the case of solving 3D structures, the sequence alignment is the best starting point to search for 3D homologous model. For the functional studies sequence alignment is very good starting point for looking possible function, active site residues.
So, in general
more than 75% - identical
40% - 60% - similar
less than 30% - not related
But as I said there are exemptions.
Hope this helps.
George.
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