I am trying to find out existence of protein domains in a set of sequences. I am using BLASTX for the task. I have made a BLASTX of my sequences with the ProDom sequences. I used an e-value cutoff of 1e-3. What should be the identity percentage and the coverage percentage of the domain so that I can say that a protein domain or it's signature is present in a particular region?
Ex:
Identity percentage is 80% (80% of the amino acids in the aligned regions are identical)
Coverage 60% (The aligned length is 60% of the total length of the domain being compared to)
What other precautions and observations should I make while making such comparison?
Dear Ravi,
Identity and coverage are both important; however, within a given family the minimum required percentage of either is not high. On the contrary, a pair sequences that have very high identity/coverage diverge structurally. Thus, without structural data it is hard to judge. By and large this type of methods are heuristics. You can employ 3D data and perform structural comparison with DALI etc. to increase your accuracy. For analogs, structure is the most important aspect. As you seem to be identifying homologs, considering both type of similarity is necessary.
Best regards.
Dear Ravi, I agree with the previous answer that you need to be critical and use 3d structures for more accuracy. However, I dont know what the purpose of comparison is. If you are interrested in an evolutionary relationship it would be best to retrieve as much sequences and domains as possible, because this could increase the accuracy of the relation. Once you have established a clear relation, you can always filter out the unwanted data later on. If you just want to see how sequences and/or domains are arranged, you maybe as critical as you want, but keep in mind what you want to compare and what you want to know.
Good luck and if you need any more help please dont hesitate to contact me.
Kind regards,
René
If you want to check the domains in your seq. you can for start use Pfam. Just simply you are putting the the aa seq and you have quick answer.
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