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Protein annotation HMMER #6

Open Ahmedbargheet opened 3 years ago

Ahmedbargheet commented 3 years ago

Hi everybody,

I am doing a functional metagenomic study. I did the annotation of protein sequences using HMMER against the Resfam database.

The question is how can I know that one of the predicted AR protein is a NOVEL??

Thanks

carden24 commented 3 years ago

Do a blast of your protein in ncbi and see the similarity there. Then you can also pick some known relatives and make a phylogenetic tree. In general you would need to have a complete protein to determine novelty, otherwise you may have regions with high similarity just because they share a domain. best of luck.

Ahmedbargheet commented 3 years ago

I mean I have a list of predicted resistance genes from the Resfam database which is responsible for antimicrobial resistance. Therefore, in my data, I have some genes that confer the resistance. How can I know if my data has a novel gene which responsible for antimicrobial resistance?

carden24 commented 3 years ago

ok. so I am reading your message again. So you have used the hmms from resfam against your metagenome and found some hits? if that is correct your results tell you that you have a sequence with high homology and from there you can assume that that gene provides resistance to antibiotics. If you want to know how new is your hit, you would need to run a blast search, or an aligment with references to calculate the similarity and determine the novelty. You can test the function experimentally by cloning the gene into a expression vector in E coli and see if it confers resistances.

If you have another type of protein that confers resistance but is not covered by the hmms, you would not see it in the results.

pd. this is my personal repository but I would be still happy to help