Low similarity gene alignment

Question

[Hsiangnan Cheng]

Hi all,

I have a ammonia monooxygenase subunit A(amoA) sequence from an autotrophic ammonia oxidizer and several heterotrophic ammonia oxidizer draft genome.

How can I find potential amoA in heterotrophic oxidizer genomes by using this autotrophic amoA gene? I guess the similarity of amoA between autotrophic and heterotrophic is quite low, lower than 40%.

Thanks for any help

[Dunois]

Sounds like you're looking for remote homologs. Have you taken a look at what HH-suite has to offer?

Answer 1

[Carlo Yague]

The standard way to do this is to BLAST the amoA gene against the genomes of interest. Because proteins sequences are usually more conserved than the gene sequences, you might have more luck with protein BLAST than with BLASTN.