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Low similarity gene alignment

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

analysis align gene
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updated by Dunois • Dunois • written by Hsiangnan Cheng • Hsiangnan Cheng

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

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written by Dunois • Dunois

1 answer

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.

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written by Carlo Yague Carlo Yague

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