This gene was not amplified by using the primers that amplified the genes in other members of group Y. Surprisingly a small portion (almost 50 %) of this gene was amplified by using primers of same synthase gene present in other genus (Pseudomonas). When blast tool used this gene showed homology as (E value= 5e-141, Query coverage=84% and identity 87%) with the synthase gene of Pseudomonas. According to my knowledge, the full genome has not been published of this Bacillus spp X and its synthase gene have never been amplified as well. Definitely, the gene is present in this bacterium X. How can I justify blast results?
Horizontal gene transfer can occur between bacteria from different genus...maybe this is the case for this one
I would design new primers eventually degenerate primers based on the sequences available from genbank - as this gene seems to be variable.
The primers that I used for bacillus spp were already degenerate. As the same primers are working for the others members of the group.
Did you use the primers for 16s rDNA? I think you can isolate this region and blast it against the microbial 16s rDNA database. This will give you a short and clear answer, I hope.
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