Blasting two protein sequences vs two nucleotide sequences

Question

[Abeer]

Hi, I am trying to hunt some toxin genes in my genomes. I used antismash to look for the secondary metabolites region and tried annotating my contig with reference sequence. blasting the two sequences, I get no similarity in nucleotide sequences but somewhat similarity when blasting protien sequences. Is this possible? I am new to metagenomics, any advice related to this problem will be great.

Answer 1

[Istvan Albert]

There are various versions of blast, that search in translated spaces, see blastx and tblastn

https://blast.ncbi.nlm.nih.gov/Blast.cgi

in addition note that blast command have many parameter settings and many scoring matrices, and those will also greatly affect the the results you are getting