The subject sequence of bacteriocin obtained at GenBank can be compared for its similarities to the reference sequences of bacteriocins in Bagel. You can upload your fast a file, select the genome from the list provided and then run it.

You will have similar sequences.

thank you dr for replying but if i have a sequence for strains by 16s RNA from gen bank can i use it for searching of bacteriocin

Dear friend,

The 16S rRNA gene sequences are used only in the phylogenetic study of an organism. The rRNA gene sequences can be searched for its similarities at any gene database for example: GenBank of NCBI.

The bagel is for the database for amino acid sequences of bacterocins. So, in bagel, you can search the amino acid sequence of your bacterocin for its similarities to the bacterocins in the database.

A similar kind of database for bacterocin is Bactibase as well.

With regards,

Dr A K Dubey

You can also try to use AntiSMASH for bacterial secondary metabolite.! This method is codded to predict not only the structural bacteriocin genes, but also will predict the sites of leader-mature peptide cleavage by protease. Moreover, different predictions of the MW of the peptide will be given based on possible Ser/Thr and C-terminal modifications.

https://antismash.secondarymetabolites.org/#!/start