how to find an ortholog of a protein of interest from a full genome sequence of a bacteria?

Question

[researcher]

hi I am a newbie trying to find a ortholog of a protein that I am interested in from a full genome sequence of a bacteria. I tried this and that (BLAST, etc) but could not figure out how to do this. could anyone help me?

I have a protein, I know the sequence of couple ortholog of the protein from different bacterial strains. I have a full genome sequence of a bacteria where I am trying to find the ortholog of the protein I am interested in.

any help is appreciated. Thanks alot!

[kamel]

you can use also orthofinder or orthomcl...for that

Answer 1

[h.mon]

Quick and dirty method:

1. If the genome you have is not annotated, annotate it (locally with Prokka, or remotely with RAST).

2. Create a blast database with the predicted proteins.

3. Blast the "couple ortholog of the protein" against this blast database, find the best high similarity hits.