Finding homologous genes in different bacteria serovars from reference locus

Question

[alejoaguirrea]

Dear all,

I'm trying to perform a comparison of a specific locus for some bacteria strains of two different serovars. On NCBI I can find the locus sequence in fasta format. However, I don't know how can I extract this locus in fasta format from the whole genomes of the strains I'm studying. How can I do this? On top of this, which tool can I use to identify the ORFs in this locus sequences and annotate them with known proteins or potential functions? I plan to perform an alignment of the whole locus and each ORF independently, to see how strains group differently depending on the ORF that's considered.

Thank you for your help