My new first objective is to annotate domains of a selected member of protein family, here named Member_1 to clarify. So seems I have to retrieve all homologs for Member_1 in the database , then run corresponding tool to annotate domains.
Query is Member_1. Some caveats are:
-Gene might have nucleotide variations what has implications for a BLAST strategy
-Gene is a member of large protein family, so I need to be accurate
Since I know up- and down-stream genes for Member_1, I thought about:
-finding 5', Member_1 and 3' genes in target genomes.
-print nucleotide sequence of Member_1 targets, including 5' and 3' genes
-for each retrieved sequence, predict protein domains.
Here you can see the 13 members of the family (paralogs):