How to Subset a Custom BLAST Database for Specific Genes of Interest?

Question

[samuel.himes]

I have a local copy of the NR protein database to run blastp. I'm interested in analyzing a specific subset of prokaryotic genes. I've already extracted prokaryotic proteins from the NR database using the following steps:

1. Extracting proteins from bacteria and archaea taxids:

blastdbcmd -db nr -taxids 2,2157 -dbtype prot -out prokaryote_sequences.fasta

2. Creating a BLAST database from the extracted sequences:

makeblastdb -in prokaryote_sequences.fasta -dbtype prot -out nr_prok

Now, I need to further subset this database to include only specific genes of interest, such as rpoB. However, I suspect that a simple grep on the FASTA headers won't be sufficient because not all rpoB sequences might have "rpoB" in their headers.

My Question:

What is the best way to filter my custom BLAST database to include only the proteins of specific genes like rpoB?

[GenoMax]

You could blast with the gene of interest against this custom DB and then extract the ID's you need as fasta to create another subset database.