As we described in a previous post, this means they now contain the GI-less proteins from the NCBI Pathogen Project and other high-throughput projects. The v5 databases are also compatible with proteins from PDB structures with multi-character chain identifiers and will include these as they become available in our other protein systems. Only the latest version of BLAST+ (2.9.0, download) will work with the updated v5 databases and allow you to access all of the most recent protein and nucleotide data. In the winter of 2019, we will stop updating the version 4 BLAST databases and offer the v5 databases as the default for download.
In addition, makeblastdb will be updated in BLAST 2.10.0, due out in October 2019, so by default it creates dbV5 formatted databases.