NCBI has been transitioning to Accession-Based BLAST. During this process we are converting the traditional (GI-based) BLAST databases into the accession-based databases. We will continue updating the traditional databases along with the new databases for some time. Eventually, we will cease updating the traditional databases. We also plan to entirely remove these databases in the fall of 2019.
If you are a BLAST+ (command-line tools) user, you can still (as of January 2019) use the traditional databases (the BLAST+ v2.8.1 executables are backward compatible). However, we urge all users to update to the accession-based databases as soon as your time permits.
To stay informed about the changes, please pay attention to our postings on the NCBI Insights blog, BLAST Mailing list, and social media (NCBI Twitter Feed or NCBI Facebook Page). We will inform you when we stop updating the traditional databases. We will post the announcement about the removal of the traditional databases three months ahead of time.