NCBI has been transitioning to Accession-Based BLAST. These changes will not affect your web BLAST searches unless you limit your search with the Entrez Query option. As of January 2019, the Entrez Query option is not available for searches against protein databases.
To continue limiting your searches with Entrez queries, please consider switching to BLAST+ (command-line tools). You will need to approach as follows:
1. Conduct your Entrez search independently from your BLAST search by using one of the following:
- Web search in the Protein database
- Entrez Programming Utilities (ESearch)
- EDirect
2. In all cases, download the results of your search as a list of accession numbers.
3. Use the accession lists in BLAST+ for Accession-Based BLAST with the following two commands -seqidlist or -negative_seqidlist.