If a nucleotide query is used with a protein database, a translated search is performed. Each ORF in the nucleotide sequence is translated, and the resulting amino acid sequences are used to search the database. Translated searches are supported by most search commands. Metagenomic gene search with ublast is the most common use case.
Each ORF is an independent search, so termination conditions are applied separately. (Note that termination conditions are disabled by default in ublast). This is because a single nucleotide sequence may span more than one gene. The -orfstyle and -mincodons options control ORF identification.