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I have a new sequence and I want to add it to a pre-constructed BLAST database containing other sequences. The makeblastdb help does not give any hint on this regard.

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You can use blastdbcmd to extract FASTA sequences from the BLAST database. Then you can append your extra sequence to the newly created FASTA file, and remake the BLAST DB using makeblastdb. Assuming you have a protein BLAST database in the current working directory, and a sequence you want to add to it in new.fa:

$ blastdbcmd -db proteindb -dbtype prot -out db.fa -entry all
    $ cat new.fa >> db.fa
$ makeblastdb -in db.fa -out newproteindb -dbtype prot

(Replace prot with nucl if you have a nucleotide database)

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You may create a new database with the new sequences and create an alias linking the old and new databases with blastdb_aliastool

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