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Probably, the easiest way to encrypt MySQL database in Ubuntu is by using ecryptfs-utils. Install ecryptfs-utils:

apt-get install ecryptfs-utils

Mount /usr/local/encrypted directory and create mdf directory for MySQL data files (you will be prompted for passphrase and other options):

mkdir /usr/local/encrypted
mount -t ecryptfs /usr/local/encrypted /usr/local/encrypted
cd /usr/local/encrypted
mkdir mdf
chug.sh mysql mdf
chmod og-rwx mdf

chug.sh is a bash script that changes user and group by calling chown and chgrp:

chown -R $1 $2
chgrp -R $1 $2

Copy all MySQL data files to encrypted directory:

service mysql stop
cp -R -p /var/lib/mysql /usr/local/encrypted/mdf

Then change datadir in /etc/mysql/my.cnf:

#datadir         = /var/lib/mysql
datadir         = /usr/local/encrypted/mdf

and start MySQL:

service mysql start

The final step is encrypting of the swap.

All database backups should be placed in /usr/local/encrypted/backup directory.

Disabling MySQL and Nginx autostart:

update-rc.d -f mysql disable
update-rc.d -f nginx disable