If you wish to run an alternative SSH agent (e.g. ssh-agent or gpg-agent, you need to disable the ssh component of GNOME Keyring. To do so in an account-local way, copy /etc/xdg/autostart/gnome-keyring-ssh.desktop to ~/.config/autostart and then append the line Hidden=true to the copied file. Then log out.
Source: https://wiki.archlinux.org/index.php/GNOME/Keyring#Disable_keyring_daemon_components