Best Practice where TLS related files are stored on a Linux OS?

I'm diving head first into TLS with java based applications, using commands like Keystore and Keytool, which I'm using to generate .pem and .jks files.

On Linux based systems, are these files stored typically under /etc/pki? Or is there a best practice? To me, it seems there isn't consistent documentation when it comes to generating, storing and managing these files.

thanks