PHP has a lot of built-in functions for interacting directly with mySQL should you wish. mysql_connect, mysql_query and so on. An abstraction layer would typically use these or similar functions to make the tasks of reading and writing data more straightforward. There are loads out there, and it's not a huge job to write your own either.
If you're talking about PHP-based database management options (something like SQL Server's enterprise manager for example) then PHP MyAdmin is a common choice, although it is lagging behind MySQL quite a bit at present. It's still perfectly serviceable for basic management and configuration, but doesn't go very far in terms of WYSIWYG.
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