Find out why mysql is very slow

I have a VPS with apache, mysql and PHP installed with out-of-the-box configuration. There seems to be a problem with mysql - it's incredibly slow. Single update query takes 0.50s to complete. Disk I/O is good: 1073741824 bytes (1.1 GB) copied, 14.207 s, 75.6 MB/s and php performance is also very good - a test script completes in 5 seconds, whereas it takes my Intel i7 SSD windows machine 17s to complete it . So I guess it's related to mysql setup and configuration. When I run the query through my windows command line (my local server) I get this: Query OK, 1 row affected (0.01 sec) Rows matched: 1 Changed: 1 Warnings: 0 Whereas when it is run on the VPS server, it's like this: Query OK, 0 rows affected (0.55 sec) Your job would be to find and eliminate the problem.