Please check :
/usr/sbin/mysqld, Version: 5.5.47-cll (MySQL Community Server (GPL)). started with:
Tcp port: 0 Unix socket: (null)
Time Id Command Argument
# Time: 160118 22:49:36
# User@Host: isalna[isalna] @ localhost []
# Query_time: 14.236989 Lock_time: 0.000025 Rows_sent: 2214 Rows_examined: 2214
SET timestamp=1453153776;
SELECT * FROM `isalna_isalna`.`qa_blobs`;
# Time: 160118 22:49:57
# User@Host: isalna[isalna] @ localhost []
# Query_time: 20.314002 Lock_time: 0.000025 Rows_sent: 257394 Rows_examined: 257394
SET timestamp=1453153797;
SELECT * FROM `isalna_isalna`.`qa_contentwords`;
# Time: 160118 22:51:33
# User@Host: isalna[isalna] @ localhost []
# Query_time: 89.548527 Lock_time: 0.000021 Rows_sent: 697562 Rows_examined: 697562
SET timestamp=1453153893;
SELECT * FROM `isalna_isalna`.`qa_eventlog`;
# Time: 160118 22:52:11
# User@Host: isalna[isalna] @ localhost []
# Query_time: 32.867167 Lock_time: 0.000019 Rows_sent: 150772 Rows_examined: 150772
SET timestamp=1453153931;
SELECT * FROM `isalna_isalna`.`qa_posts`;
# Time: 160118 22:52:43
# User@Host: isalna[isalna] @ localhost []
# Query_time: 31.306731 Lock_time: 0.000022 Rows_sent: 487888 Rows_examined: 487888
SET timestamp=1453153963;
SELECT * FROM `isalna_isalna`.`qa_sharedevents`;
# Time: 160118 22:52:57
# User@Host: isalna[isalna] @ localhost []
# Query_time: 13.837871 Lock_time: 0.000026 Rows_sent: 725838 Rows_examined: 725838
SET timestamp=1453153977;
SELECT * FROM `isalna_isalna`.`qa_titlewords`;
Each of these queries is not indexed and is taking even as high as 89 seconds to execute.