I give you samples from slow-query-log.
mysql version:5.6.14, 8gb server 6gb free memory, innodb tables
for example: id is primary key when I type this query in phpmyadmin is very fast but its still in my slow query log
# Query_time: 3.226675 Lock_time: 0.000046 Rows_sent: 0 Rows_examined: 1
SET timestamp=1385980918;
update `rsslists` set `lastTimeRead` = '1385980913', `total` = '66502', `quality` = '0.028284863613124' where `id` = '146';
or this query:
# Query_time: 2.284815 Lock_time: 0.000047 Rows_sent: 0 Rows_examined: 0
SET timestamp=1385980935;
select * from `articles` where `guid` = '1.2180130' limit 1;
explain:
'guid' is index really simple queries I have no ideas why they taking so long time sometimes
If these tables are huge and have multiple indexes, the insert can be quite slow. You should log all your queries and see how other inserts perform.
As for the select, there should be an index on guid, otherwise it will be slow if it is a large table.