One of my queries on MySQL 5.0.45 is running slow in \"sending data\" phase. The query is a simple select, returns about 300 integer ID fields as result set.
Your query spends 2.127019 to execute the query. This is probably because you have a large amount of data, and your are missing an index on the destination_id column. Try :
CREATE INDEX index_destination_id ON directions (destination_id);