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SELECT 
  feature_id 
FROM 
  cscart_product_features 
  INNER JOIN cscart_ult_objects_sharing ON (
    cscart_ult_objects_sharing.share_object_id = cscart_product_features.feature_id 
    AND cscart_ult_objects_sharing.share_company_id = 1 
    AND cscart_ult_objects_sharing.share_object_type = 'product_features'
  ) 
WHERE 
  feature_id IN (549, 548) 
  AND feature_type = 'E'

Query time 0.00049

Explain
id	select_type	table	type	possible_keys	key	key_len	ref	rows	Extra
1	SIMPLE	cscart_product_features	range	PRIMARY	PRIMARY	3		2	Using index condition; Using where
1	SIMPLE	cscart_ult_objects_sharing	eq_ref	PRIMARY	PRIMARY	159	cscart_dev_4_16.cscart_product_features.feature_id,const,const	1	Using where; Using index