There are difference explain in SELECT query and UPDATE query.

"id"	"select_type"	"table"	"type"	"possible_keys"	"key"	"key_len"	"ref"	"rows"	"Extra"

"1"	"SIMPLE"	"TB_LI_GERP_SEW_SHIP"	"range"	"TB_LI_GERP_SEW_SHIP_N04,TB_LI_GERP_SEW_SHIP_N05,TB_LI_GERP_SEW_SHIP_N02,TB_LI_GERP_SEW_SHIP_N07,TB_LI_GERP_SEW_SHIP_N01,TB_LI_GERP_SEW_SHIP_N06,TB_LI_GERP_SEW_SHIP_N08,TB_LI_GERP_SEW_SHIP_N09,TB_LI_GERP_SEW_SHIP_N11,TB_LI_GERP_SEW_SHIP_N12,TB_LI_GERP_SEW_SHIP_N13,TB_LI_GERP_SEW_SHIP_N15"	"TB_LI_GERP_SEW_SHIP_N06"	"110"	\N	"1"	"Using where"

explain

UPDATE /* AllocationExportShip.updateSEWShip */ 

 	TB_LI_GERP_SEW_SHIP

   SET PRCS_STATUS = 'Y'

     , PRCS_MESSAGE = 'SUCCESS'

     , LAST_UPDATE_DATE = NOW()

     , LAST_UPDATE_USER_ID = 'PG_LD_GERP_DAILYOUT3'

 WHERE CORP_TYPE =  'LGEKR'

   AND DC_CD = 'F01'

   AND PRCS_STATUS IN ('N','E')

   AND PG_YMD = '2016-10-20 00:00:00.0'

   AND CONTAINER_NO = 'ZCSU8646091'

   AND INTERFACE_ID = '1651217'

"id"	"select_type"	"table"	"type"	"possible_keys"	"key"	"key_len"	"ref"	"rows"	"Extra"

"1"	"SIMPLE"	"TB_LI_GERP_SEW_SHIP"	"ref"	"TB_LI_GERP_SEW_SHIP_N04,TB_LI_GERP_SEW_SHIP_N05,TB_LI_GERP_SEW_SHIP_N02,TB_LI_GERP_SEW_SHIP_N07,TB_LI_GERP_SEW_SHIP_N01,TB_LI_GERP_SEW_SHIP_N06,TB_LI_GERP_SEW_SHIP_N08,TB_LI_GERP_SEW_SHIP_N09,TB_LI_GERP_SEW_SHIP_N11,TB_LI_GERP_SEW_SHIP_N12,TB_LI_GERP_SEW_SHIP_N13,TB_LI_GERP_SEW_SHIP_N15"	"TB_LI_GERP_SEW_SHIP_N06"	"110"	"const,const,const,const,const"	"1"	"Using index condition; Using where"

explain  

select * from TB_LI_GERP_SEW_SHIP

 WHERE CORP_TYPE =  'LGEKR'

   AND DC_CD = 'F01'

   AND PRCS_STATUS IN ('N','E')

   AND PG_YMD = '2016-10-20 00:00:00.0'

   AND CONTAINER_NO = 'ZCSU8646091'

   AND INTERFACE_ID = '1651217'

"id"	"select_type"	"table"	"type"	"possible_keys"	"key"	"key_len"	"ref"	"rows"	"Extra"

"1"	"PRIMARY"	"<derived2>"	"ALL"	\N	\N	\N	\N	"2"	""

"1"	"PRIMARY"	"B"	"eq_ref"	"PRIMARY"	"PRIMARY"	"4"	"A.pk_id"	"1"	""

"2"	"DERIVED"	"TB_LI_GERP_SEW_SHIP"	"ref"	"TB_LI_GERP_SEW_SHIP_N04,TB_LI_GERP_SEW_SHIP_N05,TB_LI_GERP_SEW_SHIP_N02,TB_LI_GERP_SEW_SHIP_N07,TB_LI_GERP_SEW_SHIP_N01,TB_LI_GERP_SEW_SHIP_N06,TB_LI_GERP_SEW_SHIP_N08,TB_LI_GERP_SEW_SHIP_N09,TB_LI_GERP_SEW_SHIP_N11,TB_LI_GERP_SEW_SHIP_N12,TB_LI_GERP_SEW_SHIP_N13,TB_LI_GERP_SEW_SHIP_N15"	"TB_LI_GERP_SEW_SHIP_N06"	"110"	"const,const,const,const,const"	"1"	"Using where"

EXPLAIN

UPDATE

	(

	SELECT CORP_TYPE, DC_CD, PG_YMD, CONTAINER_NO, INTERFACE_ID, PRCS_STATUS, pk_id

	FROM TB_LI_GERP_SEW_SHIP

	 WHERE CORP_TYPE =  'LGEKR'

	   AND DC_CD = 'F01'

	   AND PRCS_STATUS IN ('N','E')

	   AND PG_YMD = '2016-10-20 00:00:00.0'

	   AND CONTAINER_NO = 'ZCSU8646091'

	   AND INTERFACE_ID = '1651217'

	) A 

JOIN TB_LI_GERP_SEW_SHIP B ON (A.pk_id=B.pk_id)

SET B.PRCS_STATUS = 'Y'

     , B.PRCS_MESSAGE = 'SUCCESS'

     , B.LAST_UPDATE_DATE = NOW()

     , B.LAST_UPDATE_USER_ID = 'PG_LD_GERP_DAILYOUT3'

;