The first thing that I'd do is rewrite the subqueries as joins:
SELECT h.alert_master_id
FROM alert_appln_header h
JOIN schedule_config c
ON c.schedule_name = 'Purging_Config'
LEFT JOIN alert_details d
ON d.alert_master_id = h.alert_master_id
AND d.end_date IS NULL
AND d.created_date < CURRENT_DATE - INTERVAL c.parameters DAY
LEFT JOIN (
alert_sara_header s
JOIN alert_sara_lines l
ON l.alert_sara_master_id = s.sara_master_id
)
ON s.alert_master_id = h.alert_master_id
AND s.end_date IS NULL
AND s.created_date < CURRENT_DATE - INTERVAL c.parameters DAY
WHERE h.created_date < CURRENT_DATE - INTERVAL c.parameters DAY
AND d.alert_master_id IS NULL
AND s.alert_master_id IS NULL
GROUP BY h.alert_master_id
LIMIT 5000
If it's still slow after that, re-examine your indexing strategy. I'd suggest indexes over:
alert_appln_header(alert_master_id,created_date)
schedule_config(schedule_name)
alert_details(alert_master_id,end_date,created_date)
alert_sara_header(sara_master_id,alert_master_id,end_date,created_date)
alert_sara_lines(alert_sara_master_id)