CAIRO, Jan 26 (Reuters) - The death toll from clashes during protests in Egypt on Saturday rose to 49, the Health Ministry said on Sunday, in violence that erupted on the third anniversary of the popular uprising which toppled autocrat Hosni Mubarak.

Nearly 250 people were wounded in Cairo and several other provinces, the ministry said.

While thousands rallied in support of army chief General Abdel Fattah al-Sisi, who overthrewEgypt's first democratically elected president in July, others protested against the military-backed government, underscoring deep and persistent divisions.

The Interior Ministry said in a statement on Sunday that it had arrested 1,079 "rioters" in possession of rifles, petrol bombs, fireworks, and other weapons. It said that a number of policemen were injured in clashes.

Egypt has been gripped by political upheaval and street violence since Mubarak's was ousted. (Reporting by Maggie Fick; Editing by Louise Ireland)