Here's some info on the Danube from the O.R.'s:

"Report of operations for the defense of Mobile, Ala., for the month of January, 1863.
ENGINEER BUREAU,
Mobile, Ala., March 11, 1863.
Ship Danube - This ship being liable to be destroyed by shells thrown low or high, it has been thought best to place her four guns (42-pounders) in the battery last named, unless additional guns can be procured. She is anchored at the Apalachee Battery and is available for service."

So, due to the date, this cannot be the large ironclad built on the Tombigbee. It still could be one of the others.

"Monthly report of operations for the defense of Mobile, Ala., during the month of October, 1864.
ENGINEER OFFiCE,
Mobile, November 3, 1864.
Conway Bayou — Two rows of piling have to be planted; scuttles to be opened on the exposed side of the ship Danube, when she will be raised and placed at the Spanish River gap in the upper lint of obstructions, ready to be sunk when ordered."

So the plan was to scuttle the Danube as an obstruction.

"ENGINEER OFFICE,
Mobile, Ala., November 27, 1864.
Weekly report of operations for the defense of Mobile, Ala., during the week ending November 26, 1864.
Conway Creek.—There are about fifty more piles to be driven and about fifty to be followed down, which, when done, will complete the obstruction proposed there. The ship Danube has settled considerably, her ports being now below water."

And, so it was sunk.

According to a communication from the Octora on Aril 3, 1965, it appears that the Danube was still a sunken obstruction.