Alex SmithThe San Francisco 49ers placed quarterback Alex Smith on injured reserve with a fractured throwing shoulder. Smith will miss the entire season.

What’s been known since Saturday night is that Smith has a fracture in the same shoulder that was badly separated last year. The results of the MRI have been examined by Dr. James Andrews, the orthopedic surgeon who operated on Smith’s shoulder in December. Presumably it was Andrews’ recommendation that prompted the 49ers to put Smith on IR. Smith has said that surgery is an option for the latest injury.

Smith’s future with the team also is dubious. Last week Scot McCloughan said that the team couldn’t afford to keep Smith next season if he is not a starter. Smith is scheduled to earn just under $10 million in base salary in 2009.

It’s kind of ironic that the same week Aaron Rodgers successfully made his debut in Green Bay, Alex Smith appears finished in San Francisco. The top two quarterbacks from the 2005 NFL Draft are heading in different directions and before this season, it looked like Rodgers was the one whose career was in flux. If J.T. O’Sullivan strings together a decent season, we’ll see how the 49ers handle the situation with Smith.