"Alex Smith lost his starting job as quarterback of the 49ers, and now he's unlikely to be available in today's season opener because of soreness in his throwing shoulder.

During Friday's practice, Smith sustained what coach Mike Nolan described Saturday as "a non-contact injury" to his right shoulder. A club spokesman said Smith didn't feel any discomfort until after the practice, and Nolan wasn't aware of it when he talked to reporters Friday afternoon.

Smith told The Chronicle on Thursday that his shoulder felt fine, but earlier in the preseason, he said it wasn't 100 percent. He said he noticed a little difficulty on long throws and some fatigue after a large number of throws.

Saturday's announcement raises the possibility that his shoulder hasn't been right all along, but that he didn't want to disclose it in the heat of the quarterback competition.

He is expected to attend the game against the Arizona Cardinals at Candlestick Park but is listed as "doubtful." That leaves Shaun Hill as the backup to J.T. O'Sullivan, who unexpectedly beat out Smith and Hill for the No. 1 job in the preseason.

Running back Michael Robinson and wide receiver Arnaz Battle both played quarterback in college. One of them could be enlisted in an emergency.

Nolan said it wasn't known specifically what's wrong with Smith's shoulder or how soon he might return.

He said Smith would consult with orthopedic surgeon Dr. James Andrews in Birmingham, Ala. Andrews performed surgery on Smith's shoulder in December to re-attach two torn ligaments.

Smith has been considered the face of the franchise since being the top player picked in the 2005 draft. After last season, the club picked up a clause in his contract that triggered the last two years of the six-year, $49.5 million deal he signed in 2005.

At the time, general manager Scot McCloughan said the move "shows we have faith in him, that he's our guy. If we didn't think he was worth it, we wouldn't do it."

That faith slipped considerably in the preseason as Smith was outplayed by O'Sullivan in the new offense installed by Mike Martz.

Last week, McCloughan acknowledged that unless Smith were the clear-cut No. 1 quarterback, the 49ers could not afford to have him on the roster next year. He would make way too much money and put too much of a hit on the salary cap to return as a backup.

Next year, he is scheduled to make $9.625 million in base salary, but none of that is guaranteed. If the 49ers release him after this season, he would cost $5.3 million against the 2009 cap. If he were retained, the cap hit would be more than $12 million.

Smith has maintained that he thought he was a good fit in the Martz offense. Yet he struggled in the exhibition season, barely completing half of his passes (28 of 55). Playing mostly with second-string players, he threw two touchdowns and two interceptions.

Many of his throws, even ones that were caught, we