SANTA CLARA, Calif. - Alex Smith's season is over with another shoulder injury. The high-priced quarterback's short career with the San Francisco 49ers is probably finished as well.

In this Aug. 8, 2008, file photo San Francisco 49ers quarterback Alex Smith throws a pass during a preseason football game against the Oakland Raiders in Oakland, Calif. The San Francisco 49ers put Smith on injured reserve Wednesday, Sept. 10, 2008, with a broken bone in his right shoulder, probably ending the former No. 1 draft pick's disappointing four-year career with the club. (AP Photo/Tony Avelar)

The 49ers put Smith on injured reserve Wednesday with a broken bone in his right shoulder. The top pick in the 2005 draft probably will require more surgery on the joint that limited him to seven games last season.

Coach Mike Nolan improbably claimed to know little about the injury that ended his former franchise quarterback's fourth NFL campaign before Smith even played in a regular-season game this fall. Smith's teammates expressed more concern than their gruff coach over his latest injury, which popped up during the club's final practice before last week's season opener.

"I feel sorry for him," said running back Frank Gore, the Niners' third-round pick in Smith's draft. "He was a great teammate and worked hard. I just hope the best for him, and hope he gets well."

After paying Smith more than $31 million during his four years with the 49ers, the bleak realities of NFL salary cap life mean the club is likely to release him before next season. General manager Scot McCloughan said last week that San Francisco can't risk paying $9 million in base salary to a backup quarterback in 2009.

Smith lost his starting job to journeyman J.T. O'Sullivan in training camp.

"I'm not going to answer any hypothetical questions about the future," said Nolan, who had an embarrassing public spat with Smith last year over the severity of the quarterback's shoulder injury. "We'll cross that bridge when we get there. My focus right now is on (Sunday's game against) Seattle."

Smith refused to comment after practice, and didn't respond to an additional request for comment Wednesday afternoon.

Smith had surgery on his shoulder in December to repair three torn ligaments, the product of a separated shoulder from a game in late September 2007. He attempted to play through pain after the injury, but obviously struggled in all three games, culminating in an awful effort in a 24-0 loss at Seattle.

"I thought he wasn't ready to go," said Seahawks linebacker Julian Peterson, Smith's former teammate in San Francisco. "I thought he just tried to tough it out for the team, and it really wasn't a smart move for the team and for himself. He tried to do it for the team, and wasn't really ready."

After several months of rehabilitation, Smith appeared to be at full strength in training camp despite losing his job to O'Sullivan, who was quicker to pick up new offensive coordinator Mike Martz's system. But Smith experienced severe pain in his shoulder last Friday while making a long throw during practice, and subsequent tests found a significant problem.

Dr. James Andrews, who performed Smith's last surgery, apparently confirmed the team's diagnosis of a broken bone in Smith's shoulder, though the quarterback and the team still don't know how it happened.

The 49ers signed 38-year-old Jamie Martin, a veteran of Martz's system who was out of football, to back up O'Sullivan and Shaun Hill.

"He worked so hard to get back, and then to have this happen to him now is so unfortunate," said Hill, who backed up Smith along with Trent Dilfer for the past two seasons. "Obviously, it's not an easy thing for him. Even last year, Trent and I were excited for what he was going to do. ... I don't think he's a bust at all. Injuries hampered him."

Smith passed for 4,679 yards with 31 interceptions and 19 touchdowns in his first three seasons with the 49ers, who selected the former Utah star with the first draft pick of Nolan's regime. He left the Utes one year early to capitalize on the excitement of their undefeated season under coach Urban Meyer, and he was rewarded with $24 million in guaranteed money as the No. 1 pick in a notoriously weak draft with no clear-cut top selections.

Smith went 11-19 as a starter, never finding a consistent NFL groove while playing for four offensive coordinators in four seasons and throwing to one of the league's worst collections of receivers. San Francisco's offense finished last in the NFL in 2005 and 2007, with Smith receiving a share of the blame even though he played only part of his rookie season and missed most of 10 games last year.

In 2006, his only full season as a starter, Smith took every snap and posted respectable numbers for offensive coordinator Norv Turner while the 49ers went 7-9. Turner then left to become San Diego's head coach.