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Niners Humbled by Rout

  • San Francisco 49ers quarterback Colin Kaepernick (7) watches his fumbled ball bounce away as Seattle Seahawks' Cliff Avril eyes it as well in the first half of an NFL football game, Sunday, Sept. 15, 2013, in Seattle. The Seahawks recovered the ball on the play. (AP Photo/Elaine Thompson)

    San Francisco 49ers quarterback Colin Kaepernick (7) watches his fumbled ball bounce away as Seattle Seahawks' Cliff Avril eyes it as well in the first half of an NFL football game, Sunday, Sept. 15, 2013, in Seattle. The Seahawks recovered the ball on the play. (AP Photo/Elaine Thompson)

  • Seattle Seahawks quarterback Russell Wilson (3) passes against the defense of San Francisco 49ers inside linebacker Patrick Willis (52) in the second half of an NFL football game, Sunday, Sept. 15, 2013, in Seattle. (AP Photo/Elaine Thompson)

    Seattle Seahawks quarterback Russell Wilson (3) passes against the defense of San Francisco 49ers inside linebacker Patrick Willis (52) in the second half of an NFL football game, Sunday, Sept. 15, 2013, in Seattle. (AP Photo/Elaine Thompson)

  • San Francisco 49ers quarterback Colin Kaepernick (7) watches his fumbled ball bounce away as Seattle Seahawks' Cliff Avril eyes it as well in the first half of an NFL football game, Sunday, Sept. 15, 2013, in Seattle. The Seahawks recovered the ball on the play. (AP Photo/Elaine Thompson)
  • Seattle Seahawks quarterback Russell Wilson (3) passes against the defense of San Francisco 49ers inside linebacker Patrick Willis (52) in the second half of an NFL football game, Sunday, Sept. 15, 2013, in Seattle. (AP Photo/Elaine Thompson)

Santa Clara, Calif. — The San Francisco 49ers are reeling in more ways than the obvious one: a rash of injuries to key players.

While the NFC West champions sustained several injuries during Sunday night’s 29-3 road defeat at the hands of division rival Seattle, including the expected season-ending ankle injury for nose tackle Ian Williams, the 49ers’ offense is left with many questions after quarterback Colin Kaepernick’s worst performance yet as a pro.

“They got nothing done. What were their numbers? What did Anquan (Boldin) do tonight?” Seahawks coach Pete Carroll said afterward. “Their quarterback threw for (412) last week. He threw for (127) tonight.”

The team had five turnovers and no touchdowns for just the third time since 1979, and had more turnovers than points for the first time since former quarterback Alex Smith’s first start as the No. 1 overall pick in 2005 — a 28-3 loss to the Colts on Oct. 9 that year.

Arizona and Tampa Bay were the only teams last year to have five turnovers and no TDs.

Jim Harbaugh was asked Monday whether he felt disbelief after taking such a lopsided loss a week after such an impressive season-opening victory against Green Bay.

“Not to stack up any, compare any other game in all the years that we’ve played or watched football,” Harbaugh said. “We were there; we had some chances. There were some missed opportunities and some momentum plays that went against us. Now, that’s on us as coaches, players. That’s also a credit to Seattle.”

Williams is expected to be sidelined for the remainder of the season with a broken left ankle. He was undergoing surgery Monday. Williams was injured in the first quarter of his first career start.

The third-year pro earned the job as the replacement for the departed Isaac Sopoaga with a strong offseason and training camp.

Williams was blocked low by J.R. Sweezy near the left knee during a 2-yard run by Marshawn Lynch and Williams flew up upon impact. Williams was down on the field for a few minutes before being helped off by a pair of trainers.

Veteran Glenn Dorsey will take over the position. Defensive tackle Ray McDonald sustained an ankle injury in the fourth quarter but Harbaugh provided no update for him.

San Francisco is left with little depth on the defensive line. Lamar Divens and Will Tukuafu were waived injured and thus can’t be re-signed until later in the season. Defensive tackles Quinton Dial and Tank Carradine won’t be available until after Week 6 because they are on the reserve/non-football injury list.

Rookie free safety Eric Reid was undergoing tests following his concussion, but Harbaugh said he wasn’t experiencing symptoms Monday. Tight end Vernon Davis was having his injured hamstring examined Monday, Harbaugh said.

San Francisco (1-1) must regroup to face another team with a top quarterback — Harbaugh’s former Stanford QB Andrew Luck — when the Indianapolis Colts (1-1) come to Candlestick Park on Sunday looking to bounce back from their home loss to Miami.

The 49ers have committed 23 penalties in two games for 206 lost yards, 12 of those for 121 yards against the Seahawks. They were flagged for two personal fouls and an unsportsmanlike conduct penalty in the fourth quarter.

Harbaugh realizes those kinds of mistakes and mental miscues must be cleaned up in a hurry with a tough stretch in a daunting schedule still ahead. After this week, the 49ers go to St. Louis, then return home to host the Houston Texans.

“It’s an obvious area that we need to improve on and hopefully we’ll see significant improvements this week in that,” Harbaugh said. “That’s something we’ll zero in on, yes.”

The 49ers had more penalty yards than yards rushing (100).

“Any time you get a lot of penalties, especially one after another, they can cost you the game,” Davis said. “So we really have to think about those things next game and get them corrected, because you can’t have those because they can cost you the game and possibly cost us the season.”