49ers show they are far from perfect

After a great showing in Week 1, Colin Kaepernick and the 49ers were humbled Sunday in Seattle. Jonathan Ferrey/Getty Images

SEATTLE -- Four weeks after being humiliated in Seattle last season, the San Francisco 49ers advanced to the Super Bowl.

So, on the second football Sunday of September, it would be naive to present the Seattle Seahawks' 29-3 victory over the 49ers as the key to the season. It’s just too early.

Just like last December, the Seahawks crushed the 49ers in a matchup of two of the best teams in the NFL. In fact, the 49ers were ranked No. 1 in ESPN.com’s Power Rankings, while the Seahawks were a spot behind them. The Seahawks surely will take over the top spot and the 49ers will fall.

But for now, the only thing it means is the Seahawks are 2-0 and the 49ers, who were flat in this rivalry game after an emotional win over Green Bay to open the season, are 1-1. This win gives Seattle, which has now outscored the 49ers by a tally of 71-16 in the teams’ last two meetings, an early advantage in the NFC West. But the game would have had much larger and lingering aftershocks if the 49ers had stolen a game at CenturyLink Field. The Seahawks haven’t lost here since 2011.

In a game that was delayed exactly an hour late in the first quarter because of a lightning storm, the Seahawks waited and then did what they do -- they dominated at home. Now the season moves on, and the 49ers and Seahawks will more than likely be playing for something when they meet in San Francisco in Week 14.

While this Seattle statement doesn’t mean too much in the overall conference race, the 49ers do need to take stock. It was an awful night for them. This loss was as worrisome as the 34-28 win over Green Bay last weekend was promising. Things did not go well at all.

“I’m certainly not proud of the way that we played tonight or coached,” coach Jim Harbaugh said. “It was not our finest hour. ... We have to bounce back. We have to bounce back in a big way.”

Regrouping will start with quarterback Colin Kaepernick. Nearly flawless last week, Kaepernick struggled Sunday night against the Seahawks’ super-studded secondary. Kaepernick threw three interceptions and lost a fumble. A week after throwing for 412 yards, Kaepernick had only 127 yards through the air. His QBR was 14.0, the worst of his 12-start NFL career. His throws were off all night and he did not look comfortable, even before the weather delay.

Kaepernick did not shed blame.

“We're not going to win games if I play like that,” he said flatly.

The Seahawks took away the instant chemistry Kaepernick had built last week with receiver Anquan Boldin in his first game as a 49er, when Boldin had 13 catches for 208 yards. Against Seattle, Boldin had one catch for 7 yards. It came with the game well out of hand. Tight end Vernon Davis had three catches for 20 yards. Last week, he had six catches for 98 yards.

According to ESPN Stats & Information, Kaepernick did not complete a pass downfield of 15 yards or longer for the first time in his career. Last week, he had eight such completions. San Francisco's offensive line, which was brilliant against the Packers, sagged some at Seattle. Kaepernick was sacked three times and was under duress 13 of the 35 times he dropped back to pass.

The 49ers also were unable to establish their run game for the second straight week. Overall, it was a poor showing by one of the most dynamic offenses in the league.

“We didn’t execute, across the board,” Boldin said. “We just didn’t do what we were supposed to do.”

This loss is on the San Francisco offense much more than the defense. But the defense did allow Seattle tailback Marshawn Lynch to have a big day. Lynch, who had run for 100-plus yards in his previous three games against the 49ers, had 98 yards rushing, 37 receiving yards and three touchdowns (two rushing, one receiving).

Discipline was also an issue for San Francisco. The 49ers were called for four personal fouls. They had 12 penalties for 121 yards. In two games, the 49ers have a whopping 23 penalties.

In addition to all the mistakes and the lack of execution, the 49ers limped out of Seattle. Nose tackle Ian Williams broke his ankle. Rookie safety Eric Reid was being tested for a concussion. Davis left with a hamstring injury. And defensive end Ray McDonald sustained an ankle injury (X-rays were negative).

This night couldn’t have gone worse for San Francisco. It has to be disturbing, and it will be the cause for great self-evaluation inside the team facility in Santa Clara. But as last year’s Seattle disaster showed, a lopsided loss here doesn’t necessarily spell ultimate doom.