San Francisco 49ers

Colin Kaepernick getting more comfortable in 49ers’ offense and in his own skin

Colin Kaepernick scrambles against Tampa Bay on Oct. 23. He has led the 49ers in rushing in three of his four starts.
Colin Kaepernick scrambles against Tampa Bay on Oct. 23. He has led the 49ers in rushing in three of his four starts. pkitagaki@sacbee.com

“I remember being up a lot and having them come rushing back. It was a great feeling to go up there, get that victory, especially against a team like that.”

Those are Colin Kaepernick’s recollections of the last time the 49ers played the New England Patriots, a 41-34 roller-coaster win in Foxborough, Mass., in 2012 and the first time Kaepernick knocked off one of the NFL’s elite teams.

Four years later, the Patriots remain at the top, and the 49ers are near the bottom. And Kaepernick? He’s somewhere in the middle but seemingly rising again.

The 49ers are winless in his four starts, but his performance has steadily improved as he becomes more comfortable in coach Chip Kelly’s system and in his own skin. He said Tuesday he’s finally back to full strength – and top speed – after recovering from surgeries to his shoulder, knee and thumb.

Kaepernick has been the team’s leading rusher in three of the last four games and, despite a limited number of starts, his 228 rushing yards rank fourth among NFL quarterbacks. Against the Arizona Cardinals’ top-ranked defense Sunday, he continually got around the edge for positive yards and, perhaps for the first time in three years, looked like the quarterback who always pressured defenses with his feet during his 2012 debut as the 49ers’ starter.

“I feel like I’m starting to get some of my wiggle back, some of the movement, starting to feel very comfortable with where my health is, how my body’s moving, those things,” Kaepernick said.

He also is just now getting up to speed with Kelly’s offense after missing most of the spring practices as well as a chunk of training camp and the preseason. He’s been well-versed in the playbook throughout the year, but he said he has a deeper understanding of Kelly’s philosophy after playing in four games.

For example, he said he now knows why certain plays are called.

“If you do it and don’t know the intention of why you’re doing it, you really don’t have a purpose,” he said. “You don’t understand why you’re doing what you’re doing. So having that complete understanding of, ‘We’re calling this play to try to get this done,’ is very helpful. It helps you get through progressions quicker and also helps you play with a clear mind.”

That progress has been reflected in his passer rating: 66.2 in his first two starts and 96.8 in his last two.

“He’s improving with his reads,” offensive coordinator Curtis Modkins said. “He’s improving with handling the offense, getting us in and out of plays. He’s done a good job of extending plays. I think he’s getting his legs. He’s strong. He’s running when he needs to.”

Of course, there’s still plenty to improve upon. Kaepernick has completed only 53.0 percent of his throws, which ranks 40th among quarterbacks with at least 50 passing attempts this year and is well below even Blaine Gabbert’s 58.0 percent over the first five weeks of the season.

Meanwhile, the 49ers are at risk of losing their ninth consecutive game – the Patriots are 12 1/2 -point favorites despite being on the road – a skid the franchise hasn’t had since 1978.

A win Sunday? Kaepernick said the effect would be a lot like the one he and his team experienced when they beat New England four years ago.

“It was huge and it was another confidence builder for our team, for myself at that point in time, that we were playing one of the best teams in the league … ,” he said. “So I think we have a similar opportunity this week to play a very good Patriots team and go out and get a victory.”

Matt Barrows: @mattbarrows, read more about the team at sacbee.com/sf49ers.

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