SANTA CLARA – Vernon Davis has to retake chemistry.

The 49ers tight end said that the rapport he established with former starting quarterback Alex Smith was years in the making. Now Davis, who has just four catches in the last four games, has to do the same with Colin Kaepernick.

"We don't have it," Davis said of the quarterback-receiver chemistry. "You have to expect (that because) he just stepped in. Me and Alex – we've been there. It takes time. It took time for me and Alex to get like that.

"It's like it's starting all over again, especially for me."

Davis has built a strong relationship with Smith, highlighted by his prolific postseason last January in which he had four touchdowns – including the game winner against New Orleans – and 292 yards in two games.

Davis called their rapport the "11-85 connection" in 2010, and he was Smith's most vocal defender when then-coach Mike Singletary lost faith in the quarterback later that year.

Davis' struggles this season, however, began when Smith still was the starter. He was held without a catch in a Week 7 game against Seattle and had fewer than 50 yards receiving in four other games that Smith started and finished.

In contrast, Kaepernick's first start, on Nov. 19 against the Bears, was one of Davis' best outings of the year. He had a season-high six catches for 83 yards and a touchdown, and he said after the game that he felt as if someone had taken the handcuffs off him.

But his receiving statistics have been meager in the four games since, and he was shut out again during a Week 12 win against New Orleans.

Kaepernick threw two passes to Davis at the goal line against the New England Patriots on Sunday, but both sailed just beyond his reach. Whether Davis could have stretched for the first of those attempts is debatable.

Asked about those opportunities, Davis said, "I get chills when I think about it."

Davis said Kaepernick might have too much respect for his speed.

"In practice, he would overthrow me," Davis said. "I think he's just kind of scared on my speed a little bit. He doesn't really know it. We don't have that timing. It'll come. Just like any quarterback and any wide receiver. It takes time. … That's what makes football that much more interesting and fun."

Other 49ers receivers have said they've had to adjust to the velocity of Kaepernick's passes. He had the strongest arm of anyone in the 2011 draft – including No. 1 overall draft pick Cam Newton – and it's certainly more powerful than Smith's.

Said Davis: "He's strong. I heard rumors of him wanting to get bigger. I said, 'Noooo, noooo. No need to get bigger.' "

Another 49ers tight end has been more involved in the offense since Kaepernick became the starter. Delanie Walker had seven catches and a touchdown in the nine games Smith started; he has eight catches and a touchdown in Kaepernick's five starts.

Back in the saddle – Coach Jim Harbaugh sounded optimistic Tuesday that defensive end Justin Smith, who left Sunday's game in the third quarter with an arm injury, would be able to practice this week.

"Well, you know his nickname is Cowboy," Harbaugh said on KNBR. "Everybody affectionately refers to Justin Smith around here as the Cowboy. So, I expect we'll see the Cowboy. Knowing what I know of Justin Smith and the situation, yeah, I think the Cowboy's going to be saddled up. … Ropin' and ridin'! … If it's humanly possible, the Cowboy will be out there ropin' and ridin'."

Smith tried to return in the fourth quarter Sunday but could not. An MRI on Monday showed that the injury would not keep the 12-year veteran out long term. Smith has started 185 consecutive games, dating to 2001.

© Copyright The Sacramento Bee. All rights reserved.

• Read more articles by Matthew Barrows

Order Reprint