SANTA CLARA – For the last few months, Colin Kaepernick had been eager to get on the field with his new coach.

For the last few months, Jim Harbaugh had been equally keen to get on the field with his new quarterback.

Finally, Kaepernick and Harbaugh came together Friday at the 49ers' facility on the first day of training camp. Both liked what they saw.

"Colin did some really good things – he made some fantastic throws," Harbaugh said. "Those were big-league throws. To come in on the first day and take snaps with a starting professional football team on the offensive unit, there's some remarkability in that."

Kaepernick is in the unusual situation of being a rookie quarterback who will get almost all the repetitions through the first six days of practice. Although Alex Smith has re-signed with the 49ers, because of oddities in the new collective bargaining agreement, Smith can't practice until Thursday.

So Kaepernick – a product of Pitman High School in Turlock – is the 49ers' de facto starting quarterback, at least for the next week. Friday, Smith, in shorts and sneakers, stood behind the line of scrimmage and participated in the offensive huddle. But Kaepernick was the lead man.

"I feel very lucky," he said. "I think it will really help my learning curve and help me pick up the offense a lot better. Even at the start of practice, everything was a little fuzzy. By the end of practice, I know what I'm doing. We're playing football out here."

It has been a long wait to play football. Kaepernick – the Nevada quarterback whom the 49ers moved up to draft in the second round – has spent the offseason and lockout studying the playbook and attending informal camps at San Jose State arranged by Smith.

He wasn't allowed to speak to Harbaugh or any of the 49ers' staff.

The advantage of those "Camp Alex" sessions was apparent.

"It's obvious they were a great benefit," Harbaugh said. "To come out on Day One, for me to go into the huddle and call a play with a quarterback and have him turn to the offense and repeat the play, that just doesn't happen on Day One."

Many NFL scouts passed on Kaepernick, thinking his running style, body type and throwing motion wouldn't work in the NFL. Kaepernick has taken those doubts as motivation.

He said he's working on his footwork and getting more comfortable. He knows he won't run as much at the NFL level. Harbaugh has said he won't change Kaepernick's throwing motion.

Kaepernick said his main priority Friday was establishing his presence.

"The biggest thing is just getting in the huddle and having that confidence and leading the team," he said. "As a young player, you have to go in there and show everybody that confidence, that I might be young, but I can still step in there and play."

Kaepernick said he was rewarded with positive feedback from his teammates, although Patrick Willis said the rookie quarterback owes him an interception since the linebacker didn't pick off a pass.

Harbaugh was hired to change the 49ers from a stone age offense to a state-of-the-art product, and he chose Kaepernick as his partner in the process.

When Harbaugh scouted Kaepernick in Reno before the draft, Kaepernick felt an instant connection and hoped the 49ers would draft him. He felt there was not only an opportunity for a young quarterback but that Harbaugh was the right coach to guide him.

He felt the connection again Friday when Harbaugh was snapping the ball and conferring with him after every throw.

"That's the biggest advantage is that he's done it before," Kaepernick said. "He's seen it before, and he can tell you exactly how you need to adjust. Coach Harbaugh brings such a great energy to the team. To have a coach out here running around for three hours makes it easier as players to be excited about practice and keeping your motor going."

It was a long wait. But the marriage that could define the 49ers' future is finally official.

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