Kaepernick a QB challenge for Harbaugh

The 49ers moved up nine spots in the second round to draft quarterback Colin Kaepernick. Jason O. Watson/US Presswire

Through four years at Michigan and seven more in the NFL, Jim Harbaugh had never seen anything like the offensive wrinkles his Indianapolis Colts were installing back in the 1990s.

Coach Lindy Infante was teaching new and varied ways to read pass routes from a quarterback's perspective. The quarterback -- Harbaugh, in this case -- could take a three-step drop, survey his options to one side, then check out the other side on a five-step tempo, for example. It's routine stuff now, but it wasn't then.

"I had never seen that before," Harbaugh said before the draft. "I didn't understand it."

Harbaugh figured it out because that's what quarterbacks do. They adapt. They learn. They grow. With persistence and a little luck, they succeed.

The San Francisco 49ers need all of the above from their newest quarterback.

Nevada's Colin Kaepernick, chosen 36th overall Friday after San Francisco moved up nine spots in the second round to select him, becomes the 49ers' best hope at the position since Alex Smith's arrival as the No. 1 overall pick in 2005. Like Smith, he's also facing a significant transition from a college offense unlike what he'll experience in the NFL. But Harbaugh doesn't care so much about college schemes or throwing motions or the related hangups that drive so much of the draft discussion regarding quarterbacks.

"Eleven-on-eleven football," Harbaugh said in laying out his criteria. "How are you at that?"

Kaepernick won 31 of 47 starts at Nevada, played well in the clutch, demonstrated a strong arm and rushed for more yards over the last four seasons (4,112) than Frank Gore has managed (3,321) with the 49ers over the same period.

The rushing stats don't matter so much at the NFL level, where guys like Patrick Willis and Adrian Wilson send running quarterbacks to the training room.

Kaepernick's mobility will translate well to Harbaugh's system, but he will have to beat teams with his arm. He'll be running a pro-style system predicated on a power running game with play-action passes.

"I fit Coach Harbaugh's offense well, their style of play," Kaepernick said. "I'm coming into an offense that has a lot of great weapons on it, from the running back, the tight end, the wide receivers. It's close to home (he is from California). Coming in with a new coaching staff, everything just fits well."

Kaepernick has come to know Andrew Luck, Harbaugh's quarterback at Stanford, and they've talked about the offense.

"A lot of things they do fit me well," Kaepernick said. "They like a mobile quarterback, a quarterback who can do a lot of things. I'm excited to get my feet wet."

Kaepernick ran a Wing-T offense in high school and a pistol attack in college. He downplayed the adjustment, as did Harbaugh.

"Figuring out how to think your way to winning is really important," Harbaugh said. "That's in a pool match, a street fight, in a football game. Things are changing when your plan meets the other team's plan. You have to be able to adapt."

Harbaugh is not a forensic scientist, but he's all about a quarterback's DNA. How is the quarterback wired mentally? How hard does he work? How competitive is he? When Harbaugh looks at Kaepernick, he sees the only quarterback in NCAA history to pass for 10,000 yards and rush for 4,000 yards over the course of his career.

"In the annals of college football," Harbaugh said with reverence.

Old quarterbacks can't move well enough to keep playing, but they can always throw a tight spiral. Harbaugh is no different. Competitive as ever, he challenged Kaepernick to a throwing competition during the pre-draft evaluation process. They competed to see which one could throw the sweetest spiral. They tested accuracy by throwing through goal posts. And because Harbaugh is no dummy, they never threw for raw distance.

Harbaugh won the first spiral competition, 5-4. Kaepernick won the second one, 5-1, and he won the accuracy competition as well.

Will Kaepernick win the starting job in San Francisco? The 49ers could still re-sign Alex Smith. They realize rookie quarterbacks aren't ready right away.

"You hear talk about Colin being a developmental quarterback," Harbaugh said. "I heard that a few times after we selected Colin. That goes for all quarterbacks. That is every quarterback who goes from college to the NFL. He is no different. He has got great gifts from Mom, Dad, God. He comes with the energy and the ability to think his way to success. All those things and more."

The 49ers haven't had much luck with quarterbacks recently. They're also trying to buck an NFL trend. Finding productive quarterbacks in the second round has been a struggle over the years. Three of the last 18 have reached a Pro Bowl. Only one, Drew Brees, has a career passer rating higher than 77.9.

Harbaugh has to be the difference for Kaepernick. He's the 49ers' first offensive-minded head coach since 2004 and the reason Kaepernick has a better chance than Smith. Mike Singletary and Mike Nolan didn't know how to manage quarterbacks. They also kept losing offensive coordinators, running through seven of them in six seasons.

Harbaugh provides insurance on that front. His coordinator, Greg Roman, takes a leading role with the scheming. But Harbaugh is the one with the quarterbacking pedigree. He's the one who played for a wide range of coaches across multiple systems spanning different eras and in various capacities. He's been the rookie first-round pick, the young backup, the promising starter, the journeyman. He's been Captain Comeback and the veteran mentor. He's played for Mike Ditka, played with Ryan Leaf and earned a spot in the Colts' Ring of Honor.

"This is a perfect situation for me," Kaepernick said.

Harbaugh must make it so.