San Francisco 49ers quarterback Josh Johnson (1) and San Francisco 49ers tackle Jason Slowey (62) of an NFL football game in San Francisco, Friday, Aug. 10, 2012. (AP Photo/Paul Sakuma)

Grant Cohn: 49ers' quarterback depth a puzzle for the preseason

SANTA CLARA — Five 49ers quarterbacks. Only three can make the team. Which three will it be?

We know Colin Kaepernick will make the team and start unless he breaks his leg or starts missing receivers by 30 yards and sailing passes into the stands.

That leaves two spots for four quarterbacks — 24-year-old former first round pick Blaine Gabbert, 25-year-old former undrafted free-agent McLeod Bethel-Thompson, 23-year-old undrafted free agent Kory Faulkner and 28-year-old former fourth round-pick Josh Johnson.

All four share key physical traits with Kaepernick. They're tall — none is shorter than 6-3. They have strong arms — Bethel-Thompson could throw 70 yards in high school. And they run relatively fast for quarterbacks — Faulkner runs a 4.7 40-yard dash, Gabbert a 4.61 and Johnson a 4.53, same as Kaepernick.

Faulkner is a rookie and a long shot to make the 53-man final roster. He started three seasons at Southern Illinois University. He played poorly his first two seasons — he threw 16 touchdowns and 18 interceptions and completed just 59 percent of his passes. He was not especially accurate and he was generally late on his throws.

He improved during his senior season. He threw 18 touchdowns and just four interceptions, and completed 61 percent of his passes in nine games before he broke a finger against North Dakota State and missed the rest of the season. He could earn a spot on the 49ers' practice squad.

McLeod Bethel-Thompson was a member of the 49ers' practice squad at the end of last season. He never has appeared in a regular-season NFL game, but he played in the preseason for the Vikings last year. He was pretty good. His quarterback rating was 83.8.

When he faced pressure, his quarterback rating plummeted to 39.6. And although he can run, he picked up only 10 yards on five rushing attempts. Bethel-Thompson probably will compete with Faulkner for a spot on the 49ers' practice squad, although Bethel-Thompson has an outside chance to make the 49ers' final roster. He already knows the 49ers' playbook.

This offseason, the 49ers' traded a sixth-round pick to the Jaguars for colossal disappointment Blaine Gabbert. The Jaguars drafted him with their first pick in 2011, drafted him instead of Colin Kaepernick whom the 49ers took in the second round. Now, Gabbert is fighting to be Kaepernick's backup. Funny how things change in three years.

Gabbert is still just 24 years old, and he has talent. But the Jaguars may have ruined him. He started 27 games for them and got sacked 74 times. Last season, he threw seven interceptions during three starts before the Jaguars benched him for the rest of the season.

He seems shell-shocked. He doesn't step up in the pocket and he throws off his back foot when he faces pressure. Most of the time, he throws the ball as quickly as possible to avoid getting hit. During last year's preseason, he took 1.98 seconds on average to get the ball and throw it. That was the fastest in the NFL. When he held onto the ball for 2.6 seconds or longer during the 2013 regular season, he was even worse. His passer rating was more like a really good figure-skating score: 13.9.

Unfortunately for Gabbert, the 49ers' offense asks the quarterback to hold onto the ball for a long time while slower possession receivers run the downfield routes Jim Harbaugh prefers. Last season, Kaepernick held the ball for 3.08 seconds on average before throwing. The season before, Alex Smith held the ball for 2.89 seconds on average before throwing. If Gabbert can't hang tough in the pocket for three seconds, he can't run the 49ers' offense.

Josh Johnson loves to hold onto the ball in the pocket. He held it for 2.92 seconds on average for the Bengals during the preseason last year. And he played pretty well overall — his passer rating was 83.9.

Like Gabbert and Bethel-Thompson, Johnson's numbers plummeted under pressure. In fact, Gabbert, Bethel-Thompson and Johnson are similar — hard throwers who aren't particularly accurate and struggle under pressure.

Johnson differentiates himself from the others with his running. He wants to run and he's good at it. During the preseason last year, he rushed 12 times for 131 yards.

Johnson tried out for the 49ers in 2012 and didn't make the team. He was one of the final cuts. "Coming here the last time, I felt like I was in the process of developing as a quarterback," Johnson said in the 49ers' media trailer on Friday. "Now, I feel like I'm past the developmental stage of my career."

Johnson didn't fit the 49ers' offense back then, either. Alex Smith, a traditional pocket quarterback, was the starter. Now the starter is Kaepernick, an athletic, running quarterback like Johnson.

"Once I talked to the coaches, they said they do things that fit my skill set at little bit more," Johnson said. "When I was here last time, the whole athletic quarterback deal wasn't as big as it is now."

Well, here's the real deal. If something happens to Kaepernick during a game next season and the 49ers need to replace him, Johnson is the only backup who can run the same plays as Kaepernick — the rollouts, the zone-reads, the designed runs. The 49ers wouldn't have to change a thing for Johnson.

Johnson probably will make the team.

The other three? Draw straws.

Grant Cohn writes sports columns and the "Inside the 49ers" blog for The Press Democrat's website. You can reach him at grantcohn@gmail.com.

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