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Trent Baalke has to be swallowing hard this morning. Blaine Gabbert, the quarterback Baalke acquired to back up Colin Kaepernick, has a passer rating of 17.6 through two exhibition games.

Trading for Blaine Gabbert was Baalke’s worst decision as an NFL general manager, worse than his decision to draft A.J. Jenkins or to trade for Jon Baldwin or to invest in a red-shirt draft choice like Marcus Lattimore who may not even pass physicals after a year of rehab. Getting Gabbert was worse than all of that.

Gabbert could be the worst quarterback in the NFL. He makes the 49ers’ previous backup QB, Colt McCoy, look like Jeff Garcia.

The 49ers owe Gabbert more than $2 million this season. It’s guaranteed money.

You almost can understand why Baalke traded for Gabbert. He was the 10th pick in the 2011 draft. He’s tall, he’s fast, he’s smart and he throws hard. Gabbert failed on the Jaguars, but they were horrible and he had a different offensive coordinator every season. The beginning of his career mirrored the beginning of Alex Smith’s career. If Jim Harbaugh could turn Smith into a good QB, Harbaugh could do the same with Gabbert, right?

That probably was Baalke’s logic. Too bad it was flawed.

Harbaugh didn’t turn Smith into a good QB – Smith already was a good QB. Smith lacked confidence from playing six seasons on a terrible 49ers’ team. Harbaugh helped Smith get back his confidence, but Smith always could play.

Not Gabbert. Despite all of his talent, he never was a good quarterback, not even in college. His final season at Missouri, he threw just 16 touchdown passes. Smith threw 32 TD passes his final season at Utah. Gabbert’s predecessor at Missouri, Chase Daniel, threw 33 TD passes his final season at Missouri. Gabbert wasn’t half the quarterback Daniel was. Daniel currently is the Chiefs’ third-string quarterback. He may not make their final roster.

Gabbert has no ability to throw downfield. He completed 30 percent of his pass attempts that traveled more than 15 yards past the line of scrimmage in college. Abysmal. Gabbert has attempted five passes that traveled more than 10 yards downfield the past two exhibition games. The result: zero completions and two interceptions. Double abysmal.

Harbaugh and the offensive coaches have been struggling just to get Gabbert into the flow of a game and to experience any semblance of success. The 49ers went almost exclusively with a three-step-drop short passing game for Gabbert Sunday against the Broncos. Still, he completed just 57 percent of his passes. He averaged 2.9 yards per pass attempt. After a dozen dinks and dunks, Harbaugh let Gabbert throw deep. Interception.

Backup quarterbacks are critical. Starters get hurt. Jay Cutler missed five games last season. The Bears won three games in his absence because they had Josh McCown, a good backup quarterback. Now, McCown is the Buccaneers’ starting quarterback – they signed him this offseason. Baalke signed McCown in 2011 and cut him a few months later after training camp. Whoops.

Gabbert cannot keep this 49ers’ team or any team in contention. If Kaepernick gets injured, the 49ers’ season is over. Gabbert cannot back him up. Neither can the 49ers’ other quarterbacks, Josh Johnson and McLeod Bethel-Thompson. After Sunday’s shutout loss, Harbaugh said the 49ers will not go out of the organization for another quarterback. They may have the worst backup quarterbacks in the NFL. Even the Raiders have better backups.

Kaepernick has not missed an NFL start due to an injury but that doesn’t mean he’s injury-proof. Quarterbacks get injured and miss games all the time. Tom Brady has missed games. Peyton Manning has missed games.

Baalke should have traded for Michael Vick instead of Gabbert. Or Baalke could have traded for Mark Sanchez – he would have been a better choice than Gabbert. The Eagles traded for Sanchez this offseason and he’s completing 81.8 percent of his passes in the preseason.

Or Baalke could have drafted a quarterback. Jim Harbaugh said David Fales was one of the five best quarterbacks in the draft. He was available in the sixth round. Baalke could have drafted him. Baalke drafted injured cornerback Keith Reaser instead. Reaser tore his ACL last year and will spend his rookie season on I.R. Fales is with the Chicago Bears under Marc Trestman where he is likely to develop into an excellent quarterback.

The best Baalke can do is wait until next year to get a better backup. It’s too late to fix this problem now. The 49ers have to protect Kaepernick at all costs and hope he misses no games.

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.