Vernon Davis has been shackled up ever since “somebody took the handcuffs off” him against the Bears. He caught six passes for 83 yards and a touchdown in that game, but he’s been held to three receptions for 19 yards and no scores since.

So what gives? This team was supposed to be lighting it up with the new gunslinger at quarterback, and Jim Harbaugh’s offense has always favored tight ends. There are a few reasons why Davis hasn’t been putting up Gronk-esque numbers lately, as the following plays show.

Play No. 1: 3rd and 4, 13:07 in the 1st quarter (0-0)

The culprit for Davis’ absence is the offensive line on this particular play. I’ve taken a look at how they’ve both helped and harmed Colin Kaepernick in his first few career starts. An example of the latter came early in the first quarter, when a forced fumble on 3rd down was recovered by Anthony Davis and the 49ers had to punt.

Vernon Davis is lined up one-on-one against a linebacker — a favorable matchup and one that Kaepernick theoretically would love to exploit. The problem is he has about two seconds to make a throw before all hell breaks loose in the pocket.

Davis is still in the development of his route as the protection collapses. It’s hard to tell from Candlestick Park’s cameras, so here’s a closer look:

Looks like Michael Crabtree is also open underneath, but Kaepernick is busy playing bumper cars with the Dolphins in a space the size of a closet.

With a little more time, Kaepernick could’ve hit a wide open Davis about 10 yards past the sticks. He had his defender going the opposite direction, but it didn’t matter because the protection didn’t hold up.

Play No. 2: 1st-and-10, 13:31 remaining in the 2nd quarter (3-0, Dolphins leading)

Sometimes it’s wise to NOT make a throw, and in this case Kaepernick made a smart decision.

They initially line up Davis in this new “full house” pistol formation, but he motions out to the slot pre-snap.

He’s going to run a simple seam route, and for a moment he looks wide open after absolutely burning the middle linebacker. But Kaepernick sees the safety getting ready to come over the top on Davis, so he opts to pass on making that throw.

The reward could’ve been high, the the risk associated with trying to connect with Davis was probably higher. So Kaepernick took the safest option, dumping it off to Gore for a 3-yard gain. Perhaps a habit he picked up from his predecessor?

Play No. 3: 1st-and-10, 7:49 remaining in the 4th quarter (20-13, 49ers leading)

Finally, here is an instance where Kaepernick just didn’t see Davis open.

They motion him out of the backfield to run a seam route again, this time on the right side. But unlike the previous play, he smokes the linebacker and the safety doesn’t watch him. In the meantime, Crabtree is running a short curl route on the right sideline.

Kaepernick hits Crabtree, but check out all of the open field Davis has at his disposal. He’s already heading to the right of the safety, and a throw shaded that way would have made for an even safer completion.

You can’t blame this one on a busted pocket either. There weren’t many of these plays, but here is an example of Kaepernick simply not seeing the long ball. Or, maybe Crabtree was his first read.

There were actually a handful of plays where Davis was watching from the sidelines. The new “full house” package has a few different personnel looks, and one of them features a bunch of linemen, two wideouts and Delanie Walker in the backfield with the runners. For the most part though, Davis’ absence from the stat sheet can be chalked up to three things: defenses keying on Davis, less than adequate protection, and conservative decision-making from the 49ers’ young quarterback at times.