Although Colin Kaepernick has seen considerably more playing time this season than your average second string quarterback, the 49ers’ backup is still a work in progress. We all know he has a unique set of physical weapons including size, speed and arm strength, but what seems to give Alex Smith the edge is his experience and field vision.

Up until Sunday, offensive coordinator Greg Roman had been using Kaepernick selectively — that is to say, he utilized Kaepernick in certain goal-to-go situations or when ground needed to be gained between the 20s. For example, Kaepernick’s insertion on the play before David Akers’s 63-yard field goal in Green Bay was a perfect time for the change up; the potential in his arm gave him just enough space to run for the yardage the 49ers needed.

There was nothing situational about Kaepernick’s snaps against the Rams. He was forced into playing due to Smith’s concussion, and his time learning on the fly eventually paid off.

Lesson #1: Kaepernick’s 10-yard scramble

When he was playing quarterback for the University of Nevada, the option to tuck the ball (or not tuck it, whatever) and run was pretty much encouraged. Running quarterbacks thrive in collegiate ball (see: Tebow, Tim), but the 49ers have been trying to teach Kaepernick to settle down and change his order of operations from “look, run, only pass if someone’s wide open” to “look, pass, only run if no one is open.” That didn’t happen on this play.

He takes the snap from under center, drops back three steps and (kind of) sets his feet, reading the field from right to left. Bruce Miller is open as an outlet option, but the pocket seems to be caving in to his right and Kaepernick can feel a bunch of open space to run between Mike Iupati and Joe Staley.

So Kaepernick does what comes very naturally to him: he takes off for the first down marker. Meanwhile, Alex Boone handles the rusher who Kaepernick thought was going to sack him. Jonathan Goodwin and Iupati are pushing out the nose tackle, forming what would have been a nice pocket from which to throw, but now the quarterback is committed to scrambling. Instead of trusting his offensive line, Kaepernick ran for the first down and got it. That’s not to say this was a bad decision, but it shows that the young quarterback was skittish and hesitant to trust his protection.

What he didn’t see was Delanie Walker wide open downfield for a considerable gain.

Lesson #2: Holding the ball too long doesn’t always result in sacks

Kaepernick grew more comfortable with his protection as the game wore on, but his field vision didn’t improve immediately. This play is a good example.

Here is where you really miss Alex Smith. Kaepernick is ready to take the snap out of the shotgun, but apparently he doesn’t bother to read the defense, because it has completely ignored Kyle Williams lined up in the slot. The Rams even pull their safety away from that side of the field, leaving plenty of open space for Williams.

Williams streaks down the field towards the end zone, hoping that Kaepernick notices him with his hand in the air. Of course the quarterback doesn’t see it, and he hangs out in the backfield for what seems like a year, evaluating his options.

Goodwin has trouble keeping his block so he has to hold the nose tackle to keep him from getting to the quarterback. Kaepernick ended up scrambling to his right before hitting Kendall Hunter for a 15-yard gain, but the whole play was negated because of the holding penalty. The quarterback did a great job of standing in the pocket on this play, but showed that he still has some work to do in terms of reading the field.

The culmination of both lessons: A 20-yard strike to Manningham

In the fourth quarter the 49ers were embarking on what would be a very important touchdown march. Kaepernick had been showing some serious improvement, and this play stands out as an example of that progress.

Right off of the snap, the Rams send three blitzing linebackers, leaving a lot of open space underneath if Kaepernick wants to run. Saying that this pocket collapsed would be an understatement, but the quarterback kept his cool and found the target he was looking for.

Truth be told, open receivers weren’t hard to find on this play. Vernon Davis and Delanie Walker are both open after running crosses around the 30-yard-line, and Manningham is open just inside the 40. Crabtree is deeper downfield, but the safety is coming to drape him, so Kaepernick hits Manningham, his deepest open target, for a 20-yard pickup.

There’s the pocket that he was throwing out of. Even with a linebacker ready to demolish him, Kaepernick delivered a perfect pass for a big gain. Nine plays later, Kaepernick scrambled into the end zone to cut their deficit to three.

There really isn’t any way to simulate the kind of experience that Kaepernick got on Sunday. “Live bullets,” as they say, are the only way for a quarterback to polish his game. It’s certainly a good sign that Kaepernick made mistakes and corrected them as this game wore on, especially if the 49ers plan on turning him into the quarterback of the future.