The 49ers had a tough go of it out of the gates this season. Not only are the Packers and Seahawks two of the best teams in the league, but they’re also two completely different teams with unique skill sets to get San Francisco out of its usual game plan.

The Packers are tough up front, and they came into the game hellbent on keeping the 49ers from running the ball. The Seahawks have the perfect defense: in the same way the 49ers can rush four with their tackles and outside linebackers, leaving their other defenders to cover and spy, the Seahawks can keep two corners and two safeties deep and let their front seven wreak havoc on the trenches.

Today they’ll face a different kind of opponent — the Indianapolis Colts are an up-and-coming team but they still have their issues. The bludgeoning in Seattle left some questions about the 49ers, and I’m hoping the Colts can answer them today.

4. Can the secondary cover and tackle?

The safest bet in the defensive backfield is Tarell Brown — He’s played 134 of the first 141 snaps this season and he’s been targeted only four times. Granted all four went for catches, but if it’s an example of how infrequently his assignment is getting open, I’ll take it.

Carlos Rogers hasn’t been fantastic, but he hasn’t been terrible either. He got picked on by Aaron Rodgers in Week 1 (three of four targets completed for 41 yards and a score), but only had one pass completed on him in Week 2.

The more important problem is one BASG addressed here with Nnamdi Asomugha — he’s been thrown at 11 times so far, giving up four catches for 63 yards and a touchdown (all courtesy of Rodgers) and missing four tackles (he whiffed on three of those in Seattle). It’s been two different problems in two different games, but Asomugha will need to correct both of them against a solid corps of Colts wideouts.

3. Is there trouble on the defensive front?

Here’s my obligatory mention of Aldon Smith’s arrest and the possible distraction it probably won’t be, but I’m more concerned about the return to 2011 this defense has yet to make in terms of clogging up the run. Trent Richardson might see more action than some people think today, and he’s the kind of tough runner usually known for giving the 49ers trouble. San Francisco was really high on Ian Williams, but with Williams gone we’ll get another look at how Glenn Dorsey is doing as their latest reclamation project. He graded out +2.4 overall and +2.0 in run defense on Pro Football Focus for his efforts last Sunday. He also registered a sack, but what I’m really looking for his how well he can hold up offensive linemen and let Patrick Willis and NaVorro Bowman work.

Quinton Patton 49ers OTAs2. Which receiver will step up?

Theoretically, the 49ers can sustain an offense based on three factors: Anquan Boldin and Vernon Davis being the only viable receiving options, the running backs producing and Colin Kaepernick’s ability to rush. Unfortunately, the run game has been a problem through two weeks (more on that in a minute) and in a perfect world, having Kaepernick run the ball should be a luxury rather than a necessity.

Kyle Williams has been quiet so far, overshadowed in Week 1 by Boldin and blanketed completely in Seattle. Quinton Patton’s snaps increased in Week 2, and I’d like to see a little more of him against a defense apt to give him a little air. One of these two needs to step up and make an impact because Boldin will probably be seeing a good amount of double-teams for the foreseeable future.

1. Where’s the running game?

You knew it was coming. It’s been the topic du jour this week, a common thread while everyone’s annual beating of the Frank Gore panic button gets an early start. I’ll have a closer eye on Gore’s blocking than I ever have — primarily on the offensive linemen shedding initial blocks and getting to the linebackers. I’ll also be watching how Garrett Celek and Vance McDonald fare.  I defended Delanie Walker’s abilities as a run-blocker last year, and I wholeheartedly agree with BASG’s assertion that the 49ers are missing him this year.

Indianapolis is the first pedestrian run defense the 49ers have come across this season. Today should be the day we see the old Gore stroll through the door.