SANTA CLARA — Here is how the 49ers (1-2) graded in their 27-7 home loss Sunday against the Indianapolis Colts (2-1):

PASS OFFENSE: Vernon Davis' first absence in 99 straight games proved glaring as no receivers stepped up to fill that complementary role next to Anquan Boldin. Colin Kaepernick had better protection than a week ago but looked out of synch (13-of-27, 150 yards). Kyle Williams and Quinton Patton each missed a catchable ball. It's time to see if former Chiefs wideout Jon Baldwin can contribute. Grade: F

RUN OFFENSE: Frank Gore understandably fumed after the game, getting only three second-half carries following a breakout first half of eight carries for 70 yards. The 49ers aren't using the zone-read scheme that Kaepernick often excelled in, and instead his runs have become desperate scrambles. The two-handed pitch wasn't a good look, either. Grade: D+

PASS DEFENSE: Five penalties, one sack and no interceptions led to a victorious Andrew Luck. Aldon Smith's presence was highly debatable, between his Friday arrest and post-game leave of absence for alcohol treatment. By playing Smith all but one snap, his upcoming replacements didn't get reps heading into Thursday's game at St. Louis. Hey guys, first cornerback to make an interception this season wins a new contract? Grade: D

RUN DEFENSE: The Colts' 179 yards were the most allowed by the 49ers since Week 3 of 2010. That bundle came in the wake of a 172-yard rushing effort by the Seahawks. Patrick Willis' groin injury didn't help matters. The Colts' final eight snaps were all run plays, producing 55 yards and two touchdowns. Grade: F

SPECIAL TEAMS: The 49ers aren't getting enough from their return game. Kyle Williams' best effort was a 14-yard punt return to midfield; he also had a pair of fair catches at the 49ers' 8. Lousy fourth-quarter kickoff returns came from Kendall Hunter (9 yards) and Quinton Patton (7 yards). Grade: D+

COACHING: Playing Aldon Smith marked possibly the biggest coaching decision -- or most controversial -- in Jim Harbaugh's tenure outside of last year's QB switch. Beyond that, the offensive calls lacked flair, and abandoning the run was highly suspect. Andrew Luck didn't seem fooled by the 49ers' defense. Harbaugh is no longer invincible to two-game losing streaks (this is his first), and adversity is piling up at 4949 Centennial Blvd. Grade: F