INDIANAPOLIS – In his second game against Colts quarterback Peyton Manning, Alex Smith had to act like, well, Peyton Manning.

The communication system between the sideline and Smith's helmet broke down twice during Sunday's 18-14 loss to Indianapolis, forcing Smith to call the plays on his own. Coach Mike Singletary said Smith handled the job with aplomb.

"All I know is that right now Alex looks very calm," Singletary said. "The game is not fast. The game has slowed down quite a bit. His mechanics are a lot better, and I think he has a better command of the offense. … He's only going to get better."

Smith and the offense struggled at times. He threw one interception – the ball glanced off Michael Crabtree's hand – in the first quarter and had three consecutive three-and-out series to open the second quarter.

But near the end of the quarter, Smith looked like he did against Houston last weekend. He drove the offense 89 yards in 1 minute, 11 seconds and completed 6 of 7 passes. The last, an eight-yard touchdown strike to tight end Vernon Davis with 33 seconds left in the half, had to be threaded through several defenders.

Smith also had the 49ers poised to score after the Colts took the lead for the first time in the fourth quarter. The 49ers marched to the Indianapolis 30-yard line – field-goal range for Joe Nedney – when they were hit with a delay-of-game penalty.

Smith said he knew time was short when he broke the huddle, but he thought he could get the snap in time.

"Maybe we could have gotten in and out of the huddle a little faster," Smith said. "That's a big play."

On the next play, defensive end Robert Mathis sacked Smith for an eight-yard loss. The 49ers were forced to punt and didn't enter Indianapolis territory again.

Pricey picture – A picture is worth 1,000 words and, as it turns out, 15 yards. That's what the officials docked the 49ers after Davis' touchdown prompted a penalty for unsportsmanlike conduct.

After the touchdown, teammates pretended to take pictures of Davis in the end zone. One, Josh Morgan, dropped to one knee. Players aren't permitted to go to the ground during an end-zone celebration.

The 49ers kicked off from their 15, and the Colts went 48 yards in four plays and kicked a 31-yard field goal with one second left in the half.

"If y'all watch the film from every game, every time he scores a touchdown, I just celebrate with him," Morgan said of Davis. "I don't think it's excessive at all. It's celebrating."

Former 49er is accused – The former fiancé of ex-49ers defensive lineman Dana Stubblefield obtained a restraining order after accusing him of harassing her and threatening her life.

Calling him "violent and unpredictable," Melanie Wade, 26, said in court papers Stubblefield once knocked her off her bicycle with his truck.

Stubblefield, 38, denied the allegations through his attorney. A former NFL Player of the Year and now the defensive-line coach at Valley Christian High School in San Jose, Stubblefield is on probation after pleading guilty to a charge of lying to a federal agent about using steroids in 2003.

Et cetera – Frank Gore's 64-yard touchdown run in the first quarter marked the first time since 2003 a player has had three runs of 60-plus yards in one season. The last 49er to do so was Garrison Hearst in 1998.

• Wide receiver Brandon Jones filled in as a punt returner after Nate Clements left the game with a broken shoulder blade. The 49ers have had trouble filling that role since releasing Allen Rossum last month.

• He had to wait until the 49ers' final possession, but Colts defensive end Dwight Freeney recorded a sack in his eighth consecutive game, tying a club record.

Read Matthew Barrows' archives and blogs at www.sacbee.com/sf49ers. The Contra Costa Times contributed to this report.