by By Daniel Brown San Jose Mercury News , Contra Costa Times

"Smith hadn't had a competitive situation in quite some time," Raye said. "But also thrown in there was a wide receiver (rookie Michael Crabtree) who had no idea, who had not been in a two-minute situation before, didn't know the alignments and the calls.

"Some formation things got screwed up. But we'll address that this week."

Needing a field goal to tie, the 49ers got the ball at their 6-yard line with 1:38 remaining against the Texans.

But the drive quickly stalled.

The biggest problem came on fourth-and-five from the 43 with about 50 seconds to play.

The 49ers coaches were trying to signal for a timeout from the sideline and Smith assumed it registered.

It didn't, and more time ticked off the clock.

"Critical," Raye said.

He said Smith should have ensured the stoppage of the clock by getting the attention of the referee.

"He didn't turn to Mike Carey and ask for it, so we got a 5-yard delay (penalty) and that 5 was big," Raye said.

Instead of a fourth-and-five, the 49ers wound up with fourth-and-10.

Smith took deep shot over the middle to Isaac Bruce, but Eugene Wilson grabbed the wayward pass for a game-clinching interception.

Chances are, the 49ers won't be running a two-minute drill against the heavily favored Colts.

But whenever the situation arises again, Raye wants the team to be better prepared.

In general, he thinks things will improve once players such as Smith and Crabtree get more time together.

"It seems to me that since we've started, there's been a different back, a different wide receiver, different quarterback, a different tackle, a different guard. There's been a different something all of the time," Raye said. "And I think continuity ."?."?. is very important to offensive Football.

"Familiarity and continuity is something you're striving to get."

For a second consecutive day, Linebacker Takeo Spikes (shoulder) sat out practice, although the 49ers remain optimistic he will be able to play. Rookie Scott McKillop is listed as Spikes' backup, with newly signed Matt Wilhelm also is capable of playing inside.

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