San Francisco 49ers

49ers notes: Fast friends? S.F. is wary of Alex Smith’s running ability

Colin Kaepernick leads all quarterbacks in rushing yards with 187 through four games. Second place? It’s not all that close, although it is a bit interesting.

The Chiefs’ Alex Smith has 103 rushing yards, and 49ers defensive coordinator Vic Fangio said his team will be wary of Smith taking off on Sunday.

“Alex is a very athletic and fast quarterback, which sometimes people forget about,” Fangio said Thursday. “But it stands out when you watch the tape. And he’s a good scrambler. So I think the offense is operating at a high level for them coming off that game Monday night, and he’s playing very well.”

When he arrived in Kansas City last year, Smith worked with former Nevada head coach Chris Ault, whom the Chiefs also brought in as a consultant. Ault is the inventor of the pistol formation and, of course, taught it to Kaepernick.

Smith spent his first offseason in Kansas City watching film of Kaepernick, the man who replaced him as the 49ers’ starter, run the pistol with the Wolf Pack; that formation is now a part of the Chiefs’ offense.

Fangio said Smith has picked up his yards both on scrambles and on designed runs.

“Much like with Colin, it’s both,” Fangio said. “I can’t give you an exact percentage, but they have designed running plays for him or the designed option where they can hand it off or keep it, which he’s done.”

Fangio, however, said Smith’s greatest strength is not his feet, but his brain. He’s able to run a complex offensive system that has an array of options, and that’s what coach Andy Reid and the Chiefs’ staff have built in Kansas City.

“And Alex is a quarterback that can handle all of that from a mental standpoint and choreograph it and orchestrate it for them on the field,” Fangio said. “They do a lot of things out of all those different packages that suit his game.”

McDonald investigation complete – San Jose police have forwarded their findings about 49ers defensive end Ray McDonald’s August arrest to the Santa Clara County district attorney’s office.

In a tweet Thursday, the DA’s office said that after reviewing the case, it will decide whether to file criminal charges or perhaps investigate the matter further. McDonald was arrested at his home in the early-morning hours of Aug. 31 on suspicion of felony domestic abuse.

McDonald has started every game for the 49ers this season at left defensive end and has not missed a practice. He has declined interview requests, saying only that the “truth will come out” and that he’s a “good-hearted person.”

Investigators have looked into the Aug. 31 event, a birthday party at McDonald’s San Jose home, as well as an incident at the same home on May 25 that involved a woman brandishing a handgun. The 49ers have said they will let “due process” play out before taking any action against McDonald.

Injuries – Tight end Vernon Davis (back), tackle Anthony Davis (knee, ankle) and cornerback Tramaine Brock (toe) missed their second practice of the week Thursday. Perrish Cox is likely to play in place of Brock on Sunday. The Davises may end up being game-day decisions.

Safety Antoine Bethea (ankle), defensive end Tony Jerod-Eddie (shoulder), center Marcus Martin (knee), tight end Vance McDonald (knee) and safety Eric Reid (hamstring) were limited participants.

Read Matt Barrows’ blogs and archives at www.sacbee.com/sf49ers .

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