Justin Smith back at 49ers practice

SANTA CLARA, Calif. -- The San Francisco 49ers' practice participation list looked better Thursday than it did Wednesday.

Defensive lineman Justin Smith (shoulder) went through limited drills after not working Wednesday. Backup running back LaMichael James (knee), meanwhile, practiced on a limited basis for the first time in the regular season. His status for Sunday's visit from the Indianapolis Colts is uncertain; I’d say it's iffy at best.

Defensive tackle Ray McDonald (both ankles sprained) did not practice for the second consecutive day -- though earlier Thursday, defensive coordinator Vic Fangio said he expects his starting group to be fine Sunday.

Rookie safety Eric Reid continued to be limited after suffering a concussion in the Week 2 loss at Seattle. He said he has passed every NFL-mandated test thus far and is on pace to play Sunday.

As expected, tight end Vernon Davis did not practice for the second day in a row while nursing a hamstring injury. He tweeted this week that he was going to rest, on doctor’s orders, but that he expected to play.

Quarterback Colin Kaepernick remains on the practice report with a foot issue. But he practiced fully the past two days and had no noticeable problems.