49ers Mailbag: Who sees more action with Manningham out?

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49ers Mailbag: Who sees more action with Manningham out?

On the eve of an ultra-intriguing regular-season game in Foxboro, Mass., we go to the 49ers Mailbag to answer some questions:

Mario Manningham is almost definitely out right? (@jmike4949blvd)
Yes.

In fact, while I was in the air Saturday on the trip from San Francisco to Boston, the 49ers made it official: Manningham will not play Sunday against the New England Patriots due to his shoulder injury.

What this means is more playing time for No. 2 tight end Delanie Walker, more playing time for fullback Bruce Miller, and more playing time for Randy Moss in two-receiver formations.

The 49ers do not figure to use three-receiver sets too often -- maybe a dozen times through the course of the game. When the 49ers go with that formation, mostly on third downs, you can expect to see rookie A.J. Jenkins get on the field. He played eight snaps last week with Manningham sidelined. He'll probably see at least that much playing time on Sunday, too.

Will LaMichael James see more carries this week? (@bjdpaskeland)
James suited up last week for the first time this season. He is taking over for Kendall Hunter, who sustained a season-ending Achilles injury in the 49ers' 11th game.

Hunter had 72 rushing attempts this season or approximately seven carries per game as Frank Gore's backup. James carried eight times for 30 yards in the 49ers' victory last week over the Miami Dolphins.

That seems about right. So, no, I do not expect James to account for a dramatically higher share of the carries. After all, Gore is still the man who makes the 49ers' offense click.

Do you think Brandon Jacobs will be on playoff roster? ‏ (@sachibub10)
Jacobs does not want to play for the 49ers, and the 49ers do not want him around. The 49ers cleared out his locker and gave it to newly re-signed outside linebacker Eric Bakhtiari.

I do not foresee any situation in which the 49ers would want Jacobs in their locker room ever again.

Jacobs will not play for any team this season. There were reports Jacobs would file a grievance against the 49ers. It might eventually come to that, but that has not happened and it would not occur until after the season.

Any grievance Jacobs might file would be all about money. It would have nothing to do with releasing Jacobs so he could sign with another team.

With the three-game suspension to end the regular season, Jacobs stands to lose $167,000 in base salary. In all likelihood, Jacobs' camp will attempt to reach some financial settlement with the 49ers to avoid filing a grievance.

What are the chances that the 49ers play a lot of nickel against the Brady led O? (‏@RichBonsall)
It's a given. Expect to see a lot of Chris Culliver and very little -- if any -- of nose tackle Isaac Sopoago, the starter in the 49ers' base defense who heads to the sideline when the 49ers go with five defensive backs.

The big question is whether the 49ers will play a lot of their dime defense. That would require fourth cornerback Perrish Cox to enter the game and send inside linebacker Patrick Willis to the sideline.

Cox played more than Willis in the first game of the season against the Green Bay Packers. Cox also played a lot against the Detroit Lions in Week 2, but he has not seen much action since that time.

The 49ers will certainly play some dime. But how much? The key is how they choose to account for tight end Aaron Hernandez. Some teams tag Hernandez as a wide receiver and use defensive backs to cover him. The Patriots also feature such pass-catching targets as Wes Welker, Brandon Lloyd, Danny Woodhead and Julian Edelman.

Bill Belichick and Co. might want to force the hand of 49ers defensive coordinator Vic Fangio, who must make the decision to keep Willis on the sideline or take his chances with a possible mismatch with Willis covering a smaller, quicker Patriots receiver.

Is Alex Boone the long-term answer at guard? (@JimKralik)
If the club remains healthy, and he's not needed elsewhere, Boone figures to be the 49ers' starting right guard through at least the 2014 season.

Right tackle Anthony Davis is signed through 2014, and he'll remain at right tackle through that time. If Davis does not sign an extension before then, the 49ers would move Boone to right tackle. Left tackle seems out of the question for a while with Joe Staley signed through 2017.

In addition to being the 49ers' starting guard, Boone also serves as the team's top backup at both tackle positions.

49ers begin final phase of offseason program

49ers begin final phase of offseason program

The 49ers have graduated back to the phase of the offseason when offense-vs.-defense drills are allowed.

Because of the hiring of Kyle Shanahan, the 49ers were allowed an additional “voluntary” minicamp before the NFL draft. That meant the 49ers were permitted to skip from the two-week conditioning phase of the offseason straight to what is allowed under Phase III.

But after the three-day minicamp in late-April, the 49ers were forced to retreat back to Phase II, when on-field drills but could not include offense vs. defense.

Beginning Monday – and over the next three weeks -- the 49ers can get back to conducting the standard one-on-one, 7-on-7, 9-on-7 and 11-on-11 "non-contact" drills. The 49ers have the maximum number of 10 organized team activities scheduled. The official offseason program concludes with a mandatory minicamp scheduled for June 13-15.

The real competition does not begin until the pads go on during training camp. but here’s a look at the team’s most notable offseason competitions (one position you will not find is quarterback, where the depth chart of Brian Hoyer, Matt Barkley and C.J. Beathard appears clearly set):

Running back: Carlos Hyde, entering the final year of his original four-year contract, has a lot of competition to hold onto his role as the featured back. He is coming off his most-productive season, finishing just 12 yards shy of the 1,000-yard mark when he sustained a knee injury with one game remaining. Shanahan and running backs coach Bobby Turner lobbied for Utah running back Joe Williams in the draft. They clearly see a fit for him within the system.

Pass-rush end: The 49ers’ pass rush was among the worst in the NFL the past two seasons. Arik Armstead will be given an opportunity to see if he can adapt to the “Leo” position. Aaron Lynch must earn the confidence of the coaching staff and front office. The 49ers added explosive, 243-pound pass Pita Taumoepenu in the sixth round.

Tight end: The 49ers confirmed Vance McDonald was available for a trade during the draft. After finding no takers, the 49ers brought back McDonald and he rejoins the competition among rookies George Kittle and Cole Hikutini, and veterans Logan Paulsen, Garrett Celek and Blake Bell.

Cornerback: Rashard Robinson is the obvious choice to start on one side. And assuming Jimmie Ward remains at free safety, the 49ers have no other player on the roster who has started a significant number of games at cornerback. Rookie Ahkello Witherspoon, a third-round draft pick, will have a legitimate opportunity to win a starting job, as long as he displays a willingness to stick his nose into the action and play with the requisite level of physicality. Dontae Johnson, Keith Reaser and Will Redmond should also be in the mix to replace Tramaine Brock, who was released shortly after his arrest after an alleged domestic incident last month.

Center: Jeremy Zuttah, a Pro Bowl performer, was added in the offseason via a trade with the Baltimore Ravens. Daniel Kilgore has been the 49ers’ center the past three seasons but injuries have limited him to just 23 starts over that period of time. Zuttah has position flexibility. The 49ers could determine the best thing for the offensive line is to move Zuttah to one of the guard positions – to challenge Zane Beadles or Joshua Garnett -- if he is not clearly better than Kilgore.

Weakside linebacker: The 49ers signed veteran Malcolm Smith on the first day of free agency, providing him with $11.5 million of fully guaranteed money. The 49ers ranked Alabama linebacker Reuben Foster as the No. 3 overall prospect in the draft. They traded up to select him at No. 31 overall. Assuming Foster is ready to compete at the beginning of training camp after undergoing offseason shoulder surgery, it appears likely he would line up in that position and compete with Smith. The 49ers’ medical staff does not believe Foster will require any additional surgery, and Foster said he expects to be cleared for the opening of camp.

Barkley continues work with personal coach of Brady, Ryan

Barkley continues work with personal coach of Brady, Ryan

Atlanta Falcons quarterback Matt Ryan spent last offseason working with Tom House and Adam Dedeaux on his throwing mechanics.

Ryan went on to set career-bests in completion percentage (69.9), yards passing (4,944), touchdowns (38), interceptions (7) and passer rating (117.1).

New 49ers quarterback Matt Barkley worked with House and Dedeaux for the fourth offseason in Southern California before reporting to Santa Clara for the team’s offseason program.

“Kyle (Shanhan) is on board with what House and those guys are doing – I think, really, because of the year Matt Ryan had,” Barkley said on “The 49ers Insider Podcast” on NBC Sports Bay Area.

“He’s a believer in that. He saw the benefits of what Matt did with some of his drops and the timing on routes, how he changed his feet on some things. So we’re kind of sticking with that plan. Everyone is a little different, but for the most part we’re all on the same page when it comes to what our drops are looking like, our footwork and how the ball is coming out.”

House is a former major league pitcher and pitching coach who founded the 3DQB training facility in Los Angeles. Dedeaux pitched at USC and is the grandson of USC baseball coaching legend Rod Dedeaux. Former NFL quarterback John Beck is a motion mechanics instructor.

Tom Brady, Drew Brees, Alex Smith and Carson Palmer are among the NFL quarterbacks who have worked with 3DQB.

“I believe in those guys and what they’re doing,” Barkley said. “They’re at the top of their game, working with Brady and a bunch of other guys. They’ve helped me.

“He won’t change your throwing motion or really tweak how the ball comes out, but he’s going to try to maximize velocity and ground force production and torque -- a lot of sports science terms. But, really, just maximizing efficiency with your motion and making sure you’re sequencing is right.”

Barkley had never played for Shanahan before signing a two-year contract with the 49ers on the first day of free agency. But there are two obvious connections. Barkley’s offensive coordinator last season with the Chicago Bears was Dowell Loggains, Shanahan’s quarterbacks coach in 2014 when Shanahan was the Cleveland Browns’ offensive coordinator. The other connection is House.

"It’s kind of funny, he worked with Atlanta’s staff all of last year, helped Matt Ryan, kind of build his base from the ground up and helped him a lot and he had an MVP year," Barkley said of House.

"There may have been talks down the pipeline, who knows. I don’t think that was the deciding factor by any means, but it never hurts.”