By Emelie Rutherford

President-elect Barack Obama confirmed yesterday Defense Secretary Robert Gates will stay on the job in the next administration, capping off negotiations with Gates over just what type of role he will have in the new setup.

No indication of when the deputy defense secretary will be named was given when Obama unveiled his new national security team in Chicago yesterday morning. Yet industry and congressional sources said they expect the deputy post to be announced in the next several weeks.

There has been talk of former Navy Secretary Richard Danzig serving as Gates’s deputy before transitioning into the secretary post, as Gates has been expected to not stay on for all of Obama’s first term. Sources said Gates was sensitive during negotiations with the Obama transition team about continuing on as defense secretary if he would serve in a limited status.

Gates has supported initiatives Obama and Democrats in Congress have resisted, including the quick deployment of European missile defense sites and development of a Reliable Replacement Warhead. Gates also has been less keen than some lawmakers to continue production of the Lockheed Martin [LMT] F-22 stealth fighter.

Obama said he will charge Gates with "responsibly ending the war in Iraq," and said together they will "ensure that we have the strategy, and resources, to succeed against al Qaeda and the Taliban," noting the war in Afghanistan.

"Going forward, we’ll continue to make the investments necessary to strengthen our military and increase our ground forces to defeat the threats of the 21st century," Obama said with Gates at his side.

Gates said he is honored to serve the military and Obama, and is "mindful that we are engaged in two wars and face other serious challenges at home and around the world."

Lawmakers on both sides of the aisle offered nothing but praise for Gates.

Senate Armed Services Committee Chairman Carl Levin (D-Mich.) highlighted Gates’s actions to restore accountability at the Pentagon, and his call for accelerating the doubling of the size of the Afghan National Army.

House Armed Services Committee Chairman Ike Skelton (D-Mo.) said Gates is "trustworthy (and) has a keen sense of duty."

Obama also announced yesterday his national security team will include retired Marine Gen. Jim Jones as national security adviser, Sen. Hillary Clinton (D-N.Y.) as secretary of state, and Gov. Janet Napolitano (D-Ariz.) as Homeland Security secretary.