BOSTON July 18, 2013 -- Stephen "Stippo" Rakes, a possible witness in the murder trial of alleged crime boss James "Whitey" Bulger, has been found dead, authorities said.

The body of Rakes, 59, had "no obvious signs of trauma" and an autopsy is being performed to determine the cause of death, Middlesex District Attorney Marian Ryan and Lincoln, Mass., Police Chief Kevin Mooney announced today.

The corpse was found on Mill Street in Lincoln yesterday at 1:30 p.m., police said.

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Rakes had been on the witness list and had been eager to testify that Bulger threatened his family at gunpoint and forced him to turn his liquor store into a front for the Winter Hill Gang. But earlier this week prosecutors informed Rakes he would not be called to testify, a decision that left Rakes "despondent," a source close to his family told ABC News.

Rakes was last seen by other Bulger victims in the courtroom Tuesday afternoon. He sent a text message to Tommy Donahue, son of victim Michael Donahue, at 2:31 p.m. Tuesday afternoon, furious that he had been dropped from the government's witness list.

"He was upset that he wasn't going to get to tell his side of the story,'' Tommy Donahue told ABC News. "He had waited for a long time for his day in court, and now he is not going to get it. I don't think it was something that he would commit suicide over there. There is something wrong with this, really wrong."

Added his mother, Patricia, who has been with her three sons Mike, Tommy and Sean every day: "We have become like a family, all the Bulger victims. Stephen Rakes was a good man. It's a sad day and it makes me worry about what could happen to my boys."

The judge overseeing the Bulger case hunkered down with lawyers in a confidential conference at the South Boston courthouse today where the trial is being held. Bulger, alleged to be a notorious and murderous crime boss and federal informant, is standing trial after being found on the lam in California two years ago.

Federal prosecutors said Rakes was supposed to testify that Bulger and associate Stephen Flemmi threatened his daughter at gunpoint, and took over his South Boston liquor store for Bulger's headquarters. Bulger sidekick Kevin Weeks testified last week Rakes' contention that Bulger's gang put a gun to his daughter's head was bogus.

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Rakes comes from a storied South Boston family. His brother Joseph Rakes was photographed in Stanley Forman's Pulitzer Prize winning photograph charging at an African-American man on Boston's City Hall with the sharp end of the American flag – which became the symbol of the racial unrest during the city's anti-busing crisis.

News of his death investigation came on the same day that Stephen "The Rifleman" Flemmi was slated to take the stand against Bulger. The two men ran the Winter Hill Gang for decades while also working as informants for the FBI, according to prosecutors and courtroom testimony.

Police told the Rakes family the death appeared to be a suicide. But a source close to the Rakes family told ABC News that "he had no phone, no wallet, and police are still looking for his car." The body of the man found in Lincoln was positively identified as Rakes this morning after a fingerprint match, sources said.

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Rakes' longtime friend Steve Davis, whose sister Debbie was allegedly murdered by Bulger, had met him for breakfast daily before court. Davis said he last saw Rakes Tuesday in court but then couldn't reach him all night Tuesday and yesterday he did not meet him in the courthouse cafeteria for breakfast.

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"Stippo would not kill himself. Absolutely not,'' Davis told ABC News this morning. "He was looking forward to taking the stand. He told me over and over he had a big bombshell to drop. He had everything to live for and was looking forward to his day in court."

Davis - who lost his sister, brother and father to homicide, and whose daughter was killed in a drunk driver accident - was devastated by the news.

"It doesn't make sense,'' Davis said.