Egypt’s first free parliament in six decades got to work on Monday, with Islamists holding by far the most seats and opponents comparing their grip on the chamber to that enjoyed by the now-defunct party of deposed president Hosni Mubarak.

With almost half the seats in the assembly, the Muslim Brotherhood is promising to cooperate with the generals who took power last February when Mubarak was overthrown, in their transition to civilian rule.

The generals will remain in charge until after a presidential election in June when they have promised to hand over power. Many Egyptians suspect the army may seek to retain influence behind the scenes after that.

Thousands of protesters who fear a deal between the Islamists and the army to carve up power cried “down with the military government” behind a police cordon near the parliament building, a reminder to those trying to rebuild Egypt’s state institutions of the power of the street.

Parliament will have the lead role in appointing a 100-strong assembly that will draw up a new constitution for Egypt. On Monday, The New York Times quoted a Western diplomat as saying the military and the Brotherhood have settled on the broad outlines of the distribution of powers to be delineated in the document.

That agreement, the paper reported, includes the creation of a mixed presidential parliamentary government, a legal system no more religious- based than the existing one and guarantees on freedom of worship and expression.

The deal would reportedly leave in place an existing constitutional clause declaring Islamic jurisprudence as the main source of Egyptian law, but not modify that clause to refer to more specific rules of Islamic law as some Islamist lawmakers had sought.

The diplomat said a mixed presidential-parliamentary system would allow parliament to oversee domestic matters, while leaving the president in charge of more contentious foreign policy issues such as relations with Israel. The Brotherhood has said it would not field a candidate in this year’s presidential elections.

The deal also reportedly includes a compromise on the thorny issue of the defense budget that would see a limited number of officials charged with determining outlays to the traditionally powerful military.

Jon Alterman, director of the Middle East Program at the Washington-based Center for Strategic and International Studies, said that if true, the deal reflects the usual back-room deals of democratic politics.

“That’s how politics work – people reach understandings in private, some of which are made public,” he said.

“That’s politics – whether American, Israeli or Egyptian.

“I’d be very surprised if there’s anything like a formal deal, but I’d also be very surprised if the two parties don’t talk to one another,” Alterman said. “It’s in both of their interests to neither surprise nor corner the other, because each has tools that it can call on that would greatly harm the interests of the other.” On Sunday, the US Embassy in Cairo tweeted that the American ambassador and other US officials had met with the Nour party, an adherent to the hardline Salafi Islamist movement and the second-biggest winner in parliamentary elections.

Last year the US administration modified a long-standing ban on official meetings with Egyptian Islamist groups, and high-level State Department representatives have met with Brotherhood figures on several occasions since Mubarak’s overthrow.

Alterman said the meeting with the Nour officials is in line with that policy.

“The US policy has been to meet with all parties in parliament,” he said. “While meeting the Salafis represents a change, it’s not a change in the policy, which is to meet with all parties in the parliament.”

Monday’s session began in a somber mood as parliament’s acting speaker – its oldest member was automatically chosen – invited deputies to hold a silent prayer in memory of the hundreds who died in the uprising that ousted Mubarak.

“The blood of the martyrs is what brought this day,” speaker Mahmoud al-Saqa, 81, said. Some deputies wore yellow sashes in protest of the army’s policy to try thousands of civilians in military courts.

The session became more raucous when one Islamist legislator, Mamdouh Ismail, read the oath that vows allegiance to the nation and its laws but added his own words, “so long as it does not oppose God’s law,” prompting the speaker to tell him to repeat it without his addition.

An angry exchange erupted later as deputies worked on their first task of electing a permanent speaker.

One candidate opposing Brotherhood nominee Mohamed Saad al-Katatni sought to introduce himself to the chamber, a move the Brotherhood opposed in a swift vote. Katatni, secretary-general of the Brotherhood’s Freedom and Justice Party (FJP), was then appointed.

In the recent elections, non- Islamists were pushed into third place behind the Freedom and Justice Party and the Salafis, the surprise runners-up. The FJP says it controls almost half the 498 elected seats, with a few re-runs to be held, but would be guided by a spirit of compromise.

“We will cooperate with everyone: with the political forces inside and outside parliament, with the interim government and with the military council until we reach safety heralded by a presidential election,” said Essam el-Erian, deputy FJP head.

Parliament’s independent voice was extinguished after a 1952 coup that toppled the king and swept military-backed autocrats to power.

Mubarak was a former air force commander and the ruling military council is now led by the man who was Mubarak’s defense minister for 20 years, Field Marshal Mohamed Hussein Tantawi.

Reuters contributed to this report.

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