The Lower Manhattan Construction Command Center, a city-state agency that coordinates construction of the World Trade Center, the new PATH Station, the MTA’s Fulton Transit Center and developer Bruce Ratner’s 75-story Beekman Tower, could be disbanded because of funding shortfalls. The agency, which is funded by the city, the state, the Metropolitan Transportation Authority and the Port Authority of New York and New Jersey, faces a budget gap about $9 million. The Lower Manhattan Development Corp. controls the Command Center, which was established by Governor George Pataki and Mayor Michael Bloomberg in 2004. The city has paid its share and says state agencies need to pay their dues.