The city of Kyoto is the capital of a bigger place , the prefecture of Kyoto . The city is connected with other part of Japan by the Meishin Expressway , which has two interchanges in the city : Kyoto Higashi ( Kyoto East ) in Yamashina-ku and Kyoto Minami ( Kyoto South ) in Fushimi-ku . The Kyoto JÅ `` kan Expressway connects the city to northern regions of Kyoto Prefecture .