While we enjoyed a period of friendship, we were far from allies for the bulk of our history leading up to the second world war.
Our modern relationship didn't get off to a good start.
If I'm honest, this event commonly remembered in history is probably overly credited for the "opening of Japan" than it deserves. The US was only one of multiple western nations involved in the military bullying of Japan, and the memory of this event was played up by both sides later on, even though the Tokugawa Shogunate realistically caved under persistent pressure rather than specifically as a result of Commodore Perry's actions.
After the Meji Restoration, the Japanese deliberately forged friendly relationships with all of the various western powers. They modeled their naval practice off of the British, and their army practice off the Germans. Meanwhile, the US was trying to flex its muscle slightly internationally, but was very far from contesting British primacy on the high seas, and thus didn't seek to make too big of a splash.
This begins to change dramatically with the US victory in the Spanish-American war and the Japanese victory in the Russo-Japanese war. The Japanese viewed the western pacific as their potential sphere of influence, and were actively growing as a new colonial and industrial power with a hungry appetite for raw materials not available domestically, and the US just made themselves a serious potential obstacle. The Japanese had bigger, more local fish yet to fry, but with the Russians out of the picture, no other western power had a strong hold on a significant holding on the border of Japan's growing sphere of influence.
The US had far less strategic interest in far eastern colonialism. This was more geopolitical grandstanding from a nation not really interested in being overly involved in the world outside of the western hemisphere. Up to the end of the First World War, the US had no real interest in directly interfering with Japan's rise.
In short, this period up until the end of the First World War, both sides were aware of the future strategic rivalry, but neither side had any interest in pursuing it, and maintained fairly friendly relations.
This all began to change, starting with the Treaty of Versailles.
The Japanese entered the First World War to pick off the pacific colonial assets held by Germany, and wasn't having any of the national self-determination bullshit that Wilson was trying to serve up. Unlike the United States, who benefited from a vast supply of domestic natural resources, Japan enjoyed no such luxury, and understood expansion as necessary to grow their economy. While fans of Wilson see his policy as outwardly benevolent, the Japanese felt directly threatened by it.
This alone didn't spoil US-Japanese relations immediately. Even the Washington Naval Treaty, while not favoring Japan in its final form, was actually something that the Japanese were OK with, as they were fully aware they could not directly outbuild the US in their current state. With China falling apart, the Japanese strategy was to appease the US while they expanded their influence further on the mainland. This was not just to cover their strategic backside, this was also to keep up trade with the western allies who still dominated most of the local raw materials market.
By the end of the 1920s, the US had retreated more towards isolationism, especially with the onset of the Great Depression. When FDR eventually was elected, he was the president of a freshly isolationist nation, even as Japan invaded China in 1937. FDR wasn't having any of this republican isolationist nonsense, and worked actively to break the country out of its shell. While he was primarily concerned with Nazi Germany, he poked sticks in all sorts of directions to get the american people interested in the global political situation.
One of these sticks was thrust against Japan, who was looking to capitalize on the fall of France and the Netherlands. The Chinese coast was not particularly easy to exploit, and not particularly resource rich. The resources the Japanese really wanted were in the Dutch East Indies (modern Indonesia), and French Indochina gave them the bases from which to reach this area. This frightened the British, as it also put the Japanese in striking range of British-held Malaysia and Singapore. The US took this as the place to put its foot down, piggy-backing on British strategic concern and public opinion against Japan stemming from atrocities in China to commit to a full scale embargo against Japan. This forced Japan's hand, and put them on the course to military confrontation starting with Pearl Harbor.
TL:DR: ~1850s -> 1905: Not many mutual fucks given ~1905 -> 1918: General friendliness, but acknowledgement of future rivalry. 1918 -> Early 1920s: Power shakeup leading to Washington Naval Treaty, ends largely in US retreat to isolationism ~1930s->July 1941: Japanese expand into china while pursuing western appeasement. Western embargo starts in July 1941. Dec 7 1941: Pearl Habor 1945: War ends, US occupation begins. Any sort of actual political alliance really begins here as the Cold War ramps up.