The Prophet is a Commander who was turned into a Prophet by the command become Prophet. You can normally have only one prophet at a time. If your prophet dies, you must wait a few turns before you get a message that you can make a new prophet. The biggest advantage of a prophet is that he spreads Dominion like your Pretender. He is also permanently blessed, even if he was not sacred. He also gets a priest skill of level 3. If he already had 3 or more priest levels, he receives a +1 bonus to his priest level.
With priest skill 3, your Prophet can cast such useful spells such as smite and divine blessing without any research.
Note: Mictlan in some Eras can spread Dominion only with the Pretender and with Blood Sacrifices.
Note: It is possible by commander-kidnapping to corrupt enemy Prophets so that you have more acting Prophets who spread your Dominion.