AFRICOM took over the Djibouti-based Combined Joint Task Force–Horn of Africa (CJTF-HOA) from CENTCOM in October 2008. Combined Task Force 151 (CTF 151) includes the US portion of the military effort to combat piracy at sea and commenced operations in January 2009. The Navy ships and sailors in CTF 151 are part of the 5th Fleet, based in Bahrain, which is under CENTCOM. CENTCOM is headquartered in Tampa, Florida and AFRICOM is headquartered in Stuttgart, Germany.
Presumably this makes sense for historic and cultural reasons, given the greater connection of Tampa Bay to buccanners and such.
For those wondering about the legal role of AFRICOM, the US federal statutory definition for such a “combatant command” is “a military command which has broad continuing missions” and in the case of the regional commands involves more than one military service. The missions are to be reviewed by the Chairman of the Joint Chiefs of Staff (in otherwords military rather than civilian leadership) “not less often” than every two years, with recommendations then reported to the President.