I believe the two minor league teams Ryan own part of are Corpus Christi Hooks (AA Astros) and Round Rock Express (AAA Astros). For some reason, it seems Clemens is part owner of one of them. I'm not sure about that, though.
I wonder if he'll sell. The conflict of interest is pretty loose, but appearances may set well.
[EDIT: Both minor league clubs are owned by Ryan-Sanders Baseball, and Clemens, Pettitte and Biggio are all minority owners
Roger Clemens, Andy Pettitte and Craig Biggio have joined the investment lineup as co-owners of the expanding minor league baseball business controlled by Houston financier Don Sanders and Hall of Fame pitcher Nolan Ryan.
The trio of Houston Astros teammates have thrown in with Ryan-Sanders Baseball, the parent company of the Round Rock Express and Corpus Christi Hooks minor league franchises. The three Major League Baseball stars signed on as minority partners in the ownership group.
Houston Business Journal]