No, they do not.

Skill ranks refer only to the number of well, ranks that you've put into the skill.

I can't find an exact reference to back that up, but they make a big deal when referring to ranks vs bonuses:

Each level, your character gains a number of skill ranks dependent upon your class plus your Intelligence modifier. Investing a rank in a skill represents a measure of training in that skill. You can never have more ranks in a skill than your total number of Hit Dice.

And

Each skill rank grants a +1 bonus on checks made using that skill.

Since you can only have a number of Ranks in a given skill equal to your level, that means that a minimum number of ranks is effectively a level requirement.

So, when for example you have an Assassin who has a requirement of minimum 5 ranks in Stealth, you must be at least 6th level before even being able to become an assassin.

Edit:

You're doing conversions! This free PDF will cover most of what you need to do: http://paizo.com/pathfinderRPG/v5748btpy89m6 (You do need a Paizo account to download it, but that too is free).

From the Prestige Classes section in the conversion guide:

Make sure to check the prestige class requirements (and the rest of the class) for any skills that have been altered or removed from the game and adjust them accordingly. In addition, the skill rank requirements should be equal to the 3.5 requirements – 3 (minimum 1 rank). Note that some of the core prestige classes do not follow this formula exactly and you should consider these requirements carefully.