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I have a Sparkfun RGB rotary encoder that I'm hooking up to an Arudino Nano. The blue and green LEDs run at 3.3v. The red led runs at 2. I figured I could run the LEDs directly off of the 3.3v line.

Since the LEDs are common anode, I need to switch them on by raising a control pin on the Nano. Basically this would mean I'm using a 5V signal pin hooked to the base of the transistor to control a 3.3V circuit. All the examples I've seen do the opposite. They'll use the lower voltage circuit to control the higher voltage one. Will it work in the other direction?
LEDs always require a current limiting resistor. I suggest you read this Sparkfun tutorial: ... iodes-leds.

You can connect the LEDs directly to the Nano without a transistor. For the 3.3V LEDs, use a 180ohm resistor in series with the LED. For the 2V LED, use a 330ohm resistor in series with the LED.