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I have an image sequence that I rendered out that contains a smoke simulation and I am trying to overlay the sequence onto a video. The background is rendered transparent to PNG's but using the compositer, I cannot figure out how to mix them properly. I have tried just using a mix node with the two input and the alpha as the factor but to no use.

enter image description here

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Your image showed that the alpha was plugged into the image input while the image was plugged into the mix factor. So if there was no alpha you would be mixing with black. However to save re-rendering you could try using a lumakey node to remove the black background:

enter image description here

or use a simple mix effect, like "screen" or "add":

enter image description here

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