To start this puzzle, bring up the Alignment Panel again. This time, the letters and colors in the sequences are a mess. The white line between the two sequences shows how well each segment matches, the thicker, the better.
Pull on the row of dots on the right of the Alignment Panel until you can see the whole sequence.
You can slide the sequences around to match them up. Try closing the gaps in the top sequence first. When there's a block of codes together, you can move them left by clicking on the rightmost code and pushing the block left.
Close all the gaps in the bottom sequence next. Now segments 1 through 12 of the top sequence match the bottom sequence. Click on segment 13 in the top sequence and slide it right. When you've moved it four spaces to the right, the rest of the two sequences should match.
Once things are lined up, click on the play button to thread the protein to the template. The protein will end up with cut at the gap in the two sequences. Shake, then wiggle until the cut turns yellow. Click on the cut to close it.
If you run into problems moving things around, there are undo, redo, and reset buttons on the left of the Alignment Panel near the play button. Also, if you click on the Name button on the right side of the panel, it becomes "Match", and shows a score showing how well your alignment matches. For this puzzle, you should be able to get a match score of 116.
Technical stuff: parts of proteins with a similar amino acid sequence tend to have the same shape. This puzzle is still a simple demonstration of the tool. In actual alignment puzzles, you get multiple templates to choose from, and can use "partial threading" on the parts that match the best.