Quite often when it comes to 5 string bass some people start playing whatever using the top (thick) string as an E-string and a reference point. You can even tell them, "that's not an E string, it's a B". However, because guitar/bass players are so used to the top string being an E it can actually take a little while to sink in.
With that in mind take a look at this animated gif. It's the G Major scale in a common box shape being played on the 3rd fret of the E string of a 5-string bass. This is a great example of good one-finger-per-fret rule fingering. Notice that each finger plays only the fret it is assigned to (EG: 1st finger 3rd fret only, 2nd finger 4th fret only, etc).
Using the E string as a reference on a 5-string bass is fine. But, you'll also have to teach yourself how to build backwards from the E-string to the B. We'll give you some hints on that at another time.
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