DO NOT turn the pickup around.

What kind of pickup is it?
Quote by conor1148
who cares if they're drawn,


Peavey Supreme 100W head
Crate 4x12 cab
Epiphone Les Paul Standard+
Modded Johnson Stratocaster
if it's a tune o matic bridge make sure each post is the same height
Dean DOF w/ Seymour Duncan Hot Rodded Pickup Set
Mesa Boogie Rect-O-Verb 50w Head
Randall KH-120 Cabinet

Marshall 1960a Cabinet
raise the pickup on that side, or maybe get new strings
Custom les paul copy with sun inlay
Epiphone les paul custom with emg 81/85
Hondo 80's star shape(project)
ESP explorer (project)
Epiphone dr200s
Epiphone ej200
mxr doubleshot distortion
Raven rg100
Is the action the same on the E string? Is there an EQ setting that lowers anything less that 55Hz?
It's possible that that string may be a lot more "dead" than the others if you play on the E that much more than the others. Try some new strings, adjust the height of the pickups, etc.
String height can play a factor. I noticed my E being really quiet too, and I had new strings, turned out lowering my string height gave it the needed volume relative to the other strings' volumes.