The default textures found in GTK actually come from the pak0.pk3 (I think that is the one). When you open up GTK, it uses any available pk3's in baseq3 as sources for textures models, etc etc.
If you have not added any of your OWN custom textures, or texture packs, then you don't need to worry about including anything of the default textures.
Try following this tutorial on how to make your pk3 with winzip (which is the way most of us do it anyway I think)
http://planetquake.com/qworkshop3/tutorials/pk3files/tut.htm