To make the Gutter Column transparent, I suggest you define it like the following:
:hi SignColumn guibg=NONE cterm=NONE term=NONE
This should come after any colorscheme command, so that it can override it, in case your colorscheme sets it. You can also place it into an ColorScheme
autocommand, so that it will automatically override any colorscheme settings:
au ColorScheme * :hi SignColumn guibg=NONE cterm=NONE term=NONE
Also, you may want to check where this was set previously, by using:
:verbose :hi SignColumn
which will tell you, in what configuration file this highlighting group was last set. It could also be set inside some plugin, that configure the sign column for you, in that case I'd recommend to check the documentation of the plugin how to configure the SignColumn properly.
:hi SignColumn guibg=NONE cterm=NONE term=NONE