Weight of a Poor Internal Reference in transitioning?

I've been working at an Back Office Ops job for a BB for about a year and am trying to make an upward move, needless to say.

I want to break into Equity Research and have developed the right relationships and contacts thus far as far as networking is concerned. I was even able to send my resume out to the Head Recruiter and a few Associates in the department that I also spoke to have mentioned that I'm in good shape after taking a look at my resume.

The only problem is that my work in my ops job hasn't been great. Not because of abillity but a sheer lack of motivation. I can't seem to get myself to work as well as I can. I do get by doing the bare minimum, though. My year-end review wasn't a trainwreck, and I did make the middle of the road rating. However, I know they're going to make an internal call for a reference, and my boss will more than likely not be of mind to recommend me.

How far can a poor reference go toward dampening my chances for a transition?

Moreover, given my relatively poor performance, any input on how to even inform my boss about my intentions before I apply, would be greatly appreciated.