Maybe you would like the "neighborhood" feature in IMG. I did a search for the FusA gene, and on the gene page clicked the 'show ortholog neighbors" and it yields this kind of graphic display that I find helpful:

My FusA is in red, you can look at the adjacent genes and check out their organization graphically. And you can link back to the genes and organisms from that type of page.

There are other things you can do, you can select subsets of species to look at, etc.

Here's the main IMG page to get started: http://img.jgi.doe.gov/

You should use the protein sequences of X and Y as queries in a sequence similarity search (such as BLAST) against the genome sequences (DNA) of bacteria. Note the coordinates of the resulting matches, including instances when either X or Y or both are not detected in the other organism. If the coordinates of the X and Y genes are very near each other or even overlap (as genes sometimes do in bacteria), you should do a little more investigation to see if another orf (open reading frame) exists between those X and Y genes.

I would make note on a copy of a bacterial phylogenetic tree where X and Y are found, where they are near physical neighbors (i.e. most likely to be in the same operon) and where they are not found.

While I do a quick search, you might want to try out STRING. It's a protein-protein interaction database, BUT one of the evidences they use are gene order/neighborhood.

If you put in a gene of interest, click "go" and then click the evidence "neighborhood" you'll see the gene of interest in the operons/gene order of your species and orthologs across species.

It's not an elegant solution, but you can answer the question. Here is a short screencast to show you what I mean.