I took one of your IDs and searched for it in NCBI::
On the right panel for GENEs I’ve got:
One gene from Caenorhabditis elegans
And on the right panel fot PROTEINs I’ve got 2 proteins (the same) with different IDs for different databases(?):
There are many options. If you are familiar with R you might want to look into
If you like raw data approach, simply download the databases you want to work with and join them with e.g. bash or something similar. Getting genes from uniprot in the easier way is probbably using this: http://www.uniprot.org/uploadlists/
If not sure it will swallow all entries, split your files and do it in steps.