Infer the new (Ban et. al) ribosomal nomenlature (ex. uL53 ) from the ribosomal protein's sequence
This is a copy-paste nearly verbatim of comments so that the question has an answer

What you are trying to do is find what genes are in what homology cluster. This is common problem and there are many solution each with some issues. 

Uniprot90 is indeed a cluster of homologues but it is too limited. Whereas you require clusters that span all the domains (universal).

COG

The nearly original grouping, is COG (cluster of orthologous genes). It is really handy for this but aren't really available from Uniprot and NCBI (its curator) has been phasing COGs out. In Uniprot records, they are patchily present as its derivative eggNOG (which has varying degrees of "scope", LUCA being the universal one):

&lt;dbReference type="eggNOG" id="COG0451"&gt;
&lt;property type="taxonomic scope" value="LUCA"/&gt;
&lt;/dbReference&gt;


Pfam

Another option that is well mapped and always present when possible in Uniprot entries is Pfam ids. These are domain family annotations and are also good option. It is a domain fold group. So domains within protein with homologous folds are grouped into one. If a protein has two known domains, it will have two Pfam entries —repeat proteins have loads, but most protein have one domain. In Uniprot XML you will find these are:

&lt;dbReference type="Pfam" id="PF01370"&gt;


Similarly there is InterPro, which is more narrow than Pfam, but generally overlaps.

DIY

Then there's always the option of making your own psi-Blast motif on the NCBI website (setting high number of hits, setting the database to refseq or even PDB and doing a few iterations), saving the motif pattern (PSSM) and using local blast with it.

Caveats

In general you may however encounter these pitfalls:


you may have two protein clusters that share a single id
you have gene fusions (one protein, 2 domains of interest). In Pfam the protein will have two ids, with COGs or similar, you'd have only an anamalous length to go by.
you may have wished to find analogues (i.e. two protein that arose independently that have the same role (a lot of ribosomal protein are simply structural). No homology clustering scheme can find these.  Say a bacterium has evolved to have a different protein with that role, yet as it has never been studied it is a domain of unknown function (guilt by association is the common strategy, but that is beyond your scope here).
you have a very small protein which is poorly conserved