Are there any databases or tools that contain a list of all RefSeq protein IDs for the interest organism/microorganism, e.g. get a specific microorganism name and return all RefSeq Protein IDs that have been identified?
How about using RefSeq itself? Say, you are interested in all E. coli proteins, you can use the query
"Escherichia coli"[Organism] AND RefSeq[Filter] here.
If you know the Taxonomy identifier for the specific organism of interest to you, it can also be used. For example, if you are interested in only "Escherichia coli str. K-12 substr. DH10B", you can use the taxonomy identifier 316385 (obtained from here) in the query
txid316385[Organism] AND RefSeq[Filter].
To extract a list of accessions and save them to a file on disk, use the "Send To" menu at the top right corner, choose "File" as destination followed by "Accession List" as the format and download the file. Alternatively, you can use E-utilities API or the EntrezDirect tool on the Unix command line to download these data programmatically.
To address the question about E. coli proteins shared between different species... There's no need to parse FTP files to get all the RefSeq proteins for a bacteria species. While it's true that some RefSeq WP proteins have taxids above species level, like Enterobacterales WP_003861789.1 where the identical protein is found in genomes from multiple species of the order Enterobacterales, those proteins are still retrieved by a species-level organism search. NCBI implemented some extra handling for the RefSeq WP proteins to treat the MULTISPECIES WPs like they belong to all of the species with genomes on which they're annotated. So of the 56947 WPs assigned as "Bacteria", 7401 are found by
"Escherichia coli"[Organism], and the species-level search will give you the full set of proteins.
You could also use the
AutonomousProtein2Genomic.gz file from the RefSeq FTP path which has a mapping of how all WPs map to specific genomic sequences, but it's a really big file and it would take a long time to grep for "Escherichia coli".