Answers.Body: <p>How about using RefSeq itself? Say, you are interested in all E. coli proteins, you can use the query <code>&quot;Escherichia coli&quot;[Organism] AND RefSeq[Filter]</code> <a href="https://www.ncbi.nlm.nih.gov/protein" rel="nofollow noreferrer">here</a>.</p>
  <p>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 &quot;Escherichia coli str. K-12 substr. DH10B&quot;, you can use the taxonomy identifier 316385 (obtained from <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=316385" rel="nofollow noreferrer">here</a>) in the query <code>txid316385[Organism] AND RefSeq[Filter]</code>.</p>
  <p>To extract a list of accessions and save them to a file on disk, use the &quot;Send To&quot; menu at the top right corner, choose &quot;File&quot; as destination followed by &quot;Accession List&quot; as the format and download the file. Alternatively, you can use E-utilities API or the <a href="https://www.ncbi.nlm.nih.gov/books/NBK179288/" rel="nofollow noreferrer">EntrezDirect</a> tool on the Unix command line to download these data programmatically.</p>
  <p>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 &quot;Bacteria&quot;, 7401 are found by <code>&quot;Escherichia coli&quot;[Organism]</code>, and the species-level search will give you the full set of proteins.</p>
  <p>You could also use the <code>AutonomousProtein2Genomic.gz</code> file from the <a href="https://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/" rel="nofollow noreferrer">RefSeq FTP</a> 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 &quot;Escherichia coli&quot;.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-06-22T17:17:04.970Z
Answers.Text: Thanks warmly for the response.
  Actually, I was looking for a database in which I can extract all RefSeq protein IDs as a .csv or .xls file.
Answers.UserDisplayName: Ehsan Salehabadi
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-06-27T09:04:07.863Z
Answers.Text: I would say,suggested query is not working as expected for refseq.Some escherichia coli refseq proteins have “lower” taxonomy rank ,for example “”Escherichia- proteins which shared between different Escherichia species.Technically ,I know only one way for now extract ALL Escherichia Coli refseq proteins
Answers.UserDisplayName: user6690
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-06-27T09:11:14.710Z
Answers.Text: retrieve all corresponding refseq assemblies from ftp and parse them
Answers.UserDisplayName: user6690
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-06-22T13:27:09.120Z
Answers.LastActivityDate: 2021-08-09T22:35:10.010Z
Answers.LastEditDate: 2021-08-09T22:35:10.010Z
Answers.UserDisplayName: vkkodali
Body: <p>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?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-15T20:20:50.990Z
Comments.Text: Please consider accepting the answer below - its good for site stats and its a good answer IMO
Comments.UserDisplayName: M__
Tags: <database><proteomics><refseq>
Title: A database for RefSeq protein accession IDs
ThreadText: # A database for RefSeq protein accession IDs
  
  (Asked by: username_0 on 2021-06-22)
  
  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?
  
  **Tags:** database, proteomics, refseq
  
  > **Comments:**
  > **username_1**: Please consider accepting the answer below - its good for site stats and its a good answer IMO  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2021-06-22. Score: 0
  
  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](https://www.ncbi.nlm.nih.gov/protein).
  
  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](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=316385)) 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](https://www.ncbi.nlm.nih.gov/books/NBK179288/) 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](https://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/) 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".
  
  > **Comments:**
  > **username_0**: Thanks warmly for the response. Actually, I was looking for a database in which I can extract all RefSeq protein IDs as a .csv or .xls file.  
  > **username_3**: I would say,suggested query is not working as expected for refseq.Some escherichia coli refseq proteins have “lower” taxonomy rank ,for example “”Escherichia- proteins which shared between different Escherichia species.Technically ,I know only one way for now extract ALL Escherichia Coli refseq proteins  
  > **username_3**: retrieve all corresponding refseq assemblies from ftp and parse them  
  
  ---
  
  