text: user727: I am attempting to run a BLAST search remotely using BLAST+.
  I can get search to work correctly at the command line with the following commands:
  blastp -query proteins.fasta -remote -db nr -out proteins_nr.txt -outfmt 6 -evalue 1e-30
  
  However, I would like to us the remote database titled "Microbial proteins from nr" which is what would be used for the microbial blast search accessing BLAST from the NCBI site.
  I'm struggling to find the correct code to access this database instead of just "nr".
  Is there a list with the codes of different databases?
  Thanks in advance
  
  user541: I believe you're looking for env_nr? It's listed as such, under Metagenomic proteins in the blastp webpage. It appears that the word within brackets should be supplied alongside the -db parameter. A quick test with a dummy amino acid fasta file does turn up a result to a valid NCBI protein accession.
  
  Edit: I followed up on this with a little more digging around, and it appears the database you're looking for is called Microbial_proteins. I ended up quote-searching Microbial proteins from nr on Google and exactly 2 hits turn up. The first hit, I think, is what the OP posted a screenshot of in a comment to this answer. The second is a list of databases along with keywords from a Spain-based bioinformatics firm: http://data.biobam.com/ncbi_blast_dbs_protein.pdf. I retried the dummy example with the Microbial_proteins database, and it seems to work. Again, I am not sure why I can't easily find this on an NCBI resource. Also, I am curious as to how different this database is from env_nr.
  
original_text: 727: <p>I am attempting to run a BLAST search remotely using BLAST+.</p>
  
  <p>I can get search to work correctly at the command line with the following commands:</p>
  
  <pre><code>blastp -query proteins.fasta -remote -db nr -out proteins_nr.txt -outfmt 6 -evalue 1e-30
  </code></pre>
  
  <p>However, I would like to us the remote database titled "Microbial proteins from nr" which is what would be used for the microbial blast search accessing BLAST from the NCBI site.</p>
  
  <p>I'm struggling to find the correct code to access this database instead of just "nr".</p>
  
  <p>Is there a list with the codes of different databases?</p>
  
  <p>Thanks in advance</p>
   541: <p>I believe you're looking for <code>env_nr</code>? It's listed as such, under <code>Metagenomic proteins</code> in the blastp webpage. It appears that the word within brackets should be supplied alongside the <code>-db</code> parameter. A quick test with a dummy amino acid fasta file does turn up a result to a valid NCBI protein accession.</p>
  
  <p><a href="https://i.stack.imgur.com/hNm3k.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/hNm3k.png" alt="partial screenshot from NCBI&#39;s blastp webpage"></a></p>
  
  <p>Edit: I followed up on this with a little more digging around, and it appears the database you're looking for is called <code>Microbial_proteins</code>. I ended up quote-searching <code>Microbial proteins from nr</code> on Google and exactly 2 hits turn up. The first hit, I think, is what the OP posted a screenshot of in a comment to this answer. The second is a list of databases along with keywords from a Spain-based bioinformatics firm: <a href="http://data.biobam.com/ncbi_blast_dbs_protein.pdf" rel="nofollow noreferrer">http://data.biobam.com/ncbi_blast_dbs_protein.pdf</a>. I retried the dummy example with the <code>Microbial_proteins</code> database, and it seems to work. Again, I am not sure why I can't easily find this on an NCBI resource. Also, I am curious as to how different this database is from <code>env_nr</code>.</p>
  