text: user3061: Is there a database with all known proteins/genes of specific pathogens such as Staph aureus and annotated whether it is a known virulence or resistance factor that idealy can be downloaded in table format?
  
  user2108: I suggest that you are looking for a resource like VFDB (virulence factor database). That table does annotate by bacterial species, so you can filter as you like.
  You can download a description table or FASTA sequences from their downloads page (see screenshot). Last update was 4 days ago, so they should be quite current.
  
  For resistance genes, you could use something like CARD (Comprehensive Antibiotic Resistance Database), which also has a downloads page where you can download a similar TSV table or FASTA sequences.
  Both resources include web tools for predicting the presence of the elements of interest in sequences.
  If you are looking for a state of the art prediction tool for such elements in genomes, you might look into seqscreen from Todd Treangen's lab.
  For a general purpose microbiological annotation and analysis resource, you might also look into BV-BRG, which succeeds PATRIC. I have only used PATRIC but BV-BRG seems very thorough.
  I think that you are unlikely to find a resource that has non-virulent/non-resistance genes annotated.
  
original_text: 3061: <p>Is there a database with all known proteins/genes of specific pathogens such as Staph aureus and annotated whether it is a known virulence or resistance factor that idealy can be downloaded in table format?</p>
   2108: <p>I suggest that you are looking for a resource like <a href="https://www.google.com/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=&amp;cad=rja&amp;uact=8&amp;ved=2ahUKEwjfw6vom4z9AhV0IX0KHZFaAa4QFnoECAkQAQ&amp;url=http%3A%2F%2Fwww.mgc.ac.cn%2FVFs%2F&amp;usg=AOvVaw1AmmhEo5WZmOQGcDHHJ4gY" rel="nofollow noreferrer">VFDB</a> (virulence factor database). That table does annotate by bacterial species, so you can filter as you like.</p>
  <p>You can download a description table or FASTA sequences from their <a href="http://www.mgc.ac.cn/VFs/download.htm" rel="nofollow noreferrer">downloads page</a> (see screenshot). Last update was 4 days ago, so they should be quite current.</p>
  <p><a href="https://i.stack.imgur.com/VD47V.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/VD47V.png" alt="enter image description here" /></a></p>
  <p>For resistance genes, you could use something like <a href="https://card.mcmaster.ca/" rel="nofollow noreferrer">CARD</a> (Comprehensive Antibiotic Resistance Database), which also has a <a href="https://card.mcmaster.ca/download" rel="nofollow noreferrer">downloads page</a> where you can download a similar TSV table or FASTA sequences.</p>
  <p>Both resources include web tools for predicting the presence of the elements of interest in sequences.</p>
  <p>If you are looking for a state of the art prediction tool for such elements in genomes, you might look into <a href="https://gitlab.com/treangenlab/seqscreen" rel="nofollow noreferrer">seqscreen</a> from Todd Treangen's lab.</p>
  <p>For a general purpose microbiological annotation and analysis resource, you might also look into <a href="https://www.bv-brc.org/" rel="nofollow noreferrer">BV-BRG</a>, which succeeds PATRIC. I have only used PATRIC but BV-BRG seems very thorough.</p>
  <p>I think that you are unlikely to find a resource that has <em>non-virulent/non-resistance</em> genes annotated.</p>
  