Answers.Body: <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.sstatic.net/VD47V.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/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>
  
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Answers.Text: Wow what a cool answer. Got to be the accepted answer, but lets wait. There are a number of microbiological bioinformaticians here.
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Answers.Text: Thanks for the input. I saw the VFDB database, but I had concers how up to date it is. I am going to check out the other resources you mentioned.
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Answers.Text: @Soren added a note- VFDB was last updated 4 days ago. See screenshot.
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Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-02-14T19:08:12.070Z
Comments.Text: Please consider accepting MP's answer. For my own stuff I found it really useful, its a good a question and really good answer.
Comments.UserDisplayName: M__
Tags: <public-databases><microbial-genomics><pathogenicity>
Title: Get a comprehensive list of virulence factors for certain or all pathogens?
ThreadText: # Get a comprehensive list of virulence factors for certain or all pathogens?
  
  (Asked by: username_0 on 2023-02-10)
  
  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?
  
  **Tags:** public-databases, microbial-genomics, pathogenicity
  
  > **Comments:**
  > **username_1**: Please consider accepting MP's answer. For my own stuff I found it really useful, its a good a question and really good answer.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2023-02-11. Score: 4
  
  I suggest that you are looking for a resource like [VFDB](https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjfw6vom4z9AhV0IX0KHZFaAa4QFnoECAkQAQ&url=http%3A%2F%2Fwww.mgc.ac.cn%2FVFs%2F&usg=AOvVaw1AmmhEo5WZmOQGcDHHJ4gY) (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](http://www.mgc.ac.cn/VFs/download.htm) (see screenshot). Last update was 4 days ago, so they should be quite current.
  
  [![enter image description here](https://i.sstatic.net/VD47V.png)](https://i.sstatic.net/VD47V.png)
  
  For resistance genes, you could use something like [CARD](https://card.mcmaster.ca/) (Comprehensive Antibiotic Resistance Database), which also has a [downloads page](https://card.mcmaster.ca/download) 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](https://gitlab.com/treangenlab/seqscreen) from Todd Treangen's lab.
  
  For a general purpose microbiological annotation and analysis resource, you might also look into [BV-BRG](https://www.bv-brc.org/), 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.
  
  > **Comments:**
  > **username_1**: Wow what a cool answer. Got to be the accepted answer, but lets wait. There are a number of microbiological bioinformaticians here.  
  > **username_0**: Thanks for the input. I saw the VFDB database, but I had concers how up to date it is. I am going to check out the other resources you mentioned.  
  > **username_2**: @Soren added a note- VFDB was last updated 4 days ago. See screenshot.  
  
  ---
  
  