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?
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$\begingroup$ Please consider accepting MP's answer. For my own stuff I found it really useful, its a good a question and really good answer. $\endgroup$– M__ ♦Feb 14 at 19:08
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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.
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1$\begingroup$ Wow what a cool answer. Got to be the accepted answer, but lets wait. There are a number of microbiological bioinformaticians here. $\endgroup$– M__ ♦Feb 11 at 1:08
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$\begingroup$ 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. $\endgroup$ Feb 14 at 17:10
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1$\begingroup$ @Soren added a note- VFDB was last updated 4 days ago. See screenshot. $\endgroup$ Feb 14 at 19:00