RefSeq predicted DB
This page lists all antiphage operon families and single proteins families as predicted in (N/A) .
Each row in the table represents a family, and examples of the family in their original genomic context can be seen by clicking on the small eye at the beginning of the line. On the right, each operon family is represented by a dot with a UMAP representation which tend to display similar operon families nearby on the plot.
Families whose any of their genes are hit by DefenseFinder are called validated, or predicted otherwise.
Validated are not necessarily known systems. Some members of the family can contain complete or partial DefenseFinder hits, but not all instances of the family contain known systems.
Validated Anti-Phage Operons are named VAPO whereas Predicted anti-Phage Operons are named PAPO.
If the operon is in fact a single gene system, they are named Validated or Predicted Anti-Phage Proteins (VAPP or PAPP). Those are not yet in the table nor represented in the umap (coming soon).
Use the search bar to filter by cluster of operon families (ex: PAPO_1234), Pfam domains (ex: SIR2) or arbitrary strings.
You can filter the results using the search bar to look for cluster of operon families (ex: PAPO_1234), Pfam domains (ex: SIR2) or arbitrary strings.
You can also select only validated (grey) or only predicted (purple) families. And finally, you can filter items based on their scores according to ESM_DF, GeneCLR_DF and defense score.
It is possible to select families on the plot as well.
To download a subset of families, select the items of interest on the list or the UMAP and click “Download”.
We call here operons any genes that are often found together on the genomes but are not necessarily cotranscribed. Operons Instances are then grouped in operon families which are further grouped into operon clusters.