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mdmparis / defense-finder

Systematic search of all known anti-phage systems.
GNU General Public License v3.0
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Where are all bit score cutoffs reported? Missing for some systems in Liste_hmm_system.md #27

Closed scubalaina closed 4 months ago

scubalaina commented 1 year ago

Hi there! I was wondering where to find the bitscore cutoff for some systems that aren't in Liste_hmm_system.md . For example, the gene AbiC or AbiC__AbiC (which is a single-gene system)? One of the proteins that I ran DefenseFinder on had hit to AbiC with a bitscore of 21.1 and E-value of 8.1e-6 (according to the genes output file). Is this a valid hit? When I searched this protein separately against HMM profiles in the EggNOG database, this gene hit to COG0325 with the function of a Pyridoxal 5'-phosphate (PLP)-binding protein and bitscore of 194.2 and evalue of 1.4e-58. I would opt to take the annotation for the highest bitscore, but sometimes novel defense genes are included in these NOG families, so it still might truly be an AbiC gene. It would be great if there was a table with the bitscores used for all defense genes so I can cite this as potential evidence that this protein is functioning as an AbiC.

Thank you for the help! :)

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github-actions[bot] commented 4 months ago

This issue has been inactive for 60 days and is now marked as stale. It will be closed in 7 days without further activity.