search

Arkadiy-Garber / FeGenie

HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes
GNU Affero General Public License v3.0
53 stars 10 forks source link

where was the data for protein DmkA obtained from？ #43

Open xdli009 opened 1 year ago

xdli009 commented 1 year ago

Hi,

Thank you for your tool. We would like to ask where the data for protein DmkA was obtained from. We didn't find the protein sequence of DmkA in NR database. And the proteins annotated as DmkA using FeGenie was re-annotated using NR database and the result was 1,4-dihydroxy-2-naphthoate octaprenyltransferase, prenyltransferase, etc.

Thank you!

Arkadiy-Garber commented 5 months ago

Hi,

Thanks for your interest in FeGenie! Apologies for the confusion with that protein family. That protein was a relatively late addition to FeGenie's database, which I think explains why there are some files missing from it - I will try to locate them!

For what it's worth, DmkA, as well as DmkB, FmnA, FmnB, Ndh2, EetA, EetB, and PplA are all part of an 8-gene locus that's thought to code for a flavin-based EET strategy: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6221200/. So I am not surprised that DmkA, is coming up as 1,4-dihydroxy-2-naphthoate octaprenyltransferase, prenyltransferase, etc. Those genes individually do not necessarily indicate capacity for EET or iron reduction, but together in the same operon or gene neighborhood (as they are in Listeria monocytogenes), is stronger evidence. Does that make sense? As far as I can tell, FeGenie should have the capacity to discriminate between singleton genes like DmkA and Ndh2 vs when they are all found together.

Let me know if you have any other questions!

Arkadiy