Supplementary dataset for Quinones in Pseudomonadota, Dataset S1, HMM profiles for quinone biosynthesis annotation

File descriptionThis archive contains the 95 protein profiles used to annotate proteins from the quinone biosynthesis pathways:
Ubiquinone (UQ) O2-dependent pathwayUQ O2-independent pathwayRquA protein for the rhodoquinone pathwayMenaquinone (MK) Men pathwayMK futalosine pathwayPlastoquinone pathwaySome profiles are to be used with GA (gathering) scores when using HMMER ('cut-ga' option):
MenA: 100MenB: 350MenH: 110MenE: 300RquA: 100RquA2: 100Note that some proteins have several corresponding profiles, and the "Allo_*" and "*decoy*" profiles are used as baits for homologous proteins with different functions.
ReferencesThis is part of the Supplementary material of the study "A dynamic quinone repertoire accompanied the diversification of energy metabolism in Pseudomonadota", submitted to The ISME Journal.
Authors' list: Sophie-Carole Chobert, Morgane Roger-Margueritat, Laura Flandrin, Safa Berraies, Christopher T. Lefèvre, Ludovic Pelosi, Ivan Junier, Nelle Varoquaux, Fabien Pierrel, Sophie S. Abby
Several of the above included profiles were published in previous studies, while most were designed for the above-listed article.
"Diversification of ubiquinone biosynthesis via gene duplications, transfers, losses, and parallel evolution", Molecular Biology and Evolution, 2023."Ubiquinone Biosynthesis over the Entire O2 Range: Characterization of a Conserved O2-Independent Pathway", mBio, 2019