Georgios A Pavlopoulos, Fotis A Baltoumas, Sirui Liu, Oguz Selvitopi, Antonio Pedro Camargo, Stephen Nayfach, Ariful Azad, Simon Roux, Lee Call, Natalia N Ivanova, I Min Chen, David Paez-Espino, Evangelos Karatzas, Ioannis Iliopoulos, Konstantinos Konstantinidis, James M Tiedje, Jennifer Pett-Ridge, David Baker, Axel Visel, Christos A Ouzounis, Sergey Ovchinnikov, Aydin Buluç, Nikos C Kyrpides
Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2 . Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes...
October 2023: Nature