In most cases, orthology was not only supported by highly significant BLAST scores (E-value below e − 100 ) but also by the presence of conserved functional domains: a PH-like domain (Pleckstrin Homology; PF04683) in ADMR1/Rpn13, a PCI domain (Proteasome Cop Initiation factor; PF01399) in PSMD3, 6, 8, 11, 12, 13, a RPN domain (Proteasome Regulatory subunit C-terminal; PF08375) in PSMD3, a JAB/MPN (Mpr1/Pad1 N-terminal; PF01398) in PSMD7/Rpn8 and PSMD14/Rpn11, and a von Willebrand Factor A domain (VWA; PF00092) responsible for the binding of PSMD4/Rpn10 to the ubiquitin-like modifier (UbL) FAT10 and possibly other UbLs ( Rani et al. 2012 ) ( supplementary fig.
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