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. 2022 Jan 20;298(3):101609. doi: 10.1016/j.jbc.2022.101609

Figure 3.

Figure 3

Maximum likelihood trees and domain architecture diagrams for UVR1 and UVR2–4 protein families. Inferred gene duplication events are indicated with blue circles at the corresponding node in the tree. Diagrams of domains were predicted by the NCBI conserved domain search tool CDsearch. Full species names and their lineage are: Arabidopsis thaliana, Angiosperms, Eudicots, Rosids, Brassicaceae; Eutrema salsugineum, Angiosperms, Eudicots, Rosids, Brassicaceae; Solanum lycopersicum, Angiosperm, Eudicots, Asterids; Oryza sativa, Angiosperms, Monocots, Poaceae; Spirodela polyrhiza, Angiosperms, Monocots; Amborella trichopoda, Angiosperms (earliest flowering plant); Selaginella moellendorffii, Lycophytes; Marchantia polymorpha, Bryophytes, Liverworts; Physcomitrella patens, Bryophytes, Mosses; Anthoceros angustus, Bryophytes, Hornwort; Mesotaenium endlicherianum, Charophytes, Green algae, Zygnemataceae (early-diverging); Chara brauna, Charophytes, Green algae; Penium margaritaceum, Charophytes, Green algae, Zygnemataceae; Botryococcus braunii, Chlorophyte, V, Trebouxiales; Ostreococcus lucimarinus, Chlorophyte, Green algae, Mamiellales; Porphyridium purpureum, Rhodophytes/Red algae; Porphyra umbilicalis, Rhodophytes/Red algae; Cyanophora paradoxa, Glaucophytes. Information about the functional domains and superfamily listed in the figure (see also Table S2): F-box-like, ∼50 amino acids long mediating protein–protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding, and translational repression; McsA, domain found in the protein-arginine kinase activator protein McsA; NTF2-like, this superfamily (IPR032710) represents a domain covering the whole length of the nuclear transport factor 2 (NTF2). It has a β-α-β insertion after the main helix. Other proteins containing this domain include protein kinases, sucrose phosphatases, bacterial ring-hydroxylating dioxygenase beta subunit, protein NXF, and many other uncharacterized proteins. Snoal_3, SnoaL-like domain (IPR037401) is found in a large number of other sequences. SnoaL is a polyketide cyclase that adopts a distorted α-β barrel fold; Snoal_3 and NTF2 are overlapping superfamilies; UVR, this domain in UvrB can interact with the homologous domain in UvrC throughout a putative coiled coil structure. PRK05298 exonuclease ABC subunit UvrB. DNase-RNase superfamily (cl00553) with pfam02577 (DNase-RNase) and COG1259 (Bifunctional DNase/RNase), overlapping with DUF151, Bifunctional nuclease domain IPR003729, and BFN Bifunctional nuclease superfamily IPR036104; Arabidopsis AT4G10925 is an F-Box and Snoal protein.