Fig. 2.

Schematic representation of nsp12 from SARS-CoV and nsp9 from EAV. A) The position of NiRAN (light grey), the RdRp domain (dark grey) and the respective motifs (white boxes; subscript “N” was added to NiRAN motifs to dicriminate them from RdRp motifs) are indicated in the figure. The exact C-terminal border of NiRAN, as well as the N-terminal border of the RdRp are not defined yet and are indicated with dashed lines. The position of ribosomal frameshifting is indicated with a triangle; translation of the preceding ORF1a products terminates shortly downstream the frameshift site (SARS-CoV nsp11 within 4 amino acids, EAV nsp8 within 1 amino acid, not indicated in the figure). NiRAN and RdRp motifs are displayed as white boxes in the figure, based on (Lehmann et al., 2015a) for NiRAN motifs, and (Xu et al., 2003) (SARS-CoV) or (Beerens et al., 2007) (EAV) for the RdRp motifs. Note that Motif D was not defined for EAV nsp9 in Beerens et al. and that the approximate position is indicated as a dashed box. The rulers indicate amino acid positions in the proteins. Question mark indicates part of the nsp that may represent a linking domain or a domain with an additional (unknown) function. B) Alignment of NiRAN motifs A, B and C from eight representative nidoviruses from all 4 families (Modified from (Lehmann et al., 2015a)). C) Alignment of RdRp motifs A, B and C from the same nidoviruses. Completely conserved residues are indicated in grey boxes. SARS-CoV, SARS coronavirus Frankfurt 1 (AY291315; Coronaviridae); MERS-CoV, Middle East respiratory syndrome coronavirus EMC/2012 (JX869059.2; Coronaviridae); GAV, Gill-associated virus (AF227196; Roniviridae); YHV, yellow head virus (EU487200; Roniviridae); CAVV, Cavally virus (HM746600; Mesoniviridae); MenoV, Meno virus (JQ957873; Mesoniviridae); PRRSV-1, porcine reproductive and respiratory syndrome virus, European genotype (GU737264.2; Arteriviridae). EAV, Equine arteritis virus (DQ846750; Arteriviridae).