Table 2.
Key functional motifs that are present, absent or variant in XtERV-S and related RVs
| Protein | Feature | Consensus sequence | Motif presence, absence or sequence variation (viral genome position)a | |||
|---|---|---|---|---|---|---|
| XtERV-S | ERV-L | FV | MLV | |||
| Gag | ||||||
| Matrix (MA) | Myristylation signal | GX2-3[S/T] | – | – | – | GQTVT (2–6) |
| Capsid (CA) | Major homology region (MHR) | QX3EX4ΦX2R | (238–257) | (281–300) | – | (357–376) |
| Nucleocapsid (NC) | Cys-His motif | CX2CX4HX4C | – | – | – | (503–511) |
| glycine-glutamine-arginine (GQR) domain | GX0-3QR | GEGIQR (324–331) | GQR (471–473) | – | – | |
| NC or P6 | Late domain | PXXP, PPXY or YXXL | PSAP (496–499) | PTAY (520–523) | PSAP (284–287) | PPPY (162–165) |
| Pol | ||||||
| Protease (Pro) (Pfam 13975) | Catalytic motif | D[T/S]G | DTG (44–46) | DTG (54–56) | DSG (24–26) | DTG (27–29) |
| Reverse transcriptase (RT) (cl02808) | D[YLF]RX2NX66-71G | DYRGLN66G (211–283) | DYRKLN55G (210–271) | DYREVNX64G (217–287) | DLREVN71G (234–311) | |
| Catalytic center | Y[V/L/I/M]DD | YIDD (312–315) | YIDD (312–315) | YVDD (312–315) | YVDD (342–345) | |
| RNaseH (cl14782) | Active site/dead box | DEDD or DEDHD | DEDD (623–745) | DEDD (621–751) | DEDD (599–740) | DEDD (644–773) |
| dUTPase | (987–1162) | (1018–1105) | – | – | ||
| Integrase (IN) (Pfam 00665) | Zinc finger domain | HX3-7HX23-32CX2C | HX4HX28CX2C (768–805) | HX4HX28CX2C (774–811) | HX3HX29CX2C (818–850) | HX3HX32CX2C (848–888) |
| Catalytic core | DX39-58DX35E | DX58DX35E (834–929) | DX58DX35E (838–933) | DX58DX35E (916–1011) | DX56DX35E (879–972) | |
| Env | ||||||
| Surface unit (SU) | Isomerase domain | CX2C | CWIC (40–43) | – | – | CWLC (336–339) |
| N-linked glycosylation sites | NX^P[S/T] | 8 SU, 1TM | – | 2 LP, 10 SU, 3 TM | 7 SU, 1 TM | |
| Furin site | K/R-X-K/R-R | RNWKR (251–255) | – | – | RHKR (466–469) | |
| Transmembrane unit (TM) | “CX6CC” | CX6CC | (344–352) | – | – | (555–563) |
| Heptad repeats | ΦX2ΦX3 | + | + | + | + | |
| “Stutter” glycosylation site | 306 | – | – | – | ||
| Immunosuppressive Domain | (327–341) | – | – | (538–551) | ||
| Membrane spanning domain | (397–417) | – | – | (606–631) | ||
| Cytoplasmic tail | (419–441) | – | – | (633–665) | ||
| Endocytosis signal | YXXΦ | YTTS (424–427) | – | – | YHQL (655 – 658) | |