Table 2 Key functional motifs that are present, absent or variant in XtERV-S and related RVs

Gag

 Matrix (MA)

Myristylation signal

GX_2-3[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

GX_0-3QR

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]RX₂NX_66-71G

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

HX_3-7HX_23-32CX₂C

HX₄HX₂₈CX₂C (768–805)

HX₄HX₂₈CX₂C (774–811)

HX₃HX₂₉CX₂C (818–850)

HX₃HX₃₂CX₂C (848–888)

Catalytic core

DX_39-58DX₃₅E

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)