Table 1.

Interactions of RNA dependent RNA polymerase (RdRp) with the regulatory elements of movement protein (MP) subgenomic promoter (SGP) region in the CGMMV genome

Regulatory elements (Co-ordinates)	Interacting nucleotides: amino acids (co-ordinates) in different interacting sites*
I (− 136 to − 144)	A(− 136):GLU11; A(− 135):ASP107, ASP13; A(− 134):ASP107; U(− 133):SER15; C(− 129): TYR67; A(− 128):LYS51, ALA90, MET92; G(− 126):HIS25, SER22; A(− 125):SER22, PHE24; A(− 124):SER22; U(− 123):TYR67; G(− 118):LYS63; U(− 117):GLN69; A(− 116):GLN56, ARG52, LYS19; A(− 115):LYS19; A(− 114):SER15, SER15, LYS16
II (− 64 to − 56)	A(− 64):GLU11, ILE9, LEU10; A(− 62):PHE83; A(− 62):ASP96; C(− 61):SER91, ALA90; U(− 58):ALA31, LYS35; A(− 57):GLU34; A(− 56):ASP40
III (− 53 to − 32)	A(− 53):TRP44; A(− 52):SER20, ILE41; A(− 50):MET45; A(− 49):CYS104; A(− 48):CYS104, ASP107, VAL75; C(− 47):LEU109, ASP107, ASP13; A(− 46):ASP13, LYS100; C(− 45):GLU11, ASP96; A(44):LEU116,ILE32; U(− 43):GLN56; U(− 42):ALA31; C(− 41):SER27; A(− 40):MET92, SER27; U(− 39):MET92, ASP23; A(− 38):LYS51; A(− 36):THR64, LEU65; C(− 35):THR64; C(− 33):LYS51; A(− 32):LE66,TYR67
IV (− 26 to − 17)	C(− 26):TYR17, LYS16; G(− 25):SER20; C(− 24):ALA90; G(− 23):LEU116; A(− 21):LYS19, LYS16; A(− 20):LYS19; A(− 19):LYS19; A(− 18):SER72; G(− 17):LYS71
V (+ 33 to + 39)	C(33):LEU116; A(34):LEU116; A(35):LEU12, ALA90; C(36):SER20; U(37):SER20; U(38):TYR68; U(39):SER22
VI (+ 99 to + 110)	A(99): LEU116; G(100): LEU116; A(102): CYS88, ALA90, MET92; C(105): LYS114; A(106): LYS35; A(108): ASP96; A(110): LYS100

*Value in parenthesis indicating the coordinates of nucleotides in the RNA with respective to translation start site (TLSS). The nucleotides located upstream of TLSS (+ 1) have (−) markings; nucleotides located downstream of TLSS have (+) markings. The interacting partners were identified from the interaction analysis between core RdRp and RNA ligands derived from complementary sequences of MP-SGP region using Patch-dock web server