Abstract: The uncharacterized alphasatellite of begomovirus associated with a common weed Verbesina encelioides was characterized by using molecular and in silico tools and techniques. Verbesina encelioides leaf curl alphasatellite (HQ631431) shows 87 % nucleotide sequence identity with Sida yellow vein disease associated DNA1 (FN806782). Translated 3-frame of HQ631431 (HQ631431/3-f.pdb) and its homologous 2HWT.pdb had respectively 67 and 77.2% residues in most favorable region of its Ramachandran plot therefore both of these two models cannot be placed in good quality. The 3d2GO server showed the hydrolase activity as possible function for HQ631431/3-f.pdb with 0.58% confidence level. In silico prediction of results can be used to confirm the begomovirus not only in host weeds but also in other crops also.