I am trying to clone a 1 kb long GPCR into the vector PENTR3C which is almost 2.2 kb in length. I am trying to clone it between the KpnI and XhoI site. I am using XL1B strains. The pentr3c vector I have has the ccdB gene replaced with another gene of interest which is around 2 kb. When I try to clone my 1 kb GPCR gene i donot get any colonies after transformation or get few colonies which gives a orangish pellet. I also use the digested vector+ligase as a control which gives no colony indicating proper digestion of my vector. When i transform the vector only i get proper colonies. Can any one suggest me what should i do? there is no problem with the ligase or restriction enzymes or competent cells.