Hii,

Getting a score of 46 from CSE stream is Okay but  the score is not upto the mark.

As you are from OBC you will qualify in the exam .You will get admission in some good private colleges but it is difficult to get admission IIT's and NIT's .

If you are serious about your Masters and want to do In a good IIT.Then give another Attempt for GATE and score well.Dont do your masters in a small private college.it won't  benefit you.

All the Best....,