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It should be there, make sure you are booting up from the SD. An easy way to know is to check this is during the booting process if the Grub menu is red you then you are not booting up from the SD, it should be blue. Another way to upload the blink sketch, remove the USB and the power and then plug the power cord again if the sketch resumes the blinking its booting up correctly. Also the files for node and python are under /usr/lib. I hope you find this useful.
Thanks JPMontero_Intel . It worked for me now!! I was having SD card boot up issue as you rightly pointed out. This was because , when I formatted my SD card , I lost the boot partition. Now it is working alright.