hello aspirant,
a b.tech final year or pass out student can apply in gate from any stream. even a mechanical engineer can opted for computer science engineering branch. however the preparation is only depends on you that how well can you prepare. now coming to your point, you may apply in gate from mechanical engineering branch, but the psu's only hires for b.tech in mechanical degree holder candidates. and for manufacturing engineering there is very low vacancy. but you can use your gate score and can pursue m.tech from top institution.
hope you may understand.
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