Yes, you can appear for GATE 2025 even if you have a supply in your 3rd year 5th semester (assuming you are currently in June 2024) as per the latest GATE eligibility criteria.

Candidates in the final year of their Bachelor's degree in Engineering/Technology/Architecture/Science/Arts/Commerce (minimum duration of 3 years) are eligible to appear for GATE.

Having a supply in a subject doesn't necessarily disqualify you from appearing for GATE.

So, you fulfill the eligibility criteria for GATE 2025 based on the current information available (June 2024).

https://engineering.careers360.com/articles/how-prepare-for-gate-in-6-months

I hope it helps!