Do you see anything wrong in the syntax???

Many things.

• You've got two opening parentheses in if(($sequence=~/ABC/), but only one closing one.
• You've not populated $sequence.
• You've not populated %hash_seqs_all.
• You've not populated $infile.
• You've not populated $id.
• You've not populated $protein.
• You're not checking for errors after opening your output file.

I'd love to try to help you, as I'm sure my brothers here in the Monastery would, but you've not given us nearly enough to work with. We'd need the following, ideally:

• Complete, syntactically correct code; a minimal test case that demonstrates the problem you're having.
• Example data.
• Expected output.
• Actual output.

As it is, we've got a code snippet that doesn't even compile, run on data we haven't seen, producing results we can only guess at. This isn't enough.

Here are some further links to get you started:

• How do I post a question effectively?
• The SSCCE: Short, Self Contained, Correct (Compilable) Example

Please help us help you!