Hi everyone! I'm doing a bioinformatics study for my thesis, but I'm having a problem. I need to derive the structure of a protein with alphafold starting from a nucleotide sequence. Now, alphafold 3 needs the amino acid sequence, so I used the Expansy-Translate tool program to derive it (remembering that I started from a nucleotide sequence). The problem, however, is precisely here: the resulting amino acid sequence (5'-3' frame reading) is missing reading ORFs in some parts, making the amino acid sequence incomplete. Alphafold can't give me an accurate structure for this very reason. I tried comparing this sequence with others from similar organisms, and with these, I had no ORF issues, and the entire sequence was highlighted as a reading ORF (for those familiar with Expansy, the ORFs are highlighted in red). Furthermore, the first ORF of all similar organisms is the same and is located on the 5'-3' strand, but in my organism this ORF is located on the 3'-5' strand and I don't understand how this is possible. Does anyone have any idea how I can obtain a better sequence to feed to alphafold? Can you recommend any programs?

p.s. I wanted to say that I'm new to the world of bioinformatics so I'm not yet very familiar with the various programs that exist, but I'm very curious and I'd like to continue studying this subject :)