Final answer:
If no BLASTX matches are found, identify a potential start codon followed by an in-frame stop codon to delineate the ORF. The protein sequence is deduced from the nucleotide sequence of the ORF, not including the stop codon. If no ORF is identified, leave the text boxes blank or indicate as such.
Step-by-step explanation:
When you do not find any BLASTX matches for your nucleotide sequence, you may still be able to predict an open reading frame (ORF). Start by examining your sequence for the presence of a potential translation start codon, typically an AUG (which codes for methionine in eukaryotes) that is reasonably close to a Kozak sequence for eukaryotic messages, or a GUG in prokaryotes. If you find such a codon, this may be the beginning of your ORF (#4). Next, scan downstream in the sequence for in-frame translation stop codons—these are UAA, UAG, or UGA. The sequence between the start codon and the first stop codon in the same reading frame constitutes the ORF. The coding sequence in the text boxes would be the nucleotide sequence that corresponds to this ORF (#3), without including the stop codon itself. The stop (#5) will be the position of the first in-frame stop codon after your start.
If you find no start codons that are followed by an appropriate in-frame stop codon, you might need to consider the possibility that your sequence does not contain a coding sequence, or that it is incomplete or contains errors. In such cases, you would leave the text boxes blank or indicate that the ORF could not be identified. Keep in mind that BLAST searches do not always yield results, and the absence of a match does not definitively conclude the nonexistence of a protein-coding sequence. It could indicate that the sequence is novel, or not well represented in the database.