There is a protein in Salmonella enterica serovar Typhi with the title "Unidentified ORF" (YP_005216057.1, GI:378958571). What does it mean ?
Since as per my thinking, ORF is concerned for nucleic acid, while the NCBI GI 378958571 contains the sequence of that protein, so why it is still 'unidentified ORF' ?
http://www.ncbi.nlm.nih.gov/protein/378958571
Refseq is a curated database at NCBI. The prefix of the accession you posted, "YP_xxxxxx" means it is a predicted protein model. That is, it was predicted from a computer algorithmic alignment of the coding DNA. Once that entry is actually confirmed, it will be replaced with an "NP_xxxxxx" accession, to indicate the identity of the predicted protein has been confirmed.
The coding accession for that protein is NC_016832 with the "NC_" prefix indicating it is a confirmed complete genomic sequenced entry. It's putative protein product will have been determined by computerized alignment with similar sequences. Since the protein is only algorithmically predicted at this point, the coding sequence itself is not considered a confirmed, identified entry yet (i.e. the genomic sequence itself is confirmed, but the assigned identity of that coding gene is not).
ORF can be computationally defined as region on a DNA sequence spanning between a start codon and a stop codon, inclusive. This seems to be the case here. Then, the computationally defined ORF is translated based on one of the 16 genetic codes; thus, there is a hypothetical peptide sequence but the ORF remains a hypothetically translatable DNA.
So, in this case, can I consider it as 'hypothetical' protein or as 'unknown' protein ?
But in NCBI Protein database, very few proteins are mentioned as 'unidentified ORF', so as per my thinking, it is something different from 'hypothetical' or 'unknown' protein.
Thank you Mr. Hugo Martins. The 'conceptual translation' comment is mentioned in many 'unknown' proteins, but not in 'hypothetical' ones, so I will consider my query GI as an 'unknown' protein.
Refseq is a curated database at NCBI. The prefix of the accession you posted, "YP_xxxxxx" means it is a predicted protein model. That is, it was predicted from a computer algorithmic alignment of the coding DNA. Once that entry is actually confirmed, it will be replaced with an "NP_xxxxxx" accession, to indicate the identity of the predicted protein has been confirmed.
The coding accession for that protein is NC_016832 with the "NC_" prefix indicating it is a confirmed complete genomic sequenced entry. It's putative protein product will have been determined by computerized alignment with similar sequences. Since the protein is only algorithmically predicted at this point, the coding sequence itself is not considered a confirmed, identified entry yet (i.e. the genomic sequence itself is confirmed, but the assigned identity of that coding gene is not).
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