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Cluster A1 gene question

| posted 12 Apr, 2018 22:14
We are having difficulty with annotation of Bones_4. This gene is in Pham 40723, and there are only 12 members of this pham, 10 of them are annotated as a hypothetical protein. Aligning the protein sequences that are from the Phamerator maps from the 12 phages in ClustalW gives the attached alignment. Bones has a long insert, and 4 of the sequences are very different from the other 8 sequences.
GeneMark shows low coding potential. Protein BLAST in NCBI shows only matches with the same 12 phages. Starterator shows 8 tracks for the 12 phages in the Pham, and Bones_4 is in its own track with a unique start site.
If this is not a gene, then there is a gap of 411 bp. However, all 10 of the annotated genes call it as a gene. Our conclusion is that this is a gene, but we would like any input from the experienced annotators.
| posted 13 Apr, 2018 14:40
I think that this is a gene and the coding potential says to use the longest start. I did not find Starterator helpful. Blast at PhagesDB and NCBI along with HHpred results did not show any functions. CLUSTALW does show the 'insert' you mention, but i don't believe there is anything to say about it at this point (not knowing function or relevance).
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