SEA-PHAGES | Phage DoRead Start at 52714 bp with 8 bp overlap vs start at 52718 with 4 bp overlap?

Link to this post \| posted 27 Mar, 2025 07:22
fbaliraine	Phage DoRead draft gene 103 (stop 52875 bp) in the +3 frame has significant coding potential (CP) only in GeneMarkS, and has an 8 bp overlap with the upstream gene which stops at 52721 bp. However, the gene in the +2 frame (stop 54067 bp) and is auto-called to start at 52907 bp has significant CP in both GeneMark_smeg & GeneMark_TB to allow it to start at 52718 bp, with a 4 bp ATGA overlap. Per Guiding Principle 12a, the ribosome is expected to prefer the operon. Keeping draft gene 103 (stop 52875 bp) means that the operon would have to go backwards to start at 52714 bp to make an 8 bp overlap rather than the ATGA overlap (start 52718 bp). So far, only phage Modragons gp104 takes this operon as the start. Several BLASTp results in phagesDB keep the 8 pb overlap start (52714 - 52875 bp) which is found in 69.5% of genes in pham. The start at 52718 which gives the 4 bp overlap is found in 54.2% of genes in pham. I also note that there is a string of operon genes with 1-4 bp overlaps starting from the two upstream genes all the way to the end of the genome (only the start at 52714 bp with an 8 bp overlap would break this pattern). What is your verdict? Change the start to 52718 bp and prefer the operon (meaning deleting the gene which stops at stop 52875 bp) or keep both genes? See attached Edited 27 Mar, 2025 07:50 220Kb

Link to this post | posted 27 Mar, 2025 07:22

Phage DoRead draft gene 103 (stop 52875 bp) in the +3 frame has significant coding potential (CP) only in GeneMarkS, and has an 8 bp overlap with the upstream gene which stops at 52721 bp. However, the gene in the +2 frame (stop 54067 bp) and is auto-called to start at 52907 bp has significant CP in both GeneMark_smeg & GeneMark_TB to allow it to start at 52718 bp, with a 4 bp ATGA overlap. Per Guiding Principle 12a, the ribosome is expected to prefer the operon. Keeping draft gene 103 (stop 52875 bp) means that the operon would have to go backwards to start at 52714 bp to make an 8 bp overlap rather than the ATGA overlap (start 52718 bp).

So far, only phage Modragons gp104 takes this operon as the start. Several BLASTp results in phagesDB keep the 8 pb overlap start (52714 - 52875 bp) which is found in 69.5% of genes in pham. The start at 52718 which gives the 4 bp overlap is found in 54.2% of genes in pham.

I also note that there is a string of operon genes with 1-4 bp overlaps starting from the two upstream genes all the way to the end of the genome (only the start at 52714 bp with an 8 bp overlap would break this pattern).

What is your verdict? Change the start to 52718 bp and prefer the operon (meaning deleting the gene which stops at stop 52875 bp) or keep both genes?
See attached

Edited 27 Mar, 2025 07:50

Link to this post \| posted 27 Mar, 2025 17:16
debbie	Fred, Cluster F1 phages are notorious for the 1-4 base overlaps. The reason I like calling the shorter version of the glycosyltransferase is that it is supported by Starterator AND the HHPred doesn't show alignments in the upstream region of PDB glycosyltransferases. Check out the glycosylation paper about Che8. It should provide more information of best call. https://pubmed.ncbi.nlm.nih.gov/37329881/ debbie Remember that no one piece of data tells the story. It is when we put all of the pieces together that we can see best choices.

Link to this post | posted 27 Mar, 2025 17:16

debbie

Fred,
Cluster F1 phages are notorious for the 1-4 base overlaps.
The reason I like calling the shorter version of the glycosyltransferase is that it is supported by Starterator AND the HHPred doesn't show alignments in the upstream region of PDB glycosyltransferases. Check out the glycosylation paper about Che8. It should provide more information of best call.
https://pubmed.ncbi.nlm.nih.gov/37329881/

debbie

Remember that no one piece of data tells the story. It is when we put all of the pieces together that we can see best choices.

Link to this post \| posted 27 Mar, 2025 18:53
fbaliraine	This helps clarify things! I have left the upstream gene intact (52714-52875 bp) and for the downstream gene (stop 54067 bp), I have changed the start to 52892 bp which is the most annotated start, also called in Che8 gp 108 and has a better RBS score than the auto-called start at 52907 bp. Thank you, Debbie! Fred Edited 27 Mar, 2025 19:02

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Phage DoRead Start at 52714 bp with 8 bp overlap vs start at 52718 with 4 bp overlap?