SEA-PHAGES | 4 bp overlap in Streptomyces phages?

Link to this post \| posted 15 Jun, 2022 21:20
kcornely	Greetings, all! We are annotating a BM cluster phage, Frankenweenie. I have a team of four students working on this annotation project this summer. This is the first time that we've annotated a phage other than a mycobacteriophage, so we will be posting a lot of questions to the forum this summer! Our first question: Do Streptomyces phages have the 4 base pair overlap that is common in mycobacteriophages? I'm looking at gp30 now, and the BLAST data and the Starterator report fit better with a -1 bp overlap start. Should we go for the -4 bp start anyway? Thanks in advance for your help! Kathleen

Link to this post | posted 15 Jun, 2022 21:20

Greetings, all! We are annotating a BM cluster phage, Frankenweenie. I have a team of four students working on this annotation project this summer. This is the first time that we've annotated a phage other than a mycobacteriophage, so we will be posting a lot of questions to the forum this summer! Our first question: Do Streptomyces phages have the 4 base pair overlap that is common in mycobacteriophages? I'm looking at gp30 now, and the BLAST data and the Starterator report fit better with a -1 bp overlap start. Should we go for the -4 bp start anyway? Thanks in advance for your help!
Kathleen

Link to this post \| posted 15 Jun, 2022 23:27
debbie	Hi Kathy, We have a bit of evidence in mass spec data that says that the -1 start is the only one that is present. So in general, we are selecting the -1 choice over the -4 when both are present. debbie

Link to this post \| posted 16 Jun, 2022 15:46
kcornely	Thank you Debbie! This is very helpful.

Link to this post \| posted 16 Jun, 2022 16:37
debbie	Welcome!

Link to this post \| posted 11 Jul, 2022 18:38
kcornely	Greetings, all! I have another comment about the 4 bp overlap. We are annotating Frankenweenie, a BM cluster phage that has only six members total. We are occasionally encountering situations where it doesn't make sense to call the start at the position that provides a 4 bp overlap. For example, for gene 95, Glimmer and GeneMark call the start at 65479, which provides a 4 bp overlap. But to us, it makes sense to call the start at 65470. The 65470 start (1) is not the SS, but is MA on Starterator, (2) it provides us with q1:s1 BLAST his to the other five BM cluster phages, and (3) the product is similar in size to the other five BM cluster phages. I'd love to hear your insights on this observation, and thanks in advance!

Link to this post | posted 11 Jul, 2022 18:38

kcornely

Greetings, all! I have another comment about the 4 bp overlap. We are annotating Frankenweenie, a BM cluster phage that has only six members total. We are occasionally encountering situations where it doesn't make sense to call the start at the position that provides a 4 bp overlap. For example, for gene 95, Glimmer and GeneMark call the start at 65479, which provides a 4 bp overlap. But to us, it makes sense to call the start at 65470. The 65470 start (1) is not the SS, but is MA on Starterator, (2) it provides us with q1:s1 BLAST his to the other five BM cluster phages, and (3) the product is similar in size to the other five BM cluster phages. I'd love to hear your insights on this observation, and thanks in advance!

Link to this post \| posted 11 Jul, 2022 20:40
cdshaffer	To me the most informative piece of evidence is the start pattern in phage genes Kradal_87, Satis_87, EhyElimayoE_87. In the current version of the starterator report those are track 3. In that track you can see that start 4 is the longest orf (so I know those annotations cannot be too long) and that start 4 in Frankenweenie is 65470. So if Kradal, Satis and EhyElimayoE can make a perfectly viable phage with only the amino acids between start 4 and the stop codon, there is no reason to believe that the other phage require more amino acids. Yes this is a negative argument but lacking evidence to the contrary I will stick with parsimony as an important consideration. That is to say, in this case where there is not good evidence to the contrary, the simple conclusion that all the phage are using the same start (4) is the best annotation. So based mostly on parsimony, this pattern suggests to me that start 4 at 65470 should be annotated and not the start with the -4 overlap. Edited 11 Jul, 2022 20:44

Link to this post | posted 11 Jul, 2022 20:40

cdshaffer

To me the most informative piece of evidence is the start pattern in phage genes Kradal_87, Satis_87, EhyElimayoE_87. In the current version of the starterator report those are track 3. In that track you can see that start 4 is the longest orf (so I know those annotations cannot be too long) and that start 4 in Frankenweenie is 65470. So if Kradal, Satis and EhyElimayoE can make a perfectly viable phage with only the amino acids between start 4 and the stop codon, there is no reason to believe that the other phage require more amino acids. Yes this is a negative argument but lacking evidence to the contrary I will stick with parsimony as an important consideration. That is to say, in this case where there is not good evidence to the contrary, the simple conclusion that all the phage are using the same start (4) is the best annotation.

So based mostly on parsimony, this pattern suggests to me that start 4 at 65470 should be annotated and not the start with the -4 overlap.

Edited 11 Jul, 2022 20:44

Link to this post \| posted 12 Jul, 2022 13:29
lhughes	Thanks for those insights, Chris. We haven't annotated a cluster BM phage yet, but I like how this case shows how important context can be when making these decisions.

Recent Activity

4 bp overlap in Streptomyces phages?