SEA-PHAGES | A wierd one: No CP but Membrane Protein function Confirmed:MrMiyagi

Link to this post \| posted 04 May, 2020 16:36
fbaliraine	Dear Phage Hunters, Here is a real weird one for phage MrMiyagi. Not autocalled in DNA Master, no Coding potential seen in GeneMark (smeg), S, or TB. But seen as in phamerator, sharing the same pharm 9086 with gene 31 in phage Fowlmouth. When inserted, shows poor RBS scores (z= 1.353, F =-6.153), but surprisingly, TmHMM & SOSUI analysis clearly show that this is a membrane protein! (See figures below). Blastp yields q11:s1 with Cuke; q16:s1, 100%, 6e-39 with Fowlmouth; no realistic way to get it to be q1:s1 with Cuke of Fowlmouth. HHPred yields no hits above 90% probability [The highest hit, at 83.65% probability (4IMM_B; PDBe ), hits the "Outer membrane assembly lipoprotein YfgL; 8-bladed beta-propeller, Protein-protein interactions, chaperone; 2.33A {Moraxella catarrhalis"]. What’s your take? Edited 04 May, 2020 16:52 313Kb

Link to this post | posted 04 May, 2020 16:36

Dear Phage Hunters,
Here is a real weird one for phage MrMiyagi. Not autocalled in DNA Master, no Coding potential seen in GeneMark (smeg), S, or TB. But seen as in phamerator, sharing the same pharm 9086 with gene 31 in phage Fowlmouth. When inserted, shows poor RBS scores (z= 1.353, F =-6.153), but surprisingly, TmHMM & SOSUI analysis clearly show that this is a membrane protein! (See figures below). Blastp yields q11:s1 with Cuke; q16:s1, 100%, 6e-39 with Fowlmouth; no realistic way to get it to be q1:s1 with Cuke of Fowlmouth. HHPred yields no hits above 90% probability [The highest hit, at 83.65% probability (4IMM_B; PDBe ), hits the "Outer membrane assembly lipoprotein YfgL; 8-bladed beta-propeller, Protein-protein interactions, chaperone; 2.33A {Moraxella catarrhalis"]. What’s your take?

Edited 04 May, 2020 16:52

Link to this post \| posted 04 May, 2020 19:59
debbie	Fred, Not that weird. First of all, it was called in the auto-annotation, just not when you did it. (or how else did it get into phamerator?) So can auto-annotations differ? Can you explain how they can differ (if they can.) Second, it has weak coding potential. Weak is different than none. It also has homology of varying degrees across the genes that it matches. That could mean a couple of different things, - like it could withstand lots of changes and still function (and has been around for a long time), or it is really just falling apart. Regardless, I would call it. and assign Hypothetical Protein as its function. Again, this is an example of why we hand curate the genomes.

Link to this post | posted 04 May, 2020 19:59

debbie

Fred,
Not that weird.
First of all, it was called in the auto-annotation, just not when you did it. (or how else did it get into phamerator?) So can auto-annotations differ? Can you explain how they can differ (if they can.)
Second, it has weak coding potential. Weak is different than none. It also has homology of varying degrees across the genes that it matches. That could mean a couple of different things, - like it could withstand lots of changes and still function (and has been around for a long time), or it is really just falling apart.
Regardless, I would call it. and assign Hypothetical Protein as its function.
Again, this is an example of why we hand curate the genomes.

Link to this post \| posted 04 May, 2020 21:11
fbaliraine	Thanks Debbie! Working on refining a student's version, needed cross-check whether had been deleted during annotation, but at least I did not see it called in the DNA Master file I am working on. Thanks! Fred

Link to this post \| posted 04 May, 2020 21:20
debbie	Fred, It may not have been called. truly. the auto-annotaion is done 'on the fly' by taking a sample of the sequence provided and using that to determine the nucleotide patterns. So that 'key' it creates to identify the orfs with coding potential is done each time GeneMark (or glimmer) is run. So there will be differences. when I ran the auot-annotation today, my output did not include it. I would look for it as I investigate the gap and call it because other auto-annotations see a wee glimmer of coding potential AND it has a 4 bp overlap with the next gene. make sense? debbie

Link to this post | posted 04 May, 2020 21:20

debbie

Fred,
It may not have been called. truly.
the auto-annotaion is done 'on the fly' by taking a sample of the sequence provided and using that to determine the nucleotide patterns. So that 'key' it creates to identify the orfs with coding potential is done each time GeneMark (or glimmer) is run. So there will be differences. when I ran the auot-annotation today, my output did not include it. I would look for it as I investigate the gap and call it because other auto-annotations see a wee glimmer of coding potential AND it has a 4 bp overlap with the next gene.
make sense?
debbie

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A wierd one: No CP but Membrane Protein function Confirmed:MrMiyagi