SEA-PHAGES | Annotation Advise: Frameshift

Link to this post \| posted 21 Apr, 2016 15:55
fbaliraine	We have identified and annotated some programmed frameshifts. When we blast our fusion protein in phagesDb, we note that some hits indicate the frameshift, whereas others do not. In phage Gideon an example of a hit for gp 15, where the frameshift information is indicated is its 1:1, 100% alignment with "Angel_15, tail assembly chaperone; -1 frameshift." Should we note this in the DNA master file? If so, where exactly: Should it be under "Logic" or beside the function i.e. "F: tail assembly chaperone; -1 frameshift", or in under "Product"? Thanks! Edited 21 Apr, 2016 15:57

Link to this post | posted 21 Apr, 2016 15:55

We have identified and annotated some programmed frameshifts. When we blast our fusion protein in phagesDb, we note that some hits indicate the frameshift, whereas others do not. In phage Gideon an example of a hit for gp 15, where the frameshift information is indicated is its 1:1, 100% alignment with "Angel_15, tail assembly chaperone; -1 frameshift." Should we note this in the DNA master file? If so, where exactly: Should it be under "Logic" or beside the function i.e. "F: tail assembly chaperone; -1 frameshift", or in under "Product"? Thanks!

Edited 21 Apr, 2016 15:57

Link to this post \| posted 22 Apr, 2016 19:17
debbie	This is difficult to answer without seeing the data. In general, you will want to choose the best start (just like any protein) for the G of the G/T tail assembly chaperone proteins. T will have the same start, so you need not repeat what you said for G. The function is Tail assembly chaperone. The source of that function info is most likely phagesDB (phamerator). I don't know what "logic" means in this context. you can add that it is a -1 frameshift in your notes. When you record your start justification 1:1 with Gideon is appropriate.

Link to this post | posted 22 Apr, 2016 19:17

debbie

This is difficult to answer without seeing the data. In general, you will want to choose the best start (just like any protein) for the G of the G/T tail assembly chaperone proteins. T will have the same start, so you need not repeat what you said for G. The function is Tail assembly chaperone. The source of that function info is most likely phagesDB (phamerator). I don't know what "logic" means in this context. you can add that it is a -1 frameshift in your notes. When you record your start justification 1:1 with Gideon is appropriate.

Link to this post \| posted 27 Apr, 2017 15:51
nancyljones249	We have identified the genes involved in the frame shift for RitaG but there are discrepancies within the middle of the gene product that do not correspond with other Phages it matches up with. We realize typically the discrepancies show where the frame shift is but it is not present within the six frame. What should we do? RitaG: MSVKKPENNGAAAREQATEFDSPFADRVLRFDDGSTMTIPPHPN LRMLDDDALEAYEAYLEEIETYDREPDLYIPDEMVLPAETRPGAVKGPP YFKDGKRVSPPREVRIVQVVLGMDSYEVLRSKQINGRPAGARDVWRAWTEQGFTIAER AESDSKSDGSSVVLETVPETDSEZ Llij: MSVKKPENNGAAAREQATEFDSPFADRVLRFDDGTTMTIPPHPN LRMLDDDALEAYEAYLEEIETYDREPDLYIPEQTVKDRDGNEMVLPAETRPGAVKGPP YFKDGKRVSPPREVRIVQVVLGMDSYEVLRSKQINGRPAGARDVWRAWTEQGFTIAER AESDSKSDGSSVVLETVPETDSE Pacc40: MSVKKPENNGAAAREQATEFDSPFADRVLRFDDGSTMTIPPHPN LRMLDDDALEAYEAYLEEIETYDREPDLYIPEQTVKDRDGNEMVLPAETRPGAVKGPP YFKDGKRVSPPREVRIVQVVLGMDSYEVLRSKQINGRPAGARDVWRAWTEQGFTIAER AESDSKSDGSSVVLETVPETDSE"

Link to this post | posted 27 Apr, 2017 15:51

nancyljones249

We have identified the genes involved in the frame shift for RitaG but there are discrepancies within the middle of the gene product that do not correspond with other Phages it matches up with. We realize typically the discrepancies show where the frame shift is but it is not present within the six frame. What should we do?

RitaG: MSVKKPENNGAAAREQATEFDSPFADRVLRFDDGSTMTIPPHPN
LRMLDDDALEAYEAYLEEIETYDREPDLYIPDEMVLPAETRPGAVKGPP
YFKDGKRVSPPREVRIVQVVLGMDSYEVLRSKQINGRPAGARDVWRAWTEQGFTIAER
AESDSKSDGSSVVLETVPETDSEZ

Llij: MSVKKPENNGAAAREQATEFDSPFADRVLRFDDGTTMTIPPHPN
LRMLDDDALEAYEAYLEEIETYDREPDLYIPEQTVKDRDGNEMVLPAETRPGAVKGPP
YFKDGKRVSPPREVRIVQVVLGMDSYEVLRSKQINGRPAGARDVWRAWTEQGFTIAER
AESDSKSDGSSVVLETVPETDSE

Pacc40: MSVKKPENNGAAAREQATEFDSPFADRVLRFDDGSTMTIPPHPN
LRMLDDDALEAYEAYLEEIETYDREPDLYIPEQTVKDRDGNEMVLPAETRPGAVKGPP
YFKDGKRVSPPREVRIVQVVLGMDSYEVLRSKQINGRPAGARDVWRAWTEQGFTIAER
AESDSKSDGSSVVLETVPETDSE"

Link to this post \| posted 27 Apr, 2017 17:05
debbie	Nancy, I am not sure what you are asking. If you look at the phamerator map of the 3 genomes that you mention, it looks like these is a deletion in the G gene of the G/T frameshift in RitaG. That doesn't have anything to do with the frameshift. The deletion occurred and it looks like the phage can get along without that portion. That shouldn't stop you from calling the appropriate frame shift. I have included how I would call the frame shift in the attached document. if you are asking something else, let me know. Edited 27 Apr, 2017 17:05 117Kb 84Kb

Link to this post | posted 27 Apr, 2017 17:05

debbie

Nancy,
I am not sure what you are asking. If you look at the phamerator map of the 3 genomes that you mention, it looks like these is a deletion in the G gene of the G/T frameshift in RitaG. That doesn't have anything to do with the frameshift. The deletion occurred and it looks like the phage can get along without that portion. That shouldn't stop you from calling the appropriate frame shift. I have included how I would call the frame shift in the attached document. if you are asking something else, let me know.

Edited 27 Apr, 2017 17:05

Link to this post \| posted 21 Feb, 2018 15:56
welkin	Dear All, I am closing this thread— if you have more specific frameshift questions, please start a new thread and include the subcluster of the phage in the title of the thread. Best, Welkin

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Annotation Advise: Frameshift