SEA-PHAGES | Tail Assembly Chaperones and Programmed Ribosmal Frameshift Call

Tail Assembly Chaperones and Programmed Ribosmal Frameshift Call

Link to this post \| posted 03 Aug, 2023 19:49
smolloy123	There is not enough evidence to support calling the tail assembly chaperone programmed ribosomal frame (PRF) in the cluster O phages. A +2 programmed ribosomal frameshift was called in most cluster O mycobacteriophage (e.g. CatDawg gp52 and 53) and they are reported in the cluster O mycobacteriophage paper (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118725). The "slippery sequence" that was identified (GAAAAGT), however, is not canonical and we really don't have any evidence that this is a slippery sequence. See the Bioinformatics guide for more information on what the canonical slippery sites are. Also, the second gene (gpGT) (e.g. MadKillah gp51 or CatDawg gp53), does not have HHPred alignments to tail assembly chaperone proteins. Because it also does not have a slippery sequence, this protein should be called "Hypothetical Protein." The first gene (gpG; MadKillah gp50) does have HHpred alignment to tail assembly chaperones and therefore should be called a tail assembly chaperone.

Link to this post | posted 03 Aug, 2023 19:49

There is not enough evidence to support calling the tail assembly chaperone programmed ribosomal frame (PRF) in the cluster O phages. A +2 programmed ribosomal frameshift was called in most cluster O mycobacteriophage (e.g. CatDawg gp52 and 53) and they are reported in the cluster O mycobacteriophage paper (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118725). The "slippery sequence" that was identified (GAAAAGT), however, is not canonical and we really don't have any evidence that this is a slippery sequence. See the Bioinformatics guide for more information on what the canonical slippery sites are.

Also, the second gene (gpGT) (e.g. MadKillah gp51 or CatDawg gp53), does not have HHPred alignments to tail assembly chaperone proteins. Because it also does not have a slippery sequence, this protein should be called "Hypothetical Protein." The first gene (gpG; MadKillah gp50) does have HHpred alignment to tail assembly chaperones and therefore should be called a tail assembly chaperone.

Link to this post \| posted 03 Apr, 2024 13:23
nietof	Hi We are annotating a cluster O phage, Alkhayr. Our sequence is not canonical. Furthermore, HHPred doesn't support calling TAC as a function for either one of the gene products (gene 50 and 51). I have attached the HHPred matches for gene T, gene 50. Regards F 210Kb

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Tail Assembly Chaperones and Programmed Ribosmal Frameshift Call