SEA-PHAGES | tail assembly chaperones

Link to this post \| posted 25 Apr, 2018 13:17
welkin	You are not off the hook for the frameshift just because your phage is a Singleton. Chances are, you can find the tape measure in a flexible tailed genome, and the two genes right upstream are good candidates for the chaperones. Look for a slippery sequences near the end of the first one— a string of 5 or 6 Gs, a string of 5 or 6 As, three As or Gs followed by three of something else, XXXYYZZ, where X is A or G, etc. Send us an email if you need help.

Link to this post | posted 25 Apr, 2018 13:17

You are not off the hook for the frameshift just because your phage is a Singleton. Chances are, you can find the tape measure in a flexible tailed genome, and the two genes right upstream are good candidates for the chaperones. Look for a slippery sequences near the end of the first one— a string of 5 or 6 Gs, a string of 5 or 6 As, three As or Gs followed by three of something else, XXXYYZZ, where X is A or G, etc.
Send us an email if you need help.

Link to this post \| posted 23 Jan, 2024 23:50
afreise	We are having a tricky time with the putative tail assembly chaperone for Singleton RomansRevenge. Its closest relatives are cluster AP phages. Most AP phages do not annotate a TAC, but several do (e.g, PureGlobe5). Please see the attached PPT for data collection. There is coding potential in the top reading frame on genemark for a potential new gene (RR_27), and the stop site looks like it would be 19980. Though the first putative TAC gene in RomansRevenge (gp26) is in the same pham as PureGlobe5's first TAC gene, there are significant sequence differences. I aligned them and looked for the slippery sequence in the same region I saw the shift in PureGlobe5, but I am not seeing any of the canonical slippery sequences in RomansRevenge_26. 257Kb

Link to this post | posted 23 Jan, 2024 23:50

afreise

We are having a tricky time with the putative tail assembly chaperone for Singleton RomansRevenge. Its closest relatives are cluster AP phages. Most AP phages do not annotate a TAC, but several do (e.g, PureGlobe5). Please see the attached PPT for data collection.

There is coding potential in the top reading frame on genemark for a potential new gene (RR_27), and the stop site looks like it would be 19980.

Though the first putative TAC gene in RomansRevenge (gp26) is in the same pham as PureGlobe5's first TAC gene, there are significant sequence differences.
I aligned them and looked for the slippery sequence in the same region I saw the shift in PureGlobe5, but I am not seeing any of the canonical slippery sequences in RomansRevenge_26.

Link to this post \| posted 24 Jan, 2024 00:49
debbie	Amanda, I see no canonical slippage in RomansRevenge either. The real trick is that I could believe that the "T" portion of a tail assembly chaperone is present, but there is really no way to call it without a useful start codon. debbie BTW The gene that precedes the tail assembly chaperones has hits to minor capsid, HK97_gp 10 and minor tail protein. While I am confident that this protein is structural, it is not clear whether it is part of the head or the tail, please call it Hypothetical Protein.

Link to this post | posted 24 Jan, 2024 00:49

debbie

Amanda,
I see no canonical slippage in RomansRevenge either.
The real trick is that I could believe that the "T" portion of a tail assembly chaperone is present, but there is really no way to call it without a useful start codon.
debbie

BTW The gene that precedes the tail assembly chaperones has hits to minor capsid, HK97_gp 10 and minor tail protein. While I am confident that this protein is structural, it is not clear whether it is part of the head or the tail, please call it Hypothetical Protein.

Link to this post \| posted 24 Jan, 2024 01:00
afreise	thanks, Debbie! and thanks for the note about the preceding gene too!

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tail assembly chaperones