SEA-PHAGES | Tail Assembly Chaperone in KaiHaiDragon

Link to this post \| posted 18 Jun, 2018 16:06
adiaz	Hello, I'm having a dilemma as to whether or not I should call genes 34 and 35 in KaiHaiDragon as the tail assembly chaperone. The evidence for the chaperones is based entirely on synteny (proximity to the tape measure) and the presence of the slippery sequences in Robsfeet and Metamorphoo, which are also found in Cluster EC. In the attached file I highlighted in blue the slippery sequence in both Robsfeet and Metamorphoo (CCCCCC), however, that sequence is missing from KaiHaiDragon, Paschalis, and Quhwah. Is it OK to still call them chaperones in KaiHaiDragon since they are in the same pham without annotating a frame shift or should I leave it as hypothetical protein in the GenBank file? Thanks for your help, Arturo 12Kb

Link to this post | posted 18 Jun, 2018 16:06

Hello,

I'm having a dilemma as to whether or not I should call genes 34 and 35 in KaiHaiDragon as the tail assembly chaperone. The evidence for the chaperones is based entirely on synteny (proximity to the tape measure) and the presence of the slippery sequences in Robsfeet and Metamorphoo, which are also found in Cluster EC. In the attached file I highlighted in blue the slippery sequence in both Robsfeet and Metamorphoo (CCCCCC), however, that sequence is missing from KaiHaiDragon, Paschalis, and Quhwah.

Is it OK to still call them chaperones in KaiHaiDragon since they are in the same pham without annotating a frame shift or should I leave it as hypothetical protein in the GenBank file?

Thanks for your help,

Arturo

Link to this post \| posted 19 Jun, 2018 14:02
welkin	Hi ARturo, Any of those are possible— can you post the .dnam5 file and then we'll take a look? thanks so much! Welkin

Link to this post \| posted 19 Jun, 2018 14:30
adiaz	Attached please find the .dnam5 file. 25Kb

Link to this post \| posted 20 Jun, 2018 12:32
kklyczek	That slippery sequence is only in 2 of the 6 EC cluster phages - see the attached alignment of the 3'end of the putative G gene (KaiHaiDragon_33, pham 45474). Karen 152Kb

Link to this post \| posted 28 Jun, 2018 16:20
welkin	Sorry it took me so long to get back to this— I think the way forward is to call them tail assembly chaperones and not to put in the slip. We probably need to remove it from the other two, as well– they are all probably using the same site and we can't identify it at this time. Thanks! Welkin

Link to this post \| posted 28 Jun, 2018 18:58
adiaz	Thanks for the clarification!

Link to this post \| posted 29 Apr, 2020 03:18
adiaz	We got another cluster EC phage this year, any updates on whether the slippery sequence has been identified for this cluster? Thank you, Arturo

Link to this post \| posted 07 Dec, 2022 16:11
debbie	Working on Microbacterium phage Jefe at the 2022 Genomics Workshop! It is one of the members of this cluster where no slippery sequence can be identified. The upstream gene of the TAC pair has a Pfam hit to tail assembly chaperone, so call it. However, there is no data to support a tail assembly chaperone call for the second gene, NOR its there a slippery sequence present. that gene is a Hypothetical Protein.

Link to this post | posted 07 Dec, 2022 16:11

debbie

Working on Microbacterium phage Jefe at the 2022 Genomics Workshop! It is one of the members of this cluster where no slippery sequence can be identified. The upstream gene of the TAC pair has a Pfam hit to tail assembly chaperone, so call it. However, there is no data to support a tail assembly chaperone call for the second gene, NOR its there a slippery sequence present. that gene is a Hypothetical Protein.

Link to this post \| posted 22 Feb, 2023 20:25
aajohnson	This was useful today! Thank you.

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Tail Assembly Chaperone in KaiHaiDragon