SEA-PHAGES | minor tail protein, tape measure, or NKF?

Link to this post \| posted 14 Mar, 2019 17:52
fbaliraine	The following sequence is for Glaske Gp 29 (120 bp): MNLTDALRTAAEVYNPDDTIDLLGLFIIGLPGSLPAIAALWVTIRGQRRGRARAQRVDAKTDEIHEHVVNTHTSNMRKDLDDLRELVVDGFRRVERDIGGIREEIRTERKERIAGDRRE I note that the majority of BLASTps show NKF for Glaske Gp 29. Although top hits show NKF, Glaske Gp 29 hits the minor tail protein of phage Xavier with q1:s1 in phages Db and NCBI. On the other hand though, HHPRED shows no minor tail protein, but hit # 5 (PF06120.11) shows 90% probability with the “tail length tape measure protein’ of phage HK97 (https://toolkit.tuebingen.mpg.de/#/jobs/Glaske_gp29 ). Nevertheless, no Chrystal structure nor related publication is shown on this hit, and even the BLAST hits were direct submissions with no related paper. Note also that Glaske has a clear, tape measure protein at Gp 17 (1217 bp); which is 10x plus longer than the Gp 29 (10bp). What’s the verdict? I am also attaching a pdf copy of HHPred in case the above hotlink expires. 85Kb

Link to this post | posted 14 Mar, 2019 17:52

The following sequence is for Glaske Gp 29 (120 bp):
MNLTDALRTAAEVYNPDDTIDLLGLFIIGLPGSLPAIAALWVTIRGQRRGRARAQRVDAKTDEIHEHVVNTHTSNMRKDLDDLRELVVDGFRRVERDIGGIREEIRTERKERIAGDRRE

I note that the majority of BLASTps show NKF for Glaske Gp 29. Although top hits show NKF, Glaske Gp 29 hits the minor tail protein of phage Xavier with q1:s1 in phages Db and NCBI. On the other hand though, HHPRED shows no minor tail protein, but hit # 5 (PF06120.11) shows 90% probability with the “tail length tape measure protein’ of phage HK97 (https://toolkit.tuebingen.mpg.de/#/jobs/Glaske_gp29 ). Nevertheless, no Chrystal structure nor related publication is shown on this hit, and even the BLAST hits were direct submissions with no related paper. Note also that Glaske has a clear, tape measure protein at Gp 17 (1217 bp); which is 10x plus longer than the Gp 29 (10bp). What’s the verdict?
I am also attaching a pdf copy of HHPred in case the above hotlink expires.

Link to this post \| posted 14 Mar, 2019 18:44
scaruso	If you look at the tape measure protein in coliphage HK97: https://www.ncbi.nlm.nih.gov/protein/NP_037710.1. It's a big protein, 1089 amino acids long. I think what HHPred is seeing is your protein looks like a small chunk of it, but clearly you have a much better candidate in gp17 for tape measure. Since it is far past tape measure, and not one of the large genes immediately following it, it's hard to justify using synteny to call it a minor tail protein. Your best HHPred hit is to a DUF, as is your second good match, then human signaling proteins. It would be hard for me to make a call on this one other than NKF. Steve Edited 14 Mar, 2019 18:45

Link to this post | posted 14 Mar, 2019 18:44

scaruso

If you look at the tape measure protein in coliphage HK97: https://www.ncbi.nlm.nih.gov/protein/NP_037710.1. It's a big protein, 1089 amino acids long. I think what HHPred is seeing is your protein looks like a small chunk of it, but clearly you have a much better candidate in gp17 for tape measure.

Since it is far past tape measure, and not one of the large genes immediately following it, it's hard to justify using synteny to call it a minor tail protein. Your best HHPred hit is to a DUF, as is your second good match, then human signaling proteins. It would be hard for me to make a call on this one other than NKF.

Steve

Edited 14 Mar, 2019 18:45

Link to this post \| posted 14 Mar, 2019 20:15
fbaliraine	Steven Caruso If you look at the tape measure protein in coliphage HK97: https://www.ncbi.nlm.nih.gov/protein/NP_037710.1. It's a big protein, 1089 amino acids long. I think what HHPred is seeing is your protein looks like a small chunk of it, but clearly you have a much better candidate in gp17 for tape measure. Since it is far past tape measure, and not one of the large genes immediately following it, it's hard to justify using synteny to call it a minor tail protein. Your best HHPred hit is to a DUF, as is your second good match, then human signaling proteins. It would be hard for me to make a call on this one other than NKF. Steve Thank you Steve! Case closed! Fred

Link to this post | posted 14 Mar, 2019 20:15

fbaliraine

Steven Caruso
If you look at the tape measure protein in coliphage HK97: https://www.ncbi.nlm.nih.gov/protein/NP_037710.1. It's a big protein, 1089 amino acids long. I think what HHPred is seeing is your protein looks like a small chunk of it, but clearly you have a much better candidate in gp17 for tape measure.

Since it is far past tape measure, and not one of the large genes immediately following it, it's hard to justify using synteny to call it a minor tail protein. Your best HHPred hit is to a DUF, as is your second good match, then human signaling proteins. It would be hard for me to make a call on this one other than NKF.

Steve

Thank you Steve! Case closed!
Fred

Recent Activity

minor tail protein, tape measure, or NKF?