SEA-PHAGES | minor tail proteins

Link to this post \| posted 03 Apr, 2018 14:11
welkin	Unlike many other clusters, the Cluster A phages have some minor tail proteins at the left end of their genome, upstream of the lysins and terminase genes (around gene 4-6ish). You can recognize these proteins due to their size. Some of them may have structural motifs that suggest long, extended proteins, like collagen-repeats, or coiled-coils.

Link to this post \| posted 06 Jun, 2019 12:51
jawsWPI	How hard and fast is the minor tail protein size range (1-3kb)? I'm reviewing an A1 annotation that has assigned the 'minor tail protein' function to 333bp, 348 bp and 447 bp ORF's, mostly based (I think) on a FEW cases in each pham that have given this functional assignment to similarly (small) sized ORFs. I want to change these all to NKF, first based on size and second based on total number of minor tails of the correct size and position.

Link to this post | posted 06 Jun, 2019 12:51

jawsWPI

How hard and fast is the minor tail protein size range (1-3kb)?
I'm reviewing an A1 annotation that has assigned the 'minor tail protein' function to 333bp, 348 bp and 447 bp ORF's, mostly based (I think) on a FEW cases in each pham that have given this functional assignment to similarly (small) sized ORFs. I want to change these all to NKF, first based on size and second based on total number of minor tails of the correct size and position.

Link to this post \| posted 17 Jun, 2020 13:31
MSMC	jawsWPI How hard and fast is the minor tail protein size range (1-3kb)? I'm reviewing an A1 annotation that has assigned the 'minor tail protein' function to 333bp, 348 bp and 447 bp ORF's, mostly based (I think) on a FEW cases in each pham that have given this functional assignment to similarly (small) sized ORFs. I want to change these all to NKF, first based on size and second based on total number of minor tails of the correct size and position. I see the same thing right now in an A3 phage. There are three minor tail proteins called as the first 3 genes: 426, 321 and 1200 bp respectively. The first two seem too short, none have any HHPRED data to support this function. It appears the functional assignment is based solely on synteny with other phages in the cluster, though only a few call these as minor tail proteins. I am thinking changing them to NKF.

Link to this post | posted 17 Jun, 2020 13:31

MSMC

jawsWPI
How hard and fast is the minor tail protein size range (1-3kb)?
I'm reviewing an A1 annotation that has assigned the 'minor tail protein' function to 333bp, 348 bp and 447 bp ORF's, mostly based (I think) on a FEW cases in each pham that have given this functional assignment to similarly (small) sized ORFs. I want to change these all to NKF, first based on size and second based on total number of minor tails of the correct size and position.

I see the same thing right now in an A3 phage. There are three minor tail proteins called as the first 3 genes: 426, 321 and 1200 bp respectively. The first two seem too short, none have any HHPRED data to support this function. It appears the functional assignment is based solely on synteny with other phages in the cluster, though only a few call these as minor tail proteins. I am thinking changing them to NKF.

Link to this post \| posted 18 Jun, 2020 14:57
jawsWPI	I would agree that the two smaller ones should be NKF but, the 1200bp is probably a minor tail. An HHPred run analysis of the 1200bp protein should give good hits to collagen-like or glycine-rich proteins if it is a minor tail. The gene count in your A3 may be off because gene 1 (HNH endonuclease) is often not included in the auto-annotation and has to be added manually.

Link to this post \| posted 18 Jun, 2020 15:07
MSMC	jawsWPI I would agree that the two smaller ones should be NKF but, the 1200bp is probably a minor tail. An HHPred run analysis of the 1200bp protein should give good hits to collagen-like or glycine-rich proteins if it is a minor tail. The gene count in your A3 may be off because gene 1 (HNH endonuclease) is often not included in the auto-annotation and has to be added manually. Thanks Joanne, I was thinking the same thing, I kept the third gene, there are some hits moderate hits to collagen-like proteins. The annotators did include the HNH.

Link to this post | posted 18 Jun, 2020 15:07

MSMC

jawsWPI
I would agree that the two smaller ones should be NKF but, the 1200bp is probably a minor tail. An HHPred run analysis of the 1200bp protein should give good hits to collagen-like or glycine-rich proteins if it is a minor tail. The gene count in your A3 may be off because gene 1 (HNH endonuclease) is often not included in the auto-annotation and has to be added manually.

Thanks Joanne, I was thinking the same thing, I kept the third gene, there are some hits moderate hits to collagen-like proteins. The annotators did include the HNH.

Link to this post \| posted 05 Apr, 2023 19:23
kcornely	We are annotating a cluster A3 phage LBerry and I found this discussion to be really helpful, because I didn't expect to find minor tail proteins on the left hand side of the genome. We have three genes, gp3, gp4, and gp5, that are candidate minor tail proteins. The gp4 and gp5 proteins seem promising because we get HHPred hits to collagen-type proteins, and BLAST hits to phage tail fiber proteins. The sizes of gp4 and gp5 also seem to be about right (945 bp and 636 bp, respectively). We're not sure about gp3. The size is smaller (321 bp), but we get some nice HHPred hits to tail fibers for L5 and the E. coli phage T5 (for example, the L subunit of phage T4; PDB code = 7QG9). Is gp3 still too short to be a minor tail protein? Or could we still call the function as a minor tail protein because gp3 might be a subunit that is part of a larger assembly?

Link to this post | posted 05 Apr, 2023 19:23

kcornely

We are annotating a cluster A3 phage LBerry and I found this discussion to be really helpful, because I didn't expect to find minor tail proteins on the left hand side of the genome. We have three genes, gp3, gp4, and gp5, that are candidate minor tail proteins. The gp4 and gp5 proteins seem promising because we get HHPred hits to collagen-type proteins, and BLAST hits to phage tail fiber proteins. The sizes of gp4 and gp5 also seem to be about right (945 bp and 636 bp, respectively). We're not sure about gp3. The size is smaller (321 bp), but we get some nice HHPred hits to tail fibers for L5 and the E. coli phage T5 (for example, the L subunit of phage T4; PDB code = 7QG9). Is gp3 still too short to be a minor tail protein? Or could we still call the function as a minor tail protein because gp3 might be a subunit that is part of a larger assembly?

Link to this post \| posted 07 Apr, 2023 16:42
debbie	Kathleen, I would careful to apply minor tail proteins to small proteins, especially when they are situated in a non-canonical place. Too often, the motifs of capsid proteins and tail proteins can look very similar - too similar to know what it is! debbie

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minor tail proteins