Link to this post | posted 25 Mar, 2019 16:45
scaruso	We used the function "major capsid and protease fusion protein," the current version of "capsid & capsid maturation protease" of the cluster AM phages (see Pham 17557). Should another function be created, perhaps that recognizes all three domains? Steve

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 13 Mar, 2019 16:24
scaruso	I don't know. I wouldn't be surprised it that wasn't an error code or below the measurable threshold code, but I don't know offhand, I'm afraid.

Link to this post | posted 11 Mar, 2019 22:40
scaruso	I know you can run OrthoANI as a stand alone program and do so. I let Ivan do that, though, since it's command line. The GUI based one has a limit of 10 genomes. It didn't seem to be particularly challenging for him. Might give him a shout if you run into any trouble. Steve

Link to this post | posted 11 Mar, 2019 19:22
scaruso	Christian, We use that one as well, and also OrthoANI, here: https://www.ezbiocloud.net/tools https://www.ezbiocloud.net/tools/ani Steve

Link to this post | posted 11 Mar, 2019 19:03
scaruso	Claire, Thank you very much for the response, that was very helpful. And I can delete Anthony now, we are done with it. Though the answer will, no doubt, be useful for other duplicates in the future. Steve

Link to this post | posted 09 Mar, 2019 22:07

scaruso

Claire, Can you tell me what the Phagesdb Function Frequency is based on? I see a list of various function assignments for a variety of PHAMS, but what brings them up? I don't see the same hits on Blastp or HHPred, always, and the PHAMS are different than the gp being examined, so I'm not clear. By the way, I posted another question about HHPred results in PECAAN and external, any thoughts about that? Thanks! Steve

Link to this post | posted 05 Mar, 2019 19:12
scaruso	Excellent. That's very helpful. Thank you! Steve

Link to this post | posted 05 Mar, 2019 03:21

scaruso

A follow up on this old post, if you don't mind. There is a recent post in the Cluster Specific Tips that continues this conversation. See: Forum Home / Science / Cluster-Specific Annotation Tips / Cluster A Annotation Tips / minor tail proteins Welkin Pope posted 03 Apr, 2018 14:11 "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." So I would like to get a little feedback if I can. Heather gp18 (a BB2) has BlastP hits to lots of "minor tail protein" calls, as well as some "tail fiber" and other similar calls. But I don't think they are justified. HHPred actually hits to collagen, not to any identified tail proteins. I think it's a rabbit hole. And then there's: The Collagen-like Protein gp12 Is a Temperature-dependent Reversible Binder of SPP1 Viral Capsids. Mohamed Zairi, Asita C. Stiege, Naima Nhiri, Eric Jacquet, and Paulo Tavares http://www.jbc.org/content/289/39/27169.full Which shows that these hits might be for other structural components, like parts of the capsid. My inclination is to leave it NKF, unless I am missing something. Any thoughts? >Heather_gp18 MTQPVETFPLPPSIETVKVHGHYRGPDGRGLQGTVTFTGPGLLTFPDADLFIAGPVVARLDEFGAFEVTLPATDNEGMNPSDWSYTVKENL TGVTGARTFALLLPKDTAEIDLADVAPADPLTPNYVPVPGPQGEPGPQGVKGDPGATGPAGANGAPGAPGAAGAPGVIQSVNGKSAASVTL VPADLGAVPTSDKGVANGVASLGADGKVPAGQLPATSNAVTSVNTKTGAVVLSASDVSAVPTSDKGAANGVATLDASTKVPTAQIPSLTST YVAVSTRGAANGVATLDGTTRLPVAQVPATLPKNTWTPQALGFQAWSCDPGGVANPGAKYLTPQRLYMTGFNITEPTTVSNVVMFARGYGG VGTNRYMAGIYKEDGTRVVASAAVALSMAGQESGALPGMVTNHIGAVPLPITSTTLQPGRYWVAWVLTVGAASDFAFYHVQNEAPVSTANF FMPTTPFARAWYLAGQSTLPTTVSQTAAGVLADHDIPIVALA Edited 05 Mar, 2019 03:24

Link to this post | posted 01 Mar, 2019 19:53
scaruso	I think you have a clear holin already as well, Esketit_Draft gene 30 (25259 - 25618 ), and it's the same length as the other BI1s (119 aa) and similar to the BI2 Scap1 that has it as well (129 aa). I don't know if we have confirmed cases of two holins (Lee?). I would be hesitant to call a second one, I think. Steve Edited 01 Mar, 2019 19:57