Link to this post | posted 01 Jun, 2023 18:54
pia1@pitt.edu	kbutela Phamerator is currently down for me and my students as of Thursday 6/1 at 2:30 pm. We just upgraded internet security services, so it's entirely possible that the site is blocked on campus wifi. Is anyone else having trouble? I'm currently on pitt campus using pitt wifi. I can't access Phamerator.

Link to this post | posted 28 Apr, 2022 18:08
pia1@pitt.edu	Would it help to add in the notes that this type of protein (IrrE-like protein) has both a metelloprotease domain and a HTH DNA binding domain?

Link to this post | posted 28 Apr, 2022 16:48
pia1@pitt.edu	I have no idea where the emoji came from but it seems to be in the place for )…

Link to this post | posted 28 Apr, 2022 16:46

pia1@pitt.edu

HI, This is Ping at University of Pittsburgh. I may have a similar case with gp39 of phage Nettuno in cluster CZ2. There is a mix of metalloprotease and HTH DNA binding domain calls in BLAST hits. The top HHpred hit for gp39 is 3DTE_A (IrrE) with 99.7% probability and 81% coverage. The alignment is gp39 aa9-128 and IrrE aa53-187. The IrrE crystal structure reveals that this protein is folded into three distinct domains: an N-terminal domain (residues 8–125) that consists of five α-helices and a three-stranded antiparallel β-sheet; a middle helix-turn-helix (HTH)-containing domain (residues 126–167); and a C-terminal domain (residues 168–263) folded into a highly twisted six-stranded antiparallel β-sheet with a short α-helix. The alignment between gp39 (aa 9-12 and IrrE (aa 53-187) corresponds to part of the metalloprotease domain, which contains a HEXXH motif and an E (glutamate) 20-30aa downstream of the HEXXH. The key motif HEXXH and the downstream E for the metalloprotease activity are indeed conserved in gp39; the alignment between gp39 and IrrE also covers the complete HTH DNA binding domain. Taken together, gp39 of Nettuno really seems to have both the metalloprotease function and HTH DNA binding domain. I'm not entirely sure which is the better function call because neither reflects the whole picture. See link to the reference below, https://www.sciencedirect.com/science/article/abs/pii/S0022283608015970?via%3Dihub

Link to this post | posted 23 Feb, 2022 04:14

pia1@pitt.edu

Hi Steve, Thanks for the quick response! I was chatting with the tech help desk at pitt. The tech expert walked me through several things. He suspected that the problem has something to do with my home wifi. But he wasn't able to solve the problem in the end after all the attempts. I saved a copy of our chat, which is attached to this post for your reference. So I decided to try Phamerator one more time before going to bed, and it's working! I'm very glad that it's working for me now. But I really don't know how the problem is fixed. Please let me know if you have any questions. Thanks! 4Kb

Link to this post | posted 23 Feb, 2022 01:23
pia1@pitt.edu	I have not been able to get Phamerator to work since yesterday. When I try to google search phamerator, the search result seems to suggest that I'm not connected to WiFi (please see attached for the screenshot), but I actually do have a working WiFi. Can someone please help? 40Kb

Link to this post | posted 22 Feb, 2022 16:55
pia1@pitt.edu	I hate to be the pest but Phamerator is still not working for me. When I try to google search phamerator, the search result seems to suggest that I don't have WiFi (please see attached for the screenshot), but I actually do have a working WiFi. Chris, is there something that you have to do from your end to get it to work? 40Kb

Link to this post | posted 22 Feb, 2022 02:36
pia1@pitt.edu	I have tried WiFi at Pitt and at home, 3 different models of Mac and 1 PC, Firefox, Safari and Chrome, none of the above can get Phamerator to load for me. The following post https://seaphages.org/forums/topic/5097/ also discussed the 502 error, but it's not clear exactly how the issue was fixed…

Link to this post | posted 21 Feb, 2022 18:50
pia1@pitt.edu	I also tried both Firefox and Chrome. Neither worked for Phamerator. Same 502 error message.

Link to this post | posted 15 Feb, 2022 17:30

pia1@pitt.edu

Debbie and I just chatted about this particular phamm today. Debbie pointed out that this pham is particularly diverse and shared the multiple sequence alignment of all members in this pham, which is attached to this post. You may need a multiple sequence alignment viewer to open the alignment and Debbie recommended the following, https://macdownload.informer.com/aliview/ The AliView tool is free for download. To reiterate the important message again, Starterator does not have all the answers for choice of start site especially when a pham is very diverse. A closer look at the specific cluster to which the phage belongs may be more informative. In addition, the gene of interest, Pytheas gp29, appears to be a lysin B coding gene. Drs. Kim Payne (a former graduate student from the Hatful lab) and Graham Hatful have published a great article on the study of mycobacteriophage endolysins in PlosOne (https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0034052&type=printable). This article revealed the diversity and modular structure of endolysin and provides very helpful background knowledge on endolysin for annotation work. 38Kb