Link to this post | posted 28 Feb, 2019 17:20

cdshaffer

These are not mutually exclusive results. Looking at the internal structure for RecA, {I used this link: [Rec A page at UniProt]} I can see that RecA includes a AAA-ATPase like domain. So both term apply, it's just a question of specificity. To me RecA is a much better description of a function than a general ATPase fold seen in diverse cellular activities {see this}. So if you have a good match to RecA across most of RecA I would say use RecA. If, on the other hand, the match is simply to the AAA ATPase as found in RecA I would go with the less specific AAA-ATPase. A detailed look at which parts of RecA is aligning to your protein by looking at the actual HHPred alignment should answer that question.

Link to this post | posted 26 Feb, 2019 18:49

cdshaffer

Just a heads up. It looks like this more recent database update had a very large number of changes. Since starterator tries to use previous results when possible, the large number of changes means this analysis requires a lot more processing and is taking much longer than is typical. I will post as soon as the results are available. Data has been posted, if you are still missing proper pham links please repost your message Edited 26 Feb, 2019 22:02

Link to this post | posted 26 Feb, 2019 16:10

cdshaffer

The most likely reason is a database version sync. There was a database update to version 256 late yesterday, the wustl website is still showing the results from version 255. The new database is being worked on by Starterator but there are approximately 15 thousand reports it just takes time, I expect all the runs to be completed in a couple more hours. If you still have trouble after the update is posted then please post a specific example or two of exactly which genes and pham numbers are giving you issues and I will investigate further.

Link to this post | posted 04 Feb, 2019 19:08

cdshaffer

It appears from your picture that you are still running an older version of Starterator. The newer version does not crash. Updating starterator is non-trivial which is one of the reasons we went with online reports. I have posted a whole phage report for phage Zolita which you can download. If you want to try to update, I can help you with that just post a followup or email me directly (address is my last name @ wustl.edu).

Link to this post | posted 28 Jan, 2019 16:11

cdshaffer

To update the database use Phamerator, just start up Phamerator, then wait for the download and install. Once Phamerator is done updating Starterator should find phage Skippy. As for "Unphamerator phage", Starterator works much better if you add the Profile in addition to the fasta file. This file gives the locations of all the genes so Starterator does not need to try and figure it out. This file is generated by opening the DNA Master file for the phage and using the default settings of the Genome -> Profile… menu to create and save a .csv file. Transfer that file to your machine running Starterator and use it for the Profile. Finally, all starterator reports are now available online if you don't want to hassle with the whole phage report. They can be accessed from the phagesdb web page for the gene. Here is an example for skippy gene 1: https://phagesdb.org/genes/SKIPPY_DRAFT_1/ On that page is a link to the most recent Starterator Report (currently pham 6729).

Link to this post | posted 24 Jan, 2019 01:19
cdshaffer	The most recent version of the database, which includes pham 60238 is now posted so you should be good to go.

Link to this post | posted 04 Oct, 2018 22:07

cdshaffer

This gene from phage Hiyaa, currently gene 75 (originally draft gene 78 ) starting at base 55288 (pham 21467) shows more than 25 HHpred hits with 100% probability and 96 to 98% coverage to adenylosuccinate lyase. Here is a link to the PDB entry for 2PFM the second best HHPRED hit to this gene. A very similar protein also in pham 21467 is gene 36 from Gordonia phage Ghobes, this gene also has the annotation of "adenylosuccinate lyase". According to KEGG, one of the primary roles for adenylosuccinate lyase (4.3.2.2) is purine biosynthesis in which it is the second of two enzymes used to convert IMP to AMP. The first step in this pathway is "adenylosuccinate synthetase, PurA-like" which is already an approved sea-phages term. These results would suggest (keeping the nomenclature parallel) adding "adenylosuccinate lyase, PurB-like" Edited 05 Oct, 2018 14:40

Link to this post | posted 10 Sep, 2018 18:22
cdshaffer	Sally had this error and solved it by deleting all projects; see the last couple of posts in this thread: https://seaphages.org/forums/topic/17/?page=8

Link to this post | posted 23 Aug, 2018 18:10

cdshaffer

Annotation of phage Gilgamesh, gene 43 (27658-28101) in PECAAN. This prediction shows 99.4% prob, with ~90% query and subject coverage HHPRED hit to MutT/NUDIX type nucleotide pyrophosphohydrolase. There is an approved term for "MazG-like nucleotide pyrophosphohydrolase". According to this paper (The Journal of Biological Chemistry 286, 30691-30705) the nucleotide pyrophosphohydrolases fall into "structurally different superfamilies, such as the MutT-related hydrolases (Nudix) (α + β), dUTPase (all-β), dITPase (Maf/HAM1) (α/β), all-α-NTP pyrophosphatases (MazG), and phospho-ribosyl-ATP pyrophosphatase (HisE)." The MazG type are a superfamily made up of all alpha helices as can been seen in this PDB crystal structure of the eponymous MazG protein 3CRA. The MutT (also called Nudix type) show a kind of sandwich with a beta sheet between alpha helices like 4KYX I would propose adding either "MutT-like nucleotide pyrophosphohydrolase" to keep a parallel structure to the other entry or just have a generic "nucleotide pyrophosphohydrolase" at the bottom of the list for those enzymes that are not in the MazG superfamily. Edited 23 Aug, 2018 18:11

Link to this post | posted 20 Jul, 2018 19:17

cdshaffer

To answer your question on Fe+2 binding, I could not find any in vivo studies but this result is a crystal of an "iron soaked" version of the protein complete with Iron bound as expected and a discussion of the conserved Asp channels that could allow ions to flow into the cavity. I agree on every single point you made. I really don't think there is a good annotation here. I think maybe the best option here is "do no harm" so we will proceed with Yaboi and annotate this gene NKF. We can always change it later.