SEA-PHAGES | All posts created by DrCatalase

Link to this post \| posted 05 Feb, 2025 19:53
DrCatalase	Okay thank you!

Posted in: DNA Master → DNA Master will not save BLAST Results

Link to this post \| posted 05 Feb, 2025 15:04
DrCatalase	Hello All, I have BLASTed our phage and gotten results for 90% of the genes and they saved properly. The others I have tried singly and reBLASTing the entire genome and they will not save. I have looked at the unpacked file and it is not missing any of the 16 files (in fact there are 32 files (no doubles)). I get XML results but they just wont save. Pictures are attached. Thank you! Sean Edited 05 Feb, 2025 15:05 97Kb 4.60Mb 4.33Mb

Link to this post | posted 05 Feb, 2025 15:04

DrCatalase

Hello All,
I have BLASTed our phage and gotten results for 90% of the genes and they saved properly. The others I have tried singly and reBLASTing the entire genome and they will not save. I have looked at the unpacked file and it is not missing any of the 16 files (in fact there are 32 files (no doubles)). I get XML results but they just wont save. Pictures are attached. Thank you!
Sean

Edited 05 Feb, 2025 15:05

Posted in: DNA Master → DNA Master will not save BLAST Results

Link to this post \| posted 17 Oct, 2024 13:58
DrCatalase	Perfect, thank you Vic!

Posted in: Phage Discovery/Isolation → A. globiformis Digest Issues?

Link to this post \| posted 17 Oct, 2024 13:31
DrCatalase	Hello All, This is our first time using A.g. and we got good DNA extraction using the basic protocol from the discovery guide. However, when we tried digestion with NspI and SacII there were no DNA fragments just the large band of uncut DNA. Is there any trick or should I just try a longer digestion time? Thank you! Sean

Posted in: Phage Discovery/Isolation → A. globiformis Digest Issues?

Link to this post \| posted 06 Mar, 2023 19:13
DrCatalase	debbie Hi! there is some confusing that can be easily remedied. Syntenically, this gene is positioned to be the capsid maturation protease (CMP). "The herpesviruses and many phages utilize a maturation protease that acts in this transition from prohead to head, and the main function of the capsid protease is to degrade the parts of the prohead that are required for prohead assembly, but must be removed to complete maturation." So if we can find it, we want this gene's protein to have some protease function. The HHPred results hit minor head protein of SPP1, putative capsid assembly protein (likely another way of saying CMP), Phage Mu protein F like - which as per our approved function list is not anything we will call), and gp15 of D29 - which is D29's capsid maturation protease. Note that all of these are based on inferred calls. I am going to agree with the work of Hatfull and Hendrix, that they were satisfied to call this gene of D29 and L5 a capsid maturation protease some 30 years ago. I would assign this gene protein the function - capsid maturation protease. Best, debbie Thank you. I was confused when I compared it to the capsid maturation protease amino acid sequence from Langerak_gp4 (from the official function list) and got no significant alignment, so it worried me. Sean

Link to this post | posted 06 Mar, 2023 19:13

DrCatalase

debbie
Hi! there is some confusing that can be easily remedied.
Syntenically, this gene is positioned to be the capsid maturation protease (CMP).

"The herpesviruses and many phages utilize a maturation protease that acts in this transition from prohead to head, and the main function of the capsid protease is to degrade the parts of the prohead that are required for prohead assembly, but must be removed to complete maturation."
So if we can find it, we want this gene's protein to have some protease function.

The HHPred results hit minor head protein of SPP1, putative capsid assembly protein (likely another way of saying CMP), Phage Mu protein F like - which as per our approved function list is not anything we will call), and gp15 of D29 - which is D29's capsid maturation protease.

Note that all of these are based on inferred calls. I am going to agree with the work of Hatfull and Hendrix, that they were satisfied to call this gene of D29 and L5 a capsid maturation protease some 30 years ago.

I would assign this gene protein the function - capsid maturation protease.

Best,
debbie

Thank you. I was confused when I compared it to the capsid maturation protease amino acid sequence from Langerak_gp4 (from the official function list) and got no significant alignment, so it worried me.
Sean

Posted in: Cluster EA Annotation Tips → EA4 gene 4

Link to this post \| posted 06 Mar, 2023 17:22
DrCatalase	DrCatalase We are looking at two EA4 phages that have what is called by others as a MuF-like minor capsid protein, minor capsid protein, capsid maturation protease, or a hypothetical protein. We are looking for some guidance, but right now, I am leaning toward hypothetical protein. I didn't see any similarity by amino acid comparison with the reference minor capsid protein and capsid maturation protease gene products.

Link to this post | posted 06 Mar, 2023 17:22

DrCatalase

DrCatalase
We are looking at two EA4 phages that have what is called by others as a MuF-like minor capsid protein, minor capsid protein, capsid maturation protease, or a hypothetical protein. We are looking for some guidance, but right now, I am leaning toward hypothetical protein.

I didn't see any similarity by amino acid comparison with the reference minor capsid protein and capsid maturation protease gene products.

Posted in: Cluster EA Annotation Tips → EA4 gene 4

Link to this post \| posted 06 Mar, 2023 16:57
DrCatalase	We are looking at two EA4 phages that have what is called by others as a MuF-like minor capsid protein, minor capsid protein, capsid maturation protease, or a hypothetical protein. We are looking for some guidance, but right now, I am leaning toward hypothetical protein.

Posted in: Cluster EA Annotation Tips → EA4 gene 4

Link to this post \| posted 22 Sep, 2022 13:54
DrCatalase	After the breakout room, Vic shared a pro-tip before we left: grass clippings, particularly partially decaying grass clippings, may be an excellent source of M. foliorum phages. I'm looking forward to trying this. Also, I am 100% from compost on Microbacterium foliorum bacteriophages, by direct isolation. Especially good is vermicompost! Edited 22 Sep, 2022 13:54

Posted in: Microbacterium → Notes from September 2022 Faculty Meeting

Link to this post \| posted 18 May, 2022 21:32
DrCatalase	scresawn Sorry about the outage - things are back up and running. Best, Steve DrCatalase Hello all, I cannot access phamerator I was able to the day on Monday but not yesterday or today. I have tried with wifi and ethernet on my computer and wifi and data on my phone. I get this message… phamerator.org took too long to respond. Try: Checking the connection Checking the proxy and the firewall Running Windows Network Diagnostics ERR_CONNECTION_TIMED_OUT Someone, please help I am trying to finish up an already late annotation (lol, sorry) Thank you, Sean Thank you, Steve! SC

Link to this post | posted 18 May, 2022 21:32

DrCatalase

scresawn
Sorry about the outage - things are back up and running.

Best,
Steve

DrCatalase
Hello all,
I cannot access phamerator I was able to the day on Monday but not yesterday or today. I have tried with wifi and ethernet on my computer and wifi and data on my phone. I get this message…

phamerator.org took too long to respond.
Try:

Checking the connection
Checking the proxy and the firewall
Running Windows Network Diagnostics
ERR_CONNECTION_TIMED_OUT

Someone, please help I am trying to finish up an already late annotation (lol, sorry)
Thank you,
Sean

Thank you, Steve!
SC

Posted in: Phamerator → Phamerator down?

Link to this post \| posted 18 May, 2022 13:20
DrCatalase	debbie Hi Sean, It should be back up this morning sometime. Steve Cresawn is aware of the problem. Thanks for checking in. debbie Thank you, I had assumed it was something on my end. Sean

Posted in: Phamerator → Phamerator down?

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