SEA-PHAGES | All posts created by plymaler

Link to this post \| posted 29 Sep, 2022 01:05
plymaler	Hi all, I am trying to use PhamNexus in the 2020 SEA VM. It asks me what database I want to use. I choose one and click "yes" when asked if I want to check the Hatfull server for the newest database version. Then, I am asked for the mySQL login info, which I do not know. Can someone tell me the login info, or if I need to change a setting in the SEA VM? I previously used this installation of the SEA VM for flatfile checking and that worked okay. Thank you!

Link to this post | posted 29 Sep, 2022 01:05

Hi all,
I am trying to use PhamNexus in the 2020 SEA VM. It asks me what database I want to use. I choose one and click "yes" when asked if I want to check the Hatfull server for the newest database version. Then, I am asked for the mySQL login info, which I do not know. Can someone tell me the login info, or if I need to change a setting in the SEA VM? I previously used this installation of the SEA VM for flatfile checking and that worked okay.

Thank you!

Posted in: Bioinformatic Tools and Analyses → PhamNexus on SEA-VM

Link to this post \| posted 02 Feb, 2022 22:44
plymaler	I haven't made it to guest additions, as I ran into an error when I tried to start the SEA VM. I downloaded and unzipped the 2017 SEA VM, put it here, /home/ruth/VirtualBox VMs/SEAVM_2017.vmdk, and followed the setup directions from https://seaphages.org/software/virtualmachine/. When I started the VM, I got this error (attached screenshot). 18Kb

Posted in: SEA-PHAGES Virtual Machine → Installing SEA VM on Linux machine

Link to this post \| posted 01 Feb, 2022 22:29
plymaler	Great! I have VirtualBox installed, and am not sure whether to download the Windows or Mac SEA VM from seaphages.org. 163Kb

Posted in: SEA-PHAGES Virtual Machine → Installing SEA VM on Linux machine

Link to this post \| posted 31 Jan, 2022 22:02
plymaler	The Mac that I was using to run the SEA VM has aged out of updates and I have installed Linux Mint on the machine. Can I run the SEA VM on this operating system? I can install VirtualBox, but then need to choose between the Mac or Windows VM download. Thank you!

Posted in: SEA-PHAGES Virtual Machine → Installing SEA VM on Linux machine

Link to this post \| posted 15 Nov, 2018 02:38
plymaler	I am confused about the role of HHpred for genes of unknown function. Is it useful to record HHpred results that are a good match, but do not provide functional information? Or should HHpred only be recorded if it supports a specific function? For example, Parada_23 (19065 to 19505 (Forward)). The top HHpred result is to "DUF2744 ; Protein of unknown function", with a 98.5% probability and 73.2877% coverage. The probability and coverage seem good, but the "DUF" in DUF2744 stands for "domain of unknown function", so this result provides no functional data. Should I / my students mark / record this result in PECAAN / when doing annotations? Or, should HHpred results only be recorded if they have good probability and coverage AND indicate a specific function? (As a note, the second result is to an anti-sigma factor, with 39% probability and 21% coverage. PhagesDB and NCBI BLAST support a function of "minor tail protein".)

Link to this post | posted 15 Nov, 2018 02:38

plymaler

I am confused about the role of HHpred for genes of unknown function. Is it useful to record HHpred results that are a good match, but do not provide functional information? Or should HHpred only be recorded if it supports a specific function?

For example, Parada_23 (19065 to 19505 (Forward)). The top HHpred result is to "DUF2744 ; Protein of unknown function", with a 98.5% probability and 73.2877% coverage. The probability and coverage seem good, but the "DUF" in DUF2744 stands for "domain of unknown function", so this result provides no functional data. Should I / my students mark / record this result in PECAAN / when doing annotations? Or, should HHpred results only be recorded if they have good probability and coverage AND indicate a specific function?

(As a note, the second result is to an anti-sigma factor, with 39% probability and 21% coverage. PhagesDB and NCBI BLAST support a function of "minor tail protein".)

Posted in: Functional Annotation → marking HHpred for unknown function

Link to this post \| posted 07 Jul, 2018 17:09
plymaler	ThetaBob is an F4 phage. ThetaBob_107 has good HHPred matches to both glycosyltransferases and methyltransferases; screenshots of the HHPred output are attached. A combined glycosyltransferase/methytransferase function is not on the approved function list and so I am not sure how to identify the function of this protein. It does not seem to lean one way or the other. ThetaBob_107 is currently in pham 3147 with 9 other non-draft proteins, all in F phage. Avani_105, Jabbawokkie_106, Zapner_106, WillSterrel_99, Llama_108, and Demsculpinboyz_115 are all labeled as glycosyltransferase/methyltransferase. Che9d_109 and Yoshi_114 are labeled as glycosyl transferase. Che8_108 is unlabeled. Can glycosyltransferase/methytransferase be added an approved function? If not, what is the recommendation for how to label ThetaBob_107? Thanks! 352Kb

Link to this post | posted 07 Jul, 2018 17:09

plymaler

ThetaBob is an F4 phage. ThetaBob_107 has good HHPred matches to both glycosyltransferases and methyltransferases; screenshots of the HHPred output are attached. A combined glycosyltransferase/methytransferase function is not on the approved function list and so I am not sure how to identify the function of this protein. It does not seem to lean one way or the other.

ThetaBob_107 is currently in pham 3147 with 9 other non-draft proteins, all in F phage. Avani_105, Jabbawokkie_106, Zapner_106, WillSterrel_99, Llama_108, and Demsculpinboyz_115 are all labeled as glycosyltransferase/methyltransferase. Che9d_109 and Yoshi_114 are labeled as glycosyl transferase. Che8_108 is unlabeled.

Can glycosyltransferase/methytransferase be added an approved function? If not, what is the recommendation for how to label ThetaBob_107?

Thanks!

Posted in: Request a new function on the SEA-PHAGES official list → methyltransferase/glycosyltransferase

Link to this post \| posted 05 Jul, 2018 17:18
plymaler	Hi all, I am annotating ThetaBob, an F4 phage. ThetaBob_32 and 33 have been labeled Lysin A and Lysin B, respectively. ThetaBob_35 (stop 28491) is in pham 48862, and seven of the eight other members of this pham are marked as holins. ThetaBob_35 has no transmembrane domains. There are five other F phage with members of this pham marked as holins–Avani_37, Che9D_37, Demsculpinboyz_38, Jabbawokkie_40, Zapner_39–none of these proteins have transmembrane domains. There is sixth F phage with a gene in his pham–Yoshi_39. Yoshi_39 is marked as NKF, and no holin has been identified in Yoshi. There are two DP phage with members of this pham marked as holins–Ronaldo_64 and Fryberger_61–both each have one transmembrane domain. ThetaBob_38 has four transmembrane domains, but is well after the lysin genes. HHPred analysis shows a pfam match to E. coli holins in the last quarter of ThetaBob_38. My plan is to mark ThetaBob_35 as NKF, not as a holin, and to mark ThetaBob_38 as a membrane protein. Thanks for your thoughts!

Link to this post | posted 05 Jul, 2018 17:18

plymaler

Hi all,
I am annotating ThetaBob, an F4 phage. ThetaBob_32 and 33 have been labeled Lysin A and Lysin B, respectively.
ThetaBob_35 (stop 28491) is in pham 48862, and seven of the eight other members of this pham are marked as holins.
ThetaBob_35 has no transmembrane domains. There are five other F phage with members of this pham marked as holins–Avani_37, Che9D_37, Demsculpinboyz_38, Jabbawokkie_40, Zapner_39–none of these proteins have transmembrane domains. There is sixth F phage with a gene in his pham–Yoshi_39. Yoshi_39 is marked as NKF, and no holin has been identified in Yoshi.
There are two DP phage with members of this pham marked as holins–Ronaldo_64 and Fryberger_61–both each have one transmembrane domain.

ThetaBob_38 has four transmembrane domains, but is well after the lysin genes. HHPred analysis shows a pfam match to E. coli holins in the last quarter of ThetaBob_38.

My plan is to mark ThetaBob_35 as NKF, not as a holin, and to mark ThetaBob_38 as a membrane protein.

Thanks for your thoughts!

Posted in: Functional Annotation → holin with zero transmembrane domains in F cluster phage?

Link to this post \| posted 16 Jun, 2016 21:13
plymaler	Hi all, I compiled a list of bioinformatic software based on this year's symposium and previous meetings. It can be found at https://docs.google.com/spreadsheets/d/15dToev8nCF_sZMfuYmQo-uKat05m-CMwKsLQi3XGDA8/edit?usp=sharing and attached. 84Kb

Posted in: Annotation → List of bioinformatic software

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