SEA-PHAGES | All posts created by smolloy123

Link to this post \| posted 15 May, 2019 21:41
smolloy123	Hi Debbie, Thanks, I aligned the first gene from Trax with the corresponding genes in Neville and Octobien14. They align overall well but mostly for about 2/3 of the sequence on the C-terminus side. Neville is shorter (or at least was called shorter) and the other two don't align well at the N-terminus. I think they don't make the Pham cut because they are too short. I will call them both hypothetical Thanks for your input so I can finish off my last genome! Cheers Sally

Link to this post | posted 15 May, 2019 21:41

Hi Debbie,
Thanks, I aligned the first gene from Trax with the corresponding genes in Neville and Octobien14. They align overall well but mostly for about 2/3 of the sequence on the C-terminus side. Neville is shorter (or at least was called shorter) and the other two don't align well at the N-terminus. I think they don't make the Pham cut because they are too short.

I will call them both hypothetical smile

Thanks for your input so I can finish off my last genome!
Cheers
Sally

Posted in: Request a new function on the SEA-PHAGES official list → membrane protein

Link to this post \| posted 15 May, 2019 18:14
smolloy123	smolloy123 Hi Welkin or others, I am QCing Trax, a DU phage. Following the lysin A genes, there are two genes that each have 1 transmembrane domain. The first gene (gp37 on phamearator) is called holin on other DU phage. I know that we are not calling genes with single TMDs "membrane proteins." I also had it in my head that holins have at least 2 TMDs. Do I call these hypothetical? Do I call one of them a holin because of being adjacent to lysin As? Based on the rules that I know I would call these hypothetical. Thanks! Sally Also, these TMDs were confirmed in other programs e.g.TMpred (can't ever get SOSUI to work)

Link to this post | posted 15 May, 2019 18:14

smolloy123

smolloy123
Hi Welkin or others,
I am QCing Trax, a DU phage. Following the lysin A genes, there are two genes that each have 1 transmembrane domain. The first gene (gp37 on phamearator) is called holin on other DU phage.

I know that we are not calling genes with single TMDs "membrane proteins."

I also had it in my head that holins have at least 2 TMDs.

Do I call these hypothetical? Do I call one of them a holin because of being adjacent to lysin As?

Based on the rules that I know I would call these hypothetical.

Thanks!
Sally

Also, these TMDs were confirmed in other programs e.g.TMpred (can't ever get SOSUI to work)

Posted in: Request a new function on the SEA-PHAGES official list → membrane protein

Link to this post \| posted 15 May, 2019 16:12
smolloy123	Hi Welkin or others, I am QCing Trax, a DU phage. Following the lysin A genes, there are two genes that each have 1 transmembrane domain. The first gene (gp37 on phamearator) is called holin on other DU phage. I know that we are not calling genes with single TMDs "membrane proteins." I also had it in my head that holins have at least 2 TMDs. Do I call these hypothetical? Do I call one of them a holin because of being adjacent to lysin As? Based on the rules that I know I would call these hypothetical. Thanks! Sally

Link to this post | posted 15 May, 2019 16:12

smolloy123

Hi Welkin or others,
I am QCing Trax, a DU phage. Following the lysin A genes, there are two genes that each have 1 transmembrane domain. The first gene (gp37 on phamearator) is called holin on other DU phage.

I know that we are not calling genes with single TMDs "membrane proteins."

I also had it in my head that holins have at least 2 TMDs.

Do I call these hypothetical? Do I call one of them a holin because of being adjacent to lysin As?

Based on the rules that I know I would call these hypothetical.

Thanks!
Sally

Posted in: Request a new function on the SEA-PHAGES official list → membrane protein

Link to this post \| posted 13 Apr, 2019 21:19
smolloy123	Hi Deb, I am going to fix those two gene function calls and then Sidious will be ready for submitting to GenBank. Right now, gp40 is RexB and gp41 is RexA. But I will confirm one more time once I make the final flat file. That will have to wait until Monday when I am at my office computer due to a BLOB that is preventing me from using the "Submit to GenBank" function in DNA Master. I'll let you know how the immunity assays turn out too. Thanks for sending the Gordi panel for us to play with! Cheers Sally

Link to this post | posted 13 Apr, 2019 21:19

smolloy123

Hi Deb,
I am going to fix those two gene function calls and then Sidious will be ready for submitting to GenBank.
Right now, gp40 is RexB and gp41 is RexA. But I will confirm one more time once I make the final flat file. That will have to wait until Monday when I am at my office computer due to a BLOB that is preventing me from using the "Submit to GenBank" function smile

in DNA Master.

I'll let you know how the immunity assays turn out too. Thanks for sending the Gordi panel for us to play with!
Cheers
Sally

Posted in: Functional Annotation → RexAB systems

Link to this post \| posted 13 Apr, 2019 21:13
smolloy123	Hi All, I am calling two Lysin A genes in a Rhodococcus phage, Whack. The first domain appears to match with high prob and coverage to M23 peptidase domain. They Payne paper refers this domain states that the M23 peptidase domain is typically observed in phage endolysins of Rhodococcus. The HHPRED hits specify M23B peptidase of various bacteria such as Helobacter pylori (as seen in Bxb1)…But also matches a Vibrio cholerae zinc peptidase (which is also mentioned in Payne paper but as M23 not M23B) Does the type of M23 peptidase need to be specified? Do you approve the call of M23 peptidase domain for lysin A and if so Can we add this to the accepted functions list? Thanks! Sally

Link to this post | posted 13 Apr, 2019 21:13

smolloy123

Hi All,
I am calling two Lysin A genes in a Rhodococcus phage, Whack.

The first domain appears to match with high prob and coverage to M23 peptidase domain. They Payne paper refers this domain states that the M23 peptidase domain is typically observed in phage endolysins of Rhodococcus.

The HHPRED hits specify M23B peptidase of various bacteria such as Helobacter pylori (as seen in Bxb1)…But also matches a Vibrio cholerae zinc peptidase (which is also mentioned in Payne paper but as M23 not M23B) Does the type of M23 peptidase need to be specified?

Do you approve the call of M23 peptidase domain for lysin A and if so Can we add this to the accepted functions list?

Thanks!
Sally

Posted in: Functional Annotation → Lysin A in Rhodococcus phage

Link to this post \| posted 11 Apr, 2019 22:12
smolloy123	Hi All, I looking for guidance on how to call two genes in Sidious (cluster CZ7) that match the RexA and RexB abortive infections system proteins of E. coli. Graham let me peek at the CarolAnn and Sbash paper and gp41 and 43 in phamerator (gp40 and 41 in PECAAN as the forward gene between them was deleted) lookk like they fit the bill. gp41 has 4 transmembrane domains (rexB?) and gp43 has a 99.8% prob and 92% coverage hit to RexA Intracellular sensor of Lambda phage, Abi component. gp43 also has the DUF4747 domain that the CarolAnn RexA protein has. Do I leave these function calls as membrane protein and NKF for gp41 and 43 or do you want the RexAB system called? If the latter, what is the exact name you would like used? Thanks! Sally

Link to this post | posted 11 Apr, 2019 22:12

smolloy123

Hi All,
I looking for guidance on how to call two genes in Sidious (cluster CZ7) that match the RexA and RexB abortive infections system proteins of E. coli. Graham let me peek at the CarolAnn and Sbash paper and gp41 and 43 in phamerator (gp40 and 41 in PECAAN as the forward gene between them was deleted) lookk like they fit the bill. gp41 has 4 transmembrane domains (rexB?) and gp43 has a 99.8% prob and 92% coverage hit to RexA Intracellular sensor of Lambda phage, Abi component. gp43 also has the DUF4747 domain that the CarolAnn RexA protein has.

Do I leave these function calls as membrane protein and NKF for gp41 and 43 or do you want the RexAB system called? If the latter, what is the exact name you would like used?

Thanks!
Sally

Posted in: Functional Annotation → RexAB systems

Link to this post \| posted 15 Feb, 2019 03:11
smolloy123	Thanks Claire and Welkin! Looking forward to using this new function with my students in class!

Posted in: PECAAN → New Features in PECAAN

Link to this post \| posted 13 Feb, 2019 23:25
smolloy123	Hi Claire and Welkin, Can someone help me navigate the new feature "Phagesdb Function Frequency" box. This just popped up this week and it caught me off guard in class when doing a demonstration with PECAAN. Thanks! Sally

Posted in: PECAAN → New Features in PECAAN

Link to this post \| posted 11 Dec, 2018 20:23
smolloy123	Hi Deb, Thanks, we are using the ARS strain R. erythropolis. Thanks! Sally

Posted in: Rhodococcus → Rhodococcus clustering

Link to this post \| posted 24 Oct, 2018 15:35
smolloy123	Viknesh Sivanathan smolloy123 Hi All, We have been growing G. terrae in PYCa broth for four days with sterile glass beads in baffled flasks. They plate like buttah! I take the glass 3-mm beads we use for archiving (a bottle is super cheap), sterilize then in culture tubes so that I can easily pour them into flasks, and I do not use Tween ( I am too lazy to take time to sub-culture). After four days of growth, the cultures are smooth and produce perfect lawns! I wash beads and re-autoclave for re-use. Just don't get these re-used beads mixed up with the beads you would use for archiving as those should not be recycled beads. I meant to post this over the summer when I discovered this but forgot! Best, Sally That's a really neat trick, Sally. Do you know if it works for M. smeg too? I'll definitely give it a try and report back. Hi Vic, It works with M. smegmatis and fairly well with some of the clumpier species of Mycobacterium. The really clumpy ones sometimes I still need to grow with tween first. Cheers!

Link to this post | posted 24 Oct, 2018 15:35

smolloy123

Viknesh Sivanathan
smolloy123
Hi All,
We have been growing G. terrae in PYCa broth for four days with sterile glass beads in baffled flasks. They plate like buttah! I take the glass 3-mm beads we use for archiving (a bottle is super cheap), sterilize then in culture tubes so that I can easily pour them into flasks, and I do not use Tween ( I am too lazy to take time to sub-culture). After four days of growth, the cultures are smooth and produce perfect lawns! I wash beads and re-autoclave for re-use. Just don't get these re-used beads mixed up with the beads you would use for archiving as those should not be recycled beads. I meant to post this over the summer when I discovered this but forgot!
Best,
Sally

That's a really neat trick, Sally. Do you know if it works for M. smeg too? I'll definitely give it a try and report back.

Hi Vic,
It works with M. smegmatis and fairly well with some of the clumpier species of Mycobacterium. The really clumpy ones sometimes I still need to grow with tween first.
Cheers!

Posted in: Gordonia → Clumping in liquid cultures

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