SEA-PHAGES | All posts created by lhughes

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Link to this post \| posted 02 Mar, 2018 15:17
lhughes	Steven Caruso We have looked very closely on all our Strep. phages (BG, BH, BI, etc.), and couldn't find them. I'm glad it's not just us. But we'll keep looking! Steve - Be careful not to confuse "B" cluster with the double letter "BB,BG" etc. clusters. Welkin is talking about just the Cluster B phages in this topic. Several of the Streptomyces-associated clusters have the Tail assembly chaperone frameshift (including Clusters BC, BD, and BL). Lee

Link to this post | posted 02 Mar, 2018 15:17

Steven Caruso
We have looked very closely on all our Strep. phages (BG, BH, BI, etc.), and couldn't find them. I'm glad it's not just us. But we'll keep looking!

Steve - Be careful not to confuse "B" cluster with the double letter "BB,BG" etc. clusters. Welkin is talking about just the Cluster B phages in this topic.

Several of the Streptomyces-associated clusters have the Tail assembly chaperone frameshift (including Clusters BC, BD, and BL).

Lee

Posted in: Cluster B Annotation Tips → Tail assembly chaperones?

Link to this post \| posted 23 Jan, 2018 19:18
lhughes	If you click the white space next to the cluster designation (not the box or the cluster letters), it will open up and show you all the members of that cluster. You can then check on just the boxes of the ones you want to view. You can do the same thing with other clusters to pick additional phages from other clusters to map. Lee

Posted in: Web Phamerator → Looking for specific phage on web phamerator

Link to this post \| posted 19 Jan, 2018 15:07
lhughes	Joseph Stukey Hi Dave - So now I do see that our other phage isolated this year - Thyatira - is shown as being phamerated but I do not find it listed on the Phamerator webpage? Is there normally a delay between before finding it on the Phamerator site or could it be an issue of it being identified as "unclustered" at phagesdb? (We like to have our students "discover" the cluster relationships.) Thanks. Joe Joe, I was just looking and see it under the "UKN" designation on the list on the web Phamerator. Lee

Link to this post | posted 19 Jan, 2018 15:07

lhughes

Joseph Stukey
Hi Dave -

So now I do see that our other phage isolated this year - Thyatira - is shown as being phamerated but I do not find it listed on the Phamerator webpage? Is there normally a delay between before finding it on the Phamerator site or could it be an issue of it being identified as "unclustered" at phagesdb? (We like to have our students "discover" the cluster relationships.)

Thanks.
Joe

Joe,

I was just looking and see it under the "UKN" designation on the list on the web Phamerator.

Lee

Posted in: Web Phamerator → Missing 2018 draft phage genomes

Link to this post \| posted 17 Jan, 2018 20:24
lhughes	Steve, I have always been successful in doing this in the past, and it gave me the same problem just now when I tried it. My DNA Master shows Build 2534 (14 Sep 2017). The only other thing that I know has changed on my computer is that I recently did an update to the most recent version of Windows 10. Help! I'm going to need to be able to download some more genomes soon for some QC I'm working on. Lee

Link to this post | posted 17 Jan, 2018 20:24

lhughes

Steve,

I have always been successful in doing this in the past, and it gave me the same problem just now when I tried it.

My DNA Master shows Build 2534 (14 Sep 2017).

The only other thing that I know has changed on my computer is that I recently did an update to the most recent version of Windows 10.

Help! I'm going to need to be able to download some more genomes soon for some QC I'm working on.

Lee

Posted in: DNA Master → %ANI

Link to this post \| posted 29 Aug, 2017 17:15
lhughes	Tamarah Adair I am having this issue also. It is returning tRNA calls, for example on Amigo, but no genes. Help please. Tammy Tammy, This post from Debbie in another thread may answer your question about the gene calls: https://www.seaphages.org/forums/post/5735/ Lee

Posted in: DNA Master → DNA Master Issue

Link to this post \| posted 27 Aug, 2017 21:21
lhughes	Another one from Abt2graduatex2: RNase adapter protein RapZ The genome has this function (not on the approved list) for gp55. I compared the HHPRED data for the equivalent gene in BabyGotBac (gp56, which was annotated as "ATPase" and found there is 100% probability, 90% coverage, and E-value of 0 to the RNase adapter protein (RapZ in E.coli). The function in Uniprot is given as "Modulates the synthesis of GlmS, by affecting the processing and stability of the regulatory small RNA GlmZ" Thoughts on this function? Lee

Link to this post | posted 27 Aug, 2017 21:21

lhughes

Another one from Abt2graduatex2: RNase adapter protein RapZ

The genome has this function (not on the approved list) for gp55. I compared the HHPRED data for the equivalent gene in BabyGotBac (gp56, which was annotated as "ATPase" smile

and found there is 100% probability, 90% coverage, and E-value of 0 to the RNase adapter protein (RapZ in E.coli).

The function in Uniprot is given as "Modulates the synthesis of GlmS, by affecting the processing and stability of the regulatory small RNA GlmZ"

Thoughts on this function?

Lee

Posted in: Functional Annotation → Functions not on the approved list

Link to this post \| posted 24 Aug, 2017 00:59
lhughes	Here is a new one to consider: Sortase This one is described in the Abt2graduatex2 genome I am QCing, but for a phage already annotated it can be found in BabyGotBac_44. Description of "sortase" below. It looks like to me that these gene products have the conserved catalytic triad. They show 98% homology in HHPRED with an E-value of 10^-9 Sortase is described in CDD as: "Sortases are cysteine transpeptidases, mainly found in Gram-positive bacteria, which either anchor surface proteins to peptidoglycans of the bacterial cell wall envelope or link proteins together to form pili by working alone, or in concert with other enzymes. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes based on sequence, membrane topology, genomic positioning, and cleavage site preference. The different classes are called class A to F sortases. Most Gram-positive bacteria contain more than one sortase and it is thought that the different sortases attach different surface protein classes. The typical eight-stranded beta-barrel fold is observed in all known sortases, along with the conserved catalytic triad consisting of cysteine, histidine and arginine residues. Some sortases contain an N-terminal signal peptide only and the C-terminus serves as a membrane anchor, which represents a type I membrane topology, with the N-terminal enzymatic portion projecting towards the bacterial surface and the C-terminal end residing in the cytoplasm. Other sortases adopt a type II membrane topology, with the N-terminal hydrophobic segment inside the cytoplasm and the C-terminal enzymatic portion located across the plasma membrane. The N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring. Sortases are also present in some Gram-negative and Archaebacterial species, but the functions of these enzymes are unknown." So, what do you think? Sortase, or cysteine transpeptidase, or not a function we add to the list? Lee

Link to this post | posted 24 Aug, 2017 00:59

lhughes

Here is a new one to consider: Sortase

This one is described in the Abt2graduatex2 genome I am QCing, but for a phage already annotated it can be found in BabyGotBac_44. Description of "sortase" below. It looks like to me that these gene products have the conserved catalytic triad. They show 98% homology in HHPRED with an E-value of 10^-9

Sortase is described in CDD as: "Sortases are cysteine transpeptidases, mainly found in Gram-positive bacteria, which either anchor surface proteins to peptidoglycans of the bacterial cell wall envelope or link proteins together to form pili by working alone, or in concert with other enzymes. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes based on sequence, membrane topology, genomic positioning, and cleavage site preference. The different classes are called class A to F sortases. Most Gram-positive bacteria contain more than one sortase and it is thought that the different sortases attach different surface protein classes. The typical eight-stranded beta-barrel fold is observed in all known sortases, along with the conserved catalytic triad consisting of cysteine, histidine and arginine residues. Some sortases contain an N-terminal signal peptide only and the C-terminus serves as a membrane anchor, which represents a type I membrane topology, with the N-terminal enzymatic portion projecting towards the bacterial surface and the C-terminal end residing in the cytoplasm. Other sortases adopt a type II membrane topology, with the N-terminal hydrophobic segment inside the cytoplasm and the C-terminal enzymatic portion located across the plasma membrane. The N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring. Sortases are also present in some Gram-negative and Archaebacterial species, but the functions of these enzymes are unknown."

So, what do you think? Sortase, or cysteine transpeptidase, or not a function we add to the list?

Lee

Posted in: Functional Annotation → Functions not on the approved list

Link to this post \| posted 14 Aug, 2017 17:59
lhughes	Working now! Thanks, Chris

Posted in: Starterator → Updates to Starterator output

Link to this post \| posted 14 Aug, 2017 16:22
lhughes	Chris - I found today that some phams aren't linking to reports from PECAAN, and then I checked your direct link above to your starterator website and found that the highest Pham # available is 32344, while the phams I was trying to view all had a higher number than that. The files all show a run date of 8/7/17. Is it possible that not all phams were updated or generated on that date? Lee

Posted in: Starterator → Updates to Starterator output

Link to this post \| posted 10 Aug, 2017 17:14
lhughes	Here is some more information: BeardedLady_37 gives hits mostly to the archael HJC on HHPRED (this is a BD1 phage) Sushi23_89 gives one hit to an E.coli HJC and the rest are RuvC (this is a BE1 phage) (data screen shots attached) 265Kb

Posted in: Functional Annotation → RuvC resolvase vs Holliday Junction Resolvase

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