SEA-PHAGES | All posts created by EWisner

Link to this post \| posted 29 Mar, 2023 12:30
EWisner	Thank you both for this information! For Culver (CQ1)the potential helicase loader (stop codon 62590 bp) is upstream for a gene we have annotated as DNA primase/helicase by ~3400 bps. The potential helicase loader gene is also directly downstream of a RepA-like replication initiator gene. With this information and the previously found evidence, I am inclined to call it the helicase loader but I wanted a second opinion on the matter. Does the helicase loader need to be directly followed by helicase, or just close? If just close by, then about how close?

Link to this post | posted 29 Mar, 2023 12:30

Thank you both for this information!

For Culver (CQ1)the potential helicase loader (stop codon 62590 bp) is upstream for a gene we have annotated as DNA primase/helicase by ~3400 bps. The potential helicase loader gene is also directly downstream of a RepA-like replication initiator gene. With this information and the previously found evidence, I am inclined to call it the helicase loader but I wanted a second opinion on the matter.

Does the helicase loader need to be directly followed by helicase, or just close? If just close by, then about how close?

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

Link to this post \| posted 24 Mar, 2023 16:35
EWisner	I’m currently working on phage Culver in the CQ1 cluster and am having an issue with calling the function of gene 37 (15874-16227). Significant BLASTp matches show a mix of head closure proteins (not listed on official function list), hypothetical proteins, and head-to-tail stopper proteins. HHPred populates multiple significant hits, one of which aligns to SPP1 gp16. In the official functions list notes for head-to-tail stopper we much “must have an HHPRED alignment to one of the following crystal structures: SPP1 16 (5A21 chain E or F in the macromolecular complex”. We do not have that match, however we do have a match with 7ZAW_1 Head completion protein gp16 of Bacteriophage SPP1, Head completion proteins, Connector Compex. Based on this, can we call this “head-to-tail stopper”?

Link to this post | posted 24 Mar, 2023 16:35

EWisner

I’m currently working on phage Culver in the CQ1 cluster and am having an issue with calling the function of gene 37 (15874-16227). Significant BLASTp matches show a mix of head closure proteins (not listed on official function list), hypothetical proteins, and head-to-tail stopper proteins. HHPred populates multiple significant hits, one of which aligns to SPP1 gp16. In the official functions list notes for head-to-tail stopper we much “must have an HHPRED alignment to one of the following crystal structures: SPP1 16 (5A21 chain E or F in the macromolecular complex”. We do not have that match, however we do have a match with 7ZAW_1 Head completion protein gp16 of Bacteriophage SPP1, Head completion proteins, Connector Compex. Based on this, can we call this “head-to-tail stopper”?

Posted in: Annotation → head-to-tail stopper

Link to this post \| posted 16 Mar, 2023 20:18
EWisner	I'm currently working on phage Culver in the CQ1 cluster, and I came across gene 9 (2199-2537) which had confusing BLAST results. I tried to find "secreted protein" in the official function list, but couldn't find it. Is this something that we no longer call? BLASTp results included as an attachment.

Posted in: Annotation → secreted protein?

Link to this post \| posted 14 Mar, 2023 19:29
EWisner	Re: Helicase Loader I am working on annotating the phage Culver (CQ1) and I am having trouble confirming the putative function of the gene with the stop codon at 62590 bps. The BLASTp shows a majority of the functions as hypothetical with a few being helicase loader. HHpred shows some matches with products similar to helicase loader, but the matches are not as strong or plentiful to be confident in this identification. Hypothetical protein or Helicase loader?

Link to this post | posted 14 Mar, 2023 19:29

EWisner

Re: Helicase Loader
I am working on annotating the phage Culver (CQ1) and I am having trouble confirming the putative function of the gene with the stop codon at 62590 bps.
The BLASTp shows a majority of the functions as hypothetical with a few being helicase loader. HHpred shows some matches with products similar to helicase loader, but the matches are not as strong or plentiful to be confident in this identification.
Hypothetical protein or Helicase loader?

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

Link to this post \| posted 14 Mar, 2023 19:29
EWisner	Re: Helicase Loader I am working on annotating the phage Culver (CQ1) and I am having trouble confirming the putative function of the gene with the stop codon at 62590 bps. The BLASTp shows a majority of the functions as hypothetical with a few being helicase loader. HHpred shows some matches with products similar to helicase loader, but the matches are not as strong or plentiful to be confident in this identification. Hypothetical protein or Helicase loader?

Link to this post | posted 14 Mar, 2023 19:29

EWisner

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

Link to this post \| posted 14 Mar, 2023 19:01
EWisner	Hey all, I am working on annotating the phage Culver (CQ1) and I am having a bit of difficulty confirming the putative function of the gene with the stop codon at 12727 bps. The BLASTp shows results that have a mix of functions between MuF-like minor capsid protein, head maturation protease, and hypothetical protein. For the MuF-like minor capsid protein, the official function list says that it should be called a hypothetical protein. HHpred only has one match that is viable which is labeled as “Gene 15 protein” further showing the gene in Culver is likely to have no known function. For the head maturation protease, none of the other programs used showed evidence of this function for the Culver gene. I am leaning towards calling the Culver gene a hypothetical protein but I wanted a second opinion if possible. Any help will be greatly appreciated!

Link to this post | posted 14 Mar, 2023 19:01

EWisner

Hey all, I am working on annotating the phage Culver (CQ1) and I am having a bit of difficulty confirming the putative function of the gene with the stop codon at 12727 bps.

The BLASTp shows results that have a mix of functions between MuF-like minor capsid protein, head maturation protease, and hypothetical protein. For the MuF-like minor capsid protein, the official function list says that it should be called a hypothetical protein. HHpred only has one match that is viable which is labeled as “Gene 15 protein” further showing the gene in Culver is likely to have no known function. For the head maturation protease, none of the other programs used showed evidence of this function for the Culver gene.

I am leaning towards calling the Culver gene a hypothetical protein but I wanted a second opinion if possible. Any help will be greatly appreciated!

Posted in: Annotation → capsid maturation protease or hypothetical protein (MuF-like minor capsid protein)

Link to this post \| posted 08 May, 2020 13:44
EWisner	Thank you Debbie!

Posted in: Gene or not a Gene → Gap or a gene?

Link to this post \| posted 07 May, 2020 12:43
EWisner	I have a gene that was called in Phamerator, but not in the DNA Master autoannotation. Without it, there is about a ~300 bp gap. It is Portcullis_Draft gene 46 (36503 - 36763 ) \| pham 18840. It would be an orpham and has no sig. hits in BLAST. The coding potential in self isn't great (see attached documents). Is it a gene, or do I just have a large gap in my genome? You might notice that there is also OK coding potential in the -1 frame. I have also looked into this by blasting the a.a. sequence but it too had no sig. results. See attached documentation 192Kb

Link to this post | posted 07 May, 2020 12:43

EWisner

I have a gene that was called in Phamerator, but not in the DNA Master autoannotation. Without it, there is about a ~300 bp gap. It is Portcullis_Draft gene 46 (36503 - 36763 ) | pham 18840. It would be an orpham and has no sig. hits in BLAST. The coding potential in self isn't great (see attached documents). Is it a gene, or do I just have a large gap in my genome? You might notice that there is also OK coding potential in the -1 frame. I have also looked into this by blasting the a.a. sequence but it too had no sig. results.

See attached documentation

Posted in: Gene or not a Gene → Gap or a gene?

Link to this post \| posted 06 May, 2020 20:48
EWisner	Can a phage have both a "capsid maturation protease and MuF-like protein" and a "capsid maturation protease"? In Portcullis (DC1) Gene stop 9453 we believe is a capsid maturation protease and MuF-like protein. We believe that Gene stop 11104 is a "capsid maturation protease". I went back to the guide, but really wasn't sure whether or not we could call both of these. Thanks! Ellen

Posted in: Functional Annotation → Cluster DC - Capsid maturation protease and MuF-like protein

Link to this post \| posted 05 May, 2020 15:22
EWisner	My class is annotating Portcullis, a DC1 phage. We called Portcullis_Draft gene 27 (18088 - 18696 ) a tail assembly chaperone, but were uncertain whether or not to call Portcullis_Draft gene 28 (18693 - 19379) also a tail assembly chaperone. The reason we were considering it is because of other phages in our cluster, specifically RogerDodger. I noticed in PECAAN that RogerDodger has two genes in a row called tail assembly chaperones (#30 & 31). Our phages (Portcullis) seems to have very similar genes 27 & 28 in PECAAN. For gene 27, based on the BLAST result I agreed with my students that we should call it a tail assembly chaperone. For 28, I am less sure because there are far fewer BLAST matches. However, gene 28 is in the same Pham as RogerDodger's gene 31. I reached out to Sally Molloy about this, as she has been helping with my annotation questions, and her group annotated RogerDodger. I will post her response below, she suggested I post here to get more feedback from you all. Thanks! Ellen From Sally: This is a very good question! There is really no evidence at all that points to RogerDoger_31 being a tail assembly chaperone other than it is between the other chaperone and tape measure. Upstream of gp 30, others have called gp29 the other chaperone and at least it has hits to HK97 tail component gp10. I am wondering if gp29 should be called the tail assembly chaperone or if to be on the safe side we should only call one tail assembly chaperone. I am leaning on the latter decision.

Link to this post | posted 05 May, 2020 15:22

EWisner

My class is annotating Portcullis, a DC1 phage. We called Portcullis_Draft gene 27 (18088 - 18696 ) a tail assembly chaperone, but were uncertain whether or not to call Portcullis_Draft gene 28 (18693 - 19379) also a tail assembly chaperone. The reason we were considering it is because of other phages in our cluster, specifically RogerDodger. I noticed in PECAAN that RogerDodger has two genes in a row called tail assembly chaperones (#30 & 31). Our phages (Portcullis) seems to have very similar genes 27 & 28 in PECAAN. For gene 27, based on the BLAST result I agreed with my students that we should call it a tail assembly chaperone. For 28, I am less sure because there are far fewer BLAST matches. However, gene 28 is in the same Pham as RogerDodger's gene 31.

I reached out to Sally Molloy about this, as she has been helping with my annotation questions, and her group annotated RogerDodger. I will post her response below, she suggested I post here to get more feedback from you all.

Thanks!
Ellen

From Sally:
This is a very good question! There is really no evidence at all that points to RogerDoger_31 being a tail assembly chaperone other than it is between the other chaperone and tape measure. Upstream of gp 30, others have called gp29 the other chaperone and at least it has hits to HK97 tail component gp10.

I am wondering if gp29 should be called the tail assembly chaperone or if to be on the safe side we should only call one tail assembly chaperone. I am leaning on the latter decision.

Posted in: Functional Annotation → Cluster DC - tail assembly chaperones

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