SEA-PHAGES | All posts created by smolloy123

Link to this post \| posted 02 Jun, 2018 10:47
smolloy123	I just found the answer on the function list. Going with most specific function of HTH DNA binding domain

Posted in: Functional Annotation → one protein with DNA binding and membrane domains

Link to this post \| posted 02 Jun, 2018 10:45
smolloy123	Hi All, I found a gene product in cluster K1 genome of Mynx that encodes both a DNA binding domain and four transmembrane (MB) domains. See attached evidence. The four MB domains run from residues 13 - 136 and the DNA binding domain is on the very C-terminus (residues 244 - 280ish). Can I call both of these domains on one protein? Thanks! Sally 390Kb

Posted in: Functional Annotation → one protein with DNA binding and membrane domains

Link to this post \| posted 31 May, 2018 20:32
smolloy123	Just for the record, I am calling gp83 of Neville as the Phosphoribosylpyrophophate synthetase.

Posted in: Functional Annotation → Phosporibosylpyrophosphate synthetase

Link to this post \| posted 31 May, 2018 12:37
smolloy123	Debbie Jacobs-Sera I think that when I called this, I decided that thymidylate synthase is a generic enough term that it would be best until more is known. I unfortunately didn't put the more generic term "thymidylate synthase" on the approved list (until today). I didn't use dihydrofolate reductase because it wasn't on the list; it surely could be. Neither are very specific or satisfying, using both seems to be too much. We could add ThyA-like thymidylate synthase, but until someone wants to look at all thymidylate synthases more closely, I think it could be problematic. Chris - thank you for your investigation on this, it was very helpful. Hi Deb, I'll go with he generic thymidylate synthase. Thanks to both you and Chris for helping me sort this cheers Sally

Link to this post | posted 31 May, 2018 12:37

smolloy123

Debbie Jacobs-Sera
I think that when I called this, I decided that thymidylate synthase is a generic enough term that it would be best until more is known. I unfortunately didn't put the more generic term "thymidylate synthase" on the approved list (until today). I didn't use dihydrofolate reductase because it wasn't on the list; it surely could be. Neither are very specific or satisfying, using both seems to be too much. We could add ThyA-like thymidylate synthase, but until someone wants to look at all thymidylate synthases more closely, I think it could be problematic. Chris - thank you for your investigation on this, it was very helpful.

Hi Deb,
I'll go with he generic thymidylate synthase. Thanks to both you and Chris for helping me sort this smile

cheers
Sally

Posted in: Functional Annotation → thymidylate synthases versus dihydrofolate reductases

Link to this post \| posted 31 May, 2018 12:36
smolloy123	Hi Chris, Thanks for this. Super helpful!

Posted in: Functional Annotation → thymidylate synthases versus dihydrofolate reductases

Link to this post \| posted 29 May, 2018 17:34
smolloy123	Hi All, I am finishing up a Microbacterium phage annotation, cluster EB phage Eden. Homologues of Eden gp57 are all called as thymidylate synthases…why? There are strong HHPRED results for a dihydrofolate reductase (see attachment or Pecaan site for Eden gene stopping at 36,681. BlastP at NCBI also points towards dihdrofolate reductases in bacterial species. Does anyone know why these genes are called as thymidylate synthases in the other EB phage? Do I go with the phamerator/phasgedb flow on this or go with the evidence? I thought maybe there is some other evidence that I don't know about that points towards thymidylate synthase. This just doesn't look like the latter to me. Thanks! Sally 344Kb

Link to this post | posted 29 May, 2018 17:34

smolloy123

Hi All,
I am finishing up a Microbacterium phage annotation, cluster EB phage Eden. Homologues of Eden gp57 are all called as thymidylate synthases…why? There are strong HHPRED results for a dihydrofolate reductase (see attachment or Pecaan site for Eden gene stopping at 36,681. BlastP at NCBI also points towards dihdrofolate reductases in bacterial species. Does anyone know why these genes are called as thymidylate synthases in the other EB phage? Do I go with the phamerator/phasgedb flow on this or go with the evidence? I thought maybe there is some other evidence that I don't know about that points towards thymidylate synthase. This just doesn't look like the latter to me.
Thanks!
Sally

Posted in: Functional Annotation → thymidylate synthases versus dihydrofolate reductases

Link to this post \| posted 16 Apr, 2018 18:51
smolloy123	Membrane protein it is! Thanks!

Posted in: Functional Annotation → Superinfection immunity proteins

Link to this post \| posted 16 Apr, 2018 18:50
smolloy123	Hi Welkin, I was thinking that this gene is for sure a PRPP synthetase and that we should add it to the function list. I guess I was worried about clouding the waters by throwing another name in for that one pham. Thanks Welkin!

Posted in: Functional Annotation → Phosporibosylpyrophosphate synthetase

Link to this post \| posted 15 Apr, 2018 21:51
smolloy123	Hi All, I found a Phosphoribosylpyrophosphate synthetase match for gene 82 in Neville (an unclustered Gordonia). The phagesdb matches have this gene called all over the board from less specific phosporibosyl transferase (Oneup_100), phosphoribosylphosphatase (thibault_115). There is also a gene called ribose-phosphate pyrophosphokinase (Snenia_73) which is the same thing as a Phosphoribosylpyrophosphate synthetase. Phosphoribosyl transferase is the only approved function call. I looked at the alignment of Neville_82 to the Bacillus subtillus PPRP synthetase (which is crystalized) and found that it had nearly all of the conserved residues and many of the less conserved residues. It has the conserved residues necessary for the pyrophosphate binding domain, for the ribose-5phosphate binding domain and the mADP binding and active site. (see attachment). Is it best just to call this a phosphoribosyl transferase or do you want the specificity of PPRP synthetase? Thanks Sally 1.31Mb

Link to this post | posted 15 Apr, 2018 21:51

smolloy123

Hi All,
I found a Phosphoribosylpyrophosphate synthetase match for gene 82 in Neville (an unclustered Gordonia). The phagesdb matches have this gene called all over the board from less specific phosporibosyl transferase (Oneup_100), phosphoribosylphosphatase (thibault_115). There is also a gene called ribose-phosphate pyrophosphokinase (Snenia_73) which is the same thing as a Phosphoribosylpyrophosphate synthetase.

Phosphoribosyl transferase is the only approved function call. I looked at the alignment of Neville_82 to the Bacillus subtillus PPRP synthetase (which is crystalized) and found that it had nearly all of the conserved residues and many of the less conserved residues. It has the conserved residues necessary for the pyrophosphate binding domain, for the ribose-5phosphate binding domain and the mADP binding and active site. (see attachment).

Is it best just to call this a phosphoribosyl transferase or do you want the specificity of PPRP synthetase?

Thanks
Sally

Posted in: Functional Annotation → Phosporibosylpyrophosphate synthetase

Link to this post \| posted 14 Apr, 2018 12:02
smolloy123	Hi All, I am QCing the cluster A15 genome of LastResort. What are people's feelings on the membrane protein in parABS cassettes that has high probability matches in HHPRED (99.7% prob, 52% coverage, e-val=8E-20) to superinfection immunity protein of T4 phage. This membrane protein excludes other T-even phage from cells already infected with T4. It also matches other superinfection immunity proteins in various bacteria in NCBI blastP (low percent identity but also low e-vals). Is it safer just to call this a membrane protein? Thanks! Sally

Link to this post | posted 14 Apr, 2018 12:02

smolloy123

Hi All,
I am QCing the cluster A15 genome of LastResort. What are people's feelings on the membrane protein in parABS cassettes that has high probability matches in HHPRED (99.7% prob, 52% coverage, e-val=8E-20) to superinfection immunity protein of T4 phage. This membrane protein excludes other T-even phage from cells already infected with T4. It also matches other superinfection immunity proteins in various bacteria in NCBI blastP (low percent identity but also low e-vals).

Is it safer just to call this a membrane protein?
Thanks!
Sally

Posted in: Functional Annotation → Superinfection immunity proteins

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