Link to this post | posted 28 Apr, 2022 14:46

smolloy123

Hi All, I am calling a gene in a singleton phage Finkle (gp42 on Phamerator and and between integrase and Immunity repressor). I noted that in AY cluster specific tips Debbie states that the gene that hits IrrE only aligns to the HTH DNA binding domain and therefore call it such. The gene I am looking at is found in a long list of phage across both Gordonia clusters and prophage clusters (CY, CZ, DN, F, MabA, P). But this protein in HHpred has high quality alignment to IrrE and includes the peptidase region (with the HEXXH motif) and the HTH DNA binding domain. Given its location between the integrase and immunity repressor my guess is that this is something like the ImmA antirepressor. But since we can't use guesses for function assignment what do we call this? metallopeptidase helix-turn-helix DNA binding protein? That is too long a name. Please send suggestions. Also the HHpred data is attached! 115Kb

Link to this post | posted 20 Mar, 2022 13:29

smolloy123

Hi All, We've discussed in the past toxins, especially those that are bacteriostatic rather than bactericidal, can exist in phage genomes without a cognate anti-toxin. I can't remember where we ended up on this topic. The CR2 phage starstruck (stop 4760, gp7 in phamerator) has very strong HHpred data supporting a HicA toxin but there is no sign of an antitoxin. It doesn't make sense to me to call it "toxin in toxin/antitoxin system, HicA-like" if there it isn't a toxin/antitoxin system. Any thoughts on this? Sally

Link to this post | posted 20 Mar, 2022 13:28

smolloy123

Hi All, We've discussed in the past toxins, especially those that are bacteriostatic rather than bactericidal, can exist in phage genomes without a cognate anti-toxin. I can't remember where we ended up on this topic. The CR2 phage starstruck (stop 4760, gp7 in phamerator) has very strong HHpred data supporting a HicA toxin but there is no sign of an antitoxin. It doesn't make sense to me to call it "toxin in toxin/antitoxin system, HicA-like" if there it isn't a toxin/antitoxin system. Any thoughts on this? Sally

Link to this post | posted 18 Feb, 2021 01:35

smolloy123

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Link to this post | posted 23 Jan, 2021 23:00
smolloy123	Thanks Chris, that is helpful. I think we will go with either pyrophosphate kinase or your diphosphate kinase…I'll let Deb decide. Who says diphosphate instead of pyrophosphate? Either way, we need to pick one name and go with it as you suggest

Link to this post | posted 23 Jan, 2021 17:57
smolloy123	Maybe these all should be pyrophosphate kinases or phosphoribosylpyrophosphate synthetase but phosphoribosyl transferase doesn't make sense if in fact it is a kinase reaction

Link to this post | posted 22 Jan, 2021 02:33

smolloy123

Ok, I just searched phosphoribosylpyrophosphate synthetase and found my own entry! I am looking at Rose_5 (Cluster L1) gene stop 49111 and it has been called a phosphoribosyl transferase. The hits are again to phosphoribosyl pyrophosphate synthetase. Looking at the accepted functions list I found hosphoribosyl pyrophosphate transferase with example gene Loadrie_73. I also found function name phosphoribosyl transferase on the accepted function list with Bantam_3 as the example gene. but Bantam_3 and Loadrie_73 are in the same Pham. And just for the record (again) Phosphoribosylpyrophosphage synthetase is not on the accepted functions list… Does anyone know about these enzymes and have a suggestion about how we should be calling these genes?

Link to this post | posted 03 Oct, 2020 15:47

smolloy123

Hi All, We are having trouble doing the autoannotation in both of our sections of SEA PHAGES this semester. All students are running DNA Master in Windows (in virtual box on Macs). I was so excited last Tuesday when all my students except for 2 had successfully installed DNa Master on their computers (usually that's our sticking point). All students failed the autoannotation with Glimmer failures or overall autoannotation failure messages. We checked and double checked DNA Master was updated and their preferences to make sure that Gene Prediction tabs and security were set up as instructed in the 2017 DNA Master Fix document (and as instructed in the Bioinformatics Guid) and yes we know the password. I did note that every single student that struggled with autoanntoations had bought a brand new Mac before school started. When I tried setting up preferences on some of their computers, I failed to complete an autoannotation. Is anyone else having trouble with autoannotations? Best Sally

Link to this post | posted 03 Oct, 2020 15:46

smolloy123

Hi All, We are having trouble doing the autoannotation in both of our sections of SEA PHAGES this semester. All students are running DNA Master in Windows (in virtual box on Macs). I was so excited last Tuesday when all my students except for 2 had successfully installed DNa Master on their computers (usually that's our sticking point). All students failed the autoannotation with Glimmer failures or overall autoannotation failure messages. We checked and double checked DNA Master was updated and their preferences to make sure that Gene Prediction tabs and security were set up as instructed in the 2017 DNA Master Fix document (and as instructed in the Bioinformatics Guid) and yes we know the password. I did note that every single student that struggled with autoanntoations had bought a brand new Mac before school started. When I tried setting up preferences on some of their computers, I failed to complete an autoannotation. Is anyone else having trouble with autoannotations? Best Sally

Link to this post | posted 04 Jun, 2020 16:47

smolloy123

After a discussion in SMART meetings we decided that a capsid maturation protease function should not be called unless there is HHPRED data indicating a protease or peptidase domain (e.g. ClpP protease). There are two genes that people have called capsid maturation protease in the DC phage and neither have HHPRED data supporting this function call. The first is gp14 in Portcullis and Jambaylaya, which has a MuF-like domain and ADP ribosyl transferase domain. This gene should be called "ADP-ribosyltransferase domain and MuF-like fusion protein." The second is gp16. This gene we are calling a hypothetical protein. There is weak evidence pointing to EEEV capsid proteases but the alignments have low probability, high E values and the the alignments don't actually include the peptidase domain.