Link to this post | posted 26 Jan, 2020 14:53

delesall

Is there a document explaining how to interpret Topcons data? I looked around the SEA-PHAGES forums, the Bioinformatics guide and found nothing. The Topcons paper is a little dense for me. In particular I'm QC.ing AwesomeSauce - an F1 which is in Pecaan. In that phage, gene 33 (start 28413) has that HHPred match to the Putative lactococcus lactis phage r1t holin which has no transmembrane domain when run through TmHmm. The Topcons summary shows different results depending on the program but the reliability box shows nothing (which is different from the easier to interpret membrane protein for gene 29 in this phage). I interpreted this as no evidence for a transmembrane domain and would thus not call this the holin. Any insight on how to interpret teh Topcons summary for this gene would be appreciated!

Link to this post | posted 17 Jun, 2019 02:26

delesall

Gene 65 in BossLady (42154,43032) and its homolog in Zartrosa show nice HHPred matches to the lytic CHAPK domain of the endolysin LysK from Staphylococcus aureus bacteriophage K among others. I attach snapshots from HHPred matches. The matches cover the length of the protein with over 99% prob and low E-values. Pasting info from HHPred hits from BossLady (uploaded in Pecaan) 4CT3_C ORF30/ORF32; VIRAL PROTEIN, PEPTIDOGLYCAN, PROTEASE; HET: EPE, GOL, CMH, MMC; 1.69A {STAPHYLOCOCCUS PHAGE K} 99.7 46.5753 26 165 1 137 9.2e-18 5UDN_B Phage-associated cell wall hydrolase; lysin, d-alanyl-l-alanine endopeptidase, CHAP domain; HET: GOL; 1.971A {Streptococcus pyogenes MGAS5005} 99.6 62.3288 1 203 2 184 4.8e-16 Can go with more generic hydrolase but PDB files suggest we can be more specific. 10Kb

Link to this post | posted 23 May, 2019 10:48
delesall	As an example - Bunnies gene 32 (immunity repressor) pham 56415 (pham number from phagesdb) report is missing

Link to this post | posted 23 May, 2019 10:46
delesall	Also checking annotations for Bunnies and seeing missing starterator reports unavailable in Pecaan and on phagesdb for phams that are not orphams!

Link to this post | posted 25 Apr, 2019 23:50
delesall	309 amino acids (930 bp including stop codon) I have identified two minor tail proteins before the lysis cassette and three after . This would be a 4th and last minor tail after the lysis cassette

Link to this post | posted 25 Apr, 2019 20:48

delesall

Annotating Begonia, a CV phage. The homolog of gene 33 (27738-28667) has been called Alpha-L-arabinofuranosidase in Lucky 10, but that is not on the approved function list. Based on location - just after a minor tail - and based on HHPred matches to Alpha-L-arabinofuranosidase, which has binding domain to arabinose as well as catalytic activity, call function minor tail protein? The Begonia protein matches this enzyme with 99.8%, covering 60% of aa sequence, and very low <10^-24 E-value

Link to this post | posted 19 Mar, 2019 00:16
delesall	I ended up calling ribonuclease toxin for my gene - somewhat generic but also informative…

Link to this post | posted 17 Mar, 2019 14:44

delesall

When I annotated Danyall (another DC phage) last year, I went with capsid morphogenesis protein and capsid maturation protease for these genes (genes 14 and 18 in KimmyK, genes 12 and 18 in Danyall) due to past annotations and to synteny (genes are between portal amd major capsid protein. The change of function call from "capsid morphogenesis protein" to "capsid maturation protease and MuF-like fusion protein" made me look more closely at these two genes. Only the early gene (the capsid maturation protease and MuF-like fusion protein) has HHPred matches that suggest a capsid maturation function (one 110 aa region with match to gp7 of SPP1 and another region at C-terminus with lots of matches to ribosyltransferase - see attached), while the other gene (gene 1 only has HHPred matches with less than 50% probability. I would thus be inclined to call a function for the first gene but not the second. What say Pittsburgh? :-) 29Kb

Link to this post | posted 16 Mar, 2019 13:58
delesall	Can you have both a gene for "capsid maturation protease and MuF-like fusion protein" and for a "capsid maturation protease" (e.g., Genes 14 and 18 in KimmyK)in the same genome? Both have been called in DC phages but there is better evidence (good HHPred matches) for the former.

Link to this post | posted 12 Mar, 2019 23:12
delesall	I see that a dehalogenase function was called for a SEA-PHAGES Gordonia phage TillyBobJoe but the function is not on the official list… I have some nice HHpred matches to both dehalogenase and polynucleotide kinase, with PDB files for the former but CDD matches favoring the latter. Any insights from folks who called dehalogenase?