Link to this post | posted 01 Jun, 2022 15:27
dtobiason	Data published in November 2020 in the PDB (6W7T) suggests that gp4 is small terminase in MortySmith. Only one cluster EF phage has been annotated and published in Genbank since this information was put into the PDB. From this data it appears that cluster EF phages may have a small and large terminase.

Link to this post | posted 22 May, 2020 15:35

dtobiason

We have finished and our ready to send out our annotations but just want to double check about ORFs and tRNAs overlapping in Nanosmite (cluster M3, only member of the subcluster). I've attached a screen shot of the two ORFs in question. gp101 is an orpham (DNAmaster notes are visible in the screenshot for this gene) with no function and basically no coding potential so we are leaning towards deleting the ORF and keeping the tRNA. gp109 (not an orpham) overlaps with a downstream tRNA by 10 bps so just want to verify that we can keep both as they are transcribed in the same direction. Thanks for your help! 314Kb

Link to this post | posted 30 Mar, 2020 15:54
dtobiason	Hi- We are seeing a discrepancy between the HHpred top results for gp11 for BigRedClifford in Pecaan (PDB 4ACV_B, 81% Prob) and after running it thru HHpred (PDB 5A21_G, 98% Prob). Based upon the 5A21_G hit, we are leaning towards calling its function as ‘tail terminator’ as many of the other EA1 phages call it a tail terminator, but can we not rely on Pecaan HHpred calls?

Link to this post | posted 12 Feb, 2020 15:41

dtobiason

Hi We just started the semester, and I've got two students running Windows 10 who also got this message: Queries table is corrupt. Reload from FTP DNA Master FTP site. We've tried hitting yes and got a long error message. They were able to import the fasta file but then trying to do other steps results in this message: TBcodonbias: cannot perform this operation on a closed data set. They are running it as administrators and we tried uninstalling and reinstalling but nothing has worked. They are running version 5.23.3 Build 2644 which I believe is the latest version. Any help is much appreciated! Deb

Link to this post | posted 11 Feb, 2020 23:59

dtobiason

Hi We just started the semester, and I've got two students running Windows 10 who also got this message: Queries table is corrupt. Reload from FTP DNA Master FTP site. We've tried hitting yes and got a long error message. They were able to import the fasta file but then trying to do other steps results in this message: TBcodonbias: cannot perform this operation on a closed data set. They are running it as administrators and we tried uninstalling and reinstalling but nothing has worked. They are running version 5.23.3 Build 2644 which I believe is the latest version. Any help is much appreciated! Deb

Link to this post | posted 17 Apr, 2019 14:51
dtobiason	Thanks Claire- that makes sense and thanks for the info about rerunning the evidence for all genes. PECAAN is super useful!

Link to this post | posted 16 Apr, 2019 14:04

dtobiason

Just to follow up. Pecaan listed the top two hits as strong hits with Mur family proteins (85% coverage and 98% probability) on HHpred for this gp, but when we just ran it thru HHpred the traditional way those hits did not exist. We asked HHpred to rerun Den3's gp55 and now the HHpred results are different and the original top hits are not there. We have been using Pecaan for annotating this semester and are concerned that we now have to go back to recheck all of the genes. We are finalizing our annotations now so please advise. Does Pecaan have a glitch? Can we still transfer Pecaan data into DNAmaster for our final file?

Link to this post | posted 11 Apr, 2019 16:35

dtobiason

In two cluster EA1 phages that we are annotating, gp55 (pham 39995) has a strong HHPred hit with a PDB crystal structure of Mur family proteins that are described as amidotransferases in the corresponding publication. Only one annotated EA1 genome calls this pham a DNA binding domain protein in Blastp with no other relevant hits. Not clear about the evidence for a DNA binding domain protein. Any help is much appreciated.

Link to this post | posted 21 Mar, 2019 16:13

dtobiason

We are annotating a cluster EA1 phage and found that pham 23434 (gp34) is coming up as a DNA recombinase based on other annotated cluster EA1 phages on BLASTp. However, HHpred has many PDB hits to replicative DNA helicases such as RepA and a few hits to RecA-like proteins from yeast and archaea- further down the list, there is a PDB hit with RecA from E.coli. It also has conserved domains with both RepA and RecA. Is there a reason that other EA1 phages did not call it a RepA-helicase?