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?

Link to this post | posted 25 Feb, 2019 19:47
delesall	I'll note that there are also nice HHPred matches to a DOC toxin in Gordonia phage Melba, a CV phage - in a reverse gene just before the integrase

Link to this post | posted 24 Jan, 2019 19:53
delesall	I have a student who is trying to install the virtual box but she gets an installation fail when she does that. Any idea of why that is the case. She is installing Virtual Box 6.0.2

Link to this post | posted 11 Aug, 2018 00:22

delesall

The product of gene 37 (28052,28756) in Darolasnstone has a couple of nice HHPred matches (95-96% probability, 61% coverage, E value of 0.027) to the Bacteriophage Mu Gam protein. "This family consists of bacterial and phage Gam proteins. The gam gene of bacteriophage Mu encodes a protein which protects linear double stranded DNA from exonuclease degradation in vitro and in vivo" http://pfam.xfam.org/family/PF07352.11 https://www.rcsb.org/structure/2P2U There is a nice paper suggesting homology between Gam and Ku (which is on approved list) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1315809/ I'd like to suggest we add Gam-like host-nuclease inhibitor protein to the function list

Link to this post | posted 06 Aug, 2018 15:48

delesall

Hi Ivan Nice detective work on this. My major criterion in situations like this is whether if you make the wrong call, it will be easily detected or propagated through the database without detection. Because of that, I would not call function as I have QC.ed too many annotations where folks just see a function in blastp data and assume it is correct without further checking. However, a wrong start should be more easy to detect and although rare longer overlap between genes can be OK. So, I would probably go with the longer call that includes all the CP. Does starterator suggest that this start is conserved in other BH phages? And it is gene 23 that you want to make longer, right? Veronique

Link to this post | posted 04 Aug, 2018 15:04
delesall	I have a student trying to install DNAMaster on her Mac. I sent her the most recent link I had to the Baylor box but that box appears to be empty… What am I missing? Thx

Link to this post | posted 19 Jul, 2018 19:45

delesall

For gp74 of Hank144, I have at least a dozen HHPred matches to an acetyltransferase. Top ten matches have probability greater than 93%, coverage 95% and E-value from 0.005 to 0.022. The best HHPred match is the Crystal structure of N-acetyltransferase from Staphylococcus aureus. That protein has 168aa - gp74 has 126. MTMRVYKVHHAIYIGALRQARRQSQLIADATSAPHEMPRSHTYYLTDDFQSGFGVAQDGTLVGLFSLIKGRGEDLVWDAILHHGATKLDCFDGFLPDYYKRFGFVETERVPNWTPGEPDVVFMSL Hank 144 is available on Pecaan if more info is needed on this request

Link to this post | posted 17 Jul, 2018 17:52

delesall

Hi Sally I had the same issue two years ago. Debbie had to go to Jeffrey Lawrence for that one! Happily I still have his email response which I paste below: "That is a warning/error form the database engine. A BLOB is a "Binary Large Object"; it is a field in the database used to store large fields of information (like a BLAST alignment for a hit). That error arises when one tries to open the same record more than once; the BLOB is already open elsewhere. This warning could arise if the same sequence is loaded form the database more than once, or if the same gene is examined in more than one way that would open a BLOB field. I would need far more details to determine the actual cause, but it may not be an error. It is only an error if it persists after it is clear that the object should have been closed. One possible source is that the record for the gene may not have been save prior to opening the BLAST tab. Try to post the record first." I can't remember what I did (it was two years ago) but the problem did resolve itself…