Link to this post | posted 24 Jun, 2020 21:17

dbolliva

I just ran into the same problem and forgot to check the forum but contacted Jeffrey Lawrence directly. I asked him what the BLOB error stood for and how to fix it. Here is his reply: >>>>> It means the database file was corrupted. Most times, this can be fixed. This is esoteric, but give it a try: Close DNA Master Go to the Helper directory in the DNA Master installation directory Look for a program called “dutil32.exe”. Run it. In the top box, click the “By Directory” button Navigate to the DNA master installation directory, then to the DMDB subdirectory On the left panel you will see the database table. Choose GenBankProjects Click “rebuild”. Repeat for the GenBank Authors and GenBankReferences tables, if needed. PLEASE NOTE: I did this as listed and the rebuilding failed, but I went back and started the .exe file using the right click then Run as adminstrator like you have to do for DNA master. When I did that, the rebuilding worked. Dave

Link to this post | posted 24 Jun, 2020 21:17

dbolliva

I just ran into the same problem and forgot to check the forum but contacted Jeffrey Lawrence directly. I asked him what the BLOB error stood for and how to fix it. Here is his reply: >>>>> It means the database file was corrupted. Most times, this can be fixed. This is esoteric, but give it a try: Close DNA Master Go to the Helper directory in the DNA Master installation directory Look for a program called “dutil32.exe”. Run it. In the top box, click the “By Directory” button Navigate to the DNA master installation directory, then to the DMDB subdirectory On the left panel you will see the database table. Choose GenBankProjects Click “rebuild”. Repeat for the GenBank Authors and GenBankReferences tables, if needed. PLEASE NOTE: I did this as listed and the rebuilding failed, but I went back and started the .exe file using the right click then Run as adminstrator like you have to do for DNA master. When I did that, the rebuilding worked. Dave

Link to this post | posted 26 Apr, 2019 16:50

dbolliva

I have been looking at the genes in Celaena, our new EB phage and see two genes close to each other (stops 38540 and 39809) that both were giving HHPred results in the 99-100 % probablility range for the bifunctional DHFR-TS. I went to look at the PDB files for the 1J3K structure and noticed that the two functions are in separate domains. The A and B chains carry the DHFR activity and the and D chains have the thymidylates synthase domains. Gene 55 of Celaena (stop 38540) is aligning with the A and B chains and Gene 57 of Celaena (stop 39809) aligns with the C and D chains. Based on this I was wondering if all of the pham members of gene 55 should be DHFR (like Bubbabear_56) and all of the pham members of gene 57 should be labeled thymidylate synthase like BubbaBear_59?

Link to this post | posted 16 Apr, 2019 15:50
dbolliva	There still is the RNAseE function on the list. Is the function you have not that specific?

Link to this post | posted 04 Apr, 2019 03:25

dbolliva

One trick we have used when starting with a new host bacterium is to do spot plating with the dilution series. If we have a lysate we would make a lawn and then spot 10 ul of the lysate onto the plate. You can also create a serial dilution series and spot 10 ul of each of the dilutions. We have had good success with this and if you do the serial dilutions you will get to a concentration where it appears there are plaques. If you are using marine agar or salt containing medium, I have also seen problems with top agar getting too high in salt if we melt it too many times in the microwave. Sometimes when isolating phages we have also run into is the growth of a different bacterium on the plate that produces a compound inhibiting growth of our host. This can be possible if the bacterium that produces the plaque like appearance is a spore-forming bacterium.

Link to this post | posted 18 Mar, 2019 21:42

dbolliva

We are looking at our phage Sucha and comparing with the previously annotated Goodman. Gene 5 in Goodman is called as a capsid maturation protease, and Sucha has a gene that shares similarity but is much shorter and only has HHpred results with minor capsid protein. In Appa a member of the same Pham as the Sucha gene has been called as a head assembly protein, which I believe you want called something different? I guess my question is whether to just call it as a minor capsid protein? It is notable theat the alignment with the capsid maturation protease is to the amino terminus but only covers a third of the protein.

Link to this post | posted 20 Feb, 2019 15:22
dbolliva	This is an issue where not everyone seems to agree and so there are examples of both calls in the databases. From what I understand from conversations I have had with Welkin indicated if you have two potential starts right in a row like this it is usually the second (-1) based on proteomics data. I could not quickly find a reference to support my memory unfortunately.

Link to this post | posted 04 Feb, 2019 20:07
dbolliva	Given what we know from experiments that the Hatfull lab has done the the second start codon is probably the correct one. You still see a 1 bp overlap and that is also highly favored. It could be ither one or both, but based on the mass spec experiments they have done, it seems that the second start would be the more likely start. Dave

Link to this post | posted 24 Jan, 2019 16:36
dbolliva	It seems that ATG and GTG are both very good start codons for bacteriophages so the GTGA overlap should be considered equally good. Dave

Link to this post | posted 19 Aug, 2018 23:00

dbolliva

This is a tougher one. Again, just my two cents. The evidence points to this having a LysM domain, but that can be a little misleading because the LysM domain essentially is a peptidoglycan binding domain. Your CDD hit is just to that part of the predicted protein. Unfortunately, there is not an approved function with just the LysM domain, so the question is do you have enough evidence for the endolysin part. There are suggestions (the LD transpeptidase hit for example) but I would suggest it is not strong enough to make this call. I personally would leave this NKF.