Link to this post | posted 23 May, 2017 19:26
washj	Lysin A in cluster CV is split into two domains. In previous annotations they have been called Lysin A, L-Ala-D-Glu peptidase domain and Lysin A, glycosyl hydrolase domain. There is also a lysin B present in the genomes. Should we add these designations to the approved list?

Link to this post | posted 02 Mar, 2017 18:25

washj

Re 5) I just checked the literature and MRE11 is a Mn dependent nuclease with several highly conserved phosphoesterase domains. http://www.genetics.org/content/195/3/739.long Phyre2 results also support the call as MRE11 with 99.1% certainty. I would propose to call the gene MRE11 double strand break nuclease. I think that it maybe even better to include exonuclease/endonuclease (instead of just nuclease - MRE11 double strand break exonuclease/endonuclease) so that when students see hits to both endo and exo it will minimize confusion but I'm concerned that the name may be too long. What do you think? 6)HTH DNA binding - hits to HTH transcriptional activator Edited 02 Mar, 2017 18:27

Link to this post | posted 01 Mar, 2017 23:59
washj	I have been using TMHMM to check for transmenbrane domains. There is a gene in Findley(K2)which has both DNA binding domain at the C terminus and 4 transmembrane domains at the N terminus. Should it be called "membrane DNA binding protein"? Thanks, Jackie

Link to this post | posted 01 Mar, 2017 23:48

washj

My apologies for the long list, but I have come across the following functional assignments which are not on the approved list. Should we use the following names? DNA polymerase I (ShayRa_47 28154-29944, Rev) - in a number of genomes but not on the approved list MRE11 nuclease - (OR MRE11 exonuclease/endonuclease OR MRE11 double strand break nuclease) - has both endonuclease and exonuclease domains. Sometimes the gene has been annotated as endonuclease, sometimes exonuclease- HHPRED 99.5% (LastHope_35, pham 5465) Polypeptide N-acetylgalactosaminyl transferase (Kingsley_110, pham 6125, 57955-59391 Forward) HHPRED prob 100% N-acetylglucosaminyl transferase (or glycosyltransferase) - Kingsley_112, pham 27754, 59597-60208, Forward - HHPRED prob 100% DNA helicase/methylase - gene has has both helicase and methylase domains Kingsley_63, pham 6161, 42315-44834 Forward HHPRED prob 100% for both helicase and methylase (also in CD) Immunity superinfection protein (sometimes called superinfection exclusion protein)- Jabith_72 (pham 25322.) It's in a number of genomes but not listed on the approved list. Thanks, Jackie

Link to this post | posted 10 Aug, 2016 18:36

washj

Hi Chris, Thanks for your help and the file! Starterator is working once again. Jackie cdshaffer Ok tried jabith once and it worked all the way through so I posted the results here. That was with the original version. As with Sprinklers I will try with the beta version see if I can get it to crash there. I will let you know how those go, please if you have time try the solutions suggested above as well and let me know if those stop the crashing.

Link to this post | posted 29 Jul, 2016 00:02
washj	Hi Chris, I tried running to generate a report for Jabith using the Beta version of Starterator and it fails at pham 18107 - #42 of 98 It seems that Starterator no longer works as I am no longer able to generate any reports even for a single pham - Itried a couple. Thanks for your help, Jackie Edited 29 Jul, 2016 00:03

Link to this post | posted 24 Sep, 2015 19:57
washj	Thanks Chris!

Link to this post | posted 24 Sep, 2015 19:51
washj	Is there a way to export the protein sequences in a single file (fasta format) for all the genes of a phage using DNA Master? Or, is there another way that I can get that info? Thanks for your help!