Link to this post | posted 25 Apr, 2017 23:12

akoga

We are working with a Gordonia phage, asapag, in the new Cluster DN. In looking at HHPred for functions of white genes, my students ran across a strong hit for Gene 93. There are a bunch of matches in the 98-99 probability range. Some say CopG-like transcriptional regulator and a few say toxin-antitoxin. We tried looking at neighboring genes to see if anything looked like the toxin to go with an antitoxin and found that Gene 91 (not a white gene) gets a hit on HHpred to a VAPC6 toxin (Probability of 84 and E=0.75). This seems really interesting, but we are not sure where to go from here. It doesn't seem like good enough evidence to call it a toxin-antitoxin, but if there is more we could do to investigate that possibility we would love to. 28Kb

Link to this post | posted 26 Apr, 2017 16:09
welkin	Hi Ann, Thanks for posting the HHPred text output. However i would also need to see how much of your protein aligns to the various matches— probability and e value alone don't get you there, as you can get some pretty high scores for pretty short motif matches. Best, Welkin

Link to this post | posted 26 Apr, 2017 17:46
akoga	Thank you, Welkin. Our predicted product is 73 aa long. I see two things that you might be looking for, so I will attempt to attach both the information that appears on the first page you see on hhpred and also the aligment viewer that shows actual aa's in a bunch of colors. This is the first time I have used HHpred, so this will be a good lesson for me. Thank you in advance. Ann 8Kb

Link to this post | posted 26 Apr, 2017 17:46
akoga	Welkin, Here is the alignment viewer picture. Ann 227Kb

Link to this post | posted 05 May, 2017 15:33

welkin

Hi Ann, thanks for the data and sorry about the lengthy wait for a reply! for 93: There are too many equally likely hits that do different things— I think the best choice is to pick HTH DNA binding protein. There are antitoxins, transcriptional regulators, and all kinds of these. HHPred is picking up that structural motif, and in this case it could be lots of things. TA systems are really difficult to untangle— the proteins are tiny, so the alignment programs don't work as well. Without bench data, I think we should be cautious. Best, Welkin

Link to this post | posted 05 May, 2017 16:34
akoga	Thank you!

Link to this post | posted 04 Oct, 2017 14:17
rlb6	Kiko_draft_36 BLAST data (attached) shows strong hits to FIC family protein in many bacteria. HHpred also hits FIC protein/domain as well as many other things (attached). What do you think is the appropriate functional call? I have also attached the product sequence if you want to take it to HHpred yourself to see the full data. Beckie Bortz Edited 04 Oct, 2017 14:22 480Kb 240Kb 47Kb