Link to this post | posted 09 Jul, 2024 17:43

aajohnson

Woohoo!! "good HHPRED hits to Vs.4 from T4 and anti-CBASS protein (Acb2) P26 from pseudomonas phage PaP2"- definitely. We could post a couple of instructions on using AlphaFold3 server here, and link it to the approved function listing. The webserver makes it as trivial as an HHPred search, but the unknown might feel like a barrier to some. See if I put enough in the attachment? Webserver link: https://alphafoldserver.com/ Settings: molecule type is protein, copies is 6 for hexamer See attachment for screenshots. [The sequence percent identities are quite wide for these phams (there are at least 3). If you're going to list a gene as a guideline as homology, proteins from the other phams won't have much homology to Wolfstar gp30-ish.] 307Kb

Link to this post | posted 11 May, 2024 14:01
aajohnson	Awesome thank you!!

Link to this post | posted 06 May, 2024 19:37

aajohnson

Hi! This is an investigation of function for Balomoji protein #102 (Pecaan) or 102 (final DNAMaster file), genome coordinates 60991-61688, pham 163488. We answer the required questions and make a pitch in this google doc for consideration of function related to cyclic trinucleotide binding anti-CBASS proteins, inspired by Dr. Bondy-Denomy's SEA Symposium presentation. Allison and two fantastic students who did this work, Harshini and Mariya 529Kb

Link to this post | posted 12 Apr, 2023 19:57
aajohnson	Thanks Debbie. Is 90% probability hit to a pfam ok for functional annotation? LittleFortune gp31 does hit a tail tube pfam: http://pfam-legacy.xfam.org/family/PF06488.14 with 90% probability in HHPred, coverage of 74% (and a terrible evalue). Allison

Link to this post | posted 12 Apr, 2023 19:57
aajohnson	Thanks Debbie. Is 90% probability hit to a pfam ok for functional annotation? LittleFortune gp31 does hit a tail tube pfam: http://pfam-legacy.xfam.org/family/PF06488.14 with 90% probability in HHPred, coverage of 74% (and a terrible evalue). AJ

Link to this post | posted 12 Apr, 2023 19:57
aajohnson	Thanks Debbie. Is 90% probability hit to a pfam ok for functional annotation? LittleFortune gp31 does hit a tail tube pfam: http://pfam-legacy.xfam.org/family/PF06488.14 with 90% probability in HHPred, coverage of 74% (and a terrible evalue). AJ

Link to this post | posted 12 Apr, 2023 19:57
aajohnson	Thanks Debbie. Is 90% probability hit to a pfam ok for functional annotation? LittleFortune gp31 does hit a tail tube pfam: http://pfam-legacy.xfam.org/family/PF06488.14 with 90% probability in HHPred, coverage of 74% (and a terrible evalue). AJ

Link to this post | posted 05 Apr, 2023 18:40

aajohnson

We are trying to figure out how/why the major tail protein (LittleFortune gene 31, pham 74364, sequence file attached) is annotated with this function in Microbacteriophages. There is no functional annotation evidence support through blastp CDD or HHPred. The Microbacteriophages paper (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0234636) describes the major tail protein twice, such as "and the major tail protein gene is atypically located upstream of some of the head-to-tail connector genes". Some maps have this label on a protein, we just can't figure out where this label is coming from. Point me in the right direction please? 173Kb

Link to this post | posted 23 Feb, 2023 13:40
aajohnson	Perfect, thank you.

Link to this post | posted 22 Feb, 2023 20:25
aajohnson	This was useful today! Thank you.