Link to this post | posted 27 Jan, 2026 18:44

aajohnson

How do we feel about blastp with clusteredNR (nr_cluster_seq) database for positional annotation? It seems like clusteredNR is the new default, not sure if this is by desigh or because it's the top of a list. For me the search returns much faster compared to non-redundant protein sequences database. I'm working on a mycobacteriophage and seeing a wider diversity of hits (non-mycobacteriophage) higher in the descriptions table which is interesting. But the alignment tab shows only 1 hit from a cluster, which doesn't really illustrate how many other sequences have a 1:1 amino acid match between query and subject. It doesn't give you a message like "See 13 other titles"- this was something I previously told my students to look for to understand the depth of matches. The number of sequence in the cluster on the descriptions tab (20) is not the number of sequences that are identical according to clusteredNR result (15- I haven't really inspected these yet) or with the number with a 1:1 match using nr database (13). [Yes, I do tell them to also use phagesdb blastp, but I want them using a tool they will use more broadly after this class.] Anyone [Chris S ] have thoughts?

Link to this post | posted 22 May, 2025 20:01

aajohnson

Hi! We annotated Faiyaz (Y) this semester and would like to propose protein 48 and an "Aca-2 like protein". The sequence is: MTPAEFRIMREYLGLPPVWMAERLGVRERTVARWEHGHAPIPPGVVDEFTDILEVTARLVDSLIIQAGATGHLVTYRTDEDYRRSGSSYAATFPASWHRAVAARVYDAVPQVQITYSTDHSDDEAPGGCGSQV My students found: 1. Best HHpred hit is to https://www.rcsb.org/structure/7VJO, an apo-Aca2 from Pectobacterium phage ZF40. This is an Anticrispr 2 associated protein. 2. Used alpha fold to model dimer structure as is observed for 7VJO. 3. Used alphafold/fold seek to produce a decent overlay of the predicted Faiyaz protein structure with 7VJO. 4. Re-created a multiple sequence alignment from the PDB article to show conservation of secondary structures as well as four residues involved in DNA binding. I get a URL request for an image…A google doc with images is here: https://docs.google.com/document/d/1TlnnNQst0vGpW8CCGbNGr9ZTynJQhjQUMWy8SBZlPU8/edit?usp=sharing Thanks for considering, Allison & the VCU Phage Lab Edited 22 May, 2025 20:01

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