Link to this post | posted 06 May, 2025 17:24

adiaz

I’m working on three cluster GK phages, all three have a podoviridae morphology and the genomes are less than 18,000 base pairs. The genome arrangements is a bit different from anything I’ve annotated before, for example, the terminase is in between two endolysins (genes 1 and 12 in phage Smelly) and two transmembrane proteins (genes 14 and 15 in Smelly). Immediately upstream of the transmembrane protein encoding genes, there’s two genes that I’m debating whether to call minor tail proteins based on HHPRED hits ( (I used these 4 databases to search: PDB, PfamA, CDD, and Uni-Prot-Swiss Protein-viral). The top hit for gene 17 (348 bp) is the L-shaped tail fiber protein p132 of phage T5, with a 99.83% probability and an e-value 1.1 e-18 (https://toolkit.tuebingen.mpg.de/jobs/5744600). The top hit for gene 18 (1131 bp) is a Collagen-like protein 1 from Acanthamoeba polyphaga mimivirus with a 96.73% probability (https://toolkit.tuebingen.mpg.de/jobs/2916481). Based on size gene 17 wouldn’t qualify to be called a minor tail protein. Any input is greatly appreciated. Thank you, Arturo

Link to this post | posted 01 May, 2025 16:06
adiaz	Debbie, As an example of including a prominent domain within our endolysin calls, based on the paper and the the SEA-PHAGES FUNCTIONAL ASSIGNMENTS we would call gp11 "endolysin, L-Ala-D-Glu peptidase domain" while gp12 would be "endolysin, protease M23 domain"? Thank you. Arturo

Link to this post | posted 05 Mar, 2025 18:12

adiaz

Greetings, Students in our bioinformatics course are working on individual projects and one of the pairs are trying to determine codon usage preference between the host bacteria and some phages that encode for 16-20 tRNAs. We tried to using COUSIN (COdon Usage Similarity INdex) but that is not working as we get an error message for the output. Does anyone know of other programs that can determine codon usage preference that do not require coding knowledge? Thank you, Arturo

Link to this post | posted 19 Feb, 2025 19:02

adiaz

Hello, We are annotated three different phages assigned to Cluster GK, all isolated from Microbacterium paraoxydans, and we're trying to determine if it's possible for podoviridae phages to have two endolysins. As reference, here's the relevant information for the two genes in phage SpiderBri: Gene 11 (Pham 199043) Start 11487, stop 12080 HHPRED: D-alanyl-D-alanine carboxypeptidase; 99.2% probability; 57% coverage; 8.6 e-11 Phagesdb BLAST: Endolysin; Footloose 23; 5 e-14 NCBI BLAST: M23 family metallopeptidase [actinomycetes]; 38% coverage; 20.7% identity; 3.83 e-14 Gene 12 (Pham 214664) Start 12150, stop 12740 HHPRED: Peptidase M23; membrane protein, 99.1% probability, 72% coverage, 2.9 e-8 Phagesdb BLAST: endolysin, protease M23 domain; Trapezoid 12, 7 e-23 NCBI BLAST: M23 family metallopeptidase; 79% coverage; 37% identity; 6.15 e-27 Conserved domain database: Peptidase family M23; 58.6% coverage; 50% identity; 1.13 e-28 Interestingly, gene 13 is a terminase while genes 14 (1 TMD) and 15 (2 TMD) are membrane proteins. Thank you, Arturo

Link to this post | posted 04 Feb, 2025 06:09
adiaz	Hi Debbie, Thank you for your feedback, much appreciated! We are currently annotating both phages assigned to Cluster GK, the region of the Pochacco genome where this orpham is located is slightly different to that of Smelly. We did a blastN for this gene in both phagesdb and NCBI and no significant similarity was found so it is truly unique, at least for now. Arturo

Link to this post | posted 03 Feb, 2025 22:17

adiaz

Hello, We are working on annotating phage Pochaccho (Cluster GK) and we're uncertain as to whether we should keep a gene call made by Glimmer but not GeneMark. Glimmer predicts a gene starting at 16,587 to 16,730. This would give an overlap of 8 nucleotides with the previous gene and a total size of 111 bp. Given that it is less than 120 bp we were about to delete it but there's coding potential and DeepTMHMM shows that there's a transmembrane domain present is there a chance that this is a potential real gene? The gene is an orpham so there's nothing else we can compare it to. Thank you for your advice. 17Kb

Link to this post | posted 01 Feb, 2024 05:34

adiaz

Hello, We are currently annotating phage Crisis(cluster EC) and I'm asking for advice on making a call for gp34 (19,345-19,749). There are no hits on Phagesdb BLAST or NCBI BLAST but there's strong evidence for a minor capsid protein from HHPRED. The probability is 99.4%, coverage of 94.77% and an e-value of 2.3e-12. In terms of location within the genome, gp34 is in between the head-to-tail adaptor and the tail assembly chaperone. None of the other cluster EC phages have made this call so I'm hesitant to call it the minor capsid protein. Any suggestions or advice are welcomed. Arturo Edited 01 Feb, 2024 05:34 259Kb

Link to this post | posted 22 Jul, 2021 22:34

adiaz

Hello, I'm going over the annotation for phage SBlackberry (cluster EJ) and I'm trying to determine the right call for gene 14. Gene 14 is part of Pham 53136 and in cluster CZ it has been annotated as a minor capsid protein whereas in cluster EJ it has been annotated as NKF. According to HHPRED there's a match to a minor capsid protein (99.4% probability, 83% coverage, 3.1e-12 e-value). Based on this info I'm leaning towards calling it a minor capsid protein but any advice is appreciated. Thanks, Arturo

Link to this post | posted 29 Apr, 2020 03:18
adiaz	We got another cluster EC phage this year, any updates on whether the slippery sequence has been identified for this cluster? Thank you, Arturo

Link to this post | posted 06 Aug, 2019 19:29
adiaz	Hi Chris, Thank you for your thorough response, that was really helpful! I'm still familiarizing myself with phage biology, it's not unusual for the genes that encode for minor tail proteins to be larger than the major tail genes?