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?

Link to this post | posted 01 Aug, 2019 18:00
adiaz	On a related note, gp22 (pham 17964) is also listed as a minor tail protein in most EA genomes but the HHPRED data matches Chitinase A (100% probability. I guess I'm having a hard time understanding how something that cleaves Chitin is related to a minor tail protein. Arturo

Link to this post | posted 01 Aug, 2019 17:42

adiaz

I'm in the process of annotating YuuY and I noticed that one of the genes is called minor tail protein (Pham 11397, coordinates 12806-15232 in Yuuy)in almost every EA cluster genome even though it is larger than the tape measure protein (Pham 11400, coordinates 9625-12036) and much larger than the major tail protein (Pham 11479, coordinates 8110-8604). HHPRED shows 99% probability (36.7% coverage) that it matches to prophage endopeptidase tail but given the size of the gene I wanted to confirm that this is the right call. Thank you, Arturo

Link to this post | posted 09 Jul, 2018 18:18

adiaz

I'm looking at Gene 61 (Start:40928, Stop: 4012 in OneinaGillian and all the evidence points to a Rad52-like DNA recombinase. The Rad52 recombinases are present in eukaryotes, however, it shows a quaternary organization similar to those of phage recombinases RecT/Redβ and ERF (Iyer LM et al, Classification and evolutionary history of the single-strand annealing proteins, RecT, Redβ, ERF and RAD52. BMC Genomics 2002). Moreover, the sporadic distribution of this family among phylogenetically distant bacteria, along with its presence in several prophages, suggests that, like the RecT/Redβ and ERF superfamilies, at least the bacterial RAD52-proteins might be of predominantly phage origin. My question is, for the sake of annotation, should we refer to this as a Rad52-like recombinase or just DNA recombinase? If it's the former then it would need to be added to the approved function list. Thanks, Arturo