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

Link to this post | posted 28 Jun, 2018 18:58
adiaz	Thanks for the clarification!

Link to this post | posted 19 Jun, 2018 14:30
adiaz	Attached please find the .dnam5 file. 25Kb

Link to this post | posted 18 Jun, 2018 16:06

adiaz

Hello, I'm having a dilemma as to whether or not I should call genes 34 and 35 in KaiHaiDragon as the tail assembly chaperone. The evidence for the chaperones is based entirely on synteny (proximity to the tape measure) and the presence of the slippery sequences in Robsfeet and Metamorphoo, which are also found in Cluster EC. In the attached file I highlighted in blue the slippery sequence in both Robsfeet and Metamorphoo (CCCCCC), however, that sequence is missing from KaiHaiDragon, Paschalis, and Quhwah. Is it OK to still call them chaperones in KaiHaiDragon since they are in the same pham without annotating a frame shift or should I leave it as hypothetical protein in the GenBank file? Thanks for your help, Arturo 12Kb