Link to this post | posted 08 Jun, 2022 00:42
delesall	Note that BE phages have a large number of tRNA genes (>40) and a tmRNA gene. Not all tRNA genes will be called by Aragorn within DNAMaster, so it is crucial to run web-based Aragorn and tRNA scan to identify all tRNA genes as well as the tmRNA.

Link to this post | posted 05 Apr, 2022 19:28
delesall	This forum post may be useful https://seaphages.org/forums/topic/4347/ Cheers

Link to this post | posted 17 Feb, 2020 03:38

delesall

If I understand your question, you want to know what MA stands for! MA = manual annotation (an annotation that has been reviewed by a human being as opposed to an auto-annotation). So for this gene, the auto-annotation has picked the start at base 1 (which is the 23rd start in this pham). When genes in this pham have been reviewed, start 23 at base 1 was picked in 190 manual annotations, while start 25 at base 10 has only 5 manual annotations. You may still want to look at CP data to see if this choice was best! Hope this helps!

Link to this post | posted 26 Jan, 2020 14:53

delesall

Is there a document explaining how to interpret Topcons data? I looked around the SEA-PHAGES forums, the Bioinformatics guide and found nothing. The Topcons paper is a little dense for me. In particular I'm QC.ing AwesomeSauce - an F1 which is in Pecaan. In that phage, gene 33 (start 28413) has that HHPred match to the Putative lactococcus lactis phage r1t holin which has no transmembrane domain when run through TmHmm. The Topcons summary shows different results depending on the program but the reliability box shows nothing (which is different from the easier to interpret membrane protein for gene 29 in this phage). I interpreted this as no evidence for a transmembrane domain and would thus not call this the holin. Any insight on how to interpret teh Topcons summary for this gene would be appreciated!

Link to this post | posted 17 Jun, 2019 02:26

delesall

Gene 65 in BossLady (42154,43032) and its homolog in Zartrosa show nice HHPred matches to the lytic CHAPK domain of the endolysin LysK from Staphylococcus aureus bacteriophage K among others. I attach snapshots from HHPred matches. The matches cover the length of the protein with over 99% prob and low E-values. Pasting info from HHPred hits from BossLady (uploaded in Pecaan) 4CT3_C ORF30/ORF32; VIRAL PROTEIN, PEPTIDOGLYCAN, PROTEASE; HET: EPE, GOL, CMH, MMC; 1.69A {STAPHYLOCOCCUS PHAGE K} 99.7 46.5753 26 165 1 137 9.2e-18 5UDN_B Phage-associated cell wall hydrolase; lysin, d-alanyl-l-alanine endopeptidase, CHAP domain; HET: GOL; 1.971A {Streptococcus pyogenes MGAS5005} 99.6 62.3288 1 203 2 184 4.8e-16 Can go with more generic hydrolase but PDB files suggest we can be more specific. 10Kb

Link to this post | posted 23 May, 2019 10:48
delesall	As an example - Bunnies gene 32 (immunity repressor) pham 56415 (pham number from phagesdb) report is missing

Link to this post | posted 23 May, 2019 10:46
delesall	Also checking annotations for Bunnies and seeing missing starterator reports unavailable in Pecaan and on phagesdb for phams that are not orphams!

Link to this post | posted 25 Apr, 2019 23:50
delesall	309 amino acids (930 bp including stop codon) I have identified two minor tail proteins before the lysis cassette and three after . This would be a 4th and last minor tail after the lysis cassette

Link to this post | posted 25 Apr, 2019 20:48

delesall

Annotating Begonia, a CV phage. The homolog of gene 33 (27738-28667) has been called Alpha-L-arabinofuranosidase in Lucky 10, but that is not on the approved function list. Based on location - just after a minor tail - and based on HHPred matches to Alpha-L-arabinofuranosidase, which has binding domain to arabinose as well as catalytic activity, call function minor tail protein? The Begonia protein matches this enzyme with 99.8%, covering 60% of aa sequence, and very low <10^-24 E-value

Link to this post | posted 19 Mar, 2019 00:16
delesall	I ended up calling ribonuclease toxin for my gene - somewhat generic but also informative…