Link to this post | posted 02 Jun, 2017 21:26
delesall	Gene 51 in Smairt (RVS 39018-37300) has interesting function calls in phages db: mostly phosphoesterase but also RDF/NrdC. Conserved domain database shows Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing. So, I'm planning to go with Phosphoesterase with intein domain. Do I get a second?

Link to this post | posted 02 Jun, 2017 21:19

delesall

In Smairt I have two genes that overlap (ca 550 bp) that both have blastp matches to the same gene porduct in JC27. I have aligned the DNA sequences to that gene and get the following (see attached file as well): Smairt 34B aligns to JC27 gene 37 from base 1 to base 588 with a 11 snps and one indel. Smairt 35 aligns from base 143 to base 688 with 8 snps and one indel. I cannot make Smairt 35 longer to include the first 142 bp with matches in JC27 and 34B cannot be made longer (darn stop codon) to include the last 100 bp that match JC27… None of these putative ORFs have known functions. Call both ORF 34B and 35 in Smairt despite 550bp overlap or just call ORF 34B (which is longer than 35? That is my dimemma 2Kb

Link to this post | posted 02 Jun, 2017 20:58
delesall	I have a cluster A1 phage (Smairt) with an ORF with nice blastp and HHPred matches (98% probability, 70% coverage) to Ead/Ea22-like protein. Call function?

Link to this post | posted 30 May, 2017 22:45
delesall	OK - I only see 4 databases as well. We have been selecting PDB and Pfam but not Scope. Since these are do novo annotation, I may add Scope95. However, the Scope database may disappear this summer per information on their web site (assuming I'm not confusing web sites) http://scop.berkeley.edu

Link to this post | posted 30 May, 2017 15:23
delesall	Hi Chris What databases do you pick to run a search? The menu of databases is much smaller, right?

Link to this post | posted 25 May, 2017 19:38
delesall	If you are annotating a podo virus, T7-like, do you go with terminase or with DNA packaging (traditionally used for T7-like pages, right?). Or are both equally OK?

Link to this post | posted 24 May, 2017 19:14

delesall

Hi all My students and I have been annotating a K1 phage and we have found some interesting HHPred matches. We are wondering whether these are sufficient to call funtion: Genes 39 and 40 - Both proteins show matches to ESAT6 family proteins - the first over only 20-25% of the aa sequence, the second over the whole aa sequence. Call function Virulence protein or NKF? Genes 94 and 95 - Nice HHPred matches - over 99%, whole length of aa sequence, very low E values -to HicB antitoxin and HicAtoxin - Call function?

Link to this post | posted 24 May, 2017 18:43
delesall	Has anybody tried to use the new HHPred web site? I'm curious about which database we should select to run query?

Link to this post | posted 24 May, 2016 20:02
delesall	I do hope his family will take some small comfort in how widely David was loved and respected. Not many people can have the wide and positive impact David had, he will be missed but he will also be remembered.

Link to this post | posted 08 Feb, 2016 01:22
delesall	I'm using HHPred tonight (Feb 7th) and can only see the databases pbd70_ and pfam_. There is no tigrfam_! Anybody knows what happened to that database? Thx, Veronique