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All posts created by welkin

| posted 31 Jul, 2017 15:12
Hi Claire,
I think we can add it back. We will just have to make a note that it should only be used if a more specific assignment can't be justified.
Posted in: Request a new function on the SEA-PHAGES official listmembrane protein
| posted 31 Jul, 2017 15:11
Hi Jackie,
I am not familiar enough with transposase classifications to know if LouisV14 meets all the criteria for the specific assignments you propose. Are there specific catalytic residues we have to look for? Or is the classification based solely on the architecture of the transposon?
Posted in: Request a new function on the SEA-PHAGES official listtnpA transposase and tnpR resolvavse
| posted 31 Jul, 2017 15:07
Hi Karen,
I think we annotated the Cluster J phages in the paper before we started using HHPred regularly. It sounds like from your comments that you are suggesting that all of pham 1260 should be reassigned to ATPase domain, is that correct?
The additional data of the other pham with the DnaB helicase assignment is interesting. Is there another DnaB helicase in any of the genomes? If that annotation is better supported, then perhaps 1260 should all be DnaB helicase, nad 1260 is a sequence variant that we haven't seen before.
Posted in: Functional Annotationcluster J pham 1260 (RecA/RepA/DNAB)
| posted 31 Jul, 2017 15:03
Sounds like it is not AlpA, and it is not likely to be excise either. I have tried to steer clear of names with just protein structures without any idea about what they do (so we don't say "alpha-helix protein", but "helix-turn-helix DNA binding protein" is OK).

Do winged helix proteins all have similar functions? Or is this a structural motif found in a variety of proteins ?
Posted in: Functional AnnotationalpA
| posted 31 Jul, 2017 14:57
Thanks Dave– this is a really helpful analysis of a tricky protein. It sounds like the phage is using a multifunction replication protein like pRN1. I am going to check in with Graham and get an official answer.
Posted in: Functional AnnotationPham 23485 repA/DNA primase polymerase
| posted 31 Jul, 2017 14:30
Nope. Post away!
Posted in: Notes and Final FilesTranslation code
| posted 31 Jul, 2017 14:30
Hi JAckie, sounds pretty solid. Do you have any thoughts on what the official name be? I don't really like either just the alphabet soup or the full length Activating Signal Cointegrator - 1 transcriptional coactivation protein.
ASC-1 transcription coactivator? IS that too long?

Posted in: Request a new function on the SEA-PHAGES official listASC 1 Activating signal cointegrator
| posted 21 Jul, 2017 15:30
Thanks for posting the data!

Based on your HHPred results and the db entries, ocr is 119 residues long, your protein is more than twice that at 295. you also have an equally good alignment to part of a restriction enzyme in the same area at the ocr alignment.
So my questions is, what do the restriction enzyme and ocr have in common?

And yes, key residues in the right spot always help, but I don't think we are there yet.
Posted in: Functional AnnotationGene with homology to T7 Ocr gene
| posted 21 Jul, 2017 15:21
The main server is currently disconnected due to construction here at Pitt. We are working on an alternate plan.
Posted in: DNA MasterDNA Master Issue
| posted 19 Jul, 2017 16:16
So I think this comes from the idea that there must be tail assembly chaperones in the Bs, and the most likely candidates are the genes between the major tail and tape measure proteins. We need two adjacent ORFs that are not in the same frame that have an overlap. Then, there are only two choices, the equivalent of FriarPreacher genes 22/23 or 25/26. 25 belongs to pham 10859, and has the hhpred hit to a tail protein (although it is the capping protein and not the assembly chaperone.) 22 also hits to some phage structural proteins that are not the assembly chaperones. Perhaps the best thing to do is to scrap all the TAC assignmnets in the Bs and set them all back to NKF.
Posted in: Functional AnnotationTail assembly chaperones in B phages