Link to this post | posted 05 Apr, 2023 18:40

aajohnson

We are trying to figure out how/why the major tail protein (LittleFortune gene 31, pham 74364, sequence file attached) is annotated with this function in Microbacteriophages. There is no functional annotation evidence support through blastp CDD or HHPred. The Microbacteriophages paper (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0234636) describes the major tail protein twice, such as "and the major tail protein gene is atypically located upstream of some of the head-to-tail connector genes". Some maps have this label on a protein, we just can't figure out where this label is coming from. Point me in the right direction please? 173Kb

Link to this post | posted 06 Apr, 2023 17:27
debbie	Alison, Hi. The hit to tail tube protein is what we call "major tail protein". Its place in EC is in the typical position in a genome. As for what should be called a tail tube protein is something that needs further investigation. debbie Edited 06 Apr, 2023 17:30

Link to this post | posted 12 Apr, 2023 19:57
aajohnson	Thanks Debbie. Is 90% probability hit to a pfam ok for functional annotation? LittleFortune gp31 does hit a tail tube pfam: http://pfam-legacy.xfam.org/family/PF06488.14 with 90% probability in HHPred, coverage of 74% (and a terrible evalue). AJ

Link to this post | posted 12 Apr, 2023 19:57
aajohnson	Thanks Debbie. Is 90% probability hit to a pfam ok for functional annotation? LittleFortune gp31 does hit a tail tube pfam: http://pfam-legacy.xfam.org/family/PF06488.14 with 90% probability in HHPred, coverage of 74% (and a terrible evalue). AJ

Link to this post | posted 12 Apr, 2023 19:57
aajohnson	Thanks Debbie. Is 90% probability hit to a pfam ok for functional annotation? LittleFortune gp31 does hit a tail tube pfam: http://pfam-legacy.xfam.org/family/PF06488.14 with 90% probability in HHPred, coverage of 74% (and a terrible evalue). AJ

Link to this post | posted 12 Apr, 2023 19:57
aajohnson	Thanks Debbie. Is 90% probability hit to a pfam ok for functional annotation? LittleFortune gp31 does hit a tail tube pfam: http://pfam-legacy.xfam.org/family/PF06488.14 with 90% probability in HHPred, coverage of 74% (and a terrible evalue). Allison

Link to this post | posted 12 Apr, 2023 20:45

debbie

Hi Alison, Using the gen numbers as found in PECAAN: 30 is a Hypothetical Protein. 31 is a hit to the major tail (tail tube), 90% probability with 73% alignment. 32 is the head-to-tail adaptor because it hits "Adaptor protein Rcc01688; "neck", "portal", "capsid", "tail tube", VIRUS; 3.58A {Rhodobacter capsulatus}".. I think that Rick Alvey and David Bollivar have been publishing about Rhodobacter capsulatus. Want to ask them about this entry. This gene is in a good place to be the head-to-tail adaptor. But it really much bigger than other head-to-tail adaptors, so there is something else there. And the something else has no hits. What do you think? debbie