Welcome to the forums at seaphages.org. Please feel free to ask any questions related to the SEA-PHAGES program. Any logged-in user may post new topics and reply to existing topics. If you'd like to see a new forum created, please contact us using our form or email us at info@seaphages.org.
Recent Activity
All posts created by ACMPhageHunters
| Link to this post | posted 08 Feb, 2024 21:42 | |
|---|---|
|
I am a student of Profesor Barmoy. I am having trouble calling a function for a gene of a Siphoviridae phage. In HHpred, I have hits for a base plate structural protein in a myoviride phage. I also have hits in HHpred for a minor tail protein. My results include no collagen-like or glycine-rich proteins to assist in calling a minor tail, but also have no directions on calling a base plate protein. Can anyone assist in which to call and why? Thank you in advance. |
| Link to this post | posted 08 Feb, 2024 21:41 | |
|---|---|
|
|
I am a student of Profesor Barmoy. I am having trouble calling a function for a gene of a Siphoviridae phage. In HHpred, I have hits for a base plate structural protein in a myoviride phage. I also have hits in HHpred for a minor tail protein. My results include no collagen-like or glycine-rich proteins to assist in calling a minor tail, but also have no directions on calling a base plate protein. Can anyone assist in which to call and why? Thank you in advance. |
| Link to this post | posted 08 Feb, 2024 21:23 | |
|---|---|
|
|
I am a student of Professor Baromy. I am having trouble calling the function of a protein. My matches on HHpred include both Holliday junction resolvase and RuvC. Per the calling instructions, I am to call a Holliday junction resolvase only if not RusA or RuvC. The way that I am interpreting this information is that I would call this gene a RuvC because my HHpred matches include more than just Holiday junction resolvase. Would my assumption be correct? I appreciate your time and help. -Brandon |
Posted in: Functional Annotation → Function calling problem
| Link to this post | posted 08 Feb, 2024 21:22 | |
|---|---|
|
|
I am a student of Professor Baromy. I am having trouble calling the function of a protein. My matches on HHpred include both Holliday junction resolvase and RuvC. Per the calling instructions, I am to call a Holliday junction resolvase only if not RusA or RuvC. The way that I am interpreting this information is that I would call this gene a RuvC because my HHpred matches include more than just Holiday junction resolvase. Would my assumption be correct? I appreciate your time and help. -Brandon |
Posted in: Functional Annotation → Function calling problem
| Link to this post | posted 12 Apr, 2023 20:31 | |
|---|---|
|
|
Adam and Chris, Thank you for your prompt replies. My background is no where close to molecular biology and I'm learning as I go, I don't know what a sigma factor is and didn't know that it had anything to do with an HTH. But now I know and I can add this topic to my summer reading! Thanks again for your kind help. Michèle |
Posted in: Annotation → helix-turn-helix binding domain or protein?
| Link to this post | posted 11 Apr, 2023 18:34 | |
|---|---|
|
|
Hello, I'm having trouble with two gene function calls regarding HTH domains. In the first gene, many of the Phagesdb Blast hits call a "helix-turn-helix DNA binding domain protein" and exact matches on the NCBI results are "HTH DNA binding protein", but I don't see any references to an HTH binding domain in the HHpred or CDD results. The second gene has similar results. I don't want to just go with the crowd on these, so without HHpred or CDD confirmation, I'm leaning towards NKF. Is there anything else I should do to check for these HTH domains? The genes in question: StolenFromERC Cluster: E PECAAN # 32 Start 29,140 Stop: 28955 Reverse PECANN #130 Start: 68,963 Stop: 68700 Reverse Thanks for your help, Michèle |
Posted in: Annotation → helix-turn-helix binding domain or protein?