SEA-PHAGES | helix-turn-helix binding domain or protein?

Link to this post \| posted 12 Apr, 2023 20:31
ACMPhageHunters	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

Link to this post \| posted 12 Apr, 2023 20:56
debbie	Hi all, My two cents - I agree with Chris. In addition, I am uncomfortable with calling something a sigma factor until I know it is a sigma factor for a particular reason, DNA binding buys us the opportunity that it is controlling DNA in some way. A safe call in my book. If we uncover a mechanistic approach to the genes that this sigma factor is controlling, then the story can change. There are many sigma factors and i have no idea what would be could be in phages….. As for whether we call it a helix-turn-helix DNA binding protein or a helix-turn-helix DNA binding domain, we have been very fickle about this. We hit a spot where I believe GenBank wouldn't take the word "domain" in the function call. So we called all of the helix-turn-helix DNA binding proteins. That is very uncomfortable when the HTH is only a small motif in an otherwise larger gene. In addition, HTH is not a functional call, but it is informative. SMART members may have a preference and over time, we may get a better handle on this. But whether you call something a helix-turn-helix DNA binding protein or a helix-turn-helix DNA binding domain, I can't see a reason to argue with it. Make best choices and when you figure it out, we'll make even better calls.

Link to this post | posted 12 Apr, 2023 20:56

debbie

Hi all,
My two cents - I agree with Chris.
In addition, I am uncomfortable with calling something a sigma factor until I know it is a sigma factor for a particular reason, DNA binding buys us the opportunity that it is controlling DNA in some way. A safe call in my book. If we uncover a mechanistic approach to the genes that this sigma factor is controlling, then the story can change.
There are many sigma factors and i have no idea what would be could be in phages…..

As for whether we call it a helix-turn-helix DNA binding protein or a helix-turn-helix DNA binding domain, we have been very fickle about this. We hit a spot where I believe GenBank wouldn't take the word "domain" in the function call. So we called all of the helix-turn-helix DNA binding proteins. That is very uncomfortable when the HTH is only a small motif in an otherwise larger gene. In addition, HTH is not a functional call, but it is informative. SMART members may have a preference and over time, we may get a better handle on this. But whether you call something a helix-turn-helix DNA binding protein or a helix-turn-helix DNA binding domain, I can't see a reason to argue with it. Make best choices and when you figure it out, we'll make even better calls.

Link to this post \| posted 07 Feb, 2024 21:17
uOttawaPHAGE	Hi Debbie Starting this thread up again with a question from a student, Ashlyn: For draft phage Superstar (BD2), the gene at the coordinates 31,549 to 31,764 (gene 47 on Phamerator) is currently being called a DNA binding protein. However, HHPRED shows high coverage and probability for a helix-turn-helix DNA binding protein. We would like to be as specific as possible for this call. According to the SEA-PHAGES FUNCTIONAL ASSIGNMENTS sheet, the alignments of the protein hitting HTHs must hit 2-3 alpha helices in the sequence separated by small spacer (turn) regions of 3-4 amino acids. However, the alignments I found are showing a spacer region of 6 amino acids between the 2nd and third helix. Is it acceptable to call this as a HTH, or should we simply call it a DNA binding protein? Attached are the top HHpred hits and the sequence comparison for the top hit. thanks Adam 150Kb

Link to this post | posted 07 Feb, 2024 21:17

uOttawaPHAGE

Hi Debbie

Starting this thread up again with a question from a student, Ashlyn:

For draft phage Superstar (BD2), the gene at the coordinates 31,549 to 31,764 (gene 47 on Phamerator) is currently being called a DNA binding protein. However, HHPRED shows high coverage and probability for a helix-turn-helix DNA binding protein. We would like to be as specific as possible for this call.

According to the SEA-PHAGES FUNCTIONAL ASSIGNMENTS sheet, the alignments of the protein hitting HTHs must hit 2-3 alpha helices in the sequence separated by small spacer (turn) regions of 3-4 amino acids. However, the alignments I found are showing a spacer region of 6 amino acids between the 2nd and third helix. Is it acceptable to call this as a HTH, or should we simply call it a DNA binding protein?

Attached are the top HHpred hits and the sequence comparison for the top hit.

thanks

Adam

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helix-turn-helix binding domain or protein?