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helix-turn-helix binding domain or protein?

| posted 04 Feb, 2022 19:19
We are annotating a gene with a HTH DNA binding domain. However in the notes column of the approved list it refers to the function HTH DNA binding protein, even though only HTH DNA binding domain is on the approved function list. I'm pretty sure you consider these two things to be the same, but it was confusing to my students. Do you consider domain and protein different annotations?
| posted 04 Feb, 2022 20:21
I think I corrected the confusion on the approved function list. Note that 'protein' was never mentioned in the first column.
The biology confusion is that "is a 'helix-turn-helix' a protein function?". That is the original of the use of domain. We are saying that this protein has a helix-turn-helix domain in it, but what it does (other than fit into DNA nicely), is varied.
Does this help?
Edited 15 Feb, 2022 13:23
| posted 15 Feb, 2022 03:39
Yes, I assumed you meant HTH DNA binding domain, not protein. It is just a motif, not a function.

Similar, but unrelated question (probably belongs in another thread?): we have annotated several membrane proteins. Again a motif, not a function. However, it seems like membrane protein doesn't get added to phamerator maps of the comparator phages even though it is is the genbank file. Why is that?
| posted 15 Feb, 2022 13:38
At the crux of the membrane protein designation is "what constitutes a membrane protein?". We have established a rule. (Know that phages don't have rules, so this is problematic.) The rule is if a protein has 2 or more transmembrane domains, call it a membrane protein. However, if it only has one, you must confirm the transmembrane domain with another transmembrane finder. Most recommended finders are TMHMM and SOSUI. PECAAN is using TopCons, which might be more helpful if we could agree on how to interpret it.

However, Phamerator does not remove anything protein labels, ever. What can happen is that at Pitt, I have a team who are curating the functional calls (discrepancies) by phams. Our 'corrections' go directly to the GenBank file. Phamerator systematically checks changes in GenBank files and updates.

You are right, membrane protein is not a functional call. It can be informative. Unfortunately, over time we have waffled on the one transmembrane call so those calls may or may not be there.
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