SEA-PHAGES | HTH or no HTH

HTH or no HTH

Link to this post \| posted 31 Jul, 2025 22:52
rdejong	We were annotating the following protein, with hits to binding proteins and HTH domain containing proteins. MPLVKTAAEINREIRSMCPPTAPPPPPASRSDRQLGPMQYALLELVRSKPYWVVDRAFWRVMARKLRVPAWRVRKVFLSLEEGGYILVSERENPRIAQATERGRR Checking for HTH on HHpred output wasn't totally clear. In the output below, I've put green boxes around possible HTH regions for both the Query and the Target. The Target has a definite HTH domain. The Query, however, is a little doubtful. One of the helices is only 3 amino acids long, and my understanding is that at least 5 aa's are needed for a stable helix. Rick Pollenz was consulted and confirmed that there is not a HTH in that protein. He used two programs to investigate: https://users.cis.fiu.edu/~giri/bioinf/GYM2/prog.html https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_hth.html Thanks Rick! Our call is going to be DNA binding protein Edited 31 Jul, 2025 22:53 89Kb

Link to this post | posted 31 Jul, 2025 22:52

We were annotating the following protein, with hits to binding proteins and HTH domain containing proteins.
MPLVKTAAEINREIRSMCPPTAPPPPPASRSDRQLGPMQYALLELVRSKPYWVVDRAFWRVMARKLRVPAWRVRKVFLSLEEGGYILVSERENPRIAQATERGRR

Checking for HTH on HHpred output wasn't totally clear. In the output below, I've put green boxes around possible HTH regions for both the Query and the Target. The Target has a definite HTH domain. The Query, however, is a little doubtful. One of the helices is only 3 amino acids long, and my understanding is that at least 5 aa's are needed for a stable helix.

Rick Pollenz was consulted and confirmed that there is not a HTH in that protein. He used two programs to investigate:
https://users.cis.fiu.edu/~giri/bioinf/GYM2/prog.html
https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_hth.html
Thanks Rick!

Our call is going to be DNA binding protein

Edited 31 Jul, 2025 22:53

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HTH or no HTH