SEA-PHAGES | All posts created by brueschhoff

Link to this post \| posted 28 Mar, 2024 15:58
brueschhoff	I have a question. In DoobyDoo, Feature 65 (on Phamerator), stop 45445, has some of the features of a RecA, but not all of them. Therefore, I do not believe we should call this a RecA recombinase. On this powerpoint, our cluster (DV), falls under the category of not having a RecA recombinase but calling it anyway. Does this mean that we should not call it a RecA recombinase, or that we should call it a RecA, even though it is not a true RecA recombinase? Thank you, Beth Rueschhoff Indiana University Southeast

Link to this post | posted 28 Mar, 2024 15:58

I have a question. In DoobyDoo, Feature 65 (on Phamerator), stop 45445, has some of the features of a RecA, but not all of them. Therefore, I do not believe we should call this a RecA recombinase. On this powerpoint, our cluster (DV), falls under the category of not having a RecA recombinase but calling it anyway. Does this mean that we should not call it a RecA recombinase, or that we should call it a RecA, even though it is not a true RecA recombinase?

Thank you,
Beth Rueschhoff
Indiana University Southeast

Posted in: SMART Function Investigations → RecA requirements

Link to this post \| posted 23 Feb, 2024 16:36
brueschhoff	Thank you so much to both of you for your help. Very interesting!

Posted in: Functional Annotation → Metalloprotease without HEXXH motif?

Link to this post \| posted 22 Feb, 2024 15:59
brueschhoff	Sure, Sorry about that! We are annotating DoobyDoo and the phamerator feature number is 10. The stop codon is 8910.

Posted in: Functional Annotation → Metalloprotease without HEXXH motif?

Link to this post \| posted 21 Feb, 2024 15:31
brueschhoff	Greetings, We are investigating the function of a protein with sequence: MEYMPADLARTLSAMARGTHNEICGFILDDWTLISVRNVAKLPTISFEMSMNAILGAVEMAAASGREILGTYHSHPGGSTEPSETDLHGWPRFIDGSYARYWVVTGDTVREFERTGEGSEIGFQLIHSIGIGVVVKRPEEGMDQSVPEDZ It belongs to a pham that indicates it is a metalloprotease. BLAST Hits indicate either a tail protein or a metalloprotease. If we look at HHPRED, many hits come as a metalloprotease, but without the HEXXH motif. Rather it has a JAMM/MPN Zinc Binding domain. Should we annotate this as a metalloprotease, even without the HEXXH motif? Thank you for your assistance! Beth Rueschhoff Indiana University Southeast Edited 21 Feb, 2024 15:32

Link to this post | posted 21 Feb, 2024 15:31

brueschhoff

Greetings,

We are investigating the function of a protein with sequence: MEYMPADLARTLSAMARGTHNEICGFILDDWTLISVRNVAKLPTISFEMSMNAILGAVEMAAASGREILGTYHSHPGGSTEPSETDLHGWPRFIDGSYARYWVVTGDTVREFERTGEGSEIGFQLIHSIGIGVVVKRPEEGMDQSVPEDZ

It belongs to a pham that indicates it is a metalloprotease. BLAST Hits indicate either a tail protein or a metalloprotease. If we look at HHPRED, many hits come as a metalloprotease, but without the HEXXH motif. Rather it has a JAMM/MPN Zinc Binding domain. Should we annotate this as a metalloprotease, even without the HEXXH motif?

Thank you for your assistance!
Beth Rueschhoff
Indiana University Southeast

Edited 21 Feb, 2024 15:32

Posted in: Functional Annotation → Metalloprotease without HEXXH motif?

Link to this post \| posted 30 Mar, 2023 16:42
brueschhoff	debbie Hi Beth, Before trying anything else, have your students close the program (maybe even restart their computer) and then try again. debbie Hi Debbie, A student just tried this and got the same error. It only seems to happen on one particular feature.

Posted in: DNA Master → DNA Master errors

Link to this post \| posted 30 Mar, 2023 15:51
brueschhoff	Greetings! Sometimes, when reblasting a gene after changing the start site, students have been getting a "range check error." This sounds vaguely familiar, but I don't remember what causes this error or what to do when they get it. Any guidance is appreciated. Thank you, Beth

Posted in: DNA Master → DNA Master errors

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