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Recent Activity
dane.bowder posted in capsid maturation protease or hypothetical protein (MuF-like minor capsid protein)
Marie Fogarty posted in capsid maturation protease or hypothetical protein (MuF-like minor capsid protein)
Debbie Jacobs-Sera posted in capsid maturation protease or hypothetical protein (MuF-like minor capsid protein)
dane.bowder posted in capsid maturation protease or hypothetical protein (MuF-like minor capsid protein)
All posts created by brueschhoff
| Link to this post | posted 28 Mar, 2024 15:58 | |
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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 | |
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Thank you so much to both of you for your help. Very interesting! |
| Link to this post | posted 22 Feb, 2024 15:59 | |
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Sure, Sorry about that! We are annotating DoobyDoo and the phamerator feature number is 10. The stop codon is 8910. |
| Link to this post | posted 21 Feb, 2024 15:31 | |
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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 |
| Link to this post | posted 30 Mar, 2023 16:42 | |
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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 | |
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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