SEA-PHAGES | All posts created by Ths44

Link to this post \| posted 29 May, 2019 17:09
Ths44	This question has been answered in the Cluster specific annotation tips for Cluster DE phages. https://seaphages.org/forums/topic/4916/?page=1#post-7305

Posted in: Functional Annotation → Cluster DE terminase/HNH endonuclease/intein

Link to this post \| posted 29 May, 2019 17:08
Ths44	Some Cluster DE phages have a much larger terminase genes than other DE phages. Zipp gp2 is an example of this longer gene product. After analysis of HHPRED data it was found there are two functional domains that this protein product has; an N-terminal homing endonuclease and a C-terminal terminase. In order to decide that this homing endonuclease was an intein further computational analysis had to be done. The first step was to discover what residues of the protein belonged to which domain. An attached image has the protein sequences color coded, highlighted and bolded for the regions that will be discussed on this post. The amino acids colored blue are the BLAST hits to terminases is cluster DE that do NOT contain the intein. The amino acids colored red are present in all gene products in the cluster that contain the intein. In order to have confidence that this protein contains an intein splice sites needed to be found. In order to do that every nucleophilic amino acid near and in the intein were highlighted. These amino acids (Cys, Ser, and Thr) are necessary at both the N- and C-terminals of the intein in order for it to splice out. The second focus was to insure that a His was located somewhere in the middle of the intein (these have been highlighted in light blue). The final amino acid sequence to find was a His-Asn dipeptide found near a nucleophilc amino acid on the C-terminus. The most probable splice sites have had their text size enlarged and bolded. Edited 31 May, 2019 12:42 611Kb

Link to this post | posted 29 May, 2019 17:08

Ths44

Some Cluster DE phages have a much larger terminase genes than other DE phages. Zipp gp2 is an example of this longer gene product. After analysis of HHPRED data it was found there are two functional domains that this protein product has; an N-terminal homing endonuclease and a C-terminal terminase.

In order to decide that this homing endonuclease was an intein further computational analysis had to be done. The first step was to discover what residues of the protein belonged to which domain. An attached image has the protein sequences color coded, highlighted and bolded for the regions that will be discussed on this post.

The amino acids colored blue are the BLAST hits to terminases is cluster DE that do NOT contain the intein. The amino acids colored red are present in all gene products in the cluster that contain the intein. In order to have confidence that this protein contains an intein splice sites needed to be found. In order to do that every nucleophilic amino acid near and in the intein were highlighted. These amino acids (Cys, Ser, and Thr) are necessary at both the N- and C-terminals of the intein in order for it to splice out. The second focus was to insure that a His was located somewhere in the middle of the intein (these have been highlighted in light blue). The final amino acid sequence to find was a His-Asn dipeptide found near a nucleophilc amino acid on the C-terminus.

The most probable splice sites have had their text size enlarged and bolded.

Edited 31 May, 2019 12:42

Posted in: Cluster DE Annotation Tips → Terminase + homing endonuclease intein

Link to this post \| posted 22 May, 2018 15:23
Ths44	Supported by HHPred investigation, the function for gp1 is adenylate kinase In the past this has been identified as a terminase, small subunit. At this time do not call this gene a terminase, small subunit. Additional edits from Welkin: This is a Graham Hatfull initiated post— not a random comment. ths44 is Ty Stoner, an excellent annotator here at Pitt— Thanks. Edited 22 May, 2018 20:05

Posted in: Cluster B Annotation Tips → B1 Gene 1

Recent Activity

All posts created by Ths44