SEA-PHAGES | Cluster K5 terminases

Link to this post \| posted 17 Jul, 2018 15:50
mdgainey	I have been annotating a cluster K5 genome (Rando14). According to the functional assignments document, if we can only find 1 terminase, then we should simply label it terminase. However, a lot of the K's have called gene5 pham 40672(shown in attached powerpoint) a small terminase, but the HHPRED does not support this (attached). I took a look at old forum posts from some faculty working on calling cluster J terminases and found a post from Jacqueline Washington that suggested looking at this paper where they found a small terminase subunit that did not have an HTH binding motif, but did have a coiled coil motif " Archives of Virology 2012 Nov. 157 (11) in which they explained that most terminase small subunits have HTH DNA binding motifs but some don't. They used the program COILS2 (http://www.ch.embnet.org/software/COILS_form.html) to identify the small terminase as it reveals the presence of a coiled coil motif (CCM) which is need for protein dimerization." I ran gene 5 through this and it does indeed seem to have a nice CCM motif (output attached). Is this enough evidence to call this a small terminase subunit, or am I just following the leader here? Thank you, Maria 458Kb

Link to this post | posted 17 Jul, 2018 15:50

I have been annotating a cluster K5 genome (Rando14). According to the functional assignments document, if we can only find 1 terminase, then we should simply label it terminase. However, a lot of the K's have called gene5 pham 40672(shown in attached powerpoint) a small terminase, but the HHPRED does not support this (attached). I took a look at old forum posts from some faculty working on calling cluster J terminases and found a post from Jacqueline Washington that suggested looking at this paper where they found a small terminase subunit that did not have an HTH binding motif, but did have a coiled coil motif " Archives of Virology 2012 Nov. 157 (11) in which they explained that most terminase small subunits have HTH DNA binding motifs but some don't. They used the program COILS2 (http://www.ch.embnet.org/software/COILS_form.html) to identify the small terminase as it reveals the presence of a coiled coil motif (CCM) which is need for protein dimerization." I ran gene 5 through this and it does indeed seem to have a nice CCM motif (output attached). Is this enough evidence to call this a small terminase subunit, or am I just following the leader here?
Thank you,
Maria

Link to this post \| posted 17 Jul, 2018 16:03
welkin	Hi Maria, I think you can use terminase small subunit here. Thanks!

Link to this post \| posted 17 Jul, 2018 16:32
mdgainey	Thanks Welkin, Maria

Recent Activity

Cluster K5 terminases