SEA-PHAGES | Frame shift in cluster ED

Link to this post \| posted 07 Mar, 2018 04:17
kklyczek	The tape measure protein (Fork_Draft_54) and the tail assembly chaperone proteins (Fork_Draft_52 and 53) were identified based on blastp homology with AQ phages (Molivia_38-40). There is a slippery sequence near the end of Fork_Draft_52, TTTTTTC (as described for phage SPP1 in the Wu 2014 paper, https://www.ncbi.nlm.nih.gov/pubmed/15469818). The attached screen shot of the 6-frame translation shows this sequence; a -1 shift at 25657 would shift to the reading frame of Fork_Draft_53. This sequence is conserved in all of the cluster ED genomes. The AQ phage genomes have a similar overall architecture to the ED phage genomes, with long direct repeats and a similar organization of structural genes. They may be helpful in identifying other ED gene functions via synteny. 231Kb

Link to this post | posted 07 Mar, 2018 04:17

The tape measure protein (Fork_Draft_54) and the tail assembly chaperone proteins (Fork_Draft_52 and 53) were identified based on blastp homology with AQ phages (Molivia_38-40). There is a slippery sequence near the end of Fork_Draft_52, TTTTTTC (as described for phage SPP1 in the Wu 2014 paper, https://www.ncbi.nlm.nih.gov/pubmed/15469818). The attached screen shot of the 6-frame translation shows this sequence; a -1 shift at 25657 would shift to the reading frame of Fork_Draft_53. This sequence is conserved in all of the cluster ED genomes.

The AQ phage genomes have a similar overall architecture to the ED phage genomes, with long direct repeats and a similar organization of structural genes. They may be helpful in identifying other ED gene functions via synteny.

Link to this post \| posted 03 Jun, 2023 15:48
robert.logan	I confirm that this also occurs in the draft genome ASegato (ED2) between the PECAAN called genes #47 and #48. Both of these genes encode for tail assembly chaperone proteins. The genomic loci are CDS join (25411. .26006;26006. .26558 ) Robert Logan, Ph.D. Assistant Professor of Biology Eastern Nazarene College, Quincy, MA 02170 Edited 05 Jun, 2023 00:51

Link to this post \| posted 03 Jun, 2023 15:51
IowaState	We believe we confirmed that StevieWelch draft also has the predicted slippery sequence at: CDS join (25746..;26342;26342..26893) a -1 shift We believed we confirmed that RunningBrook draft also has the predicted slippery sequence at: CDS join (26354..26950;26950..27501) a -1 shift

Link to this post \| posted 29 Jun, 2023 18:48
robert.logan	I confirm that this also occurs in the draft genome DejaVu (ED1) between the PECAAN called genes #51 and #52. Both of these genes encode for a tail assembly chaperone protein. The genomic loci are CDS join (24677. .25339;25339. .2655 Robert Logan, Ph.D. Assistant Professor of Biology Eastern Nazarene College, Quincy, MA 02170

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Frame shift in cluster ED