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DNA Primase

| posted 02 Apr, 2018 15:35
Like in Cluster A phages, the DNA primase of many cluster BD phages is split into two overlapping reading frames. The upstream portion of the gene is frequently missed by Glimmer and Genemark. We are not sure what happens within the cell during the infection to generate the correct full length primase, so for now, we add both parts to the annotations with a large overlap.
| posted 23 May, 2019 01:38
What about BE phages? They have a similar pattern. Several BE have a gene upstream of primase that overlaps with only fair coding potential (e.g., Karimac) that Glimmer and GM don't like. Can we call that DNA primase, too?
| posted 23 May, 2019 22:05
The CP is almost nonexistent, and it is less than 2/3 the length of the BE ones, though. Blasting the first primase of a BD (Alvy) vs the putative first primase of the BE is 30%coverage 35% aa alignment, which is intriguing not very convincing…

THe BLAST alignment for that ORF is about the same with Karimac, your BD phage, too…
Edited 23 May, 2019 22:11
| posted 09 Dec, 2019 19:35
it does not appear that the large overlap is found in the BD2 cluster. Large overlap is found in most other subclusters.
Edited 10 Dec, 2019 16:13
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