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All posts created by JPeterGo

| posted 01 Mar, 2021 22:23
Gene 1 has a stop at 129655 in Zooman and gene 2 has a stop at 130782 in Zooman.

For gene the first two other phages have e-values better the e-40:
Cross 217 rIIa-like protein 636 164 5e-40 BE1
Annadreamy 153 rIIA-like protein 639 152 2e-36 BK1
Limpid 160 rIIA-like protein 639 152 2e-36 BK1
SparkleGoddess 165 rIIA-like protein 641 152 3e-36 BK1
At NCBI a match to an
rIIA-like protein from Streptomyces phage Mildred21 has an e-value of 4.40328e-43

For the second gene:
SparkleGoddess 166 rIIB-like protein 335 146 5e-35 BK1 4397
Trina 157 rIIB-like protein 304 142 1e-33 CE 4397

And at NCBI rIIB-like protein [Streptomyces phage Mildred21]e-value of 1.0028e-32

The phams are at and

What surprises me is that many phages in phagesDB use the (correct) annotation as rIIA-like protein or rIIB-like protein, but that this annotation is not in the approved function list.
Johann Peter Gogarten
Posted in: Functional AnnotationriiA and riiB like proteins
| posted 24 Feb, 2021 22:37
In annotating Zooman (cluster GD) we have two neighboring genes that have good matches to rIIA-like protein and rIIB like protein. The homologs belong to phams 45139 and 4397. While it is unclear what these proteins do in detail (they seem to regulate the switch between different lysis pathways), they have been studied for decades, thus an annotation as riiA and riiB like proteins seems appropriate; however, I do not see them in the approved function list.
Johann Peter Gogarten
Posted in: Functional AnnotationriiA and riiB like proteins
| posted 26 Jan, 2021 00:49
The manual says to use the host trained Genemark version. The phage we are working with has a pretty large genome (192kB), and the coding potential from genemarkS looks crisper than the host trained one. (And for some of the genes host trained Genemark shows no coding potential, whereas genemarkS gives rather convincing curves.
Does anything speak against using the phage trained genemarkS output in PECAAN?
Johann Peter Gogarten
Edited 26 Jan, 2021 00:49
Posted in: PECAANGeneMarkS ?