Link to this post | posted 19 Jan, 2024 19:49
JPeterGo	Thanks Debbie! Johann Peter Gogarten

Link to this post | posted 19 Jan, 2024 19:48
JPeterGo	Thanks Debbie! Johann Peter Gogarten

Link to this post | posted 19 Jan, 2024 15:02

JPeterGo

We are annotating phage Gack this semester. In blastn a nearly identical phage in Frankin22: >Microbacterium phage Frankin22 complete sequence, 40567 bp including 10-base 3' overhang (ACTCCCGGCA), Cluster EB Length = 40567 Score = 1.105e+04 bits (5573), Expect = 0.0 Identities = 6164/6358 (96%), Gaps = 6/6358 (0%) Strand = Plus / Plus My problem is that when I try to look up Frankin22 in phagesDB, I get the message "Error: Page Not Found". The problem seems to be that the searchable databank lists the sequence as Frankin22, and in phagesDB the phage is known a Franklin22. Johann Peter Gogarten

Link to this post | posted 01 Mar, 2021 22:23

JPeterGo

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 https://phagesdb.org/phams/45139/ and https://phagesdb.org/phams/4397/ 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 337Kb

Link to this post | posted 24 Feb, 2021 22:37

JPeterGo

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. Peter Johann Peter Gogarten

Link to this post | posted 26 Jan, 2021 00:49

JPeterGo

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 267Kb