SEA-PHAGES | riiA and riiB like proteins

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 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.
Peter

Johann Peter Gogarten

Link to this post \| posted 26 Feb, 2021 13:12
debbie	Hi! I am not sure the evidence is convincing. I would like to investigate a bit.

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 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

Link to this post \| posted 02 Mar, 2021 18:41
debbie	The rIIA-like protein and rIIB-like protein assignments are now on the SEA-PHAGES Functional Assignments List. The significant hits are seen when using the UniProt-SwissProt-viral database at HHPred. debbie Also, this links to an excellent read on the proteins. Edited 02 Mar, 2021 18:43

Link to this post \| posted 02 Mar, 2021 19:46
neitzelj	Another paper on r genes: https://www.genetics.org/content/genetics/148/4/1539.full.pdf

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riiA and riiB like proteins