SEA-PHAGES | cluster J pham 1260 (RecA/RepA/DNAB)

Link to this post \| posted 20 Jul, 2017 14:30
kklyczek	Pham 1260 in cluster J phages has been annotated as RecA, RepA, and DNA B helicase. All three versions appear in the maps in the cluster J paper (Pope et al. 2013, doi:10.1371/journal.pone.0069273) where the pham is 3492: Baka_149, Courthouse_142, Optimus_140. There are HHPred hits to all of these at >90% with 50–60% coverage, as well as to many other recombination/repair proteins. It looks like the hit is to an ATPase domain that all of these share? If further investigation is needed I’ll be happy to try that, but wanted to check with those of you with more cluster J experience first. HHPred results for Klein_151 are attached. Note that some J phages have a different pham (3133) at this location which has consistently (I think) been called DNA B helicase (e.g. LittleE_149). Edited 20 Jul, 2017 14:30 1.01Mb

Link to this post | posted 20 Jul, 2017 14:30

Pham 1260 in cluster J phages has been annotated as RecA, RepA, and DNA B helicase. All three versions appear in the maps in the cluster J paper (Pope et al. 2013, doi:10.1371/journal.pone.0069273) where the pham is 3492: Baka_149, Courthouse_142, Optimus_140. There are HHPred hits to all of these at >90% with 50–60% coverage, as well as to many other recombination/repair proteins. It looks like the hit is to an ATPase domain that all of these share? If further investigation is needed I’ll be happy to try that, but wanted to check with those of you with more cluster J experience first. HHPred results for Klein_151 are attached.
Note that some J phages have a different pham (3133) at this location which has consistently (I think) been called DNA B helicase (e.g. LittleE_149).

Edited 20 Jul, 2017 14:30

Link to this post \| posted 31 Jul, 2017 15:07
welkin	Hi Karen, I think we annotated the Cluster J phages in the paper before we started using HHPred regularly. It sounds like from your comments that you are suggesting that all of pham 1260 should be reassigned to ATPase domain, is that correct? The additional data of the other pham with the DnaB helicase assignment is interesting. Is there another DnaB helicase in any of the genomes? If that annotation is better supported, then perhaps 1260 should all be DnaB helicase, nad 1260 is a sequence variant that we haven't seen before.

Link to this post | posted 31 Jul, 2017 15:07

welkin

Hi Karen,
I think we annotated the Cluster J phages in the paper before we started using HHPred regularly. It sounds like from your comments that you are suggesting that all of pham 1260 should be reassigned to ATPase domain, is that correct?
The additional data of the other pham with the DnaB helicase assignment is interesting. Is there another DnaB helicase in any of the genomes? If that annotation is better supported, then perhaps 1260 should all be DnaB helicase, nad 1260 is a sequence variant that we haven't seen before.

Link to this post \| posted 03 Aug, 2017 14:48
dbolliva	Karen, The 3133 Pham is equally suspect. The HHPred resulta are for both RepA and DnaB helicases and the CDD results include RecA and AAA domains for ATP binding. Since I had so many DNA helicase hits of both types I currently have it annotated as a DNA helicase without the type specified. I am looking at Squint right now. I am doing this in PECAAN so you should be able to go look at the results if you like. Best, Dave

Link to this post | posted 03 Aug, 2017 14:48

dbolliva

Karen,
The 3133 Pham is equally suspect. The HHPred resulta are for both RepA and DnaB helicases and the CDD results include RecA and AAA domains for ATP binding. Since I had so many DNA helicase hits of both types I currently have it annotated as a DNA helicase without the type specified. I am looking at Squint right now. I am doing this in PECAAN so you should be able to go look at the results if you like.

Best,

Dave

Link to this post \| posted 03 Aug, 2017 15:56
kklyczek	Hi David, I agree - here are the HHPred results for LittleE_149 (pham 3133), using PDB, Pfam, and TIGRfam: https://toolkit.tuebingen.mpg.de/#/jobs/9976351 . The hits are to that central ATPase domain, and most of the descriptions are recombination/repair enzymes. Interestingly, the only sequence similarity between LittleE_149 and Klein_151 (pham 1260) is the N-terminal domain, not that central region (BLAST alignment attached). And to address Welkin's question - there is not another DNA helicase called in the genomes with pham 1260 (at least not that I have seen). So maybe DNA helicase for all of these? Karen Edited 03 Aug, 2017 17:15 34Kb

Link to this post | posted 03 Aug, 2017 15:56

kklyczek

Hi David,

I agree - here are the HHPred results for LittleE_149 (pham 3133), using PDB, Pfam, and TIGRfam: https://toolkit.tuebingen.mpg.de/#/jobs/9976351 . The hits are to that central ATPase domain, and most of the descriptions are recombination/repair enzymes.

Interestingly, the only sequence similarity between LittleE_149 and Klein_151 (pham 1260) is the N-terminal domain, not that central region (BLAST alignment attached).

And to address Welkin's question - there is not another DNA helicase called in the genomes with pham 1260 (at least not that I have seen).

So maybe DNA helicase for all of these?

Karen

Edited 03 Aug, 2017 17:15

Recent Activity

cluster J pham 1260 (RecA/RepA/DNAB)