Link to this post | posted 08 Aug, 2017 20:02

kbutela

Pham 5142 (as of 8/8/17) corresponds to several members in Cluster B1, some of which are annotated as PLA2, PLA2-like domain, and PLA2-like domain protein, with PLA2 standing for phospholipase A2. According to this paper, some bacteria contain phospholipase A2, and a quick Blast search shows phospholipase A2 in Mycobacterium tuberculosis in two forms, one 512 aa long and the other designated as "membrane associated" at 111 aa long. Most members of Pham 5142 are relatively small, in the range of 40-50 aa. This gene (Virapocalypse gp73) does not match to any "PLA2" designated proteins in HHPred (attached) or in NCBI Blast other than mycobacteriophages. No conserved domains were found. I pulled the M. tuberculosis phospholipase A protein sequence (512 aa) and the one designated as "Membrane associated" as well as a sequence pulled from the crystal structure of phospholipase A from Streptomyces (1FAZ) and ran them through MUSCLE, Clustal Omega, and T-Coffee; all three give pretty lousy alignments with gp73 of Virapocalypse. I am not convinced this gene contains a PLA2 domain, but I'm not sure where the call of PLA2-like domain originated since the functional source for Virapocalpyse is ShiVal gp71 (older, annotated in 2011). Thoughts? 113Kb

Link to this post | posted 09 Aug, 2017 16:26

dbolliva

Kristen, I reviewed several B1's and found really strong HHpred results for pham 5142 being PLA2. Granted the e values are not awesome, but the hit comes out of the CDD. All three of the B1s I reviewed had similar HHpred results. Not sure why virpocalpse is giving different results, but there is support for the other ones called I think. Note that the PLA2 hit is actually not from M smeg but a plant version. Best, Dave 21Kb

Link to this post | posted 21 Mar, 2018 15:46
kaylafast	Is there any update on what the most appropriate function call for Pham 5142 is (something along the lines of phospholipase A2 domain protein, PLA2)? My B1 phage (Kwksand96 gp74) shows HHPred results very similar to Kristen's with no phospholipase hits, but many in phagesDB and NCBI Blast. I don't see a close function match in the official function list.

Link to this post | posted 21 Mar, 2018 16:19
dbolliva	It is not on the official list so I would not call it. Though there were some hits to PLA2, I think the evalues ended up not being good enough. Ultimately I think the people at Pitt will clean this up and make them all NKF.

Link to this post | posted 21 Mar, 2018 16:22
kaylafast	Thanks!

Link to this post | posted 19 Feb, 2021 23:38

nietof

Hey Retaking this thread. We are annotating Sarma624. Gene 35 blasted in phagesdb gets two hits with a PLA2-like protein domain function, Bigphil_35 and Mozy_42. It is a phospholipase A2 It doesn't appear in the list of accepted functions yet. Most of the other F1 phages have NKF for the same gene. The HHPred hits are all human actin binding protein or other not close to a phospholipase. I would be inclined to think BigPhil and Mozy's annotations are incorrect and thus to call it NKF for Sarma.

Link to this post | posted 19 Feb, 2021 23:39

nietof

Hey Retaking this thread. We are annotating Sarma624. Gene 35 blasted in phagesdb gets two hits with a PLA2-like protein domain function, Bigphil_35 and Mozy_42. It is a phospholipase A2 It doesn't appear in the list of accepted functions yet. Most of the other F1 phages have NKF for the same gene. The HHPred hits are all human actin binding protein or other not close to a phospholipase. I would be inclined to think BigPhil and Mozy's annotations are incorrect and thus to call it NKF for Sarma.

Link to this post | posted 19 Feb, 2021 23:49
debbie	I do not think that this protein (gene35 of Sarma624) has a reportable function. HHPred has no hits to an applicable function.

Link to this post | posted 20 Feb, 2021 00:02
nietof	debbie I do not think that this protein (gene35 of Sarma624) has a reportable function. HHPred has no hits to an applicable function. Debbie thanks for confirming. regards F

Link to this post | posted 20 Feb, 2021 00:03
nietof	debbie I do not think that this protein (gene35 of Sarma624) has a reportable function. HHPred has no hits to an applicable function. Debbie thanks for confirming. regards F