SEA-PHAGES | Singleton FuzzBuster Major Capsid

Link to this post \| posted 03 Jun, 2019 19:51
mdgainey	I am finishing up the new Micro singleton FuzzBuster that has some similarities to the cluster EI phages. I have not called a Major Capsid, but about half of other annotators call pham 10363 (FuzzBuster_31) a Major Capsid. I don't see any evidence for this and feel I should get nice HHPRED hits for a Major Capsid. I am not sure if this was called based on synteny alone, but perhaps I am missing something. I am leaning toward NKF.

Link to this post | posted 03 Jun, 2019 19:51

I am finishing up the new Micro singleton FuzzBuster that has some similarities to the cluster EI phages. I have not called a Major Capsid, but about half of other annotators call pham 10363 (FuzzBuster_31) a Major Capsid. I don't see any evidence for this and feel I should get nice HHPRED hits for a Major Capsid. I am not sure if this was called based on synteny alone, but perhaps I am missing something. I am leaning toward NKF.

Link to this post \| posted 22 Jan, 2021 20:44
Pollenz	The PHAM you reference is now 44108 and contains ~500 members. The majority of calls are to Major Capsid even though the HHPred hits have 25% probability, poor e scores and minimal coverage. I have tested many of these proteins and do not see any evidence of hitting to major capsid PDB entries. Even when the HHpred query is run with the pfam selected, there are no hits to phages. We are annotating a DE3 Gordonia phage (EdmundFerry) where gp19 is in this pham. It would appear that most calls are possibly based on synteny. BUT: in EdmundFerry there are also very few structural genes identified in the 5' region of the phage as in others we have annotated. So calling genes based on the location to other known structural proteins is iffy and is not supported by condition 2 of the synteny rules (2. adjacent to other structural genes of known, verifiable function ). For example we can find small and large terminases with excellent HHpred evidence (gp1 and 2), but genes 3-10 have NKF, portal (gp11, good HHpred hits), but that is about it. The Tape measure is clearly gp29 based on its size and location and there are two major tail proteins that hit low probability HHPred and pfam that are upstream of it. The call of a MuF-like minor capsid (gp13) has NO HHpred PDB HITS of any consequence, but DOES hit to low coverage pfam hits to MuF and minor capsid, BUT: gp15 (PHAM 46435) is called as a capsid maturation protease or RNA ligase with essentially NO hits to relevant proteins that have anything to do with proteases or capsids……so the sequence of clearly identifiable structural genes does not fit the standard. Any other thoughts here? RS Pollenz

Link to this post | posted 22 Jan, 2021 20:44

Pollenz

The PHAM you reference is now 44108 and contains ~500 members. The majority of calls are to Major Capsid even though the HHPred hits have 25% probability, poor e scores and minimal coverage. I have tested many of these proteins and do not see any evidence of hitting to major capsid PDB entries. Even when the HHpred query is run with the pfam selected, there are no hits to phages. We are annotating a DE3 Gordonia phage (EdmundFerry) where gp19 is in this pham. It would appear that most calls are possibly based on synteny.

BUT: in EdmundFerry there are also very few structural genes identified in the 5' region of the phage as in others we have annotated. So calling genes based on the location to other known structural proteins is iffy and is not supported by condition 2 of the synteny rules (2. adjacent to other structural genes of known, verifiable function ).

For example we can find small and large terminases with excellent HHpred evidence (gp1 and 2), but genes 3-10 have NKF, portal (gp11, good HHpred hits), but that is about it. The Tape measure is clearly gp29 based on its size and location and there are two major tail proteins that hit low probability HHPred and pfam that are upstream of it. The call of a MuF-like minor capsid (gp13) has NO HHpred PDB HITS of any consequence, but DOES hit to low coverage pfam hits to MuF and minor capsid, BUT: gp15 (PHAM 46435) is called as a capsid maturation protease or RNA ligase with essentially NO hits to relevant proteins that have anything to do with proteases or capsids……so the sequence of clearly identifiable structural genes does not fit the standard.

Any other thoughts here?

RS Pollenz

Link to this post \| posted 24 Jan, 2021 12:08
debbie	Maria, without evidence, Hypothetical Protein is the best choice. thanks, debbie

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Singleton FuzzBuster Major Capsid