SEA-PHAGES | Tail Terminator in Cluster EE

Link to this post \| posted 01 May, 2020 13:58
WCUPhage	Hi everyone, I am finishing up a new Cluster EE phage (PoRanda), and I had a question about a functional call. I am looking at gene 7 in PoRanda, and its aa sequence is below. In comparing this gene to other EE's in phamerator, as well as blast searches etc., the majority of the data says I should call this as a tail terminator. However, in the functional assignments sheet it says that to be called a tail terminator it "must have an HHPRED alignment to one of the following: SPP1 17 (5A21 chain G in the macromolecular complex) or Lambda U (3FZ2_chains A through F)". In the HHPred hits for this gene, I do see 3FZ2, with a probability just under 90%. However, the E-values for this hit (and all HHPred hits) are not good. The E-value for the 3FZ2 hit is 8.4. 5A21 is also present, with a coverage of 86.6% and an E-value of 13. Looking at the pham (Pham # 19507), the majority of genomes have this annotated as a tail terminator, while others call it a minor tail protein. I'm looking for guidance on how to call this, given then HHPred results described above. Thank you! MSTLGDLRRELADDVAGSPVELTTYDHVPARVQLPAAFVMAGAPYVEADQTFGSSIVRFGVVLLTQPSMNADETDQLDERIESVQRRLLSAGWLVERIERPEIQDLNGAEVLATALSVAAGGVTFP

Link to this post | posted 01 May, 2020 13:58

Hi everyone,

I am finishing up a new Cluster EE phage (PoRanda), and I had a question about a functional call. I am looking at gene 7 in PoRanda, and its aa sequence is below. In comparing this gene to other EE's in phamerator, as well as blast searches etc., the majority of the data says I should call this as a tail terminator. However, in the functional assignments sheet it says that to be called a tail terminator it "must have an HHPRED alignment to one of the following: SPP1 17 (5A21 chain G in the macromolecular complex) or Lambda U (3FZ2_chains A through F)". In the HHPred hits for this gene, I do see 3FZ2, with a probability just under 90%. However, the E-values for this hit (and all HHPred hits) are not good. The E-value for the 3FZ2 hit is 8.4. 5A21 is also present, with a coverage of 86.6% and an E-value of 13.

Looking at the pham (Pham # 19507), the majority of genomes have this annotated as a tail terminator, while others call it a minor tail protein. I'm looking for guidance on how to call this, given then HHPred results described above. Thank you!
MSTLGDLRRELADDVAGSPVELTTYDHVPARVQLPAAFVMAGAPYVEADQTFGSSIVRFGVVLLTQPSMNADETDQLDERIESVQRRLLSAGWLVERIERPEIQDLNGAEVLATALSVAAGGVTFP

Link to this post \| posted 01 May, 2020 20:00
debbie	Hi Jamie, I would continue to call this a tail terminator for 2 reasons. One, the minor tail protein of lambda that it hits is a tail terminator along with the SPP1 hits. Secondly, it is in the right place for it. I agree, we fall under the threshold of 90% probability, and I usually don't consider anything under 90%, but in this case I think it is a good prediction.

Link to this post \| posted 01 May, 2020 20:52
WCUPhage	Thank you, Debbie! I'll call it a tail terminator.

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Tail Terminator in Cluster EE