SEA-PHAGES | All posts created by mthomas

Link to this post \| posted 04 Apr, 2025 21:18
mthomas	stpage mthomas There are several putative SAM-degrading enzymes in HollowPurple (e.g., SAM lyase –gp#120 w/ stop codon at 62,755 – evidence is based on HHpred hits; see the entry in PECAAN). If real, these are probably a counter-defense against the bacterial restriction-modification system. (see https://doi.org/10.7554/eLife.61818). There are no SAM-degrading enzymes in other phages in seaphages.org. Thoughts on including this? Can you post the HHPRED coverage and percent identity? What do you get when you do an amino acid sequence alignment against the SAM lyase from T3? The hit is to pdb 6ZM9, coverage=86% and probability=97.6%. There is no alignment similarity vs. T3 SAM lyase. Edited 04 Apr, 2025 21:18

Link to this post | posted 04 Apr, 2025 21:18

stpage
mthomas
There are several putative SAM-degrading enzymes in HollowPurple (e.g., SAM lyase –gp#120 w/ stop codon at 62,755 – evidence is based on HHpred hits; see the entry in PECAAN). If real, these are probably a counter-defense against the bacterial restriction-modification system. (see https://doi.org/10.7554/eLife.61818). There are no SAM-degrading enzymes in other phages in seaphages.org. Thoughts on including this?

Can you post the HHPRED coverage and percent identity? What do you get when you do an amino acid sequence alignment against the SAM lyase from T3?

The hit is to pdb 6ZM9, coverage=86% and probability=97.6%. There is no alignment similarity vs. T3 SAM lyase.

Edited 04 Apr, 2025 21:18

Posted in: Cluster ED Annotation Tips → SAM lyase ?

Link to this post \| posted 03 Apr, 2025 19:34
mthomas	There are several putative SAM-degrading enzymes in HollowPurple (e.g., SAM lyase –gp#120 w/ stop codon at 62,755 – evidence is based on HHpred hits; see the entry in PECAAN). If real, these are probably a counter-defense against the bacterial restriction-modification system. (see https://doi.org/10.7554/eLife.61818). There are no SAM-degrading enzymes in other phages in seaphages.org. Thoughts on including this?

Link to this post | posted 03 Apr, 2025 19:34

mthomas

There are several putative SAM-degrading enzymes in HollowPurple (e.g., SAM lyase –gp#120 w/ stop codon at 62,755 – evidence is based on HHpred hits; see the entry in PECAAN). If real, these are probably a counter-defense against the bacterial restriction-modification system. (see https://doi.org/10.7554/eLife.61818). There are no SAM-degrading enzymes in other phages in seaphages.org. Thoughts on including this?

Posted in: Cluster ED Annotation Tips → SAM lyase ?

Link to this post \| posted 14 Mar, 2024 21:28
mthomas	Now that DeepTMHMM has replaced other tools membrane to call membrane proteins, I noticed that a call from last year (KillerTomato gene 19) is now predicted to have 2 membrane domains (rather than just one). This gives us evidence consistent with calling the gene a holin (a call made for other genes in Pham 1053), which is supported by HHPred. Could we update the NCBI report for the phage?

Posted in: Functional Annotation → Membrane protein

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