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CS2 Holin Gene
| Link to this post | posted 24 Apr, 2024 15:42 | |
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Hello! WE are in the process of calling functions for the CS2 phage, BigShaq. My students have found a gene that we are struggling with whether to call holin or not- gene 32. The genes in this pham are often called holins in other phages, but not particularly often in CS2s and I am wondering why? There are 4 transmembrane domains found by DeepTMHMM- argues in favor of the holin call It is just upstream of the two lysin A genes, also in favor. We have hits in HHPRED to holin in two chunks that are back to back (both are hitting different parts of PF16081.9), each has great probability, but low E values, I think because there are two hits separated the e value is low. Argues in favor of the holin call- kind of. I don't see any other transmembrane proteins in the region- also argues in favor. So, I would argue that we should call it a holin, but I am wondering if I am missing something that is preventing other phages from calling this holin (other CS2s are also not calling it a membrane protein) Any guidance? |
| Link to this post | posted 24 Apr, 2024 17:02 | |
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Hi Dane, See the attached picture for why I would call a lot of theses proteins membrane proteins and not holins….. yet. Too many to choose from? debbie |
392Kb| Link to this post | posted 24 Apr, 2024 18:47 | |
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Ah- There it is- I was not looking AFTER the lysins for transmembrane domains I was thinking they'd be upstream for some reason- makes total sense now. Those will all end up membrane proteins. Thanks for clarification Debbie! |
| Link to this post | posted 24 Apr, 2024 19:04 | |
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You are welcome! debbie |