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Debbie Jacobs-Sera posted in Calling start in FC phage Phrampa
Holin in D1
| Link to this post | posted 30 Jul, 2019 00:26 | |
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Has the holin in D1 been identified? There is a 4 transmembrane domain protein only called a holin in one cluster D1 phage (Nova gp37), all the rest call membrane domain or NKF. This is a conserved gene located between the lysin A and lysin B. How much evidence is needed to designate this as the holin? |
| Link to this post | posted 30 Jul, 2019 17:51 | |
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Jordan - I have a quick question (without looking) Are there any other membrane proteins in the region? If not, then it is acceptable to call this a holin. If there are other proteins that could be the holins adjacent to these 2 genes, then i would leave it at membrane protein. If it is more confusing that this and you want me to take a longer look, let me know. debbie |
| Link to this post | posted 30 Jul, 2019 18:09 | |
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Thanks, Debbie! There is an other membrane protein near by. I'll paste the sequences here if you want to take a look, but I'll go with membrane protein for now. >Helpful_37 (membrane protein) MKNLSNYWKAGIALVGTAGTAVATLAADENVRTAVGESGVTWLAVAGVALTTALTWLKRNEPTVTEAEEILRRAKERASSSSSA - TMHMM and SOSUI predict 2 TM domains and phobius predicts a signal peptide and one TM. Mixed results from TOPCONS, but def. signal peptide. >Helpful_39 (membrane protein) MFRPTDSRRLRSIFRKPRRIDHGRMYVSCMMGLWVWSLSLLVIGPVPNSTIDELTDYVQNILASCIFIGSFVCLCGIAIGTKYVLPKADIRLCYRFSLWGIPALAGSVGTYAWAIAHNTGSFWVSAYAASIGAFICLGIVWNGLDLLFEIARLNEEINYLKYGAGSEERLEDRDDERKC - 4 TM domains confirmed with TOPCONS, phobius, SOSUI and TMHMM |
| Link to this post | posted 30 Jul, 2019 18:50 | |
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Jordan, A good question, thanks for making it easy to check. I would call both Membrane proteins. debbie |