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Viknesh Sivanathan posted in did you know you can do restriction digests in the microwave?
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nic.vega posted in did you know you can do restriction digests in the microwave?
Viknesh Sivanathan posted in did you know you can do restriction digests in the microwave?
nic.vega posted in did you know you can do restriction digests in the microwave?
Excise or DNA binding protein?
| Link to this post | posted 21 Jun, 2018 16:29 | |
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GP32 PHAM in Catfish (Draft) is also found in Vendetta (GP32) the closest related phage to Catfish. Vendetta lists function as DNA binding protein. There is a good HHPred score to an excisionase. It seems that both could apply based on BLAST Hits. Excise is an approved function, so which to use, excise or DNA binding protein? Or is hypothetical protein best. Thanks |
| Link to this post | posted 22 Jun, 2018 03:11 | |
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I spent some time looking at the Catfish genes later in the genome. One of the first questions I ask when considering excise is whether there is evidence for an integrase. It is also great if there is lab evidence of lysogeny. Catfish has a strong hit to integrase in gp38 followed by a repressor at gp 40 followed by a strong hit to excise at gp41. Gp41 is likely to be the escise based on its position relative to the repressor and integrase. Although not impossible, it is pretty unlikely for there to be a second excise. Given this combination of evidence, I think the call for gp32 as a helix turn helix DNA binding protein makes more sense in the total context of the genome. |