SEA-PHAGES | Gene with homology to T7 Ocr gene

Link to this post \| posted 17 Jul, 2017 15:52
scaruso	I have a gene for which the top three HHPred hits are all >99% prob, Eval 10^-21, ident 22% to the phage T7 Ocr gene (gene 0.3), which protects DNA from attack by the host's type I restriction enzymes. So, I am wondering what to call this. In reverse order of specificity: Ocr Ocr-like protein DNA bending protein DNA binding protein Thoughts and suggestions? Steve Edited 17 Jul, 2017 15:53

Link to this post \| posted 19 Jul, 2017 15:06
welkin	hi Steve— send data! DNA Master file, screenshots? I also like to get a sense of exactly what the putative functional match is before I use something specific: here is a nice description on Ocr and its characteristics that are essential for functionality. https://academic.oup.com/nar/article/40/16/8129/1031862/Exploring-the-DNA-mimicry-of-the-Ocr-protein-of Edited 19 Jul, 2017 15:14

Link to this post \| posted 19 Jul, 2017 23:56
scaruso	Welkin, Great, thanks for taking a look. It looks interesting. MTKKLELAQYDYIEVLEDEIDVLERFNEYNGSTCVCDAITEIADAAVSIYPADLWKNAYEMKEYIEAAMSSGLCETPSGQQPDLDKI SAAGYYEYYSQLLYNNESEMYYNYIANIVNKWIETLNYEQLEKLDIDELDACIEHEKGDIDSNSYMEELEDIAKRIIAGFKVKVNKN DVWENHGDVDALDQGGIFIRPDEEQRHCYYVVKVDNLEYVTKEDKIRITDMYVDISDDWFDWAGIEAYSGTEESDDDIEKVLAVIDY HGAENFNPDIEDFEDKADAIEYLANMGIAIEEV I think you can still access HHPred links with the new system. Here are the hits: https://toolkit.tuebingen.mpg.de/#/jobs/Anthony_gp275 It doesn't extend throughout the entire length of the protein, but it is from a very different phage and is rather compelling. So, I am on the fence. As you can see. So, I suppose the way to look for a connection here is to see if the conserved residues being picked up by HHPred are the important G, A, L, and R? Steve Edited 20 Jul, 2017 13:27

Link to this post | posted 19 Jul, 2017 23:56

scaruso

Welkin,

Great, thanks for taking a look. It looks interesting.

MTKKLELAQYDYIEVLEDEIDVLERFNEYNGSTCVCDAITEIADAAVSIYPADLWKNAYEMKEYIEAAMSSGLCETPSGQQPDLDKI
SAAGYYEYYSQLLYNNESEMYYNYIANIVNKWIETLNYEQLEKLDIDELDACIEHEKGDIDSNSYMEELEDIAKRIIAGFKVKVNKN
DVWENHGDVDALDQGGIFIRPDEEQRHCYYVVKVDNLEYVTKEDKIRITDMYVDISDDWFDWAGIEAYSGTEESDDDIEKVLAVIDY
HGAENFNPDIEDFEDKADAIEYLANMGIAIEEV

I think you can still access HHPred links with the new system. Here are the hits:

https://toolkit.tuebingen.mpg.de/#/jobs/Anthony_gp275

It doesn't extend throughout the entire length of the protein, but it is from a very different phage and is rather compelling. So, I am on the fence. As you can see.

So, I suppose the way to look for a connection here is to see if the conserved residues being picked up by HHPred are the important G, A, L, and R?

Steve

Edited 20 Jul, 2017 13:27

Link to this post \| posted 21 Jul, 2017 15:30
welkin	Thanks for posting the data! Based on your HHPred results and the db entries, ocr is 119 residues long, your protein is more than twice that at 295. you also have an equally good alignment to part of a restriction enzyme in the same area at the ocr alignment. So my questions is, what do the restriction enzyme and ocr have in common? And yes, key residues in the right spot always help, but I don't think we are there yet.

Link to this post | posted 21 Jul, 2017 15:30

welkin

Thanks for posting the data!

Based on your HHPred results and the db entries, ocr is 119 residues long, your protein is more than twice that at 295. you also have an equally good alignment to part of a restriction enzyme in the same area at the ocr alignment.
So my questions is, what do the restriction enzyme and ocr have in common?

And yes, key residues in the right spot always help, but I don't think we are there yet.

Link to this post \| posted 21 Jul, 2017 15:44
scaruso	So better NKF? A shame. This is an interesting looking hit. It's compelling, and makes sense. And in fact, restriction enzymes and Ocr do have something in common, of course, right? Binding (or mimicking) DNA. Thanks for your help! Steve Edited 21 Jul, 2017 16:00

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Gene with homology to T7 Ocr gene