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Holin

| posted 28 Jun, 2018 16:59
Currently there is no holin identified in B1 phages? There are a few calls present (Xavier14) but in the homolog DonSanchon 14 the best hit was an HHpred to holin at 75% probability and 33% coverage. Thoughts on this?
| posted 28 Jun, 2018 18:00
After discussing with Welkin, there are no currently approved holin calls in the B1 phages. The gene in question is too far from the lysins combined with the relatively low hit. The gene from DonSanchon does have several predicted transmembrane domains so can be called as a membrane protein
| posted 26 Feb, 2021 18:57
There are 6 B1 phages in phagesdb calling the holin.
| posted 26 Feb, 2021 18:57
There are 6 B1 phages in phagesdb calling the holin.
| posted 26 Feb, 2021 19:51
Hi Shallee,
What genes are you referring to?
thanks,
debbie
| posted 27 Feb, 2021 19:03
in the database there are 11 phage genes with subcluster B1 they all appear in current pham 48591:

| phageid      | subcluster | gene name | notes | phamid |

| BatteryCK    | B1         | 14        | holin |  48591 |
| Beaglebox    | B1         | 14        | holin |  48591 |
| DoesntMatter | B1         | 15        | holin |  48591 |
| LeeLot       | B1         | 15        | holin |  48591 |
| Magic8       | B1         | 15        | holin |  48591 |
| Megatron     | B1         | 15        | holin |  48591 |
| Mosaic       | B1         | 14        | holin |  48591 |
| OliverWalter | B1         | 15        | holin |  48591 |
| ProfessorX   | B1         | 15        | holin |  48591 |
| Trypo        | B1         | 15        | holin |  48591 |
| Xavier       | B1         | 14        | holin |  48591 |
for the totally geeky here is the mysql query I used:
> select gene.phageid, phage.subcluster, gene.name as "gene name",
gene.notes, gene.phamid from gene join phage on gene.phageid=phage.phageid
where phage.subcluster="B1"
and gene.notes like "%holin%";
Edited 27 Feb, 2021 19:04
| posted 01 Mar, 2021 00:52
The pfam hits to holin are not great but also not shabby. The typical order of genes is not present in the B1s, so that is also not helpful. However, it is interesting that this gene has 4 transmembrane domains, and the 2 subsequent genes each have 2 transmembrane domains. So I would be inclined to call all three "membrane proteins".
Edited 01 Mar, 2021 00:52
 
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