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Recent Activity
All posts created by debbie
| Link to this post | posted 23 Aug, 2018 14:35 | |
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Cluster F genomes have 2 tyrosine integrases. |
Posted in: Cluster FF Annotation Tips → 2 integrases
| Link to this post | posted 23 Aug, 2018 14:33 | |
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Corgi gp19 and 20 HHPred hit the same domain of the crystal structure of Mycobacteriophage Pukovinik (gp37) excise. Call this a helix-turn-helix DNA binding protein because that is the domain that it hits. |
| Link to this post | posted 23 Aug, 2018 14:29 | |
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The 4 genes between capsid and tape measure (Corgi gp 8-11) include (in this order) head-to-tail adaptor, head-to-tail stopper, major tail, hypothetical protein. the hypothetical protein in these genomes hits HK97 gp10. Bob Duda of the Hendrix lab (who extensively has studied the structural genes of HK97) agrees the function of this gene, though structural, is unknown. |
| Link to this post | posted 23 Aug, 2018 14:26 | |
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No tail assembly chaperones have been found….yet. |
Posted in: Cluster FE Annotation Tips → No tail assembly chaperone
| Link to this post | posted 23 Aug, 2018 14:24 | |
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The cpapsid is fused to the capsid maturation protease (gp7 in Corgi). |
Posted in: Cluster FE Annotation Tips → capsid and protease fusion
| Link to this post | posted 22 Aug, 2018 16:01 | |
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This cluster has 2 tyrosine integrases. |
Posted in: Cluster AY Annotation Tips → Two integrases
| Link to this post | posted 22 Aug, 2018 16:00 | |
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When you come across the gene that hits IrrE in these genomes Example: Richie gp53(reverse), you will find that the domain that these genes share with IrrE is the 'helix-turn-helix DNA binding domain'. |
Posted in: Cluster AY Annotation Tips → No IrrE found here
| Link to this post | posted 22 Aug, 2018 15:56 | |
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The 6 genomes that we reviewed today *Auxilium, Hestia, Richie, SeaHorse, Faja, and Isolde all have a small terminase subunit. The large terminase subunit, except for Hestia, is split into 2 gene products: "terminase, large subunit (ATPase domain)" and "terminase, large subunit (nulcease domain)". |
Posted in: Cluster AY Annotation Tips → Large terminase in two pieces
| Link to this post | posted 22 Aug, 2018 15:52 | |
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While further investigation may yield a more specific designation, the gene products that match Lambda repressor C1 are called "helix-turn-helix DNA binding proteins". Example: Auxilium gp49(reverse) & gp50 (forward). |
Posted in: Cluster AY Annotation Tips → Repressor-like proteins
| Link to this post | posted 15 Aug, 2018 23:46 | |
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I just looked at the genome of KandZ (Cluster D1). There is a VIP2 gene in that area in other phage genomes (Troll4_gp7). For reasons I have not yet investigated, gene 6 and 7 (in most of these genomes) are in the same pham (4561). But only the second gene hits VIP2 in HHPred. In addition, that second gene can be in a different pham (5921)that is not a VIP2. This true in KandZ. (posted 8-15-1
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