SEA-PHAGES Logo

The official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program.

Welcome to the forums at seaphages.org. Please feel free to ask any questions related to the SEA-PHAGES program. Any logged-in user may post new topics and reply to existing topics. If you'd like to see a new forum created, please contact us using our form or email us at info@seaphages.org.

Recent Activity

smg366 posted in PhamNexus on SEA-VM

Debbie Jacobs-Sera posted in Assignment of gp28 as holin

nietof posted in Assignment of gp28 as holin

nietof posted in Assignment of gp28 as holin

Debbie Jacobs-Sera posted in Capsid maturation protease and MuF-like fusion protein

All posts created by debbie

| posted 23 Aug, 2018 14:38
debbie avatar
debbie
At this time (8-23-18 ), we felt it prudent to call the DNA binding proteins around the integrases "helix-turn-helix DNA binding proteins", even thought 2 of them are hitting Lambda's CI. (Genome used in this evaluation are Nandita and Ryan).
Edited 23 Aug, 2018 14:39
Posted in: Cluster FF Annotation Tips → Repressor vs HTH DNA binding proteins
| posted 23 Aug, 2018 14:35
debbie avatar
debbie
Cluster F genomes have 2 tyrosine integrases.
Posted in: Cluster FF Annotation Tips → 2 integrases
| posted 23 Aug, 2018 14:33
debbie avatar
debbie
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.
Posted in: Cluster FE Annotation Tips → hits to Pukovnik gp 37 (Excise)
| posted 23 Aug, 2018 14:29
debbie avatar
debbie
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.
Posted in: Cluster FE Annotation Tips → Genes between capsid and tape measure
| posted 23 Aug, 2018 14:26
debbie avatar
debbie
No tail assembly chaperones have been found….yet.
Posted in: Cluster FE Annotation Tips → No tail assembly chaperone
| posted 23 Aug, 2018 14:24
debbie avatar
debbie
The cpapsid is fused to the capsid maturation protease (gp7 in Corgi).
Posted in: Cluster FE Annotation Tips → capsid and protease fusion
| posted 22 Aug, 2018 16:01
debbie avatar
debbie
This cluster has 2 tyrosine integrases.
Posted in: Cluster AY Annotation Tips → Two integrases
| posted 22 Aug, 2018 16:00
debbie avatar
debbie
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
| posted 22 Aug, 2018 15:56
debbie avatar
debbie
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)".
Edited 23 Aug, 2018 16:41
Posted in: Cluster AY Annotation Tips → Large terminase in two pieces
| posted 22 Aug, 2018 15:52
debbie avatar
debbie
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).
Edited 22 Aug, 2018 15:54
Posted in: Cluster AY Annotation Tips → Repressor-like proteins