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Category:Team AOA Phagers
|Status||Page||User||Date/Time||GO Term (Aspect)||Reference||Evidence||Notes||Links|
|BPBPP:Q775C7||Kothaa, Team AOA Phagers||2017-04-05 13:52:46 CDT||GO:0019012 virion (C)||PMID:24347545||IDA|
Figure 1 shows the results of mass spectrometry from the major band of a gel that was derived from whole phage particles. From the thick black line under part B on the top of the mass spectrometry, it is evident that Bbp16 is the second most abundant protein. Mass spectrometry confirmed that the sequence obtained from the second most abundant band corresponded to capsid protein. This is a virion component because whole phage components were run as a gel.The band migrating at 15.0 kD is around the size they expected based on the sequence of the capsid.
|BPE15:Q858G8||Chigbuon, Team AOA Phagers||2017-04-12 14:00:06 CDT||GO:0019028 viral capsid (C)||Pubmed uniprot:Pubmed uniprot||ISS with/from UniProtKB:A0A0L5RKM7|
The sequence was run on blast and the results showed a lot of similarity between the major capsid protein in epsilon15 and Salmonella enterica. There was an e-value of 0.0 and a percent identity of 100%, as well as a query cover of 100. This proves that there is a capsid protein in epsilon15.
|BPE15:Q858G8||Chigbuon, Team AOA Phagers||2017-04-19 13:51:43 CDT||GO:0019028 viral capsid (C)||GO:0000100||ISS with/from UniProtKB:H2D0E5|
Comparison of the epsilon15 sequence to the sequence database using blatp showed that a region in epsilon15 and the major capsid protein in salmonella phage SPN1S have very close similarity. There was a percent Identity of a 100%, an Evalue of 0.0, and a query value of a 100. This shows that epsilon 15 has a major capsid protein.
|BPE15:Q858G8||Chigbuon, Team AOA Phagers||2017-04-19 14:04:55 CDT||GO:0019028 viral capsid (C)||0000100:0000100||ISS with/from UniProtKB:M1F234|
Comparison of the epsilon15 sequence to the sequence database using blatp showed that a region in epsilon15 and the major capsid protein in salmonella phage SPN9TCW have very close similarity. There was a percent Identity of a 100%, an Evalue of 0.0, and a query value of a 100. This shows that epsilon15 has a major capsid protein.
|BPP22:CAPSD||Hueydj, Team AOA Phagers||2017-04-26 08:50:34 CDT||GO:0039620 T=7 icosahedral viral capsid (C)||PMID:28270620||IDA|
Gp5 of Salmonella phage P22 was shown to fold into a classical HK97 capsid fold (PMID:11000116). Figure 1b shows a density map of the P22 capsid cryo-EM model. From the cryo-EM image, one asymmetrical unit, outlined in red in Figure 1b, was modeled and presented in Figure 1c with seven different colors representing each of the seven proteins folding into a T=7 icosahedral structure. This cryo-EM derived model of the protein matched closely to the molecular model of the gp5 430 amino acid sequence shown in Figure 2b. This 430 amino acid sequence number corresponds to the BLAST sequence in Uniprot for gp5, confirming that the model derived from the cryo-EM imaging was indeed gp5.
|BPBPP:Q775C7||Kothaa, Team AOA Phagers||2017-04-30 21:30:00 CDT||GO:0019028 viral capsid (C)||other:||ISS with/from UniProtKB:Q2KZ42|UniProtKB:Q775C7|
The sequence of the protein Bbp16 from the phage Bordetella phage BPP-1 was run in the BLASTp program to analyze its similarity to the protein sequences of other phages with major capsid protein sequences. The results indicated a close relationship between the major capsid protein sequences of Bordetella phage BPP-1 and Bordetella avium (strain 197N) based on the percent identity, the e-value, and the query coverage percentage. The percent identity of Bordetella avium to phage BPP-1 is 97.3% which indicates a very close similarity between the two sequences. The e-value is 0.00, and the query coverage is 100. The e-value, high query coverage, and high percent identity collectively indicate that there is a major capsid protein in Boredatella phage BPP-1.
|BPR69:Q7Y5B1||Hueydj, Team AOA Phagers||2017-04-30 22:44:42 CDT||GO:0039624 viral outer capsid (C)||PMID:19835886||ISM with/from PMID:10998631|
Figure 6a shows how the structure of the RB69 soc protein fits into a cryo EM model of the T4 capsid through trimeric interactions, where the major capsid protein gp23 of T4 has a 94% sequence identity to the major capsid protein of RB69. Fitting was done through the use of the EMFIT program, originally developed by Michael Rossmann (2000) (PMID:10998631). The stereo diagrams of the protein structure was derived from the RESOLVE program shown in Figure 2b using the amino acid sequence shown in Figure 2a. Figure 7b shows how six trimers of the soc (shown in red) assemble around each major capsid protein gp23 hexamer (each shown in blue, black, green, or magenta), acting to stabilize the connection between each capsid protein, a key characteristic of an outer capsid protein. A larger view that shows the stabilizing cage of the whole phage capsid can be seen in Figure 7a, with the red representing the soc proteins.
|9CAUD:A0A0N9ST32||Asmataa, Team AOA Phagers||2017-05-15 17:05:22 CDT||GO:0039624 viral outer capsid (C)||PMID:20826161||IDA|
The C-terminal Ig-like domain of gpV (gpVc) was fitted into cryo-EM density of the ϕ29 capsid in three structures. The domain was shown to fold into the superposition of gpVc and the intimin Big_2 domain structures. Figure 7 shows a density map of the ϕ29 capsid cryo-EM model. From the cryo-EM image, in Figure 7a, we can see only the superposition of gpVc. And in contrast, Figure 7b shows the Big_2 domain structures and how they fit into the gp8 density, further proving the presence of a capsid protein. From the combination of these two components, we can notice in Figure 7c, the lg-like domain of ϕ29 gp8.