User:Rayesd

My Annotations

Status	Page	Date/Time	GO Term (Aspect)	Reference	Evidence	Notes	Links
unacceptable	BPT4:TERL	2016-04-07 08:45:53 CDT	GO:0043493 viral terminase complex (C)	PMID:3294420	ECO:0000314 direct assay evidence used in manual assertion	gp16 and gp17 Terminase genes from T4 were over expressed in Ecoli bacteria in the presence of empty phage proheads in order to asses the headful DNA packaging abilities of the genes. Gp16 and gp17 were expressed individually and together in a complex. It was found that, "the gp16 function of the terminase complex is dispensable for packaging mature DNA, whereas gp17 is essential for packaging DNA under any condition tested." It was therefore determined that gp17 is the main Terminase protein in T4 necessary for the molecular function of DNA packaging.	challenge
updatedbyinstructor	BPSP1:TSP	2016-04-27 10:13:55 CDT	GO:0098015 virus tail (C)	PMID:6827651	ECO:0000314 direct assay evidence used in manual assertion	Fig 3. Shows the abundance of T3 and other SPO1 tail proteins through gel electrophoresis. T3 is determined to be the tail sheath protein because it is the most abundant protein, next to T6 which is smaller and determined to be the tail core.	challenge
unacceptable	BPSP1:PORTL	2016-05-01 23:05:09 CDT	GO:0046798 viral portal complex (C)	PMID:19285085	ECO:0000317 genomic context evidence used in manual assertion	Fig 3. shows synteny between the portal protein of SPO1 and phages, LP65, Twort, P100, and K/G. In all phages, the portal protein is located "immediately upstreams of the procapsid protease gene" or Gp3.2 (B6V2N5).	challenge
unacceptable	BPTWO:PORTL	2016-05-02 11:02:45 CDT	GO:0046798 viral portal complex (C)	PMID:15788529	ECO:0000317 genomic context evidence used in manual assertion	Fig 3. shows synteny between Twort and 27 other S Areus phages, including 44AHJD (Q859K6). The location of the portal gene is in the same place for compared phages- upstream of protease (Q4Z9G2) and the major capsid protein (Q6UTE7).	challenge
unacceptable	HHV11:MCP	2016-04-25 12:01:02 CDT	GO:0039622 T=16 icosahedral viral capsid (C)	PMID:12574112	ECO:0000314 direct assay evidence used in manual assertion	The authors isolate a 65kda fragment of VP5 by "limited trypsin digestion." They then identifiy this fragment as the upper domain of VP5 by x-ray crystallography. Fig 1. shows this crystalized structure of the upper domain. It identifies areas important for both interactions between VP5 proteins and interactions with other capsid proteins like VP26. The authors also identify a novel fold that is unique to the herpesvirus.	challenge
unacceptable	BPTWO:TSP	2016-04-25 20:01:54 CDT	GO:0098027 virus tail, sheath (C)	GO_REF:0000100	ECO:0000317 genomic context evidence used in manual assertion	The tail sheath protein in Staphylococcus phage Twort is an ortholog to the tail sheath protein in Bacillus phage SPO1 (B6V2P4), as well as Staphylococcus phages K (Q6Y7R8) and G1 (Q4ZA16) (PMID:19285085). Furthermore, because sequence of tail sheath proteins is generally highly conserved (PMID:19285085), BlastP shows strong sequence identity (75%) with G1 and K, and slightly weaker (26%) identity with SPO1.	challenge
unacceptable	HHV11:MCP	2016-05-04 23:18:41 CDT	GO:0039622 T=16 icosahedral viral capsid (C)	PMID:12574112	ECO:0000255 match to sequence model evidence used in manual assertion	Fig. 2 identifies VP5 as the major capsid protein through cryoelectron microscopy. The authors fit the crystalized structure of VP5ud (upper domain) on to a cryoelectron microscopy map of the HSV-1 capsid obtained from a publication by Zhou et al (PMID:10797014). They utilize Foldhunter (PMID:11352589) and the Molecular Modeling Toolkit (MMTK) to fit the x-ray structure on to the cryoelectron microscopy map of the capsid.	challenge

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unacceptable:6
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Annotations challenged by Rayesd

Status	Author,Group	Page	GO Term (Aspect)	Reference	Evidence	Links	Page history
unacceptable	Omololu1, Team Blue B	9CAUD:A0A0K2D0J0	GO:0000166 - nucleotide binding (F)	PMID:17209017	ECO:0000315 mutant phenotype evidence used in manual assertion	challenge	C: 3
unacceptable	Warrierrk, Team Snorlax	BPSP1:DPOL	GO:0004527 - exonuclease activity (F)	PMID:1324872	ECO:0000247 sequence alignment evidence used in manual assertion	challenge	C: 1
unacceptable	Jermstadsb, Team TRUMP2016	LEGPH:COAE	GO:0004140 - dephospho-CoA kinase activity (F)	PMID:25449315	ECO:0000255 match to sequence model evidence used in manual assertion	challenge	C: 1
unacceptable	TaylorBourgeois, Team T7	BPT5:HEL10	GO:0004386 - helicase activity (F)	PMID:2547651	ECO:0000247 sequence alignment evidence used in manual assertion	challenge	C: 2
unacceptable	Powellme, Team TRUMP2016	CLOTH:A3DJ38		PMID:23595150	ECO:0000255 match to sequence model evidence used in manual assertion	challenge	C: 1

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