User:RyanRichardson

My Annotations

Status	Page	Date/Time	GO Term (Aspect)	Reference	Evidence	Notes	Links
acceptable	LAMBD:TMP	2016-04-18 06:21:21 CDT	GO:0098003 viral tail assembly (P)	PMID:6096021	ECO:0000315 mutant phenotype evidence used in manual assertion	The research team selected for two phages with mutant H genes. The mutant phages were found to be active, plaque producing phages (pp. 691-692), indicating that the mutant H genes were still functional. Both of the mutant H genes were found to produce smaller H proteins than the wild type Lambda H (Fig 2, p. 692). The mutant phages were shown to have shorter tails than wild type Lambda(Fig 4, 694), and the tail length for the wild type and both mutants correlated with the size of H protein, indicating Lambda H plays a role in determining tail length.	challenge
acceptable	LAMBD:TMP	2016-04-18 08:17:28 CDT	GO:0098003 viral tail assembly (P)	PMID:2952887	ECO:0000315 mutant phenotype evidence used in manual assertion	The researcher isolated 31 lambda phage mutants with mutations in the H gene. Thirty mutants had a deletion in the H gene, while the other had a duplication. Twelve of the deletion mutants, along with the duplication mutant, were found to produce tail particles. The phages with a deletion in the H gene produced shorter tails than wild type Lambda, and the duplication mutant produced a longer tail (Fig 2, p. 74). The length of the tails of wild type Lambda and each mutant were found to be roughly proportional to the number of amino acids in their respective H proteins (Fig 3, p. 74). This indicates that the H protein plays a role in determining the length of the Lambda tail.	challenge
unacceptable	LAMBD:TMP	2016-04-18 08:17:28 CDT	GO:0098003 viral tail assembly (P)	PMID:2952887	ECO:0000315 mutant phenotype evidence used in manual assertion	The researcher isolated thirty mutants with a deletion in the H gene of Lambda. For 18 of these mutants, tails did not assemble (p. 74). This provides evidence that H protein is necessary for tail assembly in Lambda.	challenge
acceptable	BPP4:PRIM	2016-04-23 10:28:42 CDT	GO:0003896 DNA primase activity (F)	PMID:1618804	ECO:0000314 direct assay evidence used in manual assertion	The P4 alpha protein was placed under the control of the LacI operon in two different recombinant plasmids. A direct assay intended to measure the ability of a primase to initiate synthesis of DNA by measuring the amount of thymine incorporated into the strand was conducted using cells induced to produce the alpha protein via the LacI operon, non-induced cells, and purified alpha protein. The induced cells and purified alpha protein showed high amounts of incorporated thymine, indicating primase activity. The non-induced cells showed no thymine incorporation (Fig 8, p. 13068), demonstrating that the alpha protein has primase activity.	challenge
unacceptable	BPT1:SPANU	2016-04-23 14:30:31 CDT	GO:0045203 integral component of cell outer membrane (C)	PMID:17900620		The T1 gp11 was found to have a sequence that very likely predicts an outer membrane lipoprotein, just as Lambda Rz1 produces an outer membrane lipoprotein component of a spanin (p. 1098). In addition, many phages, including Lambda, have a lysis cassette, which means that the holin, endolysin, and spanin are all next to each other in the genome (p. 1100). In the case of T1, genes 12 and 13 are the endolysin and holin, respectively, providing further evidence that gp11 is an integral component of the cell outer membrane. (I've also requested a new GO term to use for gp11, since this paper indicates that the protein disrupts the outer membrane. The issue can be found here https://github.com/geneontology/go-ontology/issues/12424).	challenge

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unacceptable:2
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Annotations challenged by RyanRichardson

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