Phage Hunters Spring 2016
My Annotations
| Status | Page | Date/Time | GO Term (Aspect) | Reference | Evidence | Notes | Links |
|---|
| acceptable | BPT4:TERL | 2016-04-05 07:32:33 CDT | GO:0016887 ATPase activity (F) | PMID:19109896 | ECO:0000315 mutant phenotype evidence used in manual assertion | The ATPase protein was compared to two mutants (W533A and ΔS527G538) which had weakened interactions between their domains. The mutants were then compared to the wild-type with a Packaging ATPase assay. Both of the mutants had a loss of their ATPase activity. This is proven in figure 3e, where the concentration of cold ATP was increased every hour, for the wild-type and mutants. The third phosphate group was only cleaved in only the wild-type samples, which is seen in the appearance of the upper bands in the thin layer chromotherapy.
| challenge |
| unacceptable | ECOLI:RBN | 2016-04-24 22:45:46 CDT | GO:0004519 endonuclease activity (F) | PMID:16452444 | ECO:0000314 direct assay evidence used in manual assertion | E. Coli's ZiPD gene has been identified as an endonuclease which cleaves the 3′ extension from various tRNA precursors, which makes it a tRNase Z enzyme. This was proven by comparing the structure of E Coli's tRNase Z to the structure of various known tRNase Z structures. This comparison can be seen in figure 4.
| challenge |
| unacceptable | ECOLI:RBN | 2016-04-25 09:37:36 CDT | GO:0000100 S-methylmethionine transmembrane transporter activity (F) | other:GO REF: 10097147 | ECO:0000250 sequence similarity evidence used in manual assertion | Blastp results showed 100.0% sequence similarity with Bacillus phage Vinny and HHpred showed a 100% probability and a e-value of 3.2E-28
| challenge |
| unacceptable | LEGPH:COAE | 2016-04-25 10:08:03 CDT | GO:0004140 dephospho-CoA kinase activity (F) | PMID:25449315 | ECO:0000255 match to sequence model evidence used in manual assertion | Structure of Lp-DPCK-Bu2 was determined by molecular replacement with Phaser
| challenge |
| unacceptable | BPT4:TERL | 2016-05-01 16:59:20 CDT | GO:0004518 nuclease activity (F) | PMID:19109896 | ECO:0000314 direct assay evidence used in manual assertion | The assay experiment of the gp17 terminase can be viewed in figure 3b. Lane's 0, 1, and 2 are how many hours after the addition of isopropyl β-D-1-thiogalactopyranoside (IPTG). This induces the expression of the DNA samples. The mutant sample are then compared to the known DNA. It is then compared to the mutant types, the mutant types did not have cleaved DNA. Proving its identity as a nuclease.
| challenge |
| acceptable | BPT4:PORTL | 2016-05-01 15:25:34 CDT | GO:0046798 viral portal complex (C) | PMID:26144253 | ECO:0000314 direct assay evidence used in manual assertion | This is a ring of proteins where DNA enters and exits the phages capsid. The structure was determined by cryo-electron microscopy (cryo-EM) Figure 1.
| challenge |
| updatedbyinstructor | BPT4:TERL | 2016-05-02 09:51:58 CDT | GO:0004536 deoxyribonuclease activity (F) | PMID:19109896 | ECO:0000315 mutant phenotype evidence used in manual assertion | Figure 3b compares the mutant gp17 proteins to the wild types. Arg406 in T4 participates in binding DNA and nuclease activity. Mutant "Arg406Ala" showed that any substitutions in amino acids at the 406 position produced a null phenotype. Meaning that when they tested the phages in a plating assay the mutants failed to produce plaques. See figure 3b shows that unlike the wild-type, the mutant R406A did not degrade the DNA after 2 hours of incubation.
| challenge |
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unacceptable:4
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