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Cacao

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GO:0003678DNA helicase activityPMID:21606333IMP: Inferred from Mutant Phenotype F
This annotation made on page: BPT7:DPOL
By: AHora (group Team Green A 2018) on 2018-03-04 22:16:06 CST.




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Entry TypeChallenging User,GroupTime/DateChallenge ReasonPoints/Assessment
Public
Assessment		Ivanerill2018-04-30 05:41:21 CDTNo notes given.Acceptable
✔ Protein
✔ Publication
✔ Qualifier
✔ Go term
✔ Evidence
✔ With/From
✔ Notes
✔ Unique/Original
Public
Assessment		DanielRenfro2018-04-22 19:47:16 CDT

This annotation has been flagged because it has been edited since last assessment

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0090592 DNA synthesis involved in DNA replication PMID:21606333 IMP: Inferred from Mutant Phenotype P Figure 2 compared the activities of both gp5/trx and its mutated form Gp5-Fbpneu/trx in the presence of gp4 by looking at how much nucleotide (dTMP) had been incorporated in a sample of dsDNA . According to the paper and from the results, Gp5-Fbpneu/trx did not mediate the synthesis in the presence of gp4 over a large range of concentrations of gp5/trx and gp4. This means that a mutated gp5 would result in disrupted DNA synthesis in the presence of gp4 as compared to a normal version of gp5, showing its critical function for DNA replication. complete
CACAO 13104
on BPT7:DPOL
Flagged
Public
Assessment		Ivanerill2018-04-14 19:26:40 CDT

I assume you refer to Fig. 2? Please do not copy-paste article text extensively (a quote is acceptable). Fig. 2 does not prove anything about gp4, much less DNA replication, synthesis of RNA primer. I have moved the annotation to gp5.

Requires Changes
✗ Protein
✗ Go term
✗ Notes
Public
Assessment		DanielRenfro2018-04-08 21:35:15 CDT

This annotation has been flagged because it has been edited since last assessment

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0006269 DNA replication, synthesis of RNA primer PMID:21606333 IMP: Inferred from Mutant Phenotype P "The primase domain of gp4 catalyzes the synthesis of RNA primer for gp5/trx to initiate DNA synthesis on ssDNA template. gp5-Fbpneu/trx mediates RNA-dependent DNA synthesis on M13 ssDNA with gp4 approximately one-third to one-half as well as does wild-type gp5/trx (Fig. S2)". The figure shows that the primase activity of gp4 is important in DNA synthesis in conjunction with both gp5/trx and its mutated counterpart. complete
CACAO 13104
on BPT7:PRIM
Flagged
Public
Assessment		Ivanerill2018-04-02 10:23:22 CDT

GO term is still not correct. I see no evidence supporting DNA helicase activity. Look at what Fig.2 (or others) DO demonstrate.

Requires Changes
✔ Go term
Public
Assessment		DanielRenfro2018-03-11 23:54:24 CDT

This annotation has been flagged because it has been edited since last assessment

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0006260 DNA helicase activity PMID:21606333 IMP: Inferred from Mutant Phenotype F The experiment measures DNA replication and the impediments faced when missing gene 5. Bacteriophage T7 cannot grow in cell that have gp5, because neutral residues, Asparagine, were used instead of the basic residues. The major effects seen on T7 were a decrease in polymerase activity on the ssDNA template and reduced processivity. Perhaps, this is because of the mutations in gene 5, which changed the binding site for one or more of the other T7 replication proteins. When the C-terminal tail is removed, the ability of gp4 to mediate the strand-displacement synthesis is obliterated. Please refer to Figure 2. complete
CACAO 13104
on BPT7:PRIM
Flagged
Public
Assessment		Scaruso2018-03-08 15:51:55 CST

You are going to have to re-think what these experiments are showing you, and pick a different GO term. This experiment (fig 2) is not testing helicase activity, it's measuring DNA production and it's lack there of when gp5 and gp4 fail to interact (the mutant). That doesn't specifically demonstrate helicase activity. Instead, it contributes to DNA replication, for example, along with gp5, trx, and so on. You could use that as a GO term. Or, you can go after gp5, which is more straightforward in the paper.

Requires Changes
✔ Publication
✗ Go term
✗ Notes
✔ Unique/Original


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