Private
Assessment | Jrr | 2019-06-06 16:12:38 CDT | You need to be an instructor to view these notes. | Updated by Instructor
✔ Protein
✔ Publication
✔ Qualifier
✔ Go term
✔ Evidence
✔ With/From
✔ Notes
✔ Unique/Original
|
Private
Assessment | Jrr | 2019-06-06 16:11:03 CDT | You need to be an instructor to view these notes. | Requires Changes
✗ Qualifier
|
Public
Assessment | Ivanerill | 2018-04-30 05:47:26 CDT | Good call. Type 2 topoisomerases are known to be ATP hydrolizing, so the term applies even if hydrolizing activity is not explicitly shown in the paper
| Acceptable
✔ Protein
✔ Publication
✔ Qualifier
✔ Go term
✔ Evidence
✔ With/From
✔ Notes
✔ Unique/Original
|
Public
Assessment | DanielRenfro | 2018-04-20 13:49:57 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
|
| Contributes to |
GO:0009330 |
DNA topoisomerase complex (ATP-hydrolyzing) |
PMID:6296073 |
IMP: Inferred from Mutant Phenotype |
|
C |
In figure 7, gp60 was replaced with a mutant version, amE429 or amE594, and then the protein complex was eluted and run through a gel. Lanes 1-3 are gels of increasingly concentrated fractions of amE492 infected cells. Lane 4 uses the same fraction as lane 3, but eluted with .1M potassium phosphate buffer, as a control for the buffer. Lane 5 is the same fraction as lane 3, but eluted with .3M potassium phosphate buffer. Lane 6 is the same as lane 5, but with .5M potassium phosphate buffer. Lane 6 has the standards for the three proteins in topoisomerase, p39, p52, and p60. Lanes 8 and 9 are the same as lanes 5 and 6, respectively, but using amE594 as the mutant gene 60 instead of amE429. In lanes 5 and 8, p60 is absent (due to the mutation) and p39 is also absent. P52 is evident, meaning it was able to be eluted by the .3M buffer. In lanes 6 and 9, p60 is again absent as is p52, since it had already been eluted out. P39 is evident, as it was eluted out of fraction by .5M buffer. Since both proteins were eluted out by different concentrations of buffer, they were not bound together, which differs from past research that proves them bound together in complex. Therefore, p60 must be capable of binding them together without any conformational change of p39 or p52(both proteins' identities were confirmed after experiment). |
complete
CACAO 13106
| on BPT4:TOPS
| Flagged
|
Public
Assessment | Ivanerill | 2018-04-02 10:37:30 CDT | | Requires Changes
✔ Protein
✗ With/From
|
Public
Assessment | DanielRenfro | 2018-03-12 09:53:57 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:0060090 |
molecular adaptor activity |
PMID:6296073 |
IMP: Inferred from Mutant Phenotype |
|
F |
In figure 7, gp60 was replaced with a mutant version, amE429 or amE594, and then the protein complex was eluted and run through a gel. Lanes 1-3 are gels of increasingly concentrated fractions of amE492 infected cells. Lane 4 uses the same fraction as lane 3, but eluted with .1M potassium phosphate buffer, as a control for the buffer. Lane 5 is the same fraction as lane 3, but eluted with .3M potassium phosphate buffer. Lane 6 is the same as lane 5, but with .5M potassium phosphate buffer. Lane 6 has the standards for the three proteins in topoisomerase, p39, p52, and p60. Lanes 8 and 9 are the same as lanes 5 and 6, respectively, but using amE594 as the mutant gene 60 instead of amE429. In lanes 5 and 8, p60 is absent (due to the mutation) and p39 is also absent. P52 is evident, meaning it was able to be eluted by the .3M buffer. In lanes 6 and 9, p60 is again absent as is p52, since it had already been eluted out. P39 is evident, as it was eluted out of fraction by .5M buffer. Since both proteins were eluted out by different concentrations of buffer, they were not bound together, which differs from past research that proves them bound together in complex. Therefore, p60 must be capable of binding them together without any conformational change of p39 or p52(both proteins' identities were confirmed after experiment). |
complete
CACAO 13106
| on BPT4:TOPS
| Flagged
|
Public
Assessment | Ivanerill | 2018-03-12 05:05:02 CDT | In referring to Figures 6 and 7, the authors state:
"These experiments give clear evidence that p60 has a structural role in the T4 DNA topoisomerase complex, i.e. that this subunit is directly involved in the association of p39 and p52."
The annotation with GO:0030674 reflects the latter part of the statement. It is used mostly for eukaryotic annotations. If used, you should add the bound proteins in the WITH field.
An interesting alternative, regarding the first part of the statement (and probably Fig. 6 rather than 7) would be the use of GO:0009340 (DNA topoisomerase IV complex), but that is restricted to bacterial topoisomerase. You might consider requesting a new term for the corresponding phage complex, or annotate to the parent node.
| Requires Changes
✔ Protein
✔ Publication
✔ Qualifier
✗ Go term
✔ Evidence
✗ With/From
✔ Notes
✔ Unique/Original
|
Public
Assessment | DanielRenfro | 2018-03-11 14:12:58 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:0030674 |
protein binding, bridging |
PMID:6296073 |
IMP: Inferred from Mutant Phenotype |
|
F |
In figure 7, gp60 was replaced with a mutant version, amE429 or amE594, and then the protein complex was eluted and run through a gel. Lanes 1-3 are gels of increasingly concentrated fractions of amE492 infected cells. Lane 4 uses the same fraction as lane 3, but eluted with .1M potassium phosphate buffer, as a control for the buffer. Lane 5 is the same fraction as lane 3, but eluted with .3M potassium phosphate buffer. Lane 6 is the same as lane 5, but with .5M potassium phosphate buffer. Lane 6 has the standards for the three proteins in topoisomerase, p39, p52, and p60. Lanes 8 and 9 are the same as lanes 5 and 6, respectively, but using amE594 as the mutant gene 60 instead of amE429. In lanes 5 and 8, p60 is absent (due to the mutation) and p39 is also absent. P52 is evident, meaning it was able to be eluted by the .3M buffer. In lanes 6 and 9, p60 is again absent as is p52, since it had already been eluted out. P39 is evident, as it was eluted out of fraction by .5M buffer. Since both proteins were eluted out by different concentrations of buffer, they were not bound together, which differs from past research that proves them bound together in complex. Therefore, p60 must be capable of binding them together without any conformational change of p39 or p52(both proteins' identities were confirmed after experiment). |
complete
CACAO 13106
| on BPT4:TOPS
| Flagged
|
Public
Assessment | Ivanerill | 2018-03-08 16:09:39 CST | What figure/table are you referring to? Does it demonstrate isomerase activity? If so, can you find a more specific GO term? If not, are they just demonstrating that the protein pertains to a complex? Need to elaborate on notes, make rationale clear.
| Requires Changes
✔ Protein
✔ Publication
✔ Qualifier
✗ Go term
✔ Evidence
✔ With/From
✔ Unique/Original
|
