| Challenge | Bgabrielle,
TeamGreen | 2015-04-13 10:47:48 CDT | Suggestion: Cite figures directly from your articles to more easily follow your reasoning. Also, what do you mean by "there is relatively no morphological differences among these three phages"? Is this inferred strictly from looking at EM images? If so, this may be an appropriate location to cite a figure pulled from one of the articles used. It may also be helpful to note which ORFs produce amino acid homology, since it may be of interest if the ORF of one phage is present at the start of the sequence while the ORF taken from another phage was present at the end of a sequence.
| None, yet. |
| Challenge | Gjulie,
TeamGreen | 2015-04-13 10:43:00 CDT | What are the e-values of the sequence alignments between the 3 phage tail sheath genes and Troll's gene? Are they significant enough to infer homology?
| None, yet. |
| Challenge | Pclarence,
TeamGreen | 2015-04-13 10:42:36 CDT | Reference is not a GO term.
| None, yet. |
Private
Assessment | Jrr | 2019-06-06 15:51:52 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 15:51:22 CDT | You need to be an instructor to view these notes. | Requires Changes
✗ Qualifier
|
Private
Assessment | Jrr | 2019-06-06 15:49:46 CDT | You need to be an instructor to view these notes. | Requires Changes
✗ Qualifier
|
Private
Assessment | Ivanerill | 2015-05-12 14:33:37 CDT | You need to be an instructor to view these notes. | Acceptable
✔ Protein
✔ Publication
✔ Qualifier
✔ Go term
✔ Evidence
✔ With/From
✔ Notes
✔ Unique/Original
|
Public
Assessment | DanielRenfro | 2015-05-08 14:00:52 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:0098027 |
virus tail, sheath |
GO_REF:0000100 |
ISA: Inferred from Sequence Alignment |
UniProtKB:Q37916
|
C |
Troll's tail sheath genome obtained good BLASTP hits towards Listeria Bacteriophage A511's tail sheath protein, tsh. With a 98% query cover, E-value of 9e-156 and 45% identity, it suggests that A511's tsh gene shows an significant homology towards Troll's tail sheath protein gene.
|
complete
CACAO 10855
| on 9CAUD:S5Y0L8
| Flagged
|
Public
Assessment | DanielRenfro | 2015-05-08 13:44:40 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:0098027 |
virus tail, sheath |
GO_REF:0000100 |
ISA: Inferred from Sequence Alignment |
UniProtKB:Q37916
|
C |
Troll's tail sheath genome obtained BLASTP hits towards Listeria Bacteriophage A511 (98% query cover, E-value: 9e-156, 45% identity), Lactobacillus plantarum bacteriophage LP65 (98% query cover, E-value: 1e-100, 36% identity), and Staphylococcus aureus Bacteriophage K (98% query cover, E-value: 2e-128, 39% identity), all of which show significance towards a homology with Troll.
From PMID:18567664, we see in Figure 1 the electron micrographs of the 3 phages, showing relatively little morphological differences among them.
Figure 3 of the same article shows an multiple sequence alignment of these 3 phages' genomes using ClustalW, revealing amino acid homologies for DNA packaging, structural genes, cell lysis, and DNA replication and description.
By comparing their morphologies and genomes, it is concluded that all of these three phages belong to a SPO1-like group of the Myoviridae in the order Caudovirales, to which they all feature a long, contractile, nonflexible tail.
These homologies suggests their function is similar: after tail contraction, a tube extends from the tail, then enters through the cell wall. However, even though the tube contacts the cell membrane, how the process of DNA injection by phage infecting the bacterial host still needs to be evaluated.||complete
CACAO 10855
| on 9CAUD:S5Y0L8
| Flagged
|
Public
Assessment | DanielRenfro | 2015-05-08 13:40:45 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:0098027 |
virus tail, sheath |
GO_REF:0000100 |
ISA: Inferred from Sequence Alignment |
UniProtKB:Q37916
|
C |
Troll's tail sheath genome obtained BLASTP hits towards Listeria Bacteriophage A511 (98% query cover, E-value: 9e-156, 45% identity), Lactobacillus plantarum bacteriophage LP65 (98% query cover, E-value: 1e-100, 36% identity), and Staphylococcus aureus Bacteriophage K (98% query cover, E-value: 2e-128, 39% identity), all of which show significance towards a homology with Troll.
From PMID:18567664, we see in Figure 1 the electron micrographs of the 3 phages, showing relatively little morphological differences among them.
Figure 3 of the same article shows an multiple sequence alignment of these 3 phages' genomes using ClustalW, revealing amino acid homologies for DNA packaging, structural genes, cell lysis, and DNA replication and description.
By comparing their morphologies and genomes, it is concluded that all of these three phages belong to a SPO1-like group of the Myoviridae in the order Caudovirales, to which they all feature a long, contractile, nonflexible tail.
These homologies suggests their function is similar: after tail contraction, a tube extends from the tail, then enters through the cell wall. However, even though the tube contacts the cell membrane, how the process of DNA injection by phage infecting the bacterial host still needs to be evaluated.||complete
CACAO 10855
| on 9CAUD:S5Y0L8
| Flagged
|
Public
Assessment | Ivanerill | 2015-05-04 08:55:14 CDT | You are conflating annotations. If this is a transfer annotation to Troll, you only need to specify the methodology (which you do) and the corresponding gene with experimental evidence. You don't need to cite the PMID.
Your note seems to imply that you are making the annotation on these three genes as part of this annotation. It is also not clear that there is solid evidence for the cellular component annotation you are making in that paper but, if there, is those annotations should be made apart (referencing the PMID), and then the genes simply be used in the WITH field of the transfer annotation (referencing the GO_REF).
| Requires Changes
✔ Protein
✗ Publication
✔ Qualifier
✗ Go term
✗ Evidence
✗ With/From
✗ Notes
✔ Unique/Original
|
Public
Assessment | DanielRenfro | 2015-04-21 22:32:37 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:0098027 |
virus tail, sheath |
GO_REF:0000100 |
ISA: Inferred from Sequence Alignment |
PMID:15489418
PMID:18567664
PMID:24459260
UniProtKB:Q37916
|
C |
Troll's tail sheath genome obtained BLASTP hits towards Listeria Bacteriophage A511 (98% query cover, E-value: 9e-156, 45% identity), Lactobacillus plantarum bacteriophage LP65 (98% query cover, E-value: 1e-100, 36% identity), and Staphylococcus aureus Bacteriophage K (98% query cover, E-value: 2e-128, 39% identity), all of which show significance towards a homology with Troll.
From PMID:18567664, we see in Figure 1 the electron micrographs of the 3 phages, showing relatively little morphological differences among them.
Figure 3 of the same article shows an multiple sequence alignment of these 3 phages' genomes using ClustalW, revealing amino acid homologies for DNA packaging, structural genes, cell lysis, and DNA replication and description.
By comparing their morphologies and genomes, it is concluded that all of these three phages belong to a SPO1-like group of the Myoviridae in the order Caudovirales, to which they all feature a long, contractile, nonflexible tail.
These homologies suggests their function is similar: after tail contraction, a tube extends from the tail, then enters through the cell wall. However, even though the tube contacts the cell membrane, how the process of DNA injection by phage infecting the bacterial host still needs to be evaluated.||complete
CACAO 10855
| on 9CAUD:S5Y0L8
| Flagged
|
