Phage Hunters Spring 2016
My Annotations
| Status | Page | Date/Time | GO Term (Aspect) | Reference | Evidence | Notes | Links |
|---|
| updatedbyinstructor | BPDPK:Q8SCY7 | 2016-04-11 04:44:53 CDT | GO:0019082 viral protein processing (P) | PMID:22429790 | ECO:0000314 direct assay evidence used in manual assertion | Figure 5 shows "SDS-PAGE of an expression vector assay of the φKZ protease showing cleavage of φKZ head protein gp93."
| challenge |
| unacceptable | BPDPK:Q8SD18 | 2016-04-11 04:44:54 CDT | GO:0006508 proteolysis (P) | PMID:22429790 | ECO:0000250 sequence similarity evidence used in manual assertion | From first two paragraphs under the "Identification of φKZ gp175 as the morphogenetic protease" says "we used local implementations of the Sequence Analysis and Modeling System and HHpred.The E-value of this match was only 3, however the HHpred P-value, which takes secondary structure into account, was 2.5E-05. This match was solidified using a custom T4 gp21 HHM powerful enough to detect an HHM based on the U35 peptidase family at E-values of 3.5E-05. Members of the U35 peptidase family contain diverged, but known, homologs to the T4 protease, such as the HK97 protease."
| challenge |
| unacceptable | BPDPK:Q8SD18 | 2016-04-11 04:44:54 CDT | GO:0006508 proteolysis (P) | PMID:22429790 | ECO:0000314 direct assay evidence used in manual assertion | Figure 2 shows the location of the phage DNA where the prohead protease cleaves.
| challenge |
| unacceptable | BPDPK:Q8SD18 | 2016-04-11 04:44:54 CDT | GO:0006508 proteolysis (P) | PMID:22429790 | ECO:0000314 direct assay evidence used in manual assertion | Figure 1. SDS-Page and Mass Spec shows the size and boundaries of the genes cleaved by the prohead protease.
| challenge |
| unacceptable | BPT4:D9IEK7 | 2016-04-11 04:44:58 CDT | GO:0006508 proteolysis (P) | PMID:15273316 | ECO:0000250 sequence similarity evidence used in manual assertion | From the fourth paragraph under results,"in the course of expanding the U35.001 family, we found statistical evidence that the U9 family and the U35.001 family are remote homologs. For example, starting with the U35.001 representative HK97 gp4 protease (gi|9634157, residues 1–225), PSI-BLAST search found a close homolog gi|26988298 with e-value 2e-18 in the first iteration. Using this sequence as query to run PSI-BLAST (default parameters in NCBI Web site), we found a U9 family member (gi|30044105) in the third iteration with a significant e-value 0.003."
| challenge |
| unacceptable | BPT4:D9IEK7 | 2016-04-11 04:52:49 CDT | GO:0006508 proteolysis (P) | PMID:15273316 | ECO:0000247 sequence alignment evidence used in manual assertion | Figure 2A Euclidian distance map. "In distance mapping, each sequence is represented by a point in a multidimensional Euclidian space and the distances between these points reflect the evolutionary distances between the sequences. A two-dimensional projection of this space is shown in Figure 2A ▶ (below). This plot offers a visualization of the sequence clustering; each family or subfamily appears as a rather distinct group, except for U35.002.a and U35.002.c. These two subfamilies are divided on the basis of sequence conservation and insertion/ deletion patterns."
| challenge |
| unacceptable | BPDPK:Q8SD18 | 2016-04-11 04:58:29 CDT | GO:0006508 proteolysis (P) | PMID:11916376 | ECO:0000250 sequence similarity evidence used in manual assertion | Blastp with T4 phage shows correlation to prohead protease of T4
| challenge |
acceptable:0
unacceptable:6
requires_changes:0
flagged:0
Annotations challenged by Iac1
| Status | Author,Group | Page | GO Term (Aspect) | Reference | Evidence | Links | Page history |
|---|
| unacceptable | Tracy.Pham,
Team Espresso my genes | LEGPH:ACON | GO:0003729 - mRNA binding (F) | PMID:8366052 | ECO:0000314 direct assay evidence used in manual assertion | challenge | C: 2
|
| updatedbyinstructor | Ttran13,
Team Asian persuasian | TRYBB:FCA2 | GO:0051701 - biological process involved in interaction with host (P) | PMID:20418379 | ECO:0000315 mutant phenotype evidence used in manual assertion | challenge | C: 1
|
| updatedbyinstructor | Nathan.Marsh,
Team Grapes of Staph | ALIFS:LUXI | GO:0052043 - obsolete modification by symbiont of host cellular component (P) | PMID:10913092 | ECO:0000315 mutant phenotype evidence used in manual assertion | challenge | C: 1
|
| unacceptable | Jsbautista,
Team Asian persuasian | MOUSE:RIT1 | GO:0000302 - response to reactive oxygen species (P) | PMID:23123784 | ECO:0000314 direct assay evidence used in manual assertion | challenge | C: 1
|
| updatedbyinstructor | Jkwan2,
Team Asian persuasian | BACSU:A3F475 | GO:0043138 - 3'-5' DNA helicase activity (F) | PMID:25246477 | ECO:0000314 direct assay evidence used in manual assertion | challenge | C: 1
fixed by Iac1 |
| unacceptable | Nur.Isaak,
Team Grapes of Staph | ALIFS:Q6WEJ3 | GO:0003677 - DNA binding (F) | PMID:25962099 | ECO:0000315 mutant phenotype evidence used in manual assertion | challenge | C: 1
|
| updatedbyinstructor | Jonathan.Yuen,
Team Not Very Creative | RAT:SMAD3 | GO:0005634 - nucleus (C) | PMID:16690606 | ECO:0000314 direct assay evidence used in manual assertion | challenge | C: 1
|
| unacceptable | Zach.Bailey,
Team Not Very Creative | CRYNV:A0A024QYR7 | GO:0005934 - cellular bud tip (C) | PMID:25367976 | ECO:0000314 direct assay evidence used in manual assertion | challenge | C: 1
|
| updatedbyinstructor | Dre.E.Steinwehr,
Team The Herd | HUMAN:RRAS | GO:1904906 - positive regulation of endothelial cell-matrix adhesion via fibronectin (P) | PMID:22825554 | ECO:0000315 mutant phenotype evidence used in manual assertion | challenge | C: 1
fixed by Iac1 |
| unacceptable | Zach.Bailey,
Team Not Very Creative | CRYNV:A0A024QYR7 | GO:0005933 - cellular bud (C) | PMID:25367976 | ECO:0000314 direct assay evidence used in manual assertion | challenge | C: 1
|
| unacceptable | Cdiop,
Team T2 | DROME:Q9W4K0 | GO:0005783 - endoplasmic reticulum (C) | PMID:9649432 | ECO:0000314 direct assay evidence used in manual assertion | challenge | C: 1
|
| unacceptable | Iac1,
Team Purple B | BPDPK:Q8SD18 | GO:0006508 - proteolysis (P) | PMID:22429790 | ECO:0000250 sequence similarity evidence used in manual assertion | challenge | C: 2
|
| unacceptable | Spanch1,
Team Red B | 9CAUD:A0A0K2D0G3 | GO:0005298 - proline:sodium symporter activity (F) | PMID:3488191 | ECO:0000250 sequence similarity evidence used in manual assertion | challenge | C: 1
|
| unacceptable | Spanch1,
Team Red B | 9CAUD:A0A0K2D0G3 | GO:0098772 - molecular function regulator activity (F) | PMID:3488191 | ECO:0000250 sequence similarity evidence used in manual assertion | challenge | C: 1
|
| unacceptable | Cardosa1,
Team Blue B | 9CAUD:A0A0K2CZY5 | GO:0051131 - chaperone-mediated protein complex assembly (P) | PMID:15469818 | ECO:0000250 sequence similarity evidence used in manual assertion | challenge | C: 2
|
| updatedbyinstructor | Mnguy1,
Team Blue B | ECOLI:CYSH | GO:0004604 - phosphoadenylyl-sulfate reductase (thioredoxin) activity (F) | PMID:7588765 | ECO:0000315 mutant phenotype evidence used in manual assertion | challenge | C: 1
fixed by Iac1 |
3 annotations fixed by Iac1
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