Phage Hunters Spring 2016
My Annotations
| Status | Page | Date/Time | GO Term (Aspect) | Reference | Evidence | Notes | Links |
|---|
| unacceptable | 9CAUD:A0A0K2D089 | 2016-03-28 04:35:04 CDT | GO:0046798 viral portal complex (C) | PMID:12239300 | ECO:0000316 genetic interaction evidence used in manual assertion | | challenge |
| unacceptable | 9CAUD:A0A0K2D089 | 2016-04-11 04:13:05 CDT | GO:0046798 viral portal complex (C) | PMID:18567664 | ECO:0000250 sequence similarity evidence used in manual assertion | Blastp of protein sequences from TsarBomba showed e value of 0 with protein gp83 [Listeria phage A511]
| challenge |
| unacceptable | 9CAUD:A0A0K2CZY5 | 2016-03-28 05:01:05 CDT | GO:0051131 chaperone-mediated protein complex assembly (P) | PMID:23911548 | ECO:0000315 mutant phenotype evidence used in manual assertion | "The requirement for co-expression of gpG and gpGT with gpH and the demonstration of a physical interaction between gpG and gpH argue that the nascent gpH polypeptide might require the binding of gpG and gpGT to fold correctly. This is consistent with the observation that gpG is expressed in a large amount similar to the level of the major tail protein gpV. Since gpG interacts with more than one part of gpH, the amount of gpG expressed is probably enough to coat the entire gpH. The large amount of gpG might ensure that gpH is properly chaperoned over its entire length. Since gpGT also uses its G part to interact with gpH, it is likely that some part of gpH is also bound with gpGT molecules. The observation that tail assembly can be disrupted by altering the ratio of gpG and gpGT production argues that the amount of gpGT incorporated is probably determined by the ratio of gpG versus gpGT, rather than by some sort of mechanism that assembles the “correct” ratio of gpGT to gpG regardless of the ratio in the unassembled pool. It also argues that having the correct ratio of gpGT to gpG in complex with gpH is important for successful assembly."
| challenge |
| unacceptable | 9CAUD:A0A0K2CZV8 | 2016-04-11 12:49:11 CDT | GO:0003896 DNA primase activity (F) | PMID:11279245 | ECO:0000247 sequence alignment evidence used in manual assertion | "An altered gene 4 protein that does not form functional hexamers and consequently lacks detectable DNA unwinding activity was created. Remarkably, this monomeric primase readily primes DNA synthesis by T7 DNA polymerase on single-stranded templates. The monomeric gene 4 protein forms a specific and stable complex with T7 DNA polymerase and thereby delivers the RNA primer to the polymerase for the onset of DNA synthesis. These results show that a single subunit of the primase-helicase hexamer contains all of the residues required for primer synthesis and for utilization of primers by T7 DNA polymerase."
| challenge |
| updatedbyinstructor | PYRFU:HJC | 2016-03-28 05:42:35 CDT | GO:0048476 Holliday junction resolvase complex (C) | PMID:11286886 | ECO:0000315 mutant phenotype evidence used in manual assertion | | challenge |
| updatedbyinstructor | BPT7:PRIM | 2016-04-11 12:45:27 CDT | GO:0003896 DNA primase activity (F) | PMID:11279245 | ECO:0000314 direct assay evidence used in manual assertion | Figs. 5, 6. "An altered gene 4 protein that does not form functional hexamers and consequently lacks detectable DNA unwinding activity was created. Remarkably, this monomeric primase readily primes DNA synthesis by T7 DNA polymerase on single-stranded templates. The monomeric gene 4 protein forms a specific and stable complex with T7 DNA polymerase and thereby delivers the RNA primer to the polymerase for the onset of DNA synthesis. These results show that a single subunit of the primase-helicase hexamer contains all of the residues required for primer synthesis and for utilization of primers by T7 DNA polymerase."
| challenge |
| unacceptable | BPA51:A8AST6 | 2016-04-11 04:36:07 CDT | GO:0098025 virus tail, baseplate (C) | PMID:18567664 | ECO:0000314 direct assay evidence used in manual assertion | Fig 1
For the first time, we are able to document the presence of long tail fibers with a sixfold symmetry attached to the base plate regions of A511, P100, and K (Fig. 1). These whiskers are distinct from the short tail spikes present on the lower side of the base plate structure, which are best visible in images of contracted phage tails (e.g., Fig. 1D), and also exhibit a sixfold symmetry. Interestingly, the base plates of all three phages seem to undergo quite dramatic conformational changes during tail contraction, allowing better visualization of its structure and components (Fig. 1A, C, D, and F). As a result of contraction triggering, the base plate moves upwards and the tail tube is exposed and extends beneath the base plate and tail sheath. Similar observations have been made for another SPO1-like phage, LP65 of Lactobacillus (9), which also appears to resembles A511 in morphology and approximate dimensions. Via the tips of exposed tail tubes in the contracted state, virions frequently adhere to some unstructured material, probably representing cell wall debris from lysed host cells (Fig. 1F).
| challenge |
| unacceptable | 9CAUD:A0A0K2D047 | 2016-04-11 04:36:58 CDT | GO:0098025 virus tail, baseplate (C) | other:Blastp | ECO:0000250 sequence similarity evidence used in manual assertion | The protein sequence for this underwent a BLASTp and gave an e value of 2e-54 with gp102 [Listeria phage A511]
| challenge |
acceptable:0
unacceptable:6
requires_changes:0
flagged:0
Annotations challenged by Amariam1
| Status | Author,Group | Page | GO Term (Aspect) | Reference | Evidence | Links | Page history |
|---|
| unacceptable | Jheins2,
Team Green B | ECOLX:A0A023Z1P7 | GO:2000966 - regulation of cell wall polysaccharide catabolic process (P) | PMID:16615077 | ECO:0000250 sequence similarity evidence used in manual assertion | challenge | C: 2
|
| unacceptable | Jheins2,
Team Green B | NEIME:A0A0G4BQJ3 | GO:2000966 - regulation of cell wall polysaccharide catabolic process (MltA is a lytic transglycosylase of Gram-negative bacteria that cleaves the beta-1,4 glycosidic linkages between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) in peptidoglycan. We have determined the crystal structures of MltA from Neisseria gonorrhoeae and Escherichia coli (NgMltA and EcMltA), which have only 21.5% sequence identity but have 2 main domains separated by a deep grove pointing that they are both MltA proteins.) | PMID:16618494 | ISS: Inferred from Sequence Similarity UniProtKB:A0A023Z1P7
| challenge | C: 3
|
| unacceptable | Parimaj1,
Team Blue A | BPSPP:PORTL | GO:0046798 - viral portal complex (C) | PMID:8467790 | ECO:0000314 direct assay evidence used in manual assertion | challenge | C: 1
|
| unacceptable | Chensi1,
Team Red A | 9CAUD:A0A0K2D047 | GO:0098025 - virus tail, baseplate (C) | other:Blast | ECO:0000250 sequence similarity evidence used in manual assertion | challenge | C: 5
|
| unacceptable | Gilliabb,
Team ContaminatorZ | 9CAUD:A0A024AZP1 | GO:0098015 - virus tail (C) | PMID:25100842 | ECO:0000314 direct assay evidence used in manual assertion | challenge | C: 5
|
| unacceptable | All5,
Team You can't B. cereus | 9CAUD:A0A0K2CZV8 | GO:0008193 - tRNA guanylyltransferase activity (F) | PMID:23844012 | ECO:0000314 direct assay evidence used in manual assertion | challenge | C: 6
|
0 annotations fixed by Amariam1
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