Phage Hunters Spring 2016
My Annotations
| Status | Page | Date/Time | GO Term (Aspect) | Reference | Evidence | Notes | Links |
|---|
| unacceptable | 9CAUD:A0A0K2CZS7 | 2016-03-28 10:31:25 CDT | GO:0016987 sigma factor activity (F) | PMID:11274153 | ECO:0000315 mutant phenotype evidence used in manual assertion | The authors created a plasmid construct with a promoterless Lacz and a random segment of E.coli Genomic DNA and transformed E.coli with it. RNA polymerase Sigma E factor fuctions under heat shock conditions. The colonies were placed under heat shock conditions. Those expressing Lacz were selected. These then went through a further selection process in order to determine the genes the sigma factor regualtes and the promoters it target. They also used mutants of RseA, which antagonized the sigma factor, to determine if RseA also regulates those genes effected by the sigma factor, as well as finding more promoters acted on by the sigma factor.
| challenge |
| unacceptable | ECOLI:RPOE | 2016-04-04 06:58:10 CDT | GO:0016987 sigma factor activity (F) | PMID:11274153 | ECO:0000315 mutant phenotype evidence used in manual assertion | The authors created a plasmid construct with a promoterless Lacz and a random segment of E.coli Genomic DNA and transformed E.coli with it. RNA polymerase Sigma E factor fuctions under heat shock conditions. The colonies were placed under heat shock conditions. Those expressing Lacz were selected. These then went through a further selection process in order to determine the genes the sigma factor regualtes and the promoters it target. They also used mutants of RseA, which antagonized the sigma factor, to determine if RseA also regulates those genes effected by the sigma factor, as well as finding more promoters acted on by the sigma factor.
| challenge |
| unacceptable | BACSU:RPSB | 2016-04-10 06:49:08 CDT | GO:0080134 regulation of response to stress (P) | PMID:10383961 | ECO:0000315 mutant phenotype evidence used in manual assertion | The authors used a null mutation of the sigma b factor to determine whether it would effect the survival of the bacteria under various conditions. A large drop in survival was found in bacteria with the null mutation under heat, ethanol, shock, salt, and acid stress.
| challenge |
| unacceptable | BACSU:RPSB | 2016-04-10 07:15:37 CDT | GO:0016987 sigma factor activity (F) | PMID:8320211 | ECO:0000315 mutant phenotype evidence used in manual assertion | The authors performed transformations on B. subtilis in order to inactivate the sigma B factor by introducing a null sigma B factor mutation. These bacteria had a socB1 frameshift mutation which inhibited a negative regulator of Sigma B factor, thus increasing the amount of sigma B factor produced in cells without the null mutation of sigma B factor, increasing the experiments sensitivity. They then monitored the gene expression of the bacteria by measuring the amount of b-galactosidase activity produced within them due to a lacz fusion with random genes on the B.subtilis genome. By locating the the fusion and measuring their activity, they found which genes were dependent to an extent on sigma B factor for activation by finding those with altered B-galactosidase activity.
| challenge |
| unacceptable | 9CAUD:A0A0K2D0H6 | 2016-04-11 01:24:42 CDT | GO:0016987 sigma factor activity (F) | PMID:8320211 | ECO:0000317 genomic context evidence used in manual assertion | HHpred consistently showed the first section of the gene being homologous to a B.subtilis sigma factor followed by a translocase. For its similarity to sigma B factor, it had a probability of 99.97 and a E-value of 1.3e-28. In addition, numerous blast results showed many B. subtitles sigma factors with reasonable similarity to the first portion of the gene. The best blast result for sigma factor B had a query cover of 43% and a E-value of 5e-27. This strongly suggests that this gene is homologous to sigma factor B as well as sigma factors from B. subtilis in general, suggesting that it likely functions as one.
| challenge |
| unacceptable | BACIU:A0A0D5D509 | 2016-04-10 11:48:33 CDT | GO:0009294 DNA mediated transformation (The authors purified DprA, RecA, SsbA, and SsbB. They then measured the ssDNA-dependent dATP hydrolysis activity of RecA after the ssDNA was coated with nothing, DprA, SsbA and SsbB, or SsbA and SsbB followed by DprA. It was found that DprA facilitated RecA nucleation onto SSB coated ssDNA and DNA strand annealing. Experimentation with RecA in the presence of DprA also showed that DprA assisted in DNA strand exchange. In addition, it was found that DprA was important in plasmid transformation as plasmid transformation was impaired in ΔdprA ΔrecA mutant cells.) | PMID:25138221 | IDA: Inferred from Direct Assay | | challenge |
acceptable:0
unacceptable:6
requires_changes:0
flagged:0
Annotations challenged by Di46616
| Status | Author,Group | Page | GO Term (Aspect) | Reference | Evidence | Links | Page history |
|---|
| 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 | Natjack1,
Team Green B | 9CAUD:A0A0K2CZV8 | GO:0003896 - DNA primase activity (F) | GO_REF:0000100 | ECO:0000250 sequence similarity evidence used in manual assertion | challenge | C: 3
|
| unacceptable | Natjack1,
Team Green B | 9CAUD:A0A0K2CZZ1 | GO:0004604 - phosphoadenylyl-sulfate reductase (thioredoxin) activity (F) | GO_REF:0000100 | ECO:0000250 sequence similarity evidence used in manual assertion | challenge | C: 3
|
| acceptable | Eleo1,
Team Red B | BPTU2:Q9AYV6 | GO:0098023 - virus tail, tip (C) | PMID:15150235 | ECO:0000314 direct assay evidence used in manual assertion | challenge | C: 4
|
| unacceptable | Carsonrm,
Team ContaminatorZ | 9CAUD:A0A024B1E1 | GO:0098027 - virus tail, sheath (C) | PMID:25517898 | ECO:0000314 direct assay evidence used in manual assertion | challenge | C: 6
|
| unacceptable | Tukrunmi,
Team Phages Woo! | 9CAUD:A0A024B0B2 | GO:0046798 - viral portal complex (C) | PMID:26621622 | ECO:0000250 sequence similarity evidence used in manual assertion | challenge | C: 3
|
| unacceptable | Heatheca,
Team ContaminatorZ | 9CAUD:A0A024B0X2 | GO:0098020 - obsolete virus tail, minor subunit (C) | PMID:22923442 | ECO:0000314 direct assay evidence used in manual assertion | challenge | C: 5
|
| unacceptable | Odilia1,
Team Green B | 9CAUD:A0A0K2CZX3 | GO:0016491 - oxidoreductase activity (F) | PMID:10769150 | ECO:0000266 sequence orthology evidence used in manual assertion | challenge | C: 3
|
| unacceptable | Nwang4,
Team Purple B | HUMAN:PGK1 | GO:0005739 - mitochondrion (C) | PMID:26942675 | ECO:0000314 direct assay evidence used in manual assertion | challenge | C: 2
|
| unacceptable | Di46616,
Team Red A | 9CAUD:A0A0K2CZS7 | GO:0016987 - sigma factor activity (F) | PMID:11274153 | ECO:0000315 mutant phenotype evidence used in manual assertion | challenge | C: 2
|
| unacceptable | Di46616,
Team Red A | BACSU:RPSB | GO:0080134 - regulation of response to stress (P) | PMID:10383961 | ECO:0000315 mutant phenotype evidence used in manual assertion | challenge | C: 4
|
| unacceptable | Di46616,
Team Red A | 9CAUD:A0A0K2D0H6 | GO:0016987 - sigma factor activity (F) | PMID:8320211 | ECO:0000317 genomic context evidence used in manual assertion | challenge | C: 2
|
0 annotations fixed by Di46616
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