User:Bionzc

My Annotations

Status	Page	Date/Time	GO Term (Aspect)	Reference	Evidence	Notes	Links
acceptable	ECOLI:NIRC	2011-10-20 22:00:32 CDT	GO:0016021 integral to membrane (C)	PMID:2200672	ECO:0000255 match to sequence model evidence used in manual assertion	Figure 5: shows the hydrophobicity of a few nitrate reductase proteins. NirB, NirD, and CysG had relatively equal values of hydrophobic and hydrophilic residues, which indicated that it more closely resembled a protein found inside the cell such as a cytoplasmic protein. On the other hand, NirC had an abundance of hydrophobic residues, which indicates it may be part of the membrane. NirC has also been found to be comparable to a subunit that is part of the cytochrome oxidase polypeptide 1, which is a membrane bound chain of amino acids. Eisenberg and McLachlan created a model to calculate hydrophobicity and amphiphilcity that was used to determine the hydrophobicity of all of these proteins.	challenge
acceptable	CUPNE:Q44012	2011-10-22 13:32:16 CDT	GO:0050421 nitrite reductase (NO-forming) activity (F)	PMID:9023961	ECO:0000315 mutant phenotype evidence used in manual assertion	Figure 3: The wild type and mutants were able to convert nitrate to nitrite. Nitrite added up in the medium and was not able to be reduced to nitrogen oxide. But, with the nirS it was able to.	challenge
acceptable	AZOVI:NIFL	2011-11-05 16:09:57 CDT	GO:0006355 regulation of transcription, DNA-dependent (P)	PMID:8700899	ECO:0000314 direct assay evidence used in manual assertion	Figure 2:NIFL is a regulatory protein that directs the transcriptional activities of nitrogen fixation genes. It does this by interacting with NIFA, which is an enhancer binding protein. Since previous research has shown that NIFL is a flavoprotein, this gene gets reduced in the presence of sodium dithionite. Transcription in inhibited when NIFL is oxidized. Transcriptional activiation can be measured by looking at the formation of open promoter complexes. This figure shows that sodium dithionite did not affect NIFA since the open promoter complexes were formed with or without the addition of sodium dithionite. This figure also shows that with the addition of sodium dithionite to NIFL and NIFA together, which would mean that NIFL is reduced, open promoter complexes were able to be formed. On the other hand, without sodium dithionite, NIFL is oxidized, and no open promoter complexes could be formed.	challenge
acceptable	KLEPN:NTRC	2011-11-05 19:59:26 CDT	GO:0006355 regulation of transcription, DNA-dependent (P)	PMID:2041769	ECO:0000315 mutant phenotype evidence used in manual assertion	Figure 4: NTRC often prohibits transcriptional activation at promoters that need o54. Both the wild-type NTRC-phosphate and the mutant phenotype yielded the protection of -25, -24, and -13 guanine residues; these resides may be necessary for Eo54 recognition. However, -8 and -9 may be responsible for open promoter complexes, and the mutant phenotype is unable to express high levels of -8 and -9, causing the promoter to remain in closed form.	challenge

acceptable:4
unacceptable:0
requires_changes:0
flagged:0

Annotations challenged by Bionzc

Status	Author,Group	Page	GO Term (Aspect)	Reference	Evidence	Links	Page history
acceptable	Dhaase1, Team Step 1 Nitrification	9CREN:Q701V3	GO:0004497 - monooxygenase activity (F)	PMID:16533068	ECO:0000317 genomic context evidence used in manual assertion	challenge	C: 1
acceptable	Lrodgers, Team KremlinOnTheCrum	CRYNJ:PACC	GO:0006351 - DNA-templated transcription (P)	PMID:20174553	ECO:0000315 mutant phenotype evidence used in manual assertion	challenge	C: 3
acceptable	Bionzc, Team Denitrifiers	CUPNE:Q44012	GO:0050421 - nitrite reductase (NO-forming) activity (F)	PMID:9023961	ECO:0000315 mutant phenotype evidence used in manual assertion	challenge	C: 2

0 annotations fixed by Bionzc