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My Annotations

StatusPageDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
acceptableECOLI:NIRC2011-10-20 22:00:32 CDTGO:0016021 integral to membrane (C)PMID:2200672ECO: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.

acceptableCUPNE:Q440122011-10-22 13:32:16 CDTGO:0050421 nitrite reductase (NO-forming) activity (F)PMID:9023961ECO: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.

acceptableAZOVI:NIFL2011-11-05 16:09:57 CDTGO:0006355 regulation of transcription, DNA-dependent (P)PMID:8700899ECO: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.

acceptableKLEPN:NTRC2011-11-05 19:59:26 CDTGO:0006355 regulation of transcription, DNA-dependent (P)PMID:2041769ECO: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.



Annotations challenged by Bionzc

StatusAuthor,GroupPageGO Term (Aspect)ReferenceEvidenceLinksPage history
Team Step 1 Nitrification
9CREN:Q701V3GO:0004497 - monooxygenase activity (F)PMID:16533068ECO:0000317 genomic context evidence used in manual assertionchallengeC: 1
Team KremlinOnTheCrum
CRYNJ:PACCGO:0006351 - DNA-templated transcription (P)PMID:20174553ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 3
Team Denitrifiers
CUPNE:Q44012GO:0050421 - nitrite reductase (NO-forming) activity (F)PMID:9023961ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 2

0 annotations fixed by Bionzc