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Contributes toGO:0009927histidine phosphotransfer kinase activity17237174:17237174ECO:0000275 IDA: Inferred from Direct AssayMolecular Function
In a microarray experiment, B-glucuronidase activity was used to determine relative expression levels of uidA+ transcription fusion proteins (Fig 2). Smc00888 is a regulatory factor involved in c-di-GMP signaling that encodes a histidine kinase. During stationary phase, SMc00888 locus expression decreased three-fold in the cbrA::Tn5 mutant compared to WT. The cbrA gene putatively encodes for histidine kinase and was found to be a regulator of the ci-di-GMP signaling pathway.
complete
This annotation made on page: RHIME:Q92RW9
By: CXie (group Team Red B 2019) on 2019-03-31 16:42:15 CDT.




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Entry TypeChallenging User,GroupTime/DateChallenge ReasonPoints/Assessment
ChallengePMariano,
Team Blue B 2019
2019-04-15 09:29:57 CDT

If your annotation is categorized as a biological process, I think you can just leave the qualifier blank. In addition, there appears to be positive regulation of histidine kinase that is supported by beta-glucuronidase transcription fusion evidence.

2
ChallengeKAtanasoff,
Team Blue A 2019
2019-04-01 10:23:50 CDT

Beta-glucuronidase activity is not measured using an expression microarray assay (as your ECO term specifies), since it's not directly measuring the actual transcription levels of a particular gene. Rather, it looks like in the paper, the experimenters generated a cbrA deletion mutant, which was then used to show (in figure 2) that the CbrA protein affects expression of different regulatory proteins. So I think your GO term as well as your ECO term is inappropriate for this particular annotation.

None, yet.
Public
Assessment
Ivanerill2019-04-22 09:36:01 CDT

As mentioned before, Fig. 2 does not demonstrate "protein histidine kinase activity", just transcriptional regulation of a gene with such activity. Notes should clearly map to the experimental support for the specific GO term being asserted.

Requires Changes
Protein
Publication
Qualifier
Go term
Evidence
With/From
Notes
Unique/Original
Public
Assessment
DanielRenfro2019-04-21 17:16:19 CDT

This annotation has been flagged because it has been edited since last assessment

Qualifier GO ID GO term name Reference ECO ID ECO term name with/from Aspect Extension Notes Status
GO:0004673 protein histidine kinase activity PMID:17237174 ECO:0005641 IMP: Inferred from Mutant Phenotype F B-glucuronidase activity was used to determine relative gene expression levels of uidA+ transcription fusion proteins, Smc00887 and Smc00888 (Fig 2). Smc00888 encodes a histidine kinase. During stationary phase, SMc00888 locus expression decreased three-fold in the cbrA::Tn5 mutant compared to WT. complete
CACAO 13661
on RHIME:Q92RW9
Flagged
Public
Assessment
Ivanerill2019-04-18 11:00:51 CDT

Remove "The cbrA gene putatively encodes for histidine kinase." from the notes. The evidence does not support that "histidine kinase activity" is regulated, just the expression of the gene that encodes it. Check http://geneontology.org/docs/go-annotations/ for use of qualifiers.

Requires Changes
Protein
Publication
Qualifier
Go term
Evidence
With/From
Notes
Unique/Original
Public
Assessment
DanielRenfro2019-04-17 10:37:49 CDT

This annotation has been flagged because it has been edited since last assessment

Qualifier GO ID GO term name Reference ECO ID ECO term name with/from Aspect Extension Notes Status
GO:0010864 regulation of gene expression PMID:17237174 ECO:0005641 IMP: Inferred from Mutant Phenotype P B-glucuronidase activity was used to determine relative gene expression levels of uidA+ transcription fusion proteins, Smc00887 and Smc00888 (Fig 2). Smc00888 encodes a histidine kinase. During stationary phase, SMc00888 locus expression decreased three-fold in the cbrA::Tn5 mutant compared to WT. The cbrA gene putatively encodes for histidine kinase. complete
CACAO 13661
on RHIME:Q92RW9
Flagged
Public
Assessment
DanielRenfro2019-04-15 09:29:57 CDT

This annotation has been flagged because it has been challenged since last assessment

Flagged
Public
Assessment
Ivanerill2019-04-08 17:06:33 CDT

See http://geneontology.org/docs/go-annotations/ for usage of the "contributes to" qualifier. Use cross-product of evidence with "manual assertion" for your ECO. The type of regulation is demonstrated quite clearly in the Figure. You should annotate to that more specific term. This (Fig.2) is not a microarray analysis result. Read the paper carefully. Your notes also have more conclusions than what the figure warrants.

Requires Changes
Protein
Publication
Qualifier
Go term
Evidence
With/From
Notes
Public
Assessment
DanielRenfro2019-04-03 09:54:36 CDT

This annotation has been flagged because it has been edited since last assessment

Qualifier GO ID GO term name Reference ECO ID ECO term name with/from Aspect Extension Notes Status
Contributes to GO:0010468 regulation of gene expression PMID:17237174 ECO:0001804 IMP: Inferred from Mutant Phenotype P In a microarray experiment, B-glucuronidase activity was used to determine relative gene expression levels of uidA+ transcription fusion proteins, Smc00887 and Smc00888 (Fig 2). Smc00888 is a regulatory factor involved in c-di-GMP signaling that encodes a histidine kinase. During stationary phase, SMc00888 locus expression decreased three-fold in the cbrA::Tn5 mutant compared to WT. The cbrA gene putatively encodes for histidine kinase and was found to be a regulator of the ci-di-GMP signaling pathway. complete
CACAO 13661
on RHIME:Q92RW9
Flagged