Table of contents

Summary

GAF summary

Found 312 annotations in 317 lines.

GAF Validation Summary Errors are reported first.

For rule GO_AR:0000014 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000014) Valid GO term ID, there are 9 violations with type Error.

For rule GO_AR:0000014 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000014) Valid GO term ID, there are 14 violations with type Warning.

GAF Prediction Summary

Found 2 predictions, see prediction file for details.

Used Ontology Summary

go/extensions/go-gaf

Report

SUMMARY

STATISTICS

MESSAGES

ERROR

WARNING

OWLTools check

#Line number RuleID ViolationType Message Line
#------------
#------------
# Validation for #312 annotations in 317 lines
#------------
#Line number RuleID ViolationType Message Line
#------------
# GO_AR:0000014 Valid GO term ID Error count: 9
30 GO_AR:0000014 Error The id 'GO:0016563' in the annotation is an obsolete class ASAP ABF-0015085 ompR GO:0016563 PMID:17573480 IMP F DNA-binding response regulator in two-component regulatory system with EnvZ gene taxon:198628 20080212 ASAP
31 GO_AR:0000014 Error The id 'GO:0016564' in the annotation is an obsolete class ASAP ABF-0015085 ompR GO:0016564 PMID:17573480 IMP F DNA-binding response regulator in two-component regulatory system with EnvZ gene taxon:198628 20080212 ASAP
40 GO_AR:0000014 Error The id 'GO:0016563' in the annotation is an obsolete class ASAP ABF-0015577 hrpL GO:0016563 PMID:7592386 ISA ASAP:ACW-0293760 F RNA polymerase sigma-54 factor rpoN gene taxon:198628 20080225 ASAP
84 GO_AR:0000014 Error The id 'GO:0030528' in the annotation is an obsolete class ASAP ABF-0016089 pecS GO:0030528 PMID:18790868 IMP F DNA-binding transcriptional regulatory protein PecS gene taxon:198628 20080130 ASAP
89 GO_AR:0000014 Error The id 'GO:0016564' in the annotation is an obsolete class ASAP ABF-0016544 scrR GO:0016564 PMID:10986236 ISA ASAP:ACW-0289472 F "Fructose repressor FruR, LacI family" gene taxon:198628 20080117 ASAP
167 GO_AR:0000014 Error The id 'GO:0016563' in the annotation is an obsolete class ASAP ABF-0018901 rhaS GO:0016563 PMID:14982630 IMP F "DNA-binding transcriptional activator, L-rhamnose-binding" JW3876|rhaC|ECK3898 gene taxon:198628 20080123 ASAP
191 GO_AR:0000014 Error The id 'GO:0016564' in the annotation is an obsolete class ASAP ABF-0019414 expR GO:0016564 PMID:16831870 IDA F DNA-binding transcriptional regulatory protein ExpR gene taxon:198628 20080208 ASAP
221 GO_AR:0000014 Error The id 'GO:0016563' in the annotation is an obsolete class ASAP ABF-0019594 hrpS GO:0016563 PMID:7592386 ISA ASAP:ACW-0293740 F HrpS type III protein secretion system regulatory protein gene taxon:198628 20080225 ASAP
260 GO_AR:0000014 Error The id 'GO:0016564' in the annotation is an obsolete class ASAP ABF-0020117 kdgR GO:0016564 PMID:1840643 IDA F DNA-binding transcriptional regulatory protein KdgR gene taxon:198628 20080115 ASAP
#------------
# GO_AR:0000014 Valid GO term ID Warning count: 14
28 GO_AR:0000014 Warning The id 'GO:0045941' in the annotation is an alternate id for: GO:0045893 ASAP ABF-0015085 ompR GO:0045941 PMID:17573480 IMP P DNA-binding response regulator in two-component regulatory system with EnvZ gene taxon:198628 20080212 ASAP
29 GO_AR:0000014 Warning The id 'GO:0016481' in the annotation is an alternate id for: GO:0045892 ASAP ABF-0015085 ompR GO:0016481 PMID:17573480 IMP P DNA-binding response regulator in two-component regulatory system with EnvZ gene taxon:198628 20080212 ASAP
37 GO_AR:0000014 Warning The id 'GO:0032022' in the annotation is an alternate id for: GO:0090606 ASAP ABF-0015577 hrpL GO:0032022 PMID:15629935 IMP P RNA polymerase sigma-54 factor rpoN gene taxon:198628 20080131 ASAP
39 GO_AR:0000014 Warning The id 'GO:0045941' in the annotation is an alternate id for: GO:0045893 ASAP ABF-0015577 hrpL GO:0045941 PMID:7592386 ISA ASAP:ACW-0293760 P RNA polymerase sigma-54 factor rpoN gene taxon:198628 20080225 ASAP
86 GO_AR:0000014 Warning The id 'GO:0045449' in the annotation is an alternate id for: GO:0006355 ASAP ABF-0016089 pecS GO:0045449 PMID:18790868 IMP P DNA-binding transcriptional regulatory protein PecS gene taxon:198628 20080130 ASAP
88 GO_AR:0000014 Warning The id 'GO:0016481' in the annotation is an alternate id for: GO:0045892 ASAP ABF-0016544 scrR GO:0016481 PMID:10986236 ISA ASAP:ACW-0289472 P "Fructose repressor FruR, LacI family" gene taxon:198628 20080117 ASAP
166 GO_AR:0000014 Warning The id 'GO:0045941' in the annotation is an alternate id for: GO:0045893 ASAP ABF-0018901 rhaS GO:0045941 PMID:14982630 IMP P "DNA-binding transcriptional activator, L-rhamnose-binding" JW3876|rhaC|ECK3898 gene taxon:198628 20080123 ASAP
207 GO_AR:0000014 Warning The id 'GO:0032022' in the annotation is an alternate id for: GO:0090606 ASAP ABF-0019590 hrcJ GO:0032022 PMID:15629935 IMP P "Type III secretion bridge between inner and outermembrane lipoprotein (YscJ,HrcJ,EscJ, PscJ)" gene taxon:198628 20080131 ASAP
214 GO_AR:0000014 Warning The id 'GO:0032022' in the annotation is an alternate id for: GO:0090606 ASAP ABF-0019593 hrpA GO:0032022 PMID:15629935 IMP P Hrp pili protein hrpA gene taxon:198628 20080131 ASAP
218 GO_AR:0000014 Warning The id 'GO:0032022' in the annotation is an alternate id for: GO:0090606 ASAP ABF-0019594 hrpS GO:0032022 PMID:15629935 IMP P HrpS type III protein secretion system regulatory protein gene taxon:198628 20080131 ASAP
220 GO_AR:0000014 Warning The id 'GO:0045941' in the annotation is an alternate id for: GO:0045893 ASAP ABF-0019594 hrpS GO:0045941 PMID:7592386 ISA ASAP:ACW-0293740 P HrpS type III protein secretion system regulatory protein gene taxon:198628 20080225 ASAP
225 GO_AR:0000014 Warning The id 'GO:0032022' in the annotation is an alternate id for: GO:0090606 ASAP ABF-0019598 hrpY GO:0032022 PMID:15629935 IMP P "DNA-binding response regulator, LuxR family, near polyamine transporter" gene taxon:198628 20080131 ASAP
229 GO_AR:0000014 Warning The id 'GO:0032022' in the annotation is an alternate id for: GO:0090606 ASAP ABF-0019600 hrpX GO:0032022 PMID:15629935 IMP P type III protein secretion system sensor kinase gene taxon:198628 20080131 ASAP
259 GO_AR:0000014 Warning The id 'GO:0016481' in the annotation is an alternate id for: GO:0045892 ASAP ABF-0020117 kdgR GO:0016481 PMID:1840643 IDA P DNA-binding transcriptional regulatory protein KdgR gene taxon:198628 20080115 ASAP
#------------

Predictions

GO:0006508 proteolysis AnnotationPropagation P GO:0008237 metallopeptidase activity IDA
GO:0010466 negative regulation of peptidase activity AnnotationPropagation P GO:0030414 peptidase inhibitor activity IDA

Predictions (experimental)

N/A