Escherichia coli K-12 MG1655
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Working With: Genome: Escherichia coli K-12 MG1655 Version: v3

ABE-0000923 (yagF) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0000923 showshow history
Names
yagF JW0262 ECK0270 b0269
Product
CP4-6 prophage; predicted dehydratase
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 283201 285168 1968 656
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR000581 (IPR000581 Dihydroxy-acid/6-phosphogluconate dehydratase) Apr 2008
Automated Process Approved IPR017798 (IPR017798 D-xylonate dehydratase YjhG/YagF) Jul 2018
Automated Process Approved IPR037237 (IPR037237 IlvD/EDD, N-terminal domain) Jul 2018
Automated Process Approved PF00920 (PF00920 Dehydratase family) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Automated Process Approved GO biological process GO:0008152 metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000581
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO cellular component GO:0005737 cytoplasm GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Automated Process Uncurated GO molecular function GO:0050401 xylonate dehydratase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR017798
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0003824 catalytic activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000581
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name yagF Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym ECK0270 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym JW0262 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b0269 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product CP4-6 prophage; predicted dehydratase Published Annotation - PubMed ID: 16397293 Jan 2006
Person Uncurated alternate product name CP4-6 prophage; putative dehydratase Published Annotation - Database Name: GenProtEC Jan 2006
Person Approved alternate product name putative dehydratase Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Protein Family
Automated Process Approved protein family IPR017798 D-xylonate dehydratase YjhG/YagF Protein Sequence Similarity - InterPro Domain: IPR017798
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR000581 Dihydroxy-acid/6-phosphogluconate dehydratase Protein Sequence Similarity - InterPro Domain: IPR000581
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR037237 IlvD/EDD, N-terminal domain Protein Sequence Similarity - InterPro Domain: IPR037237
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF00920 Dehydratase family Protein Sequence Similarity - PFAM Model Name: PF00920
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Automated Process Uncurated EC number 4.2.1.82 Published Annotation - Database Name: EC2GO: GO:0050401
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Person Uncurated EC number 4.2.1.9 Protein Sequence Similarity - InterPro Domain: IPR000581
Reference: Escherichia coli K-12 MG1655 		Dec 2008
Person Uncurated MultiFun 8.1 (extrachromosomal; prophage genes and phage related functions) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Automated Process Approved codon start 1 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG13345 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:944928 Published Annotation - Entrez Gene Database ID: 944928
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref GI:1786464 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P77596 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0000923 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P77596 Published Annotation - Swiss-Prot Accession Number: P77596 Jan 2005
Automated Process Approved function Phage or Prophage Related Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved note putative dehydratase Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC73372.1 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Uncurated subcellular localization Cytoplasmic Predicted by PSORTb - PSORTb Final_Score: 8.96
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Automated Process Approved transl table 11 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Gene Ontology
Automated Process Approved GO biological process GO:0008152 metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000581
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO cellular component GO:0005737 cytoplasm GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Automated Process Uncurated GO molecular function GO:0050401 xylonate dehydratase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR017798
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0003824 catalytic activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000581
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Comparative to toptop
Author Approval Details Genome Feature Name Type
Member
Automated Process Uncurated Go view OrthoMCL (14 enterobacteria) AMM-0004169 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0005176 yagF CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0005498 yagF CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0008114 yagF CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0005285 yagF CDS
Ortholog
Automated Process Uncurated Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0003881 ilvD_5 CDS
Experimental to toptop
SelectSetNameSetDetailsNotes
stringent responsetranscriptional profile of the stringent responseNone
Recombinant heat-shock dataexpression data for recombinant strain under heat shockThese data are from the Harcum laboratory. (Jeremy Glasner)
Suppressor tRNA expressionexperiment comparing transcript levels in cells with and without suppressor tRNA expressionThese data were reported in the paper: Herring and Blattner. 2004. Global transcriptional effects of a suppressor tRNA and the inactivation of the regulator frmR. J. Bacteriol. 186(20):6714-20. Link to Abstract (Jeremy Glasner)
Recombinant E. coli expressionexperiment comparing expression of wild-type E. coli with the same strain harboring a plasmid that expresses protein when induced with IPTG These data were reported in the paper: F. T. Haddadin, S. W. Harcum (2005) Transcriptome profiles for high-cell-density recombinant and wild-type Escherichia coli, Biotechnology and Bioengineering, 90:127-153. Link to Abstract (Jeremy Glasner)
Aerobic shiftAerobic shiftThese data were reported in the paper: Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. 2004. Integrating high-throughput and computational data elucidates bacterial networks. Nature. 2004 May 6;429(6987):92-6. Link to Abstract (Jeremy Glasner)
CalibratorCalibrated microarray experiments (50 hybridizations)This data was used in the paper: Allen et al., J. Bacteriol. 185(21):6392-9 (Jeremy Glasner)
AffyData1Affymetrix Experiments (data from 41 chip hybridizations)This data was used in the paper: Allen et al., J. Bacteriol. 185(21):6392-9 (Jeremy Glasner)
Context Table to toptop

Listed below are features that lie nearby this feature. Features encoded in multiple intervals may appear more than once in the table. Features that span the origin will have a left endpoint greater than the right endpoint.

Features overlapping the region 278201 to 290168
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0234205CP4-6prophageforward262958297265Contains
ABE-0285342misc_featureforward262958297265Contains
ABE-0000898afuCCDScomplement277756278802Upstream
ABE-0000900afuBpseudogenecomplement278814279162Upstream
ABE-0000902mobile_elementcomplement279163279930Upstream
ABE-0000906insB-2CDScomplement279178279681Upstream
ABE-0000909insA-2CDScomplement279600279875Upstream
ABE-0000910mobile_elementforward279931280111Upstream
ABE-0285317insI1pseudogeneforward279931280104Upstream
ABE-0285026insXpseudogenecomplement280112280362Upstream
ABE-0285345mobile_elementcomplement280114280425Upstream
ABE-0000912yagBpseudogenecomplement280427280735Upstream
ABE-0000915yagACDScomplement280829281983Upstream
ABE-0000921yagECDSforward282278283186Upstream
ABE-0000923yagFCDSforward283201285168Matches
ABE-0000929yagGCDSforward285395286777Downstream
ABE-0000931yagHCDSforward286789288399Downstream
ABE-0000933xynRCDScomplement288404289162Downstream
ABE-0000939argFCDScomplement289301290305Downstream
Release Notes to toptop
All MG1655 annotations and sequence data are publicly available, and investigators can use these data in publications without contacting the genome curators. This version of the sequence was the source of GenBank record U00096.3. Ongoing annotation updates to that GenBank record are being generated from a collaboration that includes ASAP, EcoGene, the Coli Genetic Stock Center, EcoliHub, EcoCyc, RegulonDB and UniProtKB/Swiss-Prot.