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

ABE-0013975 (idnD) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0013975 showshow history
Names
idnD yjgV JW4224 ECK4260 b4267
Product
L-idonate 5-dehydrogenase
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 4493375 4494406 1032 344
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR013149 (IPR013149 Alcohol dehydrogenase, C-terminal) Apr 2008
Automated Process Approved IPR002085 (IPR002085 (DEPRECATED) Alcohol dehydrogenase superfamily, zinc-type) Apr 2008
Automated Process Approved IPR011032 (IPR011032 GroES-like superfamily) Apr 2008
Automated Process Approved IPR013154 (IPR013154 Alcohol dehydrogenase, N-terminal) Apr 2008
Automated Process Approved IPR036291 (IPR036291 NAD(P)-binding domain superfamily) Jul 2018
Automated Process Approved PF00107 (PF00107 Zinc-binding dehydrogenase) Jul 2018
Automated Process Approved PF08240 (PF08240 Alcohol dehydrogenase GroES-like domain) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Automated Process Uncurated GO biological process GO:0055114 (OBSOLETE) oxidation-reduction process GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR013149, IPR013154
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Person Uncurated GO biological process GO:0016052 carbohydrate catabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
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 Approved GO molecular function GO:0016491 oxidoreductase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR002085
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0008270 zinc ion binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR002085
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name idnD Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym ECK4260 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym JW4224 Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved synonym yjgV Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved locus tag b4267 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product L-idonate 5-dehydrogenase Published Annotation - PubMed ID: 16397293
Reference: Escherichia coli K-12 		Oct 2021
Person Uncurated alternate product name L-idonate 5-dehydrogenase, NAD-binding Published Annotation - Database Name: GenProtEC Jan 2006
Person Uncurated alternate product name L-idonate dehydrogenase Experimental - PubMed ID: 9658018
Reference: Escherichia coli 		Jan 2006
Protein Family
Automated Process Approved protein family IPR013149 Alcohol dehydrogenase, C-terminal Protein Sequence Similarity - InterPro Domain: IPR013149
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR002085 (DEPRECATED) Alcohol dehydrogenase superfamily, zinc-type Protein Sequence Similarity - InterPro Domain: IPR002085
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR013154 Alcohol dehydrogenase, N-terminal Protein Sequence Similarity - InterPro Domain: IPR013154
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR036291 NAD(P)-binding domain superfamily Protein Sequence Similarity - InterPro Domain: IPR036291
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF00107 Zinc-binding dehydrogenase Protein Sequence Similarity - PFAM Model Name: PF00107
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF08240 Alcohol dehydrogenase GroES-like domain Protein Sequence Similarity - PFAM Model Name: PF08240
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR011032 GroES-like superfamily Protein Sequence Similarity - InterPro Domain: IPR011032
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Other
Person Approved EC number 1.1.1.264 Published Annotation - Swiss-Prot Accession Number: P39346 Feb 2006
Person Uncurated MultiFun 1.1.1 (metabolism; carbon utilization; carbon compounds) 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
Person Approved db xref UniProtKB:P39346 Published Annotation - Swiss-Prot Accession Number: P39346 Jan 2005
Automated Process Approved db xref GeneID:944769 Published Annotation - Entrez Gene Database ID: 944769
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref GI:1790718 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P39346 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0013975 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG12541 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved function putative enzyme; Not classified Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved note GO_process: GO:0016052 - carbohydrate catabolic process Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC77224.1 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: 9.26
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Person Uncurated subsystem component of in silico model iMC1010 Experimental - PubMed ID: 15129285
Reference: Escherichia coli K-12 MG1655 		Mar 2009
Person Uncurated subsystem component of in silico model iAF1260 Experimental - PubMed ID: 17593909
Reference: Escherichia coli K-12 MG1655 		Jan 2009
Person Uncurated subsystem component of in silico model iJR904 Experimental - PubMed ID: 12952533
Reference: Escherichia coli K-12 MG1655 		Feb 2009
Automated Process Approved transl table 11 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Gene Ontology
Person Uncurated GO biological process GO:0016052 carbohydrate catabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Uncurated GO biological process GO:0055114 (OBSOLETE) oxidation-reduction process GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR013149, IPR013154
Reference: Escherichia coli K-12 MG1655 		Jul 2018
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 Approved GO molecular function GO:0008270 zinc ion binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR002085
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0016491 oxidoreductase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR002085
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-0004137 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0004025 idnD CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0003835 idnD CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0003184 idnD CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0004318 idnD CDS
Ortholog
Automated Process Uncurated Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0003918 idnD CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0004568 CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0004411 idnD CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0009143 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0081582 idnD CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0005692 idnD CDS
Automated Process Approved Go view Escherichia coli HS ADR-0009211 idnD CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0003943 idnD CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0004356 idnD CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0179110 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0004740 idnD CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0004883 idnD CDS
Automated Process Uncurated Go view Ewingella americana ATCC 33852 [T] AMA-0003600 CDS
Automated Process Uncurated Go view Musicola paradisiaca Ech703 AGA-0004607 CDS
Automated Process Uncurated Go view Pantoea sp. At-9b AGM-0011208 CDS
Automated Process Uncurated Go view Pectobacterium brasiliensis 1692 AED-0003092 CDS
Person Uncurated Go view Pectobacterium carotovorum WPP14 ADT-0002379 CDS
Automated Process Uncurated Go view Salmonella Agona SL483 BBX-0008929 CDS
Person Uncurated Go view Salmonella Choleraesuis SC-B67 ADB-0005117 idnD CDS
Automated Process Uncurated Go view Salmonella Dublin CT_02021853 BCB-0009107 CDS
Automated Process Uncurated Go view Salmonella Enteritidis P125109 BCF-0014000 idnD CDS
Automated Process Uncurated Go view Salmonella Gallinarum 287/91 BCG-0013242 idnD CDS
Automated Process Uncurated Go view Salmonella Hadar RI_05P066 BBT-0006953 CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL476 BBV-0009242 CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL486 BBW-0007678 CDS
Automated Process Uncurated Go view Salmonella Javiana GA_MM04042433 BCA-0004215 CDS
Automated Process Uncurated Go view Salmonella Kentucky CDC 191 BBZ-0007190 CDS
Automated Process Uncurated Go view Salmonella Kentucky CVM29188 BBP-0008293 CDS
Automated Process Uncurated Go view Salmonella Newport SL254 BBQ-0009177 CDS
Automated Process Uncurated Go view Salmonella Newport SL317 BBR-0006204 CDS
Automated Process Uncurated Go view Salmonella Paratyphi A AKU_12601 BCH-0004317 CDS
Person Uncurated Go view Salmonella Paratyphi A ATCC 9150 ADA-0004279 idnD CDS
Automated Process Uncurated Go view Salmonella Paratyphi B SPB7 BCC-0005666 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA23 BBN-0004549 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA29 BBM-0006519 CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund CVM19633 BBO-0008800 CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund SL480 BBY-0004128 CDS
Automated Process Uncurated Go view Salmonella Typhimurium 14028S AJR-0005388 idnD CDS
Person Approved Go view Salmonella Typhimurium LT2 [T] ABU-0103776 idnD CDS
Automated Process Uncurated Go view Salmonella Virchow SL491 BBS-0004650 CDS
Automated Process Uncurated Go view Salmonella Weltevreden SL484 BBU-0007365 CDS
Automated Process Uncurated Go view Salmonella enterica CVM23701 BBL-0005610 CDS
Automated Process Uncurated Go view Serratia marcescens subsp. marcescens ATCC 13880 [T] AMF-0002431 CDS
Person Approved Go view Shigella sonnei 046 ADD-0004834 idnD 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 4488375 to 4499406
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0013960lptGCDSforward44873184488400Downstream
ABE-0285696repeat_regionforward44885054488540Downstream
ABE-0013963yjgRCDScomplement44885614490063Downstream
ABE-0013966idnRCDScomplement44901414491139Downstream
ABE-0013969idnTCDScomplement44912064492525Downstream
ABE-0013971idnOCDScomplement44925874493351Downstream
ABE-0013975idnDCDScomplement44933754494406Matches
ABE-0013980idnKCDSforward44946234495186Upstream
ABE-0013982ahrCDScomplement44951904496209Upstream
ABE-0013986leuXtRNAforward44964054496489Upstream
ABE-0234214KpLE2prophageforward44965404536609Upstream
ABE-0013992intBpseudogeneforward44966754497940Upstream
ABE-0013997is_elementcomplement44981814499511Upstream
ABE-0285697mobile_elementforward44981814499511Upstream
ABE-0013999insC-6CDSforward44982724498637Upstream
ABE-0014001insD-6CDSforward44985954499500Upstream
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.