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

ABE-0009773 (glcD) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0009773 showshow history
Names
glcD yghM gox JW2946 ECK2974 b2979
Product
glycolate dehydrogenase subunit
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 3126522 3128021 1500 500
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR004490 (IPR004490 Glycolate oxidase subunit GlcD) Apr 2008
Automated Process Approved IPR006094 (IPR006094 FAD linked oxidase, N-terminal) Apr 2008
Automated Process Approved IPR004113 (IPR004113 FAD-linked oxidase, C-terminal) Apr 2008
Automated Process Approved IPR016164 (IPR016164 FAD-linked oxidase-like, C-terminal) Jul 2018
Automated Process Approved IPR036318 (IPR036318 FAD-binding, type PCMH-like superfamily) Jul 2018
Automated Process Approved PF02913 (PF02913 FAD linked oxidases, C-terminal domain) Jul 2018
Automated Process Approved PF01565 (PF01565 FAD binding 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: IPR006094
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO biological process GO:0006118 (OBSOLETE) electron transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR006094
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Uncurated GO biological process GO:0016052 carbohydrate catabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO cellular component GO:0009339 glycolate oxidase complex GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004490
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:0016491 oxidoreductase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR006094
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Uncurated GO molecular function GO:0050660 flavin adenine dinucleotide binding GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR004113, IPR006094, IPR016164, IPR036318
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Uncurated GO molecular function GO:0003824 catalytic activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR004113, IPR016164
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0008891 glycolate oxidase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004490
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name glcD Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved synonym yghM Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved synonym gox Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved synonym JW2946 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK2974 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b2979 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product glycolate dehydrogenase subunit Published Annotation - EcoCyc Accession Number: G7545
Reference: Escherichia coli K-12 MG1655 		Oct 2021
Person Approved alternate product name glycolate oxidase subunit, FAD-linked Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved alternate product name glycolate oxidase subunit D Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Person Uncurated alternate product name glycolate oxidase, FAD-linked subunit Published Annotation - Database Name: GenProtEC Jan 2006
Protein Family
Automated Process Approved protein family PF01565 FAD binding domain Protein Sequence Similarity - PFAM Model Name: PF01565
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR036318 FAD-binding, type PCMH-like superfamily Protein Sequence Similarity - InterPro Domain: IPR036318
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF02913 FAD linked oxidases, C-terminal domain Protein Sequence Similarity - PFAM Model Name: PF02913
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR016164 FAD-linked oxidase-like, C-terminal Protein Sequence Similarity - InterPro Domain: IPR016164
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR004113 FAD-linked oxidase, C-terminal Protein Sequence Similarity - InterPro Domain: IPR004113
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR004490 Glycolate oxidase subunit GlcD Protein Sequence Similarity - InterPro Domain: IPR004490
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR006094 FAD linked oxidase, N-terminal Protein Sequence Similarity - InterPro Domain: IPR006094
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Other
Automated Process Uncurated EC number 1.-.-.- Published Annotation - Database Name: EC2GO: GO:0016491
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Person Uncurated EC number 1.3.1.98 Protein Sequence Similarity - InterPro Domain: IPR006094
Reference: Escherichia coli K-12 MG1655 		Mar 2014
Person Uncurated EC number 2.5.1.26 Protein Sequence Similarity - InterPro Domain: IPR004113
Reference: Escherichia coli K-12 MG1655 		Dec 2008
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
Automated Process Approved db xref GeneID:947353 Published Annotation - Entrez Gene Database ID: 947353
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref ASAP:ABE-0009773 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P0AEP9 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG12997 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P0AEP9 Published Annotation - Swiss-Prot Accession Number: P0AEP9 Jan 2006
Automated Process Approved db xref GI:1789351 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved function enzyme; Degradation of small molecules: Carbon compounds Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved note glycolate oxidase subunit D; 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 AAC76015.1 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
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
Automated Process Uncurated GO biological process GO:0055114 (OBSOLETE) oxidation-reduction process GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR006094
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 Approved GO biological process GO:0006118 (OBSOLETE) electron transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR006094
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 Approved GO cellular component GO:0009339 glycolate oxidase complex GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004490
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO molecular function GO:0050660 flavin adenine dinucleotide binding GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR004113, IPR006094, IPR016164, IPR036318
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Uncurated GO molecular function GO:0016491 oxidoreductase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR006094
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Uncurated GO molecular function GO:0003824 catalytic activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR004113, IPR016164
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0008891 glycolate oxidase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004490
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 (205 gammaproteobacteria) APP-0004826 glcD CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0005867 glcD CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0004042 glcD CDS
Ortholog
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0002544 glcD CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0005788 glcD CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0003087 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0008147 glcD CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0003050 glcD CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0001217 glcD CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0006183 CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0010015 GlcD CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0079880 glcD CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0003426 glcD CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0004033 glcD CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0005681 glcD CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0005512 glcD CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0003476 glcD CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0007873 glcD CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0006792 CDS
Automated Process Approved Go view Escherichia coli HS ADR-0007834 glcD CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0003488 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0002780 glcD CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0003050 glcD CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0003617 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0003399 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0003567 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0003424 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0177593 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0003319 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0003255 glcD CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0003403 glcD CDS
Person Uncurated Go view Pseudomonas syringae pv. tomato DC3000 ADG-0003613 glcD CDS
Person Uncurated Go view Shigella flexneri 2457T ABQ-0074400 glcD pseudogene
Person Uncurated Go view Shigella flexneri 301 ABT-0256096 glcD pseudogene
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)
Strains to toptop

Strains with mutations in this feature.

Strain NameStrain TypeStrain InformationStrain RequestFeatureIDNameMutation DetailsExperiments Using StrainSubmitter
FB20998mutantTn5 InsertionRequest the StrainABE-0009773glcDglcD::Tn5KAN-I-SceI at position 1106 in Minus orientation ,+ pKD460Blattner Laboratory
FB20999mutantTn5 InsertionRequest the StrainABE-0009773glcDglcD::Tn5KAN-I-SceI at position 1106 in Minus orientation ,- pKD465Blattner Laboratory
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 3121522 to 3133021
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0009767glcBCDScomplement31216343123805Downstream
ABE-0009769glcGCDScomplement31238273124231Downstream
ABE-0174097glcFCDScomplement31242363125459Downstream
ABE-0174098glcECDScomplement31254703126522Overlaps Downstream
ABE-0009773glcDCDScomplement31265223128021Matches
ABE-0009777glcCCDSforward31282723129036Upstream
ABE-0009779yghOpseudogenecomplement31290433130145Upstream
ABE-0009781is_elementcomplement31301463131340Upstream
ABE-0285567mobile_elementforward31301463131340Upstream
ABE-0009783insH9CDSforward31302143131194Upstream
ABE-0009786yghQpseudogenecomplement31313403132408Upstream
ABE-0285163yghQ_1CDSpcomplement31313413132408Upstream
ABE-0009789yghRCDScomplement31324543133212Upstream
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.