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

ABE-0007826 (oxc) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0007826 showshow history
Names
oxc yfdU JW2370 ECK2369 b2373
Product
oxalyl-CoA decarboxylase
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 2490256 2491950 1695 565
Sequence

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View sequence with flanking regions: bases upstream and bases downstream

Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR000399 (IPR000399 TPP-binding enzyme, conserved site) Apr 2008
Automated Process Approved IPR012275 (IPR012275 (DEPRECATED) 2-hydroxyphytanoyl-CoA lyase/oxalyl-CoA decarboxylase) Apr 2008
Automated Process Approved IPR012001 (IPR012001 Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain) Apr 2008
Automated Process Approved IPR012000 (IPR012000 Thiamine pyrophosphate enzyme, central domain) Apr 2008
Automated Process Approved IPR011766 (IPR011766 Thiamine pyrophosphate enzyme, C-terminal TPP-binding) Apr 2008
Automated Process Approved IPR017660 (IPR017660 Oxalyl-CoA decarboxylase) Jul 2018
Automated Process Approved IPR029035 (IPR029035 DHS-like NAD/FAD-binding domain superfamily) Jul 2018
Automated Process Approved IPR029061 (IPR029061 Thiamin diphosphate-binding fold) Jul 2018
Automated Process Approved PF00205 (PF00205 Thiamine pyrophosphate enzyme, central domain) Jul 2018
Automated Process Approved PF02775 (PF02775 Thiamine pyrophosphate enzyme, C-terminal TPP binding domain) Jul 2018
Automated Process Approved PF02776 (PF02776 Thiamine pyrophosphate enzyme, N-terminal TPP binding domain) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Automated Process Uncurated GO biological process GO:0033611 oxalate catabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR017660
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Uncurated GO molecular function GO:0008949 oxalyl-CoA decarboxylase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR017660
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Uncurated GO molecular function GO:0046872 metal ion binding GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR017660
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:IPR011766
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0030976 thiamine pyrophosphate binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000399
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0000287 magnesium ion binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000399
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0016740 transferase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000399
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0016830 carbon-carbon lyase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR012275
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name oxc Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK2369 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym yfdU Published Annotation - Swiss-Prot Accession Number: P78093 Jan 2006
Person Approved synonym JW2370 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b2373 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product oxalyl-CoA decarboxylase Published Annotation - EcoCyc Accession Number: G7236
Reference: Escherichia coli K-12 MG1655 		Oct 2021
Automated Process Approved alternate product name oxalyl CoA decarboxylase, ThDP-dependent Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved alternate product name predicted oxalyl-CoA decarboxylase Published Annotation - PubMed ID: 16397293 Jan 2006
Person Uncurated alternate product name putative oxalyl-CoA decarboxylase Published Annotation - Database Name: GenProtEC Jan 2006
Person Uncurated alternate product name probable oxalyl-CoA decarboxylase Published Annotation - Swiss-Prot Accession Number: P78093 Jan 2006
Protein Family
Automated Process Approved protein family IPR012275 (DEPRECATED) 2-hydroxyphytanoyl-CoA lyase/oxalyl-CoA decarboxylase Protein Sequence Similarity - InterPro Domain: IPR012275
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR000399 TPP-binding enzyme, conserved site Protein Sequence Similarity - InterPro Domain: IPR000399
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR012001 Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain Protein Sequence Similarity - InterPro Domain: IPR012001
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR029061 Thiamin diphosphate-binding fold Protein Sequence Similarity - InterPro Domain: IPR029061
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR011766 Thiamine pyrophosphate enzyme, C-terminal TPP-binding Protein Sequence Similarity - InterPro Domain: IPR011766
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR017660 Oxalyl-CoA decarboxylase Protein Sequence Similarity - InterPro Domain: IPR017660
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF00205 Thiamine pyrophosphate enzyme, central domain Protein Sequence Similarity - PFAM Model Name: PF00205
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF02775 Thiamine pyrophosphate enzyme, C-terminal TPP binding domain Protein Sequence Similarity - PFAM Model Name: PF02775
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR029035 DHS-like NAD/FAD-binding domain superfamily Protein Sequence Similarity - InterPro Domain: IPR029035
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF02776 Thiamine pyrophosphate enzyme, N-terminal TPP binding domain Protein Sequence Similarity - PFAM Model Name: PF02776
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR012000 Thiamine pyrophosphate enzyme, central domain Protein Sequence Similarity - InterPro Domain: IPR012000
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Other
Person Approved EC number 4.1.1.8 Published Annotation - Swiss-Prot Accession Number: P0AFI0 Feb 2006
Person Uncurated MultiFun 1.7.1 (metabolism; central intermediary metabolism; unassigned reversible reactions) 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 UniProtKB/Swiss-Prot:P0AFI0 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P0AFI0 Published Annotation - Swiss-Prot Accession Number: P0AFI0 Jan 2006
Automated Process Approved db xref ASAP:ABE-0007826 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:946845 Published Annotation - Entrez Gene Database ID: 946845
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref GI:1788716 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG14143 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved function enzyme; Oxalate catabolism Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC75432.1 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Uncurated subcellular localization Unknown Predicted by PSORTb - PSORTb Final_Score: 2.00
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 Uncurated GO biological process GO:0033611 oxalate catabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR017660
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0016740 transferase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000399
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0000287 magnesium ion binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000399
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0030976 thiamine pyrophosphate binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000399
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO molecular function GO:0046872 metal ion binding GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR017660
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Uncurated GO molecular function GO:0008949 oxalyl-CoA decarboxylase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR017660
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:IPR011766
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0016830 carbon-carbon lyase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR012275
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-0005197 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0003811 oxc CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0004155 oxc CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003550 oxc CDS
Ortholog
Person Uncurated Go view Dickeya dadantii 3937 ABF-0016185 oxc CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0005380 CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0002416 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0008859 oxc CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0002348 CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0001917 oxc CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0006869 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0008244 CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0005537 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0079047 oxc CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0002721 oxc CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0003191 oxc CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0008246 CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0005983 CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0002717 oxc CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0007095 CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0005475 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0006947 oxc CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0005469 oxc CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0006909 CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0006494 CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0008445 oxc CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0005491 CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0006232 oxc CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0009325 CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0010354 CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0009117 CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0008434 CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0007594 CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0027347 oxc CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0008993 oxc CDS
Automated Process Approved Go view Escherichia coli HS ADR-0007183 CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0002927 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0002236 oxc CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0002451 oxc CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0002903 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0002822 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0002782 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0002738 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0176898 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0002712 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0002522 CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0133265 oxc CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0003567 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0002713 CDS
Automated Process Uncurated Go view Musicola paradisiaca Ech703 AGA-0007340 CDS
Person Approved Go view Shigella boydii 227 ADV-0002653 CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0008151 oxc CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0005338 CDS
Person Approved Go view Shigella dysenteriae 197 ADU-0002952 CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0073723 CDS
Person Approved Go view Shigella flexneri 301 ABT-0088700 CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0002604 CDS
Person Approved Go view Shigella sonnei 046 ADD-0002698 oxc 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)
Strains to toptop

Strains with mutations in this feature.

Strain NameStrain TypeStrain InformationStrain RequestFeatureIDNameMutation DetailsExperiments Using StrainSubmitter
FB22626mutantTn5 InsertionRequest the StrainABE-0007826oxcb2373::Tn5KAN-I-SceI at position 1248 in Minus orientation ,+ pKD460Blattner 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 2485256 to 2496950
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0007819evgSCDSforward24843742487967Downstream
ABE-0007821yfdECDScomplement24880232489168Downstream
ABE-0007824yfdVCDScomplement24892422490186Downstream
ABE-0007826oxcCDScomplement24902562491950Matches
ABE-0007828frcCDScomplement24920042493254Upstream
ABE-0007835yfdXCDScomplement24937672494402Upstream
ABE-0007839ypdICDSforward24946982494973Upstream
ABE-0007841yfdYCDScomplement24950502495292Upstream
ABE-0007848lpxPCDSforward24956452496565Upstream
ABE-0285223ypdKCDSforward24969212496992Upstream
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.