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

ABE-0010242 (tdcE) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0010242 showshow history
Names
tdcE yhaS JW5522 ECK3103 b3114
Product
pyruvate formate-lyase 4/2-ketobutyrate formate-lyase
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 3260124 3262418 2295 765
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 IPR005949 (IPR005949 Formate acetyltransferase) Apr 2008
Automated Process Approved IPR001150 (IPR001150 Glycine radical domain) Apr 2008
Automated Process Approved IPR004184 (IPR004184 Pyruvate formate lyase domain) Apr 2008
Automated Process Approved PF01228 (PF01228 Glycine radical) Jul 2018
Automated Process Approved PF02901 (PF02901 Pyruvate formate lyase-like) 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:IPR001150
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Uncurated GO biological process GO:0009063 cellular amino acid catabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO biological process GO:0005975 carbohydrate metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR005949
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO biological process GO:0006006 glucose metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004184
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Uncurated GO biological process GO:0009061 anaerobic respiration Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Person Uncurated GO biological process GO:0006113 fermentation Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO cellular component GO:0005737 cytoplasm GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR005949
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO cellular component GO:0005737 cytoplasm GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Person Approved GO cellular component GO:0005737 cytoplasm Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO molecular function GO:0003824 catalytic activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001150
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0008861 formate C-acetyltransferase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR005949
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name tdcE Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym ECK3103 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym JW5522 Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved synonym yhaS Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved locus tag b3114 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product pyruvate formate-lyase 4/2-ketobutyrate formate-lyase Published Annotation - PubMed ID: 16397293 Jan 2006
Person Uncurated alternate product name pyruvate formate-lyase 4/2-ketobutyrate formate-lyase Published Annotation - Database Name: GenProtEC Jan 2006
Person Approved alternate product name probable formate acetyltransferase 3 Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Protein Family
Automated Process Approved protein family IPR004184 Pyruvate formate lyase domain Protein Sequence Similarity - InterPro Domain: IPR004184
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF02901 Pyruvate formate lyase-like Protein Sequence Similarity - PFAM Model Name: PF02901
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR001150 Glycine radical domain Protein Sequence Similarity - InterPro Domain: IPR001150
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF01228 Glycine radical Protein Sequence Similarity - PFAM Model Name: PF01228
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR005949 Formate acetyltransferase Protein Sequence Similarity - InterPro Domain: IPR005949
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Other
Person Approved EC number 2.3.1.- Published Annotation - Swiss-Prot Accession Number: P42632 Feb 2006
Person Uncurated MultiFun 1.3.5 (metabolism; energy metabolism, carbon; fermentation) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 1.3.7 (metabolism; energy metabolism, carbon; anaerobic respiration) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 1.1.3 (metabolism; carbon utilization; amino acids) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 1.7.30 (metabolism; central intermediary metabolism; threonine catabolism) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 7.1 (location of gene products; cytoplasm) 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 ASAP:ABE-0010242 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG12758 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P42632 Published Annotation - Swiss-Prot Accession Number: P42632 Jan 2005
Automated Process Approved db xref GeneID:947623 Published Annotation - Entrez Gene Database ID: 947623
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref GI:48994926 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P42632 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved function putative enzyme; Energy metabolism, carbon: Anaerobic respiration Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved note probable formate acetyltransferase 3; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0009063 - cellular amino acid catabolic process; GO_process: GO:0006113 - fermentation; GO_process: GO:0009061 - anaerobic respiration Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAT48170.1 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved sequence correction version m56: frameshift error corrected, altering C-term. Experimental - GenBank Accession Number: AG613272
Reference: Escherichia coli 		May 2004
Automated Process Uncurated subcellular localization Cytoplasmic Predicted by PSORTb - PSORTb Final_Score: 9.97
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 Approved GO biological process GO:0005975 carbohydrate metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR005949
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO biological process GO:0008152 metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001150
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Uncurated GO biological process GO:0009061 anaerobic respiration Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Person Uncurated GO biological process GO:0009063 cellular amino acid catabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Person Uncurated GO biological process GO:0006113 fermentation Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO biological process GO:0006006 glucose metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004184
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO cellular component GO:0005737 cytoplasm GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR005949
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Approved GO cellular component GO:0005737 cytoplasm Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved 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:0003824 catalytic activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001150
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0008861 formate C-acetyltransferase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR005949
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Comparative to toptop
Author Approval Details Genome Feature Name Type
Homolog
Person Uncurated Go view Shewanella oneidensis MR-1 ACY-0266522 pflB CDS
Member
Automated Process Uncurated Go view OrthoMCL (14 enterobacteria) AMM-0000082 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0000035 pflB CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0000038 pflB CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0001109 pflB CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0000031 pflB CDS
Ortholog
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0000635 tdcE CDS
Automated Process Approved Go view Citrobacter freundii ATCC 8090 [T] AVI-0004743 tdcE CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0003237 CDS
Automated Process Uncurated Go view Escherichia coli APEC O1 (APEC) AEG-0003188 tdcE CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0001070 tdcE CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0006015 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0080044 tdcE CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0003581 CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0004206 CDS
Automated Process Uncurated Go view Escherichia coli E2348/69 (EPEC) BCI-0003627 tdcE CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0008022 pflB1 CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0009263 pflB1 CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0028139 tdcE CDS
Automated Process Uncurated Go view Escherichia coli F11 (UPEC) ADQ-0007276 tdcE CDS
Automated Process Approved Go view Escherichia coli HS ADR-0007986 pflB1 CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0003636 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0002906 tdcE CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0003182 tdcE CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0003761 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0003683 pflB CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0003415 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0003585 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0177747 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0003461 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0003408 pflB1 CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0134052 tdcE CDS
Person Approved Go view Escherichia coli UTI89 (UPEC) AEA-0003558 tdcE CDS
Person Uncurated Go view Salmonella Choleraesuis SC-B67 ADB-0003725 tdcE CDS
Person Uncurated Go view Salmonella Paratyphi A ATCC 9150 ADA-0003109 tdcE CDS
Person Uncurated Go view Salmonella Typhi CT18 ABX-0112222 tdcE CDS
Person Uncurated Go view Salmonella Typhi Ty2 ABS-0084880 tdcE CDS
Person Uncurated Go view Salmonella Typhimurium LT2 [T] ABU-0100070 tdcE CDS
Person Uncurated Go view Shigella boydii 227 ADV-0003269 tdcE CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0008657 pflB1 CDS
Person Uncurated Go view Shigella dysenteriae 197 ADU-0003766 tdcE CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0074560 tdcE CDS
Person Approved Go view Shigella flexneri 301 ABT-0089395 tdcE CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0003360 tdcE CDS
Person Approved Go view Shigella sonnei 046 ADD-0003574 tdcE 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
FB23293mutantTn5 InsertionRequest the StrainABE-0010242tdcEtdcE::Tn5KAN-I-SceI at position 1108 in Plus 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 3255124 to 3267418
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0010219yhaLCDSforward32550433255207Downstream
ABE-0285584repeat_regionforward32552173255319Downstream
ABE-0174100cyuACDScomplement32553413256651Downstream
ABE-0010228cyuPCDScomplement32566793258010Downstream
ABE-0174101tdcGCDScomplement32582853259649Downstream
ABE-0010240tdcFCDScomplement32597213260110Downstream
ABE-0010242tdcECDScomplement32601243262418Matches
ABE-0010245tdcDCDScomplement32624523263660Upstream
ABE-0010247tdcCCDScomplement32636863265017Upstream
ABE-0010249tdcBCDScomplement32650393266028Upstream
ABE-0010252tdcACDScomplement32661273267065Upstream
ABE-0010255tdcRCDSforward32673803267598Upstream
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.