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

ABE-0005991 (dmlA) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0005991 showshow history
Names
dmlA JW1789 ECK1798 ttuC yeaU b1800
Product
D-malate/3-isopropylmalate dehydrogenase
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 1881912 1882997 1086 362
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR001804 (IPR001804 (DEPRECATED) Isocitrate and isopropylmalate dehydrogenases family) Apr 2008
Automated Process Approved IPR011829 (IPR011829 Tartrate dehydrogenase) Apr 2008
Automated Process Approved IPR024084 (IPR024084 Isopropylmalate dehydrogenase-like domain) Jul 2018
Automated Process Approved PF00180 (PF00180 Isocitrate/isopropylmalate dehydrogenase) 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: IPR024084, IPR011829
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO biological process GO:0008152 metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001804
Reference: Escherichia coli K-12 MG1655 		Apr 2008
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 - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Automated Process Approved GO molecular function GO:0051287 NAD binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR011829
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0009027 tartrate dehydrogenase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR011829
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001804
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Automated Process Approved name dmlA Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved synonym yeaU Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym JW1789 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK1798 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ttuC Published Annotation - Database Name: GenProtEC Jul 2002
Person Approved locus tag b1800 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product D-malate/3-isopropylmalate dehydrogenase Published Annotation - EcoCyc Accession Number: G6986
Reference: Escherichia coli K-12 MG1655 		Oct 2021
Person Approved alternate product name putative tartrate dehydrogenase Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Person Approved alternate product name predicted dehydrogenase Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved alternate product name D-malate oxidase, NAD-dependent; probable tartrate dehydrogenase Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Protein Family
Automated Process Approved protein family IPR001804 (DEPRECATED) Isocitrate and isopropylmalate dehydrogenases family Protein Sequence Similarity - InterPro Domain: IPR001804
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR024084 Isopropylmalate dehydrogenase-like domain Protein Sequence Similarity - InterPro Domain: IPR024084
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR011829 Tartrate dehydrogenase Protein Sequence Similarity - InterPro Domain: IPR011829
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF00180 Isocitrate/isopropylmalate dehydrogenase Protein Sequence Similarity - PFAM Model Name: PF00180
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Automated Process Uncurated EC number 1.1.1.- Published Annotation - Database Name: EC2GO: GO:0016616
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Person Approved EC number 1.1.1.93 Published Annotation - Swiss-Prot Accession Number: P76251 Feb 2006
Person Approved EC number 4.1.1.73 Published Annotation - Swiss-Prot Accession Number: P76251 Feb 2006
Person Approved EC number 1.1.1.83 Published Annotation - Swiss-Prot Accession Number: P76251 Feb 2006
Person Uncurated MultiFun 1.3.5 (metabolism; energy metabolism, carbon; fermentation) 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-0005991 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:946319 Published Annotation - Entrez Gene Database ID: 946319
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref GI:1788101 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P76251 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P76251 Published Annotation - Swiss-Prot Accession Number: P76251 Jan 2005
Automated Process Approved db xref EcoGene:EG13507 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved note putative tartrate dehydrogenase; GO_process: GO:0006113 - fermentation Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC74870.1 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved 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 iAF1260 Experimental - PubMed ID: 17593909
Reference: Escherichia coli K-12 MG1655 		Jan 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:0006113 fermentation 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: IPR024084, IPR011829
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO biological process GO:0008152 metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001804
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
Automated Process Approved GO molecular function GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001804
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0051287 NAD binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR011829
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0009027 tartrate dehydrogenase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR011829
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-0003058 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0003051 yeaU CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0002913 yeaU CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0004554 dmlA CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003327 dmlA CDS
Ortholog
Automated Process Uncurated Go view Brenneria salicis ATCC 15712 [T] AMK-0000161 CDS
Automated Process Uncurated Go view Brenneria sp. EniD312 AKG-0002826 CDS
Automated Process Uncurated Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0002587 dmlA CDS
Automated Process Uncurated Go view Citrobacter freundii ATCC 8090 [T] AVI-0003235 dmlA CDS
Automated Process Uncurated Go view Dickeya chrysanthemi Ech1591 AFK-0008271 CDS
Person Uncurated Go view Dickeya dadantii 3937 ABF-0016830 CDS
Automated Process Uncurated Go view Dickeya parazeae Ech586 AGC-0000889 CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0004367 ttuC CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0008961 ttuC CDS
Person Uncurated Go view Escherichia coli 536 (UPEC) AEF-0004822 yeaU pseudogene
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0010384 ttuC CDS
Person Uncurated Go view Escherichia coli ATCC 11775 [T] AMC-0002588 yeaU pseudogene
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0007520 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0009851 ttuC CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0009306 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0081783 dmlA pseudogene
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0002018 CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0002338 CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0010008 ttuC CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0010352 ttuC CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0006463 ttuC CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0006320 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0005913 ttuC CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0010213 ttuC CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0008773 ttuC CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0007489 ttuC CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0007366 ttuC CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0007532 ttuC CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0010740 ttuC CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0010000 ttuC CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0010194 ttuC CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0009798 ttuC CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0008750 ttuC CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0008518 ttuC CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0026593 yeaU CDS
Automated Process Approved Go view Escherichia coli HS ADR-0006562 ttuC CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0001695 yeaU CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0001847 yeaU CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0002262 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0002166 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0002100 CDS
Person Uncurated Go view Escherichia coli Nissle 1917 AML-0002014 dmlA pseudogene
Automated Process Approved Go view Escherichia coli SE11 AFS-0002005 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0001387 ttuC CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0132493 yeaU CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0004057 CDS
Person Uncurated Go view Escherichia coli UTI89 (UPEC) AEA-0005364 yeaU pseudogene
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0001019 CDS
Automated Process Uncurated Go view Musicola paradisiaca Ech703 AGA-0008128 CDS
Automated Process Uncurated Go view Pantoea agglomerans IG1 APM-0003452 CDS
Automated Process Uncurated Go view Pantoea agglomerans SL1-M5 ALY-0002282 CDS
Automated Process Uncurated Go view Pantoea ananatis AJ13355 AOV-0003577 yeaU CDS
Automated Process Uncurated Go view Pantoea ananatis B1-9 APL-0000402 CDS
Automated Process Uncurated Go view Pantoea ananatis LMG 20103 AKB-0000347 yeaU CDS
Automated Process Uncurated Go view Pantoea ananatis PA13 APK-0004038 CDS
Automated Process Uncurated Go view Pantoea sp. At-9b AGM-0008140 CDS
Automated Process Uncurated Go view Pantoea sp. aB AJV-0003860 CDS
Automated Process Uncurated Go view Pantoea stewartii DC283 ACV-0289006 yeaU CDS
Automated Process Uncurated Go view Pantoea vagans C9-1 ALK-0007345 yeaU CDS
Person Uncurated Go view Pseudomonas syringae pv. tomato DC3000 ADG-0002707 CDS
Automated Process Uncurated Go view Serratia marcescens subsp. marcescens ATCC 13880 [T] AMF-0001763 CDS
Person Approved Go view Shigella boydii 227 ADV-0001424 yeaU CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0007467 ttuC CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0006063 ttuC CDS
Person Approved Go view Shigella dysenteriae 197 ADU-0001964 yeaU CDS
Person Approved Go view Shigella sonnei 046 ADD-0001478 yeaU CDS
Person Uncurated Go view Trabulsiella guamensis ATCC 49490 [T] APH-0004387 CDS
Person Uncurated Go view Xenorhabdus nematophila ATCC 19061 [T] ADW-0000940 yeaU CDS
Person Uncurated Go view Yersinia pestis 91001 (biovar Microtus) ACQ-0239816 leuB1 CDS
Automated Process Uncurated Go view Yersinia pestis Angola (biovar Pestoides) ADI-0005870 CDS
Automated Process Uncurated Go view Yersinia pestis Antiqua (biovar Antiqua) BAE-0002406 CDS
Automated Process Uncurated Go view Yersinia pestis B42003004 (biovar Antiqua) BAL-0007870 CDS
Automated Process Uncurated Go view Yersinia pestis CA88-4125 (biovar Orientalis) BAF-0000968 CDS
Person Approved Go view Yersinia pestis CO92 (biovar Orientalis) ABY-0123605 CDS
Automated Process Uncurated Go view Yersinia pestis E1979001 (biovar Antiqua) BAM-0004640 CDS
Automated Process Uncurated Go view Yersinia pestis F1991016 (biovar Orientalis) BAQ-0005539 CDS
Automated Process Uncurated Go view Yersinia pestis FV-1 (biovar Orientalis) BAK-0003313 CDS
Automated Process Uncurated Go view Yersinia pestis IP275 (biovar Orientalis) BAC-0006858 CDS
Automated Process Uncurated Go view Yersinia pestis K1973002 (biovar Mediaevalis) BAO-0008297 CDS
Person Uncurated Go view Yersinia pestis KIM (biovar Mediaevalis) ABI-0031382 CDS
Automated Process Uncurated Go view Yersinia pestis MG05-1020 (biovar Orientalis) BAP-0008268 CDS
Automated Process Uncurated Go view Yersinia pestis Nepal516 (biovar Antiqua) BAD-0002519 CDS
Automated Process Uncurated Go view Yersinia pestis Pestoides F (biovar Pestoides) BAI-0002288 CDS
Automated Process Uncurated Go view Yersinia pestis UG05-0454 (biovar Antiqua) BAN-0005826 CDS
Automated Process Uncurated Go view Yersinia pseudotuberculosis IP31758 ADS-0005478 CDS
Person Uncurated Go view Yersinia pseudotuberculosis IP32953 ACZ-0002620 CDS
Automated Process Uncurated Go view Yersinia pseudotuberculosis PB1/+ AFV-0003135 CDS
Automated Process Uncurated Go view Yersinia pseudotuberculosis YPIII AFW-0001899 CDS
Molecular Interactions to toptop
Author Approval Feature Name Technique Evidence Comment Annotated
Person Approved ABE-0005991 dmlA lambda repressor assay Doodle - bnumber: b1800 Oct 2003
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
FB22726mutantTn5 InsertionRequest the StrainABE-0005991dmlAyeaU::Tn5KAN-I-SceI at position 603 in Plus orientation ,+ pKD460Blattner Laboratory
FB23155mutantTn5 InsertionRequest the StrainABE-0005991dmlAyeaU::Tn5KAN-I-SceI at position 603 in Plus orientation ,- pKD465Tim Durfee (durf@genome.wisc.edu)
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 1876912 to 1887997
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0005964yeaOCDSforward18769091877256Upstream
ABE-0005966yoaFCDScomplement18772781877532Upstream
ABE-0005972dgcPCDSforward18777151878740Upstream
ABE-0285219yoaKCDSforward18787731878871Upstream
ABE-0285218yoaJCDSforward18788741878948Upstream
ABE-0005974yeaQCDScomplement18790071879255Upstream
ABE-0005976yoaGCDScomplement18794031879585Upstream
ABE-0005979yeaRCDScomplement18795891879948Upstream
ABE-0005984leuECDScomplement18801211880759Upstream
ABE-0005987dmlRCDScomplement18808861881809Upstream
ABE-0005991dmlACDSforward18819121882997Matches
ABE-0005995yeaVpseudogeneforward18831511884633Downstream
ABE-0005997yeaWCDSforward18846651885789Downstream
ABE-0006000yeaXCDSforward18858451886810Downstream
ABE-0006003rndCDScomplement18868641887991Downstream
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.