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

ABE-0010056 (ttdT) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0010056 showshow history
Names
ttdT ygjC JW3035 ECK3053 ygjE b3063
Product
L-tartrate:succinate antiporter
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 3208024 3209487 1464 488
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 IPR001898 (IPR001898 Solute carrier family 13) Apr 2008
Automated Process Approved IPR030676 (IPR030676 Citrate carrier CitT-related) Jul 2018
Automated Process Approved PF00939 (PF00939 Sodium:sulfate symporter transmembrane region) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Automated Process Approved GO biological process GO:0006814 sodium ion transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001898
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO biological process GO:0055085 transmembrane transport GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR001898
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO cellular component GO:0016020 membrane GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001898
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Uncurated GO cellular component GO:0019866 organelle inner membrane Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Uncurated GO cellular component GO:0005886 plasma membrane GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Automated Process Approved GO molecular function GO:0005215 transporter activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001898
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Uncurated name ttdT Published Annotation - PubMed ID: 17172328
Reference: Escherichia coli K-12 MG1655 		Apr 2009
Person Approved synonym ygjE Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved synonym ygjC Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved synonym JW3035 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK3053 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b3063 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product L-tartrate:succinate antiporter Experimental - PubMed ID: 17172328
Reference: Escherichia coli K-12 MG1655 		Apr 2009
Automated Process Approved alternate product name L-tartrate/succinate antiporte Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Uncurated alternate product name putative tartrate:succinate antiporter (DASS family) Published Annotation - Database Name: GenProtEC Jan 2006
Protein Family
Automated Process Approved protein family PF00939 Sodium:sulfate symporter transmembrane region Protein Sequence Similarity - PFAM Model Name: PF00939
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR030676 Citrate carrier CitT-related Protein Sequence Similarity - InterPro Domain: IPR030676
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR001898 Solute carrier family 13 Protein Sequence Similarity - InterPro Domain: IPR001898
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Other
Person Uncurated MultiFun 4.2.A.47 (transport; Electrochemical potential driven transporters; Porters (Uni-, Sym- and Antiporters); The Divalent Anion:Na+ Symporter (DASS) Family) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 6.1 (cell structure; membrane) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 7.3 (location of gene products; inner membrane) 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 EcoGene:EG12393 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0010056 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P39414 Published Annotation - Swiss-Prot Accession Number: P39414 Jan 2005
Automated Process Approved db xref GI:1789444 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:947576 Published Annotation - Entrez Gene Database ID: 947576
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref UniProtKB/Swiss-Prot:P39414 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved note GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC76099.1 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Uncurated subcellular localization Cytoplasmic Membrane Predicted by PSORTb - PSORTb Final_Score: 10.00
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 iJR904 Experimental - PubMed ID: 12952533
Reference: Escherichia coli K-12 MG1655 		Feb 2009
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
Automated Process Uncurated GO biological process GO:0055085 transmembrane transport GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR001898
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO biological process GO:0006814 sodium ion transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001898
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Uncurated GO cellular component GO:0019866 organelle inner membrane Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Uncurated GO cellular component GO:0005886 plasma membrane GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Automated Process Approved GO cellular component GO:0016020 membrane GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001898
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0005215 transporter activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001898
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-0002082 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0003275 ttdT CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0000445 citT CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0000946 citT CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0002906 ttdT CDS
Ortholog
Automated Process Uncurated Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0000694 ttdT CDS
Automated Process Approved Go view Citrobacter freundii ATCC 8090 [T] AVI-0004635 ttdT_3 CDS
Person Uncurated Go view Dickeya dadantii 3937 ABF-0017821 CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0002434 CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0005694 CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0003183 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0008053 CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0003147 ygjE CDS
Automated Process Uncurated Go view Escherichia coli ATCC 11775 [T] AMC-0001115 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0006079 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0005505 CDS
Person Uncurated Go view Escherichia coli B7A (ETEC) ADK-0011152 pseudogene
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0079985 ttdT CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0003526 ttdT CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0004127 CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0005592 CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0005602 CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0003576 ttdT CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0007961 CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0000335 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0007715 CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0006232 CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0008490 CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0010802 CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0009211 CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0005954 CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0007016 CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0005997 CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0005819 CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0005403 CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0006248 CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0028090 ygjE CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0007558 ttdT CDS
Automated Process Approved Go view Escherichia coli HS ADR-0007926 CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0003589 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0002860 ygjE CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0003132 ygjE CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0003296 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0003470 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0003530 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0177702 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0003406 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0003354 CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0134003 ygjE CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0005905 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0003508 ygjE CDS
Automated Process Uncurated Go view Ewingella americana ATCC 33852 [T] AMA-0003019 CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0001551 CDS
Automated Process Uncurated Go view Musicola paradisiaca Ech703 AGA-0009042 CDS
Automated Process Uncurated Go view Pantoea agglomerans IG1 APM-0003889 CDS
Person Uncurated Go view Shigella boydii 227 ADV-0003208 ygjE CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0004053 CDS
Person Approved Go view Shigella dysenteriae 197 ADU-0003700 ygjE CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0074496 ygjE CDS
Person Approved Go view Shigella flexneri 301 ABT-0089349 ygjE CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0003306 ygjE CDS
Person Approved Go view Shigella sonnei 046 ADD-0003493 ygjE 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
FB22690mutantTn5 InsertionRequest the StrainABE-0010056ttdTygjE::Tn5KAN-I-SceI at position 222 in Plus orientation ,+ pKD460Blattner Laboratory
FB23282mutantTn5 InsertionRequest the StrainABE-0010056ttdTygjE::Tn5KAN-I-SceI at position 222 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 3203024 to 3214487
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0010031ccaCDSforward32018913203129Upstream
ABE-0285573repeat_regionforward32031443203268Upstream
ABE-0010034bacACDScomplement32033103204131Upstream
ABE-0010036folBCDScomplement32042213204589Upstream
ABE-0010042plsYCDSforward32046943205311Upstream
ABE-0010045ttdRCDScomplement32053243206256Upstream
ABE-0010050ttdACDSforward32064633207374Upstream
ABE-0010052ttdBCDSforward32073713207976Upstream
ABE-0010056ttdTCDSforward32080243209487Matches
ABE-0285574repeat_regionforward32094993209518Downstream
ABE-0010058tsaDCDScomplement32095303210543Downstream
ABE-0010063rpsUCDSforward32107813210996Downstream
ABE-0010065dnaGCDSforward32111073212852Downstream
ABE-0010070rpoDCDSforward32130473214888Downstream
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.