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

ABE-0013503 (dcuB) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0013503 showshow history
Names
dcuB JW4084 ECK4116 genF b4123
Product
C4-dicarboxylate antiporter
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 4347404 4348744 1341 447
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR004668 (IPR004668 Anaerobic c4-dicarboxylate membrane transporter) Apr 2008
Automated Process Approved PF03605 (PF03605 Anaerobic c4-dicarboxylate membrane transporter) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
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:0015740 C4-dicarboxylate transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004668
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO cellular component GO:0016021 integral component of membrane GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004668
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:0015556 C4-dicarboxylate transmembrane transporter activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004668
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name dcuB Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym ECK4116 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym JW4084 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym genF Published Sequence Analysis - PubMed ID: 9729611 Aug 2003
Person Approved locus tag b4123 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product C4-dicarboxylate antiporter Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved alternate product name C4-dicarboxylate transporter, anaerobic; DcuS co-sensor Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved alternate product name anaerobic dicarboxylate transport Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Person Uncurated alternate product name anaerobic C4-dicarboxylate transport protein (Dcu family) Published Annotation - Database Name: GenProtEC Jan 2006
Protein Family
Automated Process Approved protein family PF03605 Anaerobic c4-dicarboxylate membrane transporter Protein Sequence Similarity - PFAM Model Name: PF03605
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR004668 Anaerobic c4-dicarboxylate membrane transporter Protein Sequence Similarity - InterPro Domain: IPR004668
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Other
Person Uncurated MultiFun 1.1.1 (metabolism; carbon utilization; carbon compounds) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 4.2.A.13 (transport; Electrochemical potential driven transporters; Porters (Uni-, Sym- and Antiporters); The C4-Dicarboxylate Uptake (Dcu) Family) 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
Person Uncurated MultiFun 4.S.46 (transport; substrate; dicarboxylate) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 6.1 (cell structure; 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 GeneID:948641 Published Annotation - Entrez Gene Database ID: 948641
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Person Approved db xref UniProtKB:P0ABN9 Published Annotation - Swiss-Prot Accession Number: P0ABN9 Jan 2006
Automated Process Approved db xref GI:1790565 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P0ABN9 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0013503 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG10006 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved function transport; Transport of small molecules: Carbohydrates, organic acids, alcohols Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved note anaerobic dicarboxylate transport; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane; 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 AAC77084.1 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
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:0015740 C4-dicarboxylate transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004668
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 Approved GO cellular component GO:0016021 integral component of membrane GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004668
Reference: Escherichia coli K-12 MG1655 		Apr 2008
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:0015556 C4-dicarboxylate transmembrane transporter activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004668
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-0002213 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0002252 dcuB CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0002233 dcuB CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0003795 dcuB CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0002255 dcuB CDS
Ortholog
Automated Process Uncurated Go view Brenneria salicis ATCC 15712 [T] AMK-0003748 CDS
Automated Process Uncurated Go view Brenneria sp. EniD312 AKG-0004221 CDS
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0004103 dcuB CDS
Automated Process Approved Go view Citrobacter freundii ATCC 8090 [T] AVI-0000128 dcuB CDS
Automated Process Uncurated Go view Dickeya chrysanthemi Ech1591 AFK-0007611 CDS
Person Uncurated Go view Dickeya dadantii 3937 ABF-0018628 dcuB CDS
Automated Process Uncurated Go view Dickeya parazeae Ech586 AGC-0002689 CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0001935 dcuB CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0006409 dcuB CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0004416 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0006843 dcuB CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0004204 dcuB CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0004680 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0010052 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0006339 dcuB CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0005741 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0081334 dcuB CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0004793 dcuB CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0005389 CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0006211 dcuB CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0006673 dcuB CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0004747 dcuB CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0003185 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0008963 dcuB CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0007477 dcuB CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0007122 dcuB CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0006202 dcuB CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0010467 dcuB CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0007137 dcuB CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0008281 dcuB CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0007254 dcuB CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0005832 dcuB CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0006580 dcuB CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0005952 dcuB CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0005102 dcuB CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0029299 dcuB CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0008530 dcuB CDS
Automated Process Approved Go view Escherichia coli HS ADR-0009052 dcuB CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0004734 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0003813 dcuB CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0004212 dcuB CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0004732 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0004843 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0004544 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0004778 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0178952 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0004521 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0004581 dcuB CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0135217 dcuB CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0003378 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0004725 dcuB CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0004416 dcuB CDS
Person Uncurated Go view Pectobacterium atrosepticum SCRI1043 ABL-0061786 dcuB CDS
Automated Process Uncurated Go view Pectobacterium brasiliensis 1692 AED-0000875 dcuB CDS
Person Uncurated Go view Pectobacterium carotovorum WPP14 ADT-0000399 dcuB CDS
Automated Process Uncurated Go view Pectobacterium parmentieri WPP163 AFJ-0001811 dcuB CDS
Automated Process Uncurated Go view Pectobacterium sp. PC1 AFL-0006160 CDS
Automated Process Uncurated Go view Salmonella Agona SL483 BBX-0008726 dcuB CDS
Automated Process Uncurated Go view Salmonella Arizonae CDC 346-86 BCD-0003506 CDS
Person Uncurated Go view Salmonella Choleraesuis SC-B67 ADB-0004922 dcuB CDS
Automated Process Uncurated Go view Salmonella Dublin CT_02021853 BCB-0008935 dcuB CDS
Automated Process Uncurated Go view Salmonella Enteritidis P125109 BCF-0013492 dcuB CDS
Automated Process Uncurated Go view Salmonella Hadar RI_05P066 BBT-0007794 CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL476 BBV-0009001 CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL486 BBW-0007407 CDS
Automated Process Uncurated Go view Salmonella Javiana GA_MM04042433 BCA-0004041 CDS
Automated Process Uncurated Go view Salmonella Kentucky CDC 191 BBZ-0005783 CDS
Automated Process Uncurated Go view Salmonella Kentucky CVM29188 BBP-0008110 CDS
Automated Process Uncurated Go view Salmonella Newport SL254 BBQ-0008992 dcuB CDS
Automated Process Uncurated Go view Salmonella Newport SL317 BBR-0008298 CDS
Automated Process Uncurated Go view Salmonella Paratyphi A AKU_12601 BCH-0004154 CDS
Person Uncurated Go view Salmonella Paratyphi A ATCC 9150 ADA-0004114 dcuB CDS
Automated Process Uncurated Go view Salmonella Paratyphi B SPB7 BCC-0005328 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA23 BBN-0004344 dcuB CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA29 BBM-0007443 dcuB CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund CVM19633 BBO-0008618 CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund SL480 BBY-0006308 CDS
Person Approved Go view Salmonella Typhi CT18 ABX-0114552 dcuB CDS
Person Uncurated Go view Salmonella Typhi Ty2 ABS-0085935 dcuB CDS
Automated Process Uncurated Go view Salmonella Typhimurium 14028S AJR-0005180 dcuB CDS
Person Uncurated Go view Salmonella Typhimurium LT2 [T] ABU-0103252 dcuB CDS
Automated Process Uncurated Go view Salmonella Virchow SL491 BBS-0004842 dcuB CDS
Automated Process Uncurated Go view Salmonella Weltevreden SL484 BBU-0007511 dcuB CDS
Automated Process Uncurated Go view Salmonella enterica CVM23701 BBL-0005823 CDS
Automated Process Uncurated Go view Serratia marcescens subsp. marcescens ATCC 13880 [T] AMF-0003987 CDS
Person Uncurated Go view Shewanella oneidensis MR-1 ACY-0268069 dcuB CDS
Person Approved Go view Shigella boydii 227 ADV-0004711 dcuB CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0004693 dcuB CDS
Person Uncurated Go view Shigella dysenteriae 197 ADU-0004770 dcuB CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0074848 dcuB CDS
Person Approved Go view Shigella flexneri 301 ABT-0090315 dcuB CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0004363 dcuB CDS
Person Approved Go view Shigella sonnei 046 ADD-0004669 dcuB CDS
Person Uncurated Go view Vibrio cholerae N16961 ADH-0003094 VCA0205 CDS
Automated Process Uncurated Go view Yersinia bercovieri ATCC 43970 [T] AEK-0003060 CDS
Automated Process Uncurated Go view Yersinia enterocolitica 8081 BAH-0002615 CDS
Automated Process Uncurated Go view Yersinia frederiksenii ATCC 33641 [T] AEI-0003991 dcuB CDS
Automated Process Uncurated Go view Yersinia intermedia ATCC 29909 [T] AEH-0003728 dcuB CDS
Automated Process Uncurated Go view Yersinia mollaretii ATCC 43969 [T] AEJ-0003297 CDS
Automated Process Uncurated Go view Yersinia pseudotuberculosis IP31758 ADS-0007231 dcuB CDS
Person Uncurated Go view Yersinia pseudotuberculosis IP32953 ACZ-0000886 CDS
Automated Process Uncurated Go view Yersinia pseudotuberculosis PB1/+ AFV-0001037 CDS
Automated Process Uncurated Go view Yersinia pseudotuberculosis YPIII AFW-0003982 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)
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 4342404 to 4353744
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0013493melACDSforward43419114343266Downstream
ABE-0013495melBCDSforward43433694344790Downstream
ABE-0285680repeat_regionforward43448154344909Downstream
ABE-0013498yjdFCDScomplement43449294345558Downstream
ABE-0013501fumBCDScomplement43456804347326Downstream
ABE-0013503dcuBCDScomplement43474044348744Matches
ABE-0013507dcuRCDScomplement43493154350034Upstream
ABE-0013509dcuSCDScomplement43500314351662Upstream
ABE-0013513yjdICDSforward43518434352073Upstream
ABE-0013515yjdJCDSforward43520854352357Upstream
ABE-0013518ghoSCDSforward43525844352880Upstream
ABE-0285080ghoTCDSforward43529084353081Upstream
ABE-0013520lysUCDScomplement43532004354717Upstream
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.