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

ABE-0004949 (ddpD) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0004949 showshow history
Names
ddpD yddP JW1479 ECK1478 b1484
Product
ATP-binding component of an ABC superfamily D-ala-D-ala transporter
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 1558031 1559017 987 329
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR010066 (IPR010066 (DEPRECATED) Oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal) Apr 2008
Automated Process Approved IPR003439 (IPR003439 ABC transporter-like) Apr 2008
Automated Process Approved IPR003593 (IPR003593 AAA+ ATPase domain) Apr 2008
Automated Process Approved IPR013563 (IPR013563 Oligopeptide/dipeptide ABC transporter, C-terminal) Apr 2008
Automated Process Approved IPR027417 (IPR027417 P-loop containing nucleoside triphosphate hydrolase) Jul 2018
Automated Process Approved PF08352 (PF08352 Oligopeptide/dipeptide transporter, C-terminal region) Jul 2018
Automated Process Approved PF00005 (PF00005 ABC transporter) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Automated Process Approved GO biological process GO:0015833 peptide transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR010066
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO cellular component GO:0005737 cytoplasm GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 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
Person Uncurated GO cellular component GO:0005737 cytoplasm Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO molecular function GO:0017111 nucleoside-triphosphatase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR003593
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0000166 nucleotide binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR003593
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0005524 ATP binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR010066
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0015197 (DEPRECATED) peptide transporter activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR010066
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0016887 ATPase GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR003439
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name ddpD Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym yddP Published Annotation - Swiss-Prot Accession Number: P77268 Jan 2006
Person Approved synonym JW1479 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK1478 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b1484 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product ATP-binding component of an ABC superfamily D-ala-D-ala transporter Published Annotation - PubMed ID: 16397293
Reference: Escherichia coli K-12 		Mar 2008
Automated Process Approved alternate product name D,D-dipeptide permease system, ATP-binding component Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Protein Family
Automated Process Approved protein family IPR013563 Oligopeptide/dipeptide ABC transporter, C-terminal Protein Sequence Similarity - InterPro Domain: IPR013563
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF08352 Oligopeptide/dipeptide transporter, C-terminal region Protein Sequence Similarity - PFAM Model Name: PF08352
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF00005 ABC transporter Protein Sequence Similarity - PFAM Model Name: PF00005
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR027417 P-loop containing nucleoside triphosphate hydrolase Protein Sequence Similarity - InterPro Domain: IPR027417
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR003439 ABC transporter-like Protein Sequence Similarity - InterPro Domain: IPR003439
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR003593 AAA+ ATPase domain Protein Sequence Similarity - InterPro Domain: IPR003593
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR010066 (DEPRECATED) Oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal Protein Sequence Similarity - InterPro Domain: IPR010066
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Other
Automated Process Uncurated EC number 3.6.1.3 Published Annotation - Database Name: EC2GO: GO:0016887
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Person Uncurated MultiFun 7.1 (location of gene products; cytoplasm) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 4.3.A.1.a (transport; Primary Active Transporters; Pyrophosphate Bond (ATP, GTP, P2) Hydrolysis-driven Active Transporters; The ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake Permeases; ABC superfamily ATP binding cytoplasmic component) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 4.S.47 (transport; substrate; dipeptide) 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:EG13787 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0004949 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:946002 Published Annotation - Entrez Gene Database ID: 946002
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref GI:1787759 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P77268 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P77268 Published Annotation - Swiss-Prot Accession Number: P77268 Jan 2005
Automated Process Approved note ATP-binding component of ABC superfamily; GO_component: GO:0005737 - cytoplasm Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC74557.1 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Uncurated subcellular localization Cytoplasmic Predicted by PSORTb - PSORTb Final_Score: 5.76
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Automated Process Uncurated subcellular localization Cytoplasmic Membrane Predicted by PSORTb - PSORTb Final_Score: 3.91
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
Automated Process Approved GO biological process GO:0015833 peptide transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR010066
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO cellular component GO:0005737 cytoplasm GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 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
Person Uncurated GO cellular component GO:0005737 cytoplasm Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO molecular function GO:0005524 ATP binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR010066
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0015197 (DEPRECATED) peptide transporter activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR010066
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0017111 nucleoside-triphosphatase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR003593
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0000166 nucleotide binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR003593
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0016887 ATPase GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR003439
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-0004803 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0003945 ddpD CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0003563 ddpD CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0004157 ddpD CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003755 ddpD CDS
Ortholog
Automated Process Uncurated Go view Brenneria salicis ATCC 15712 [T] AMK-0003683 CDS
Automated Process Uncurated Go view Brenneria sp. EniD312 AKG-0000649 CDS
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0002254 oppD_1 CDS
Automated Process Approved Go view Citrobacter freundii ATCC 8090 [T] AVI-0002910 oppD_1 CDS
Automated Process Uncurated Go view Enterobacter cloacae subsp. cloacae ATCC 13047 [T] (AToL DRAFT) AMB-0002787 CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0005492 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0010082 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0007925 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0005349 CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0005068 CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0001657 CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0001917 CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0005251 CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0007978 CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0006112 CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0003355 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0005474 CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0009839 CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0008019 CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0007045 CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0006936 CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0006921 CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0011411 CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0008078 CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0008424 CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0007012 CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0007117 CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0008772 CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0025999 ddpD CDS
Automated Process Approved Go view Escherichia coli HS ADR-0006245 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0001393 ddpD CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0001525 ddpD CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0001755 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0001793 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0001716 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0001603 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0001688 CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0132058 ddpD CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0002030 CDS
Automated Process Uncurated Go view Ewingella americana ATCC 33852 [T] AMA-0004353 CDS
Automated Process Uncurated Go view Pantoea ananatis AJ13355 AOV-0003046 yddP CDS
Automated Process Uncurated Go view Pantoea ananatis B1-9 APL-0000941 CDS
Automated Process Uncurated Go view Pantoea ananatis LMG 20103 AKB-0003868 yddP CDS
Automated Process Uncurated Go view Pantoea ananatis PA13 APK-0000286 CDS
Automated Process Uncurated Go view Pantoea sp. At-9b AGM-0007144 CDS
Automated Process Uncurated Go view Pantoea stewartii DC283 ACV-0288421 ddpD CDS
Person Uncurated Go view Pseudomonas syringae pv. tomato DC3000 ADG-0004612 CDS
Automated Process Uncurated Go view Serratia marcescens subsp. marcescens ATCC 13880 [T] AMF-0002916 CDS
Person Approved Go view Shigella boydii 227 ADV-0001736 CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0007156 CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0004133 CDS
Person Uncurated Go view Shigella flexneri 2457T ABQ-0072969 CDS
Person Uncurated Go view Shigella flexneri 301 ABT-0256000 CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0001852 CDS
Person Approved Go view Shigella sonnei 046 ADD-0001784 ddpD 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 1553031 to 1564017
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0004928adhPCDScomplement15528281553838Downstream
ABE-0004931maeACDScomplement15539721555669Downstream
ABE-0004935sraCDScomplement15558261555963Downstream
ABE-0004938bdmCDScomplement15560651556280Downstream
ABE-0004944osmCCDSforward15566251557056Downstream
ABE-0285455repeat_regionforward15570631557081Downstream
ABE-0004947ddpFCDScomplement15571121558038Overlaps Downstream
ABE-0004949ddpDCDScomplement15580311559017Matches
ABE-0004953ddpCCDScomplement15590141559910Overlaps Upstream
ABE-0004955ddpBCDScomplement15599071560929Upstream
ABE-0004958ddpACDScomplement15609311562481Upstream
ABE-0004960ddpXCDScomplement15624951563076Upstream
ABE-0285725matS13protein_bindforward15632821563294Upstream
ABE-0004963dosPCDScomplement15633341565733Upstream
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.