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

ABE-0004958 (ddpA) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0004958 showshow history
Names
ddpA yddS JW5240 ECK1481 b1487
Product
periplasmic-binding component of an ABC superfamily D-ala-D-a la transporter
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 1560931 1562481 1551 517
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR000914 (IPR000914 Solute-binding protein family 5 domain) Apr 2008
Automated Process Approved PF00496 (PF00496 Bacterial extracellular solute-binding proteins, family 5 Middle) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Automated Process Approved GO biological process GO:0006810 transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000914
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO cellular component GO:0030288 outer membrane-bounded periplasmic space GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Person Uncurated GO cellular component GO:0042597 periplasmic space Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO molecular function GO:0005215 transporter activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000914
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name ddpA Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK1481 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym yddS Published Annotation - Swiss-Prot Accession Number: P76128 Jan 2006
Person Approved synonym JW5240 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b1487 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product periplasmic-binding component of an ABC superfamily D-ala-D-a la transporter Published Annotation - PubMed ID: 16397293
Reference: Escherichia coli K-12 		Mar 2008
Automated Process Approved alternate product name D-ala-D-a la transporter subunit Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Protein Family
Automated Process Approved protein family PF00496 Bacterial extracellular solute-binding proteins, family 5 Middle Protein Sequence Similarity - PFAM Model Name: PF00496
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR000914 Solute-binding protein family 5 domain Protein Sequence Similarity - InterPro Domain: IPR000914
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Other
Person Uncurated MultiFun 4.S.47 (transport; substrate; dipeptide) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 4.3.A.1.p (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, periplasmic binding component) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 7.2 (location of gene products; periplasmic space) 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:EG13790 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P76128 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:946052 Published Annotation - Entrez Gene Database ID: 946052
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref ASAP:ABE-0004958 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GI:1787762 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P76128 Published Annotation - Swiss-Prot Accession Number: P76128 Jan 2005
Automated Process Approved note periplasmic-binding component of ABC superfamily; GO_component: GO:0042597 - periplasmic space Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC74560.1 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Uncurated subcellular localization Periplasmic Predicted by PSORTb - PSORTb Final_Score: 9.94
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:0006810 transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000914
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Uncurated GO cellular component GO:0042597 periplasmic space Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Uncurated GO cellular component GO:0030288 outer membrane-bounded periplasmic space 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:IPR000914
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-0004805 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0004148 ddpA CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0003853 ddpA CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0004142 ddpA CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003782 ddpA CDS
Ortholog
Automated Process Uncurated Go view Brenneria salicis ATCC 15712 [T] AMK-0003680 CDS
Automated Process Uncurated Go view Brenneria sp. EniD312 AKG-0000652 CDS
Automated Process Uncurated Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0002251 dppA_2 CDS
Automated Process Uncurated Go view Citrobacter freundii ATCC 8090 [T] AVI-0002907 dppA_2 CDS
Automated Process Uncurated Go view Enterobacter cloacae subsp. cloacae ATCC 13047 [T] (AToL DRAFT) AMB-0002784 CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0005495 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0010085 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0007921 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0005352 CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0005065 CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0001660 CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0005248 CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0007981 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0005477 CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0009842 CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0008022 CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0007042 CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0006939 CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0006918 CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0011414 CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0008081 CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0008421 CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0007009 CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0007114 CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0008769 CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0025996 ddpA CDS
Automated Process Approved Go view Escherichia coli HS ADR-0006248 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0001396 ddpA CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0001528 ddpA CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0001752 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0001796 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0001713 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0001606 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0001685 CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0132061 ddpA CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0002027 CDS
Automated Process Uncurated Go view Pantoea ananatis AJ13355 AOV-0003043 yddS CDS
Automated Process Uncurated Go view Pantoea ananatis B1-9 APL-0000944 CDS
Automated Process Uncurated Go view Pantoea ananatis LMG 20103 AKB-0003865 yddS CDS
Automated Process Uncurated Go view Pantoea ananatis PA13 APK-0000289 CDS
Automated Process Uncurated Go view Pantoea sp. At-9b AGM-0007147 CDS
Automated Process Uncurated Go view Pantoea stewartii DC283 ACV-0288424 ddpA CDS
Person Approved Go view Shigella boydii 227 ADV-0001733 CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0007159 CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0004137 CDS
Person Approved Go view Shigella sonnei 046 ADD-0001781 ddpA 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
FB22174mutantTn5 InsertionRequest the StrainABE-0004958ddpAb1487::Tn5KAN-I-SceI at position 392 in Minus orientation ,+ pKD460Blattner Laboratory
FB23107mutantTn5 InsertionRequest the StrainABE-0004958ddpAb1487::Tn5KAN-I-SceI at position 392 in Minus 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 1555931 to 1567481
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0004935sraCDScomplement15558261555963Downstream
ABE-0004938bdmCDScomplement15560651556280Downstream
ABE-0004944osmCCDSforward15566251557056Downstream
ABE-0285455repeat_regionforward15570631557081Downstream
ABE-0004947ddpFCDScomplement15571121558038Downstream
ABE-0004949ddpDCDScomplement15580311559017Downstream
ABE-0004953ddpCCDScomplement15590141559910Downstream
ABE-0004955ddpBCDScomplement15599071560929Downstream
ABE-0004958ddpACDScomplement15609311562481Matches
ABE-0004960ddpXCDScomplement15624951563076Upstream
ABE-0285725matS13protein_bindforward15632821563294Upstream
ABE-0004963dosPCDScomplement15633341565733Upstream
ABE-0004965dosCCDScomplement15657581567140Upstream
ABE-0285781yddYCDScomplement15671781567219Upstream
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.