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

ABE-0004809 (ydcV) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0004809 showshow history
Names
ydcV JW1438 ECK1437 b1443
Product
membrane component of an ABC superfamily predicted spermidine/putrescine transporter
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 1514762 1515556 795 265
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 IPR000515 (IPR000515 ABC transporter type 1, transmembrane domain MetI-like) Apr 2008
Automated Process Approved IPR035906 (IPR035906 MetI-like superfamily) Jul 2018
Automated Process Approved PF00528 (PF00528 Binding-protein-dependent transport system inner membrane component) 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:IPR000515
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: IPR000515
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:IPR000515
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:IPR000515
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name ydcV Published Annotation - Swiss-Prot Accession Number: P77505 Aug 2002
Person Approved synonym JW1438 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK1437 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b1443 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product membrane component of an ABC superfamily predicted spermidine/putrescine transporter Published Annotation - PubMed ID: 16397293
Reference: Escherichia coli K-12 		Mar 2008
Person Uncurated alternate product name putative ABC transporter permease protein Published Annotation - Swiss-Prot Accession Number: P77505 Jan 2006
Person Uncurated alternate product name putative sperimidine/putrescine transport protein (ABC superfamily, membrane) Published Annotation - Database Name: GenProtEC Jan 2006
Automated Process Approved alternate product name predicted spermidine/putrescine transporter subunit Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Protein Family
Automated Process Approved protein family PF00528 Binding-protein-dependent transport system inner membrane component Protein Sequence Similarity - PFAM Model Name: PF00528
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR000515 ABC transporter type 1, transmembrane domain MetI-like Protein Sequence Similarity - InterPro Domain: IPR000515
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR035906 MetI-like superfamily Protein Sequence Similarity - InterPro Domain: IPR035906
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Person Uncurated MultiFun 4.3.A.1.m (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, membrane component) 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 4.S.166 (transport; substrate; putrescine/spermidine) 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 GeneID:945903 Published Annotation - Entrez Gene Database ID: 945903
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Person Approved db xref UniProtKB:P0AFR9 Published Annotation - Swiss-Prot Accession Number: P0AFR9 Jan 2006
Automated Process Approved db xref GI:1787714 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P0AFR9 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0004809 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG13765 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved function putative transport; Not classified Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved note membrane component of ABC superfamily; 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 AAC74525.1 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 iAF1260 Experimental - PubMed ID: 17593909
Reference: Escherichia coli K-12 MG1655 		Jan 2009
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
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: IPR000515
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO biological process GO:0006810 transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000515
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:IPR000515
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:IPR000515
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 (205 gammaproteobacteria) APP-0003674 ydcV CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0003578 ydcV CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0003654 ydcV CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003273 ydcV CDS
Ortholog
Automated Process Uncurated Go view Buttiauxella agrestis ATCC 33320 [T] APC-0002166 ydcV CDS
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0002308 ydcV_2 CDS
Automated Process Approved Go view Citrobacter freundii ATCC 8090 [T] AVI-0002974 ydcV_2 CDS
Automated Process Uncurated Go view Enterobacter cloacae subsp. cloacae ATCC 13047 [T] (AToL DRAFT) AMB-0002854 CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0004015 ydcV CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0005449 ydcV CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0001457 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0010030 ydcV CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0001423 CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0002901 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0007974 CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0005118 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0081934 ydcV CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0001554 ydcV CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0001875 CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0005301 ydcV CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0006295 ydcV CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0001696 ydcV CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0006062 ydcV CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0003305 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0005427 ydcV CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0009792 ydcV CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0007971 ydcV CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0007093 ydcV CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0006888 ydcV CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0006969 ydcV CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0011363 ydcV CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0008028 ydcV CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0008472 ydcV CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0007061 ydcV CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0007165 ydcV CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0008821 ydcV CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0026050 ydcV CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0008004 ydcV_1 CDS
Automated Process Approved Go view Escherichia coli HS ADR-0006204 ydcV CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0001862 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0001352 ydcV CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0001484 ydcV CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0001337 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0001740 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0001529 CDS
Person Uncurated Go view Escherichia coli Nissle 1917 AML-0001676 pseudogene
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0175814 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0001554 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0001730 ydcV CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0132015 ydcV CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0002081 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0001669 CDS
Person Uncurated Go view Hafnia alvei ATCC 13337 [T] AMD-0001601 CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0001930 ydcV CDS
Automated Process Uncurated Go view Leclercia adecarboxylata ATCC 23216 [T] AME-0000043 CDS
Automated Process Uncurated Go view Serratia marcescens subsp. marcescens ATCC 13880 [T] AMF-0002061 CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0004096 ydcV CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0073004 CDS
Person Uncurated Go view Shigella flexneri 301 ABT-0088075 CDS
Automated Process Uncurated Go view Shigella flexneri 8401 BAG-0001891 CDS
Person Approved Go view Shigella sonnei 046 ADD-0001847 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 43003 APO-0013342 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 49455 [T] AMG-0003907 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
FB22166mutantTn5 InsertionRequest the StrainABE-0004809ydcVb1443::Tn5KAN-I-SceI at position 248 in Plus orientation ,+ pKD460Blattner Laboratory
FB23098mutantTn5 InsertionRequest the StrainABE-0004809ydcVb1443::Tn5KAN-I-SceI at position 248 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 1509762 to 1520556
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0004796hicBCDSforward15095081509924Upstream
ABE-0004800ydcRCDSforward15100031511409Upstream
ABE-0004803ydcSCDSforward15116541512799Upstream
ABE-0004805ydcTCDSforward15128171513830Upstream
ABE-0004807ydcUCDSforward15138311514772Overlaps Upstream
ABE-0004809ydcVCDSforward15147621515556Matches
ABE-0285723matS11protein_bindforward15149541514966Contained Within
ABE-0004813patDCDSforward15155781517002Downstream
ABE-0285182yncLCDScomplement15170991517194Downstream
ABE-0004818ortTCDSforward15173891517562Downstream
ABE-0004821ydcYCDSforward15176481517881Downstream
ABE-0004823ydcZCDScomplement15178821518331Downstream
ABE-0004827mnaTCDScomplement15183281518846Downstream
ABE-0004834curACDSforward15190271520064Downstream
ABE-0004837mcbRCDSforward15202621520927Downstream
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.