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

ABE-0011360 (nikD) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0011360 showshow history
Names
nikD JW3444 ECK3463 hydD hydC b3479
Product
ATP-binding component of an ABC superfamily nickel transporter
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 3617015 3617779 765 255
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR003439 (IPR003439 ABC transporter-like) Apr 2008
Automated Process Approved IPR003593 (IPR003593 AAA+ ATPase domain) Apr 2008
Automated Process Approved IPR014138 (IPR014138 Nickel import ATP-binding protein NikD) Apr 2008
Automated Process Approved IPR027417 (IPR027417 P-loop containing nucleoside triphosphate hydrolase) Jul 2018
Automated Process Approved PF00005 (PF00005 ABC transporter) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Person Uncurated GO biological process GO:0009060 aerobic respiration Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Uncurated GO biological process GO:0015675 nickel cation transport GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR014138
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Person Uncurated GO biological process GO:0009061 anaerobic respiration Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved 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 Uncurated GO cellular component GO:0005737 cytoplasm 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 Uncurated GO molecular function GO:0015413 ABC-type nickel transporter activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR014138
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Uncurated GO molecular function GO:0016151 nickel cation binding GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR014138
Reference: Escherichia coli K-12 MG1655 		Jul 2018
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:IPR003439
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 nikD Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym hydC Published Sequence Analysis - PubMed ID: 9729611 Aug 2003
Person Approved synonym hydD Published Sequence Analysis - PubMed ID: 9729611 Aug 2003
Person Approved synonym JW3444 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK3463 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b3479 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product ATP-binding component of an ABC superfamily nickel transporter Published Annotation - PubMed ID: 16397293
Reference: Escherichia coli K-12 		Mar 2008
Person Uncurated alternate product name nickel transport protein (ABC superfamily, atp_bind) Published Annotation - Database Name: GenProtEC Jan 2006
Automated Process Approved alternate product name nickel transporter subunit Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved alternate product name ATP-binding protein of nickel transport system Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Protein Family
Automated Process Approved protein family IPR014138 Nickel import ATP-binding protein NikD Protein Sequence Similarity - InterPro Domain: IPR014138
Reference: Escherichia coli K-12 MG1655 		Apr 2008
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 PF00005 ABC transporter Protein Sequence Similarity - PFAM Model Name: PF00005
Reference: Escherichia coli K-12 MG1655 		Jul 2018
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 IPR003439 ABC transporter-like Protein Sequence Similarity - InterPro Domain: IPR003439
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Other
Person Approved EC number 3.6.3.24 Published Annotation - Swiss-Prot Accession Number: P33593 Feb 2006
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 1.3.6 (metabolism; energy metabolism, carbon; aerobic respiration) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 1.3.7 (metabolism; energy metabolism, carbon; anaerobic respiration) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
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.143 (transport; substrate; Ni++) 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:EG12078 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0011360 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P33593 Published Annotation - Swiss-Prot Accession Number: P33593 Jan 2005
Automated Process Approved db xref GeneID:947989 Published Annotation - Entrez Gene Database ID: 947989
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref GI:1789890 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P33593 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved function transport; Transport of small molecules: Cations Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved note ATP-binding protein of nickel transport system; ATP-binding component of ABC superfamily; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0009060 - aerobic respiration; GO_process: GO:0009061 - anaerobic respiration Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC76504.1 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: 3.91
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Automated Process Uncurated subcellular localization Cytoplasmic Predicted by PSORTb - PSORTb Final_Score: 5.76
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 Uncurated GO biological process GO:0015675 nickel cation transport GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR014138
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Person Uncurated GO biological process GO:0009060 aerobic respiration Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Person Uncurated GO biological process GO:0009061 anaerobic respiration Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved 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 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 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 Uncurated GO molecular function GO:0016151 nickel cation binding GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR014138
Reference: Escherichia coli K-12 MG1655 		Jul 2018
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 Uncurated GO molecular function GO:0015413 ABC-type nickel transporter activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR014138
Reference: Escherichia coli K-12 MG1655 		Jul 2018
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
Automated Process Approved GO molecular function GO:0005524 ATP binding 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 (205 gammaproteobacteria) APP-0003620 nikD CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0003928 nikD CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003383 nikD CDS
Ortholog
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0000274 nikD CDS
Automated Process Uncurated Go view Dickeya chrysanthemi Ech1591 AFK-0007033 CDS
Person Uncurated Go view Enterobacter sp. 638 AEL-0002269 nikD CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0001423 nikD CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0004844 nikD CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0003612 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0007613 nikD CDS
Person Approved Go view Escherichia coli APEC O1 (APEC) AEG-0003533 nikD CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0000710 nikD CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0005595 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0006502 nikD CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0005386 NikD CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0080448 nikD CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0003968 nikD CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0004614 nikD CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0005268 nikD CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0003959 nikD CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0008396 nikD CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0004772 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0008156 nikD CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0006669 nikD CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0006215 nikD CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0005208 nikD CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0009653 nikD CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0005293 nikD CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0007467 nikD CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0005248 nikD CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0005316 nikD CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0005155 nikD CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0005045 nikD CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0005644 nikD CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0028523 nikD CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0005479 nikD CDS
Automated Process Approved Go view Escherichia coli HS ADR-0008367 nikD CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0003980 nikD CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0003240 nikD CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0003892 nikD CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0004125 nikD CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0004119 nikD CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0003825 nikD CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0003984 nikD CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0178131 nikD CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0003818 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0003760 nikD CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0134418 nikD CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0002697 CDS
Person Approved Go view Escherichia coli UTI89 (UPEC) AEA-0004005 nikD CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0003901 nikD CDS
Person Approved Go view Shigella boydii 227 ADV-0003795 nikD CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0009261 nikD CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0003419 nikD CDS
Person Approved Go view Shigella dysenteriae 197 ADU-0004114 nikD CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0075568 nikD CDS
Person Approved Go view Shigella flexneri 301 ABT-0089730 nikD CDS
Person Approved Go view Shigella flexneri 8401 BAG-0003696 nikD CDS
Person Approved Go view Shigella sonnei 046 ADD-0004052 nikD 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 3612015 to 3622779
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0011347yhhTCDSforward36118653612914Upstream
ABE-0011351acpTCDSforward36129693613556Upstream
ABE-0011354nikACDSforward36136673615241Upstream
ABE-0011356nikBCDSforward36152413616185Upstream
ABE-0011358nikCCDSforward36161823617015Overlaps Upstream
ABE-0011360nikDCDSforward36170153617779Matches
ABE-0011362nikECDSforward36177763618582Overlaps Downstream
ABE-0011366nikRCDSforward36185883618989Downstream
ABE-0011371rhsBCDSforward36191923623427Downstream
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.