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

ABE-0011358 (nikC) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0011358 showshow history
Names
nikC JW3443 ECK3462 hydD hydC b3478
Product
membrane component of an ABC superfamily nickel transporter
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 3616182 3617015 834 278
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 IPR014157 (IPR014157 Nickel ABC transporter, permease subunit NikC) Apr 2008
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
Automated Process Uncurated GO cellular component GO:0016021 integral component of membrane GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR014157
Reference: Escherichia coli K-12 MG1655 		Jul 2018
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:0019866 organelle inner membrane Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Uncurated GO molecular function GO:0015099 nickel cation transmembrane transporter activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR014157
Reference: Escherichia coli K-12 MG1655 		Jul 2018
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 nikC Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym hydD Published Sequence Analysis - PubMed ID: 9729611 Aug 2003
Person Approved synonym JW3443 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK3462 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym hydC Published Sequence Analysis - PubMed ID: 9729611 Aug 2003
Person Approved locus tag b3478 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product membrane component of an ABC superfamily nickel transporter Published Annotation - PubMed ID: 16397293
Reference: Escherichia coli K-12 		Mar 2008
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 transport of nickel, membrane protein Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Person Uncurated alternate product name nickel transport proein (ABC superfamily, membrane) Published Annotation - Database Name: GenProtEC Jan 2006
Protein Family
Automated Process Approved protein family IPR035906 MetI-like superfamily Protein Sequence Similarity - InterPro Domain: IPR035906
Reference: Escherichia coli K-12 MG1655 		Jul 2018
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 IPR014157 Nickel ABC transporter, permease subunit NikC Protein Sequence Similarity - InterPro Domain: IPR014157
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Other
Person Approved EC number 3.6.3.24 Published Annotation - Swiss-Prot Accession Number: P0AFA9 Feb 2006
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.143 (transport; substrate; Ni++) 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 ASAP:ABE-0011358 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG12077 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:947990 Published Annotation - Entrez Gene Database ID: 947990
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref UniProtKB/Swiss-Prot:P0AFA9 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GI:1789889 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P0AFA9 Published Annotation - Swiss-Prot Accession Number: P0AFA9 Jan 2006
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 transport of nickel, membrane protein; 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 AAC76503.1 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
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 Uncurated GO cellular component GO:0016021 integral component of membrane GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR014157
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
Automated Process Uncurated GO molecular function GO:0015099 nickel cation transmembrane transporter activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR014157
Reference: Escherichia coli K-12 MG1655 		Jul 2018
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 (14 enterobacteria) AMM-0003054 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0003581 nikC CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0003855 nikC CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003358 nikC CDS
Ortholog
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0000275 nikC CDS
Person Uncurated Go view Enterobacter sp. 638 AEL-0002267 nikC CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0001422 nikC CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0004845 nikC CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0003611 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0007614 nikC CDS
Person Approved Go view Escherichia coli APEC O1 (APEC) AEG-0003532 nikC CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0000711 nikC CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0005596 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0006501 nikC CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0005387 NikC CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0080447 nikC CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0003967 nikC CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0004613 nikC CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0005269 nikC CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0003958 nikC CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0008394 nikC CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0004771 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0008155 nikC CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0006668 nikC CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0006214 nikC CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0005209 nikC CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0009652 nikC CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0005294 nikC CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0007466 nikC CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0005247 nikC CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0005315 nikC CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0005154 nikC CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0005044 nikC CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0005643 nikC CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0028522 nikC CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0005480 nikC CDS
Automated Process Approved Go view Escherichia coli HS ADR-0008366 nikC CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0003981 nikC CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0003239 nikC CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0003893 nikC CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0004124 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0004118 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0003826 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0003983 nikC CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0178130 nikC CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0003817 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0003759 nikC CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0134417 nikC CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0002696 CDS
Person Approved Go view Escherichia coli UTI89 (UPEC) AEA-0004004 nikC CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0003900 nikC CDS
Person Approved Go view Shigella boydii 227 ADV-0003794 nikC CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0009262 nikC CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0003420 nikC CDS
Person Approved Go view Shigella dysenteriae 197 ADU-0004113 nikC CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0075569 nikC CDS
Person Approved Go view Shigella flexneri 301 ABT-0089729 nikC CDS
Person Approved Go view Shigella flexneri 8401 BAG-0003695 nikC CDS
Person Approved Go view Shigella sonnei 046 ADD-0004051 nikC 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
FB21229mutantTn5 InsertionRequest the StrainABE-0011358nikCnikC::Tn5KAN-I-SceI at position 240 in Plus orientation ,- pKD460Blattner Laboratory
FB21230mutantTn5 InsertionRequest the StrainABE-0011358nikCnikC::Tn5KAN-I-SceI at position 240 in Plus orientation ,+ pKD460Blattner Laboratory
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 3611182 to 3622015
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0011344yhhSCDScomplement36105163611733Upstream
ABE-0011347yhhTCDSforward36118653612914Upstream
ABE-0011351acpTCDSforward36129693613556Upstream
ABE-0011354nikACDSforward36136673615241Upstream
ABE-0011356nikBCDSforward36152413616185Overlaps Upstream
ABE-0011358nikCCDSforward36161823617015Matches
ABE-0011360nikDCDSforward36170153617779Overlaps Downstream
ABE-0011362nikECDSforward36177763618582Downstream
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.