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

ABE-0011356 (nikB) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0011356 showshow history
Names
nikB JW3442 ECK3461 hydD hydC b3477
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 3615241 3616185 945 315
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR014156 (IPR014156 Nickel ABC transporter, permease subunit NikB) 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:0035444 nickel cation transmembrane transport GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR014156
Reference: Escherichia coli K-12 MG1655 		Jul 2018
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 Uncurated GO molecular function GO:0015099 nickel cation transmembrane transporter activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR014156
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 nikB 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 JW3442 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK3461 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym hydC Published Sequence Analysis - PubMed ID: 9729611 Aug 2003
Person Approved locus tag b3477 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 protein (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 IPR014156 Nickel ABC transporter, permease subunit NikB Protein Sequence Similarity - InterPro Domain: IPR014156
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Other
Person Approved EC number 3.6.3.24 Published Annotation - Swiss-Prot Accession Number: P33591 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-0011356 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG12076 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:947986 Published Annotation - Entrez Gene Database ID: 947986
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref UniProtKB/Swiss-Prot:P33591 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GI:1789888 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P33591 Published Annotation - Swiss-Prot Accession Number: P33591 Jan 2005
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 AAC76502.1 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:0035444 nickel cation transmembrane transport GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR014156
Reference: Escherichia coli K-12 MG1655 		Jul 2018
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 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:0005886 plasma membrane GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Automated Process Uncurated GO molecular function GO:0015099 nickel cation transmembrane transporter activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR014156
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-0003055 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0003438 nikB CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0003480 nikB CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003235 nikB CDS
Ortholog
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0000276 nikB CDS
Automated Process Uncurated Go view Dickeya chrysanthemi Ech1591 AFK-0007685 CDS
Automated Process Uncurated Go view Dickeya parazeae Ech586 AGC-0001389 CDS
Person Uncurated Go view Enterobacter sp. 638 AEL-0002265 nikB CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0001421 nikB CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0004846 nikB CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0003610 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0007615 nikB CDS
Person Approved Go view Escherichia coli APEC O1 (APEC) AEG-0003531 nikB CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0000712 nikB CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0005598 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0006500 nikB CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0005388 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0080446 nikB CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0003966 CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0004612 nikB CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0005270 nikB CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0003957 nikB CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0008392 nikB CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0004769 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0008154 nikB CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0006667 nikB CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0006213 nikB CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0005210 nikB CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0009651 nikB CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0005295 nikB CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0007465 nikB CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0005246 nikB CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0005314 nikB CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0005153 nikB CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0005043 nikB CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0005642 nikB CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0028521 nikB CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0005481 nikB CDS
Automated Process Approved Go view Escherichia coli HS ADR-0008365 nikB CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0003982 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0003238 nikB CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0003894 nikB CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0004123 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0004117 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0003827 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0003982 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0003816 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0003758 nikB CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0134416 nikB CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0002694 CDS
Person Approved Go view Escherichia coli UTI89 (UPEC) AEA-0004003 nikB CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0003899 nikB CDS
Automated Process Uncurated Go view Musicola paradisiaca Ech703 AGA-0004667 CDS
Person Approved Go view Shigella boydii 227 ADV-0003793 nikB CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0009263 nikB CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0003421 nikB CDS
Person Approved Go view Shigella dysenteriae 197 ADU-0004112 nikB CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0075570 nikB CDS
Person Approved Go view Shigella flexneri 301 ABT-0089728 nikB CDS
Person Approved Go view Shigella flexneri 8401 BAG-0003694 nikB CDS
Person Approved Go view Shigella sonnei 046 ADD-0004050 nikB 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 3610241 to 3621185
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0011342dcrBCDSforward36099553610512Upstream
ABE-0011344yhhSCDScomplement36105163611733Upstream
ABE-0011347yhhTCDSforward36118653612914Upstream
ABE-0011351acpTCDSforward36129693613556Upstream
ABE-0011354nikACDSforward36136673615241Overlaps Upstream
ABE-0011356nikBCDSforward36152413616185Matches
ABE-0011358nikCCDSforward36161823617015Overlaps Downstream
ABE-0011360nikDCDSforward36170153617779Downstream
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.