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

ABE-0011354 (nikA) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0011354 showshow history
Names
nikA JW3441 ECK3460 hydD hydC b3476
Product
periplasmic-binding component of an ABC superfamily nickel transporter
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 3613667 3615241 1575 525
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR011980 (IPR011980 Nickel ABC transporter, substrate-binding protein NikA) Apr 2008
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
Person Approved GO biological process GO:0015675 nickel cation transport GO Inferred from Direct Assay - PubMed ID: 12270829
Reference: Escherichia coli HPX72 		Jul 2006
Person Uncurated GO biological process GO:0042330 taxis 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
Person Uncurated GO cellular component GO:0042597 periplasmic space Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Uncurated GO molecular function GO:0020037 heme binding GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR011980
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: IPR011980
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:IPR000914
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Uncurated GO molecular function GO:0015099 nickel cation transmembrane transporter activity GO Inferred from Direct Assay - PubMed ID: 12270829
Reference: Escherichia coli HPX72 		Jul 2006
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name nikA Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym ECK3460 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym JW3441 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym hydD Published Sequence Analysis - PubMed ID: 9729611 Aug 2003
Person Approved synonym hydC Published Sequence Analysis - PubMed ID: 9729611 Aug 2003
Person Approved locus tag b3476 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product periplasmic-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, peri_bind) Published Annotation - Database Name: GenProtEC Jan 2006
Person Approved alternate product name periplasmic binding protein for nickel Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Automated Process Approved alternate product name nickel-binding, heme-binding periplasmic protein Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Protein Family
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
Automated Process Approved protein family IPR011980 Nickel ABC transporter, substrate-binding protein NikA Protein Sequence Similarity - InterPro Domain: IPR011980
Reference: Escherichia coli K-12 MG1655 		Apr 2008
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
Other
Person Approved EC number 3.6.3.24 Published Annotation - Swiss-Prot Accession Number: P33590 Feb 2006
Person Uncurated MultiFun 7.2 (location of gene products; periplasmic space) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 5.3 (cell processes; motility (incl. chemotaxis, energytaxis, aerotaxis, redoxtaxis)) 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 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
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:EG12075 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0011354 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:947981 Published Annotation - Entrez Gene Database ID: 947981
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Person Approved db xref UniProtKB:P33590 Published Annotation - Swiss-Prot Accession Number: P33590 Jan 2005
Automated Process Approved db xref UniProtKB/Swiss-Prot:P33590 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GI:1789887 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Uncurated function functions in nickel transport Experimental - PubMed ID: 12270829
Reference: Escherichia coli HPX72 		Jul 2006
Person Approved function transport; Transport of small molecules: Cations Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Uncurated mutant phenotype nikA null mutant; null mutant shows loss of nickel transporter activity Experimental - PubMed ID: 12270829
Reference: Escherichia coli HPX72 		Jul 2006
Automated Process Approved note periplasmic binding protein for nickel; periplasmic-binding component of ABC superfamily; GO_component: GO:0042597 - periplasmic space; GO_process: GO:0042330 - taxis Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC76501.1 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: 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 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 Approved GO biological process GO:0015675 nickel cation transport GO Inferred from Direct Assay - PubMed ID: 12270829
Reference: Escherichia coli HPX72 		Jul 2006
Person Uncurated GO biological process GO:0042330 taxis Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
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 Uncurated GO molecular function GO:0016151 nickel cation binding GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR011980
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Uncurated GO molecular function GO:0020037 heme binding GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR011980
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:IPR000914
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Uncurated GO molecular function GO:0015099 nickel cation transmembrane transporter activity GO Inferred from Direct Assay - PubMed ID: 12270829
Reference: Escherichia coli HPX72 		Jul 2006
Comparative to toptop
Author Approval Details Genome Feature Name Type
Member
Automated Process Uncurated Go view OrthoMCL (14 enterobacteria) AMM-0003056 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0003326 nikA CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0003210 nikA CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003145 nikA CDS
Ortholog
Automated Process Uncurated Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0000277 nikA CDS
Automated Process Uncurated Go view Dickeya chrysanthemi Ech1591 AFK-0007687 CDS
Automated Process Uncurated Go view Dickeya parazeae Ech586 AGC-0001388 CDS
Person Uncurated Go view Enterobacter sp. 638 AEL-0002263 nikA CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0001420 nikA CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0004847 nikA CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0003609 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0007616 nikA CDS
Person Approved Go view Escherichia coli APEC O1 (APEC) AEG-0003530 nikA CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0000713 nikA CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0005600 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0006499 nikA CDS
Person Uncurated Go view Escherichia coli B7A (ETEC) ADK-0010548 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0080445 nikA CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0003965 nikA CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0004611 nikA CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0005271 nikA CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0003956 nikA CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0008391 nikA CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0004768 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0008153 nikA CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0006666 nikA CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0006212 nikA CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0005211 nikA CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0009650 nikA CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0005296 nikA CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0007464 nikA CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0005245 nikA CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0005313 nikA CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0005152 nikA CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0005042 nikA CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0005641 nikA CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0028520 nikA CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0005482 nikA CDS
Automated Process Approved Go view Escherichia coli HS ADR-0008364 nikA CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0003983 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0003237 nikA CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0003895 nikA CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0004122 nikA CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0004116 nikA CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0003828 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0003981 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0178128 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0003815 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0003757 nikA CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0134415 nikA CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0002693 CDS
Person Approved Go view Escherichia coli UTI89 (UPEC) AEA-0004002 nikA CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0003898 nikA CDS
Automated Process Uncurated Go view Musicola paradisiaca Ech703 AGA-0004665 CDS
Person Approved Go view Shigella boydii 227 ADV-0003792 nikA CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0009264 nikA CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0003422 nikA CDS
Person Approved Go view Shigella dysenteriae 197 ADU-0004111 nikA CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0075571 nikA CDS
Person Approved Go view Shigella flexneri 301 ABT-0089727 nikA CDS
Person Approved Go view Shigella flexneri 8401 BAG-0003693 nikA CDS
Person Approved Go view Shigella sonnei 046 ADD-0004049 nikA 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
FB21228mutantTn5 InsertionRequest the StrainABE-0011354nikAnikA::Tn5KAN-I-SceI at position 943 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 3608667 to 3620241
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0011336tusACDScomplement36087513608996Upstream
ABE-0011340yhhQCDSforward36092173609882Upstream
ABE-0011342dcrBCDSforward36099553610512Upstream
ABE-0011344yhhSCDScomplement36105163611733Upstream
ABE-0011347yhhTCDSforward36118653612914Upstream
ABE-0011351acpTCDSforward36129693613556Upstream
ABE-0011354nikACDSforward36136673615241Matches
ABE-0011356nikBCDSforward36152413616185Overlaps Downstream
ABE-0011358nikCCDSforward36161823617015Downstream
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.