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

ABE-0013348 (nrfD) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0013348 showshow history
Names
nrfD yjcK JW4034 ECK4066 b4073
Product
putative menaquinol-cytochrome c reductase subunit
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 4290476 4291432 957 319
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR005614 (IPR005614 NrfD family) Apr 2008
Automated Process Approved IPR014366 (IPR014366 (DEPRECATED) Polysulphide reductase, subunit C) Apr 2008
Automated Process Approved IPR017566 (IPR017566 NrfD) Jul 2018
Automated Process Approved PF03916 (PF03916 Polysulphide reductase, NrfD) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Person Uncurated GO biological process GO:0009061 anaerobic respiration 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
Person Uncurated GO cellular component GO:0019866 organelle inner membrane Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name nrfD Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym JW4034 Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved synonym yjcK Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved synonym ECK4066 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b4073 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product putative menaquinol-cytochrome c reductase subunit Published Annotation - EcoCyc Accession Number: EG11947
Reference: Escherichia coli K-12 MG1655 		Oct 2021
Person Approved alternate product name formate-dependent nitrite reductase, membrane subunit Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved alternate product name formate-dependent nitrate reductase complex; transmembrane protein Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Person Uncurated alternate product name putative nitrate reductase, formate-dependent Published Annotation - Database Name: GenProtEC Jan 2006
Protein Family
Automated Process Approved protein family IPR014366 (DEPRECATED) Polysulphide reductase, subunit C Protein Sequence Similarity - InterPro Domain: IPR014366
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR005614 NrfD family Protein Sequence Similarity - InterPro Domain: IPR005614
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF03916 Polysulphide reductase, NrfD Protein Sequence Similarity - PFAM Model Name: PF03916
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR017566 NrfD Protein Sequence Similarity - InterPro Domain: IPR017566
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Person Uncurated MultiFun 7.3 (location of gene products; inner membrane) 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 6.1 (cell structure; 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 GI:1790509 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P32709 Published Annotation - Swiss-Prot Accession Number: P32709 Jan 2005
Automated Process Approved db xref GeneID:948580 Published Annotation - Entrez Gene Database ID: 948580
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref UniProtKB/Swiss-Prot:P32709 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0013348 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG11947 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved function enzyme; Energy metabolism, carbon: Anaerobic respiration Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved note formate-dependent nitrate reductase complex; transmembrane protein; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane; 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 AAC77043.1 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
Person Uncurated GO biological process GO:0009061 anaerobic respiration Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
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
Comparative to toptop
Author Approval Details Genome Feature Name Type
Member
Automated Process Uncurated Go view OrthoMCL (14 enterobacteria) AMM-0003276 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0002734 nrfD CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0002861 nrfD CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0008499 nrfD CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0002718 nrfD CDS
Ortholog
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0004140 nrfD CDS
Automated Process Approved Go view Citrobacter freundii ATCC 8090 [T] AVI-0000184 nrfD CDS
Automated Process Uncurated Go view Dickeya chrysanthemi Ech1591 AFK-0008289 CDS
Person Uncurated Go view Dickeya dadantii 3937 ABF-0016811 nrfD CDS
Automated Process Uncurated Go view Dickeya parazeae Ech586 AGC-0000877 CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0001957 nrfD CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0006354 nrfD CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0004357 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0006897 nrfD CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0004150 nrfD CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0004739 nrfD CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0010115 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0006282 nrfD CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0009221 NrfD CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0081277 nrfD CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0004739 nrfD CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0005341 nrfD CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0006163 nrfD CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0006619 nrfD CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0004693 nrfD CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0009066 nrfD CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0003130 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0008906 nrfD CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0007419 nrfD CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0007064 nrfD CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0006260 nrfD CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0010408 nrfD CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0007080 nrfD CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0008224 nrfD CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0007194 nrfD CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0005776 nrfD CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0006523 nrfD CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0006010 nrfD CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0005045 nrfD CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0029247 nrfD CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0007040 CDS
Automated Process Approved Go view Escherichia coli HS ADR-0009006 nrfD CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0004676 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0003766 nrfD CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0004160 nrfD CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0004781 nrfD CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0004788 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0004598 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0004721 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0178889 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0004468 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0004527 nrfD CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0135167 nrfD CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0003321 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0004672 nrfD CDS
Automated Process Uncurated Go view Musicola paradisiaca Ech703 AGA-0008145 CDS
Person Uncurated Go view Pectobacterium atrosepticum SCRI1043 ABL-0062137 nrfD CDS
Automated Process Uncurated Go view Pectobacterium brasiliensis 1692 AED-0001035 nrfD CDS
Person Uncurated Go view Pectobacterium carotovorum WPP14 ADT-0000485 nrfD CDS
Automated Process Uncurated Go view Pectobacterium parmentieri WPP163 AFJ-0002114 nrfD CDS
Automated Process Uncurated Go view Pectobacterium sp. PC1 AFL-0007403 CDS
Automated Process Uncurated Go view Salmonella Agona SL483 BBX-0008701 nrfD CDS
Automated Process Uncurated Go view Salmonella Arizonae CDC 346-86 BCD-0003556 CDS
Person Uncurated Go view Salmonella Choleraesuis SC-B67 ADB-0004893 nrfD CDS
Automated Process Uncurated Go view Salmonella Dublin CT_02021853 BCB-0008913 nrfD CDS
Automated Process Uncurated Go view Salmonella Enteritidis P125109 BCF-0013409 nrfD CDS
Automated Process Uncurated Go view Salmonella Gallinarum 287/91 BCG-0012672 nrfD CDS
Automated Process Uncurated Go view Salmonella Hadar RI_05P066 BBT-0007818 nrfD CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL476 BBV-0008978 nrfD CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL486 BBW-0007383 nrfD CDS
Automated Process Uncurated Go view Salmonella Javiana GA_MM04042433 BCA-0004017 nrfD CDS
Automated Process Uncurated Go view Salmonella Kentucky CDC 191 BBZ-0005759 nrfD CDS
Automated Process Uncurated Go view Salmonella Kentucky CVM29188 BBP-0008086 nrfD CDS
Automated Process Uncurated Go view Salmonella Newport SL254 BBQ-0008970 nrfD CDS
Automated Process Uncurated Go view Salmonella Newport SL317 BBR-0008275 nrfD CDS
Automated Process Uncurated Go view Salmonella Paratyphi A AKU_12601 BCH-0004133 CDS
Person Uncurated Go view Salmonella Paratyphi A ATCC 9150 ADA-0004092 nrfD CDS
Automated Process Uncurated Go view Salmonella Paratyphi B SPB7 BCC-0005300 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA23 BBN-0004321 nrfD CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA29 BBM-0007466 nrfD CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund CVM19633 BBO-0008595 nrfD CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund SL480 BBY-0006284 nrfD CDS
Person Approved Go view Salmonella Typhi CT18 ABX-0114498 nrfD CDS
Person Uncurated Go view Salmonella Typhi Ty2 ABS-0085913 nrfD CDS
Automated Process Uncurated Go view Salmonella Typhimurium 14028S AJR-0005152 nrfD CDS
Person Uncurated Go view Salmonella Typhimurium LT2 [T] ABU-0103178 nrfD CDS
Automated Process Uncurated Go view Salmonella Virchow SL491 BBS-0004865 nrfD CDS
Automated Process Uncurated Go view Salmonella Weltevreden SL484 BBU-0007534 nrfD CDS
Automated Process Uncurated Go view Salmonella enterica CVM23701 BBL-0005800 nrfD CDS
Person Uncurated Go view Shewanella oneidensis MR-1 ACY-0268228 nrfD-2 CDS
Person Approved Go view Shigella boydii 227 ADV-0004468 nrfD CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0010013 nrfD CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0004637 nrfD CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0074811 nrfD CDS
Person Approved Go view Shigella flexneri 301 ABT-0090346 nrfD CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0004395 nrfD CDS
Person Approved Go view Shigella sonnei 046 ADD-0004621 nrfD CDS
Automated Process Uncurated Go view Yersinia bercovieri ATCC 43970 [T] AEK-0003311 CDS
Automated Process Uncurated Go view Yersinia frederiksenii ATCC 33641 [T] AEI-0003580 CDS
Automated Process Uncurated Go view Yersinia mollaretii ATCC 43969 [T] AEJ-0002718 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
FB21645mutantTn5 InsertionRequest the StrainABE-0013348nrfDnrfD::Tn5KAN-I-SceI at position 230 in Plus orientation ,- pKD465Blattner Laboratory
FB21646mutantTn5 InsertionRequest the StrainABE-0013348nrfDnrfD::Tn5KAN-I-SceI at position 230 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 4285476 to 4296432
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0013337acsCDScomplement42854134287371Upstream
ABE-0285850ytcBCDSforward42876114287667Upstream
ABE-0013342nrfACDSforward42877644289200Upstream
ABE-0013344nrfBCDSforward42892454289811Upstream
ABE-0013346nrfCCDSforward42898084290479Overlaps Upstream
ABE-0013348nrfDCDSforward42904764291432Matches
ABE-0013350nrfECDSforward42915124293170Downstream
ABE-0013352nrfFCDSforward42931634293546Downstream
ABE-0013354nrfGCDSforward42935434294139Downstream
ABE-0013357gltPCDSforward42944814295794Downstream
ABE-0285674repeat_regionforward42958354296434Downstream
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.