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

ABE-0005307 (ynfF) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0005307 showshow history
Names
ynfF JW5260 ECK1583 b1588
Product
oxidoreductase subunit
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 1660556 1662979 2424 808
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 IPR006311 (IPR006311 Twin-arginine translocation pathway, signal sequence) Apr 2008
Automated Process Approved IPR011888 (IPR011888 Anaerobic dimethyl sulphoxide reductase, subunit A, DmsA/YnfE) Apr 2008
Automated Process Approved IPR009010 (IPR009010 Aspartate decarboxylase-like domain superfamily) Apr 2008
Automated Process Approved IPR006963 (IPR006963 Molybdopterin oxidoreductase, 4Fe-4S domain) Apr 2008
Automated Process Approved IPR006656 (IPR006656 Molybdopterin oxidoreductase) Apr 2008
Automated Process Approved IPR006657 (IPR006657 Molybdopterin dinucleotide-binding domain) Apr 2008
Automated Process Approved IPR006655 (IPR006655 Molybdopterin oxidoreductase, prokaryotic, conserved site) Apr 2008
Automated Process Approved PF00384 (PF00384 Molybdopterin oxidoreductase) Jul 2018
Automated Process Approved PF04879 (PF04879 Molybdopterin oxidoreductase Fe4S4 domain) Jul 2018
Automated Process Approved PF01568 (PF01568 Molydopterin dinucleotide binding domain) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Automated Process Uncurated GO biological process GO:0055114 (OBSOLETE) oxidation-reduction process GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR006656, IPR006963, IPR006657, IPR011888
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO biological process GO:0006118 (OBSOLETE) electron transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR006655
Reference: Escherichia coli K-12 MG1655 		Apr 2008
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:0043546 molybdopterin cofactor binding GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR006657
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0016491 oxidoreductase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR006963
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0009389 dimethyl sulfoxide reductase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR011888
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0030151 molybdenum ion binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR011888
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0051539 4 iron, 4 sulfur cluster binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR011888
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name ynfF Published Annotation - Swiss-Prot Accession Number: P77783 Aug 2002
Person Approved synonym JW5260 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK1583 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b1588 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product oxidoreductase subunit Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved alternate product name S- and N-oxide reductase, A subunit, periplasmic Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Uncurated alternate product name putative reductase subunit Published Annotation - Database Name: GenProtEC Jan 2006
Person Uncurated alternate product name putative dimethyl sulfoxide reductase, major subunit Published Annotation - Swiss-Prot Accession Number: P77783 Jan 2006
Protein Family
Automated Process Approved protein family IPR009010 Aspartate decarboxylase-like domain superfamily Protein Sequence Similarity - InterPro Domain: IPR009010
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR006311 Twin-arginine translocation pathway, signal sequence Protein Sequence Similarity - InterPro Domain: IPR006311
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR011888 Anaerobic dimethyl sulphoxide reductase, subunit A, DmsA/YnfE Protein Sequence Similarity - InterPro Domain: IPR011888
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF01568 Molydopterin dinucleotide binding domain Protein Sequence Similarity - PFAM Model Name: PF01568
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR006657 Molybdopterin dinucleotide-binding domain Protein Sequence Similarity - InterPro Domain: IPR006657
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR006655 Molybdopterin oxidoreductase, prokaryotic, conserved site Protein Sequence Similarity - InterPro Domain: IPR006655
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR006656 Molybdopterin oxidoreductase Protein Sequence Similarity - InterPro Domain: IPR006656
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR006963 Molybdopterin oxidoreductase, 4Fe-4S domain Protein Sequence Similarity - InterPro Domain: IPR006963
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF00384 Molybdopterin oxidoreductase Protein Sequence Similarity - PFAM Model Name: PF00384
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF04879 Molybdopterin oxidoreductase Fe4S4 domain Protein Sequence Similarity - PFAM Model Name: PF04879
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Automated Process Uncurated EC number 1.-.-.- Published Annotation - Database Name: EC2GO: GO:0016491
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Person Approved EC number 1.8.99.- Published Annotation - Swiss-Prot Accession Number: P77783 Feb 2006
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-0005307 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P77783 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P77783 Published Annotation - Swiss-Prot Accession Number: P77783 Jan 2006
Automated Process Approved db xref EcoGene:EG13844 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:945268 Published Annotation - Entrez Gene Database ID: 945268
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref GI:171474008 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved function putative enzyme; Not classified Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved protein id AAC74660.4 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: 9.76
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:0055114 (OBSOLETE) oxidation-reduction process GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR006656, IPR006963, IPR006657, IPR011888
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO biological process GO:0006118 (OBSOLETE) electron transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR006655
Reference: Escherichia coli K-12 MG1655 		Apr 2008
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 Approved GO molecular function GO:0009389 dimethyl sulfoxide reductase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR011888
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO molecular function GO:0043546 molybdopterin cofactor binding GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR006657
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0016491 oxidoreductase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR006963
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0051539 4 iron, 4 sulfur cluster binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR011888
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0030151 molybdenum ion binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR011888
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-0001757 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0000011 dmsA CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0000013 ynfE CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0004112 ynfE CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0000004 dmsA CDS
Paralog
Person Approved Go view Escherichia coli K-12 MG1655 ABE-0003044 dmsA CDS
Ortholog
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0002198 dmsA_4 CDS
Automated Process Uncurated Go view Escherichia coli APEC O1 (APEC) AEG-0001511 ynfF CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0002800 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0007772 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0078093 ynfF CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0001790 CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0002071 ynfF CDS
Automated Process Uncurated Go view Escherichia coli E2348/69 (EPEC) BCI-0001786 ynfF CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0006232 CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0026375 ynfF CDS
Automated Process Approved Go view Escherichia coli HS ADR-0006336 CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0001988 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0001490 ynfF CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0001630 ynfF CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0001941 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0002328 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0001738 CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0132275 ynfF CDS
Person Approved Go view Escherichia coli UTI89 (UPEC) AEA-0001782 ynfF CDS
Person Approved Go view Salmonella Choleraesuis SC-B67 ADB-0001760 ynfF CDS
Person Approved Go view Salmonella Typhi CT18 ABX-0108233 ynfF CDS
Person Approved Go view Salmonella Typhi Ty2 ABS-0083133 ynfF CDS
Person Approved Go view Salmonella Typhimurium LT2 [T] ABU-0094981 ynfF CDS
Person Approved Go view Shigella boydii 227 ADV-0001707 ynfF CDS
Person Approved Go view Shigella dysenteriae 197 ADU-0001808 ynfF pseudogene
Person Approved Go view Shigella flexneri 2457T ABQ-0072827 ynfF pseudogene
Person Approved Go view Shigella flexneri 301 ABT-0087922 ynfF pseudogene
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
FB23552mutantTn5 InsertionRequest the StrainABE-0005307ynfFb1588::Tn5KAN-I-SceI at position 595 in Plus orientation ,- pKD460Blattner Laboratory
FB23671mutantTn5 InsertionRequest the StrainABE-0005307ynfFb1588::Tn5KAN-I-SceI at position 595 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 1655556 to 1667979
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0005279ynfACDScomplement16553471655673Upstream
ABE-0005284ynfBCDSforward16558081656149Upstream
ABE-0005286speGCDSforward16561841656744Upstream
ABE-0005288ynfCCDScomplement16567471657457Upstream
ABE-0005297ynfDCDSforward16575651657870Upstream
ABE-0285459repeat_regionforward16578881657908Upstream
ABE-0005302ynfECDSforward16580691660495Upstream
ABE-0005307ynfFCDSforward16605561662979Matches
ABE-0005309ynfGCDSforward16629901663607Downstream
ABE-0005311ynfHCDSforward16636091664463Downstream
ABE-0005314dmsDCDSforward16645061665120Downstream
ABE-0285460repeat_regionforward16651361665166Downstream
ABE-0285729matS17protein_bindforward16651751665187Downstream
ABE-0005317clcBCDSforward16653151666571Downstream
ABE-0005319bidACDScomplement16665241667219Downstream
ABE-0005323mlcCDScomplement16673441668564Downstream
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.