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

ABE-0008179 (hyfA) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0008179 showshow history
Names
hyfA yffE JW2466 ECK2477 hydA b2481
Product
hydrogenase 4 component A
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 2601201 2601818 618 206
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR001450 (IPR001450 (DEPRECATED) 4Fe-4S binding domain) Apr 2008
Automated Process Approved IPR017896 (IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain) Jul 2018
Automated Process Approved PF12798 (PF12798 4Fe-4S binding domain) Jul 2018
Automated Process Approved PF00037 (PF00037 4Fe-4S binding domain) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Automated Process Approved GO biological process GO:0006118 (OBSOLETE) electron transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001450
Reference: Escherichia coli K-12 MG1655 		Apr 2008
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:0005737 cytoplasm GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Automated Process Approved GO molecular function GO:0051536 iron-sulfur cluster binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001450
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0009055 electron transfer activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001450
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name hyfA Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym hydA Published Annotation - Database Name: GenProtEC Jul 2002
Automated Process Approved synonym yffE Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved synonym JW2466 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK2477 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b2481 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product hydrogenase 4 component A Published Annotation - EcoCyc Accession Number: EG11150
Reference: Escherichia coli K-12 MG1655 		Oct 2021
Person Approved alternate product name hydrogenase 4, 4Fe-4S subunit Published Annotation - PubMed ID: 16397293 Jan 2006
Protein Family
Automated Process Approved protein family IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain Protein Sequence Similarity - InterPro Domain: IPR017896
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR001450 (DEPRECATED) 4Fe-4S binding domain Protein Sequence Similarity - InterPro Domain: IPR001450
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF00037 4Fe-4S binding domain Protein Sequence Similarity - PFAM Model Name: PF00037
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF12798 4Fe-4S binding domain Protein Sequence Similarity - PFAM Model Name: PF12798
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Person Approved EC number 1.-.-.- Published Annotation - Swiss-Prot Accession Number: P23481 Feb 2006
Person Uncurated MultiFun 1.3.7 (metabolism; energy metabolism, carbon; anaerobic respiration) 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:EG11150 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P23481 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:946959 Published Annotation - Entrez Gene Database ID: 946959
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref GI:87082114 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P23481 Published Annotation - Swiss-Prot Accession Number: P23481 Jan 2005
Automated Process Approved db xref ASAP:ABE-0008179 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved note hydrogenase 4 Fe-S subunit; 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 AAC75534.2 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Uncurated subcellular localization Cytoplasmic Predicted by PSORTb - PSORTb Final_Score: 9.26
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:0006118 (OBSOLETE) electron transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001450
Reference: Escherichia coli K-12 MG1655 		Apr 2008
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:0005737 cytoplasm GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Automated Process Approved GO molecular function GO:0051536 iron-sulfur cluster binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001450
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0009055 electron transfer activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001450
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-0002654 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0003872 hyfA CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0001718 hyfA CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0004091 hyfA CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003641 hyfA CDS
Ortholog
Automated Process Uncurated Go view Dickeya chrysanthemi Ech1591 AFK-0007618 CDS
Person Approved Go view Dickeya dadantii 3937 ABF-0015735 hyfA CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0006783 hyfA CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0008747 hyfA CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0006744 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0006786 hyfA CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0007914 CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0002824 CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0003316 CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0006756 hyfA CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0008539 hyfA CDS
Automated Process Uncurated Go view Escherichia coli E24377A (ETEC) ADO-0007197 CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0000821 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0007046 hyfA CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0005567 hyfA CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0005041 hyfA CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0006625 hyfA CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0008543 hyfA CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0006274 hyfA CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0006335 hyfA CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0008194 hyfA CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0007992 hyfA CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0006674 hyfA CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0006591 hyfA CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0008119 hyfA CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0027447 hyfA CDS
Automated Process Uncurated Go view Escherichia coli HS ADR-0007286 hyfA CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0002337 hyfA CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0002551 hyfA CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0003108 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0002901 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0002813 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0002627 hyfA CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0133362 hyfA CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0003668 CDS
Automated Process Uncurated Go view Musicola paradisiaca Ech703 AGA-0005880 CDS
Person Uncurated Go view Pectobacterium atrosepticum SCRI1043 ABL-0061493 hyfA CDS
Person Uncurated Go view Shigella boydii 227 ADV-0002762 hyfA pseudogene
Automated Process Uncurated Go view Shigella boydii BS512 ADJ-0008261 hyfA CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0004405 hyfA CDS
Person Approved Go view Shigella dysenteriae 197 ADU-0003060 hyfA CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0073825 hyfA CDS
Person Approved Go view Shigella flexneri 301 ABT-0088781 hyfA CDS
Automated Process Uncurated Go view Shigella flexneri 8401 BAG-0002701 hyfA CDS
Person Approved Go view Shigella sonnei 046 ADD-0002798 hyfA CDS
Automated Process Uncurated Go view Yersinia bercovieri ATCC 43970 [T] AEK-0001153 CDS
Automated Process Uncurated Go view Yersinia frederiksenii ATCC 33641 [T] AEI-0002223 hyfA CDS
Automated Process Uncurated Go view Yersinia mollaretii ATCC 43969 [T] AEJ-0003594 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
FB20825mutantTn5 InsertionRequest the StrainABE-0008179hyfAhyfA::Tn5KAN-I-SceI at position 153 in Plus orientation ,+ pKD460Blattner Laboratory
FB20826mutantTn5 InsertionRequest the StrainABE-0008179hyfAhyfA::Tn5KAN-I-SceI at position 153 in Plus orientation ,- pKD465Blattner 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 2596201 to 2606818
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0008153ypfJCDScomplement25958742596737Upstream
ABE-0008156purCCDScomplement25969052597618Upstream
ABE-0285524repeat_regionforward25976732597718Upstream
ABE-0008161bamCCDScomplement25978312598865Upstream
ABE-0008163dapACDScomplement25988822599760Upstream
ABE-0008168gcvRCDSforward25999062600478Upstream
ABE-0008171bcpCDSforward26004782600948Upstream
ABE-0008179hyfACDSforward26012012601818Matches
ABE-0008181hyfBCDSforward26018182603836Overlaps Downstream
ABE-0008183hyfCCDSforward26038472604794Downstream
ABE-0008185hyfDCDSforward26048112606250Downstream
ABE-0008188hyfECDSforward26062622606912Downstream
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.