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

ABE-0008185 (hyfD) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0008185 showshow history
Names
hyfD JW2469 ECK2480 b2484
Product
hydrogenase 4 component D
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 2604811 2606250 1440 480
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR003916 (IPR003916 (DEPRECATED) NADH-ubiquinone oxidoreductase, chain 5) Apr 2008
Automated Process Approved IPR001750 (IPR001750 NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit) Apr 2008
Automated Process Approved IPR001516 (IPR001516 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal) Jul 2018
Automated Process Approved PF00662 (PF00662 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus) Jul 2018
Automated Process Approved PF00361 (PF00361 Proton-conducting membrane transporter) 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 hyfD Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym JW2469 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK2480 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b2484 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product hydrogenase 4 component D Published Annotation - EcoCyc Accession Number: G7301
Reference: Escherichia coli K-12 MG1655 		Oct 2021
Person Uncurated alternate product name hydrogenase 4, D membrane subunit Published Annotation - Database Name: GenProtEC Jan 2006
Person Approved alternate product name hydrogenase 4 membrane subunit Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Person Approved alternate product name hydrogenase 4, membrane subunit Published Annotation - PubMed ID: 16397293 Jan 2006
Protein Family
Automated Process Approved protein family IPR003916 (DEPRECATED) NADH-ubiquinone oxidoreductase, chain 5 Protein Sequence Similarity - InterPro Domain: IPR003916
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR001516 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal Protein Sequence Similarity - InterPro Domain: IPR001516
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF00361 Proton-conducting membrane transporter Protein Sequence Similarity - PFAM Model Name: PF00361
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR001750 NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit Protein Sequence Similarity - InterPro Domain: IPR001750
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF00662 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus Protein Sequence Similarity - PFAM Model Name: PF00662
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Person Approved EC number 1.-.-.- Published Annotation - Swiss-Prot Accession Number: P77416 Feb 2006
Person Uncurated MultiFun 7.3 (location of gene products; inner membrane) 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 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 UniProtKB/Swiss-Prot:P77416 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GI:1788829 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P77416 Published Annotation - Swiss-Prot Accession Number: P77416 Jan 2005
Automated Process Approved db xref ASAP:ABE-0008185 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:947290 Published Annotation - Entrez Gene Database ID: 947290
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref EcoGene:EG14212 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 hydrogenase 4 membrane subunit; 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 AAC75537.1 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-0003114 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0004169 hyfD CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0003916 hyfD CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0008438 hyfD CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003359 hyfD CDS
Ortholog
Automated Process Uncurated Go view Brenneria salicis ATCC 15712 [T] AMK-0003724 CDS
Automated Process Uncurated Go view Brenneria sp. EniD312 AKG-0004243 CDS
Automated Process Uncurated Go view Dickeya chrysanthemi Ech1591 AFK-0007622 CDS
Person Approved Go view Dickeya dadantii 3937 ABF-0015738 hyfD CDS
Automated Process Uncurated Go view Dickeya parazeae Ech586 AGC-0002698 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0008743 CDS
Automated Process Uncurated Go view Escherichia coli ATCC 8739 AEM-0006740 hyfD pseudogene
Person Uncurated Go view Escherichia coli B7A (ETEC) ADK-0011095 pseudogene
Person Uncurated Go view Escherichia coli BL21(DE3) AHL-0005494 pseudogene
Person Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0002832 hyfD pseudogene
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0003319 CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0000824 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0007049 CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0005570 CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0005044 hyfD CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0006622 hyfD CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0008546 CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0006271 hyfD CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0006338 CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0008197 hyfD CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0007995 hyfD CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0006677 hyfD CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0006594 hyfD CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0008122 hyfD CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0027450 hyfD CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0002340 hyfD CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0002554 hyfD CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0002898 CDS
Automated Process Uncurated Go view Escherichia coli SE11 AFS-0002817 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0002630 hyfD CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0133365 hyfD CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0003671 CDS
Person Uncurated Go view Hafnia alvei ATCC 13337 [T] AMD-0003150 CDS
Automated Process Uncurated Go view Musicola paradisiaca Ech703 AGA-0005875 CDS
Person Approved Go view Pectobacterium atrosepticum SCRI1043 ABL-0061490 hyfD CDS
Person Uncurated Go view Shigella boydii 227 ADV-0002765 hyfD pseudogene
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0004408 hyfD CDS
Person Uncurated Go view Shigella dysenteriae 197 ADU-0003063 hyfD pseudogene
Person Approved Go view Shigella flexneri 2457T ABQ-0073828 hyfD CDS
Person Approved Go view Shigella flexneri 301 ABT-0088783 hyfD CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0002704 hyfD CDS
Person Approved Go view Shigella sonnei 046 ADD-0002801 hyfD CDS
Automated Process Uncurated Go view Yersinia bercovieri ATCC 43970 [T] AEK-0001150 CDS
Automated Process Uncurated Go view Yersinia enterocolitica 8081 BAH-0008062 hyfD CDS
Automated Process Uncurated Go view Yersinia frederiksenii ATCC 33641 [T] AEI-0002226 hyfD CDS
Automated Process Uncurated Go view Yersinia intermedia ATCC 29909 [T] AEH-0001335 hyfD CDS
Automated Process Uncurated Go view Yersinia mollaretii ATCC 43969 [T] AEJ-0003597 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 43003 APO-0008224 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 49455 [T] AMG-0002190 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
FB22430mutantTn5 InsertionRequest the StrainABE-0008185hyfDhyfD::Tn5KAN-I-SceI at position 469 in Plus orientation ,+ pKD460Blattner Laboratory
FB23576mutantTn5 InsertionRequest the StrainABE-0008185hyfDhyfD::Tn5KAN-I-SceI at position 1101 in Plus orientation ,- pKD460Blattner Laboratory
FB23700mutantTn5 InsertionRequest the StrainABE-0008185hyfDhyfD::Tn5KAN-I-SceI at position 1101 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 2599811 to 2611250
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0008168gcvRCDSforward25999062600478Upstream
ABE-0008171bcpCDSforward26004782600948Upstream
ABE-0008179hyfACDSforward26012012601818Upstream
ABE-0008181hyfBCDSforward26018182603836Upstream
ABE-0008183hyfCCDSforward26038472604794Upstream
ABE-0008185hyfDCDSforward26048112606250Matches
ABE-0008188hyfECDSforward26062622606912Downstream
ABE-0008191hyfFCDSforward26069172608497Downstream
ABE-0008194hyfGCDSforward26084872610154Downstream
ABE-0008196hyfHCDSforward26101642610709Downstream
ABE-0008198hyfICDSforward26107062611464Downstream
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.