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

ABE-0003288 (hyaB) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0003288 showshow history
Names
hyaB JW0955 ECK0964 b0973
Product
hydrogenase 1 large subunit
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 1033254 1035047 1794 598
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 IPR001501 (IPR001501 Nickel-dependent hydrogenase, large subunit) Apr 2008
Automated Process Approved IPR029014 (IPR029014 [NiFe]-hydrogenase, large subunit) Jul 2018
Automated Process Approved PF00374 (PF00374 Nickel-dependent hydrogenase) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Person Uncurated GO biological process GO:0009060 aerobic respiration Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO biological process GO:0006118 (OBSOLETE) electron transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001501
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: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:0019866 organelle inner membrane Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO molecular function GO:0016151 nickel cation binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001501
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0008901 ferredoxin hydrogenase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001501
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Uncurated GO molecular function GO:0009053 (DEPRECATED) electron donor activity Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name hyaB Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym ECK0964 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym JW0955 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b0973 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product hydrogenase 1 large subunit Published Annotation - PubMed ID: 16397293
Reference: Escherichia coli K-12 		Oct 2021
Person Uncurated alternate product name hydrogenase-1, large subunit Published Annotation - Database Name: GenProtEC Jan 2006
Person Approved alternate product name hydrogenase-1 large subunit Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Protein Family
Automated Process Approved protein family PF00374 Nickel-dependent hydrogenase Protein Sequence Similarity - PFAM Model Name: PF00374
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR001501 Nickel-dependent hydrogenase, large subunit Protein Sequence Similarity - InterPro Domain: IPR001501
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR029014 [NiFe]-hydrogenase, large subunit Protein Sequence Similarity - InterPro Domain: IPR029014
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Person Approved EC number 1.12.99.6 Published Annotation - Swiss-Prot Accession Number: P0ACD8 Feb 2006
Person Uncurated MultiFun 1.3.6 (metabolism; energy metabolism, carbon; aerobic respiration) 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 7.3 (location of gene products; inner membrane) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 1.4.1 (metabolism; energy production/transport; electron donor) 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 ASAP:ABE-0003288 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG10469 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P0ACD8 Published Annotation - Swiss-Prot Accession Number: P0ACD8 Jan 2006
Automated Process Approved db xref GeneID:945580 Published Annotation - Entrez Gene Database ID: 945580
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref GI:1787207 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P0ACD8 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved function enzyme; Energy metabolism, carbon: Aerobic respiration Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved note hydrogenase-1 large subunit; GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0009060 - aerobic respiration; 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 AAC74058.1 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: 9.44
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
Person Uncurated subsystem component of in silico model iMC1010 Experimental - PubMed ID: 15129285
Reference: Escherichia coli K-12 MG1655 		Mar 2009
Person Uncurated subsystem component of in silico model iJR904 Experimental - PubMed ID: 12952533
Reference: Escherichia coli K-12 MG1655 		Feb 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:0009060 aerobic respiration Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO biological process GO:0006118 (OBSOLETE) electron transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001501
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: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:0019866 organelle inner membrane Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Person Uncurated GO molecular function GO:0009053 (DEPRECATED) electron donor activity Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO molecular function GO:0016151 nickel cation binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001501
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0008901 ferredoxin hydrogenase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001501
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-0006670 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0002552 hyaB CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0003106 hyaB CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0002751 hyaB CDS
Ortholog
Automated Process Approved Go view Citrobacter freundii ATCC 8090 [T] AVI-0001586 hyaB CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0003591 hyaB CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0007309 hyaB CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0000987 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0005506 hyaB CDS
Person Approved Go view Escherichia coli APEC O1 (APEC) AEG-0000912 hyaB CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0003396 CDS
Person Uncurated Go view Escherichia coli ATCC 8739 AEM-0008476 hyaB pseudogene
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0009645 hyaB CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0006723 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0077208 hyaB CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0001058 hyaB CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0008550 hyaB CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0010317 hyaB CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0001006 hyaB CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0005531 hyaB CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0005047 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0009913 hyaB CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0008957 hyaB CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0007562 hyaB CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0005591 hyaB CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0006049 hyaB CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0009644 hyaB CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0009816 hyaB CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0006251 hyaB CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0006904 hyaB CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0008782 hyaB CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0008327 hyaB CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0007782 hyaB CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0025204 hyaB CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0007450 hyaB CDS
Automated Process Approved Go view Escherichia coli HS ADR-0005759 hyaB CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0001207 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0000936 hyaB CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0000982 hyaB CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0001271 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0001273 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0001125 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0001065 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0001061 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0002143 hyaB CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0131050 hyaB CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0003442 CDS
Person Approved Go view Escherichia coli UTI89 (UPEC) AEA-0001044 hyaB CDS
Person Uncurated Go view Salmonella Choleraesuis SC-B67 ADB-0002089 hyaB pseudogene
Person Uncurated Go view Salmonella Paratyphi A ATCC 9150 ADA-0001086 hyaB CDS
Person Uncurated Go view Salmonella Typhi CT18 ABX-0108850 hyaB CDS
Person Approved Go view Salmonella Typhi Ty2 ABS-0082803 hyaB CDS
Person Approved Go view Salmonella Typhimurium LT2 [T] ABU-0095815 hyaB CDS
Person Approved Go view Shigella boydii 227 ADV-0002502 hyaB CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0007754 hyaB CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0004926 hyaB CDS
Person Approved Go view Shigella dysenteriae 197 ADU-0001067 hyaB CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0072078 hyaB CDS
Person Approved Go view Shigella flexneri 301 ABT-0087326 hyaB CDS
Person Approved Go view Shigella flexneri 8401 BAG-0001041 hyaB CDS
Person Approved Go view Shigella sonnei 046 ADD-0001052 hyaB 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
FB20075mutantTn5 InsertionRequest the StrainABE-0003288hyaBhyaB::Tn5KAN-2 at position 1627 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 1028254 to 1040047
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0003267yccUCDSforward10279461028359Upstream
ABE-0285415repeat_regionforward10283661028389Upstream
ABE-0003269hspQCDScomplement10284041028721Upstream
ABE-0003272rlmICDScomplement10287791029969Upstream
ABE-0003276yccXCDSforward10300641030342Upstream
ABE-0003278tusECDScomplement10303391030668Upstream
ABE-0003280yccACDScomplement10307591031418Upstream
ABE-0003283serTtRNAcomplement10316251031712Upstream
ABE-0003286hyaACDSforward10321391033257Overlaps Upstream
ABE-0003288hyaBCDSforward10332541035047Matches
ABE-0003290hyaCCDSforward10350661035773Downstream
ABE-0003292hyaDCDSforward10357701036357Downstream
ABE-0003294hyaECDSforward10363541036752Downstream
ABE-0003296hyaFCDSforward10367491037606Downstream
ABE-0003300appCCDSforward10377401039284Downstream
ABE-0003302appBCDSforward10392961040432Downstream
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.