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

ABE-0008946 (hycD) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0008946 showshow history
Names
hycD hevD JW2692 ECK2717 b2722
Product
formate hydrogenlyase subunit
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 2846489 2847412 924 308
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR001694 (IPR001694 NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H) Apr 2008
Automated Process Approved PF00146 (PF00146 NADH dehydrogenase) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Person Uncurated GO biological process GO:0006113 fermentation Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Uncurated GO biological process GO:0055114 (OBSOLETE) oxidation-reduction process GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR001694
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:IPR001694
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO cellular component GO:0016020 membrane GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001694
Reference: Escherichia coli K-12 MG1655 		Apr 2008
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
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name hycD Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym JW2692 Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved synonym hevD Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved synonym ECK2717 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b2722 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product formate hydrogenlyase subunit Published Annotation - EcoCyc Accession Number: EG10477
Reference: Escherichia coli K-12 MG1655 		Oct 2021
Person Approved alternate product name hydrogenase 3, membrane subunit Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved alternate product name membrane-spanning protein of hydrogenase 3 (part of FHL complex) Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Person Uncurated alternate product name hydrogenase 3, membrane subunit (part of FHL complex) Published Annotation - Database Name: GenProtEC Jan 2006
Protein Family
Automated Process Approved protein family PF00146 NADH dehydrogenase Protein Sequence Similarity - PFAM Model Name: PF00146
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR001694 NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H Protein Sequence Similarity - InterPro Domain: IPR001694
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Other
Person Uncurated EC number 1.6.-.- Protein Sequence Similarity - InterPro Domain: IPR001694
Reference: Escherichia coli K-12 MG1655 		Dec 2008
Person Uncurated MultiFun 1.3.5 (metabolism; energy metabolism, carbon; fermentation) 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 7.3 (location of gene products; inner 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 EcoGene:EG10477 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:948994 Published Annotation - Entrez Gene Database ID: 948994
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Person Approved db xref UniProtKB:P16430 Published Annotation - Swiss-Prot Accession Number: P16430 Jan 2005
Automated Process Approved db xref UniProtKB/Swiss-Prot:P16430 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GI:1789077 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0008946 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved function enzyme; Energy metabolism, carbon: Fermentation Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved note membrane-spanning protein of hydrogenase 3 (part of FHL complex); GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0006113 - fermentation Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC75764.1 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 iMC1010 Experimental - PubMed ID: 15129285
Reference: Escherichia coli K-12 MG1655 		Mar 2009
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 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
Automated Process Approved GO biological process GO:0006118 (OBSOLETE) electron transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001694
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Uncurated GO biological process GO:0006113 fermentation Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Uncurated GO biological process GO:0055114 (OBSOLETE) oxidation-reduction process GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR001694
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO cellular component GO:0016020 membrane GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001694
Reference: Escherichia coli K-12 MG1655 		Apr 2008
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
Comparative to toptop
Author Approval Details Genome Feature Name Type
Member
Automated Process Uncurated Go view OrthoMCL (14 enterobacteria) AMM-0002656 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0002777 hycD CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0001575 hyfC CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0004150 hyfC CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0002723 hycD CDS
Ortholog
Automated Process Uncurated Go view Buttiauxella agrestis ATCC 33320 [T] APC-0004193 hyfC CDS
Automated Process Uncurated Go view Cedecea davisae ATCC 33431 [T] ALZ-0004206 CDS
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0003546 hycD CDS
Automated Process Approved Go view Citrobacter freundii ATCC 8090 [T] AVI-0004274 hycD CDS
Automated Process Uncurated Go view Enterobacter cloacae subsp. cloacae ATCC 13047 [T] (AToL DRAFT) AMB-0004942 CDS
Person Uncurated Go view Enterobacter sp. 638 AEL-0003894 hycD CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0002830 hycD CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0008265 hycD CDS
Person Approved Go view Escherichia coli 536 (UPEC) AEF-0002714 hycD CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0008441 hycD CDS
Person Approved Go view Escherichia coli APEC O1 (APEC) AEG-0002721 hycD CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0001571 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0006499 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0007425 hycD CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0007014 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0079438 hycD CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0003109 CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0003617 CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0008158 hycD CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0008826 hycD CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0003180 hycD CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0007447 hycD CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0001289 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0007312 hycD CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0005833 hycD CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0005308 hycD CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0008065 hycD CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0008809 hycD CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0007389 hycD CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0006603 hycD CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0007427 hycD CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0008245 hycD CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0008464 hycD CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0007913 hycD CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0008280 hycD CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0027700 hycD CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0006367 hycD CDS
Automated Process Approved Go view Escherichia coli HS ADR-0007533 hycD CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0003198 hycD CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0002551 hycD CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0002791 hycD CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0003571 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0003205 hycD CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0003138 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0003038 hycD CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0177286 hycD CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0003027 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0002845 hycD CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0133614 hycD CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0000870 CDS
Person Approved Go view Escherichia coli UTI89 (UPEC) AEA-0003094 hycD CDS
Person Uncurated Go view Hafnia alvei ATCC 13337 [T] AMD-0001499 CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0003068 hycD CDS
Automated Process Uncurated Go view Leclercia adecarboxylata ATCC 23216 [T] AME-0001392 CDS
Automated Process Uncurated Go view Pantoea sp. At-9b AGM-0007656 CDS
Automated Process Uncurated Go view Salmonella Agona SL483 BBX-0007138 hycD CDS
Automated Process Uncurated Go view Salmonella Arizonae CDC 346-86 BCD-0000125 CDS
Person Approved Go view Salmonella Choleraesuis SC-B67 ADB-0003260 hycD CDS
Automated Process Uncurated Go view Salmonella Dublin CT_02021853 BCB-0007416 hycD CDS
Automated Process Uncurated Go view Salmonella Enteritidis P125109 BCF-0008804 hycD CDS
Automated Process Uncurated Go view Salmonella Gallinarum 287/91 BCG-0008351 hycD CDS
Automated Process Uncurated Go view Salmonella Hadar RI_05P066 BBT-0006552 hycD CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL476 BBV-0007397 hycD CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL486 BBW-0006355 hycD CDS
Automated Process Uncurated Go view Salmonella Javiana GA_MM04042433 BCA-0005395 hycD CDS
Automated Process Uncurated Go view Salmonella Kentucky CDC 191 BBZ-0005412 hycD CDS
Automated Process Uncurated Go view Salmonella Kentucky CVM29188 BBP-0006520 hycD CDS
Automated Process Uncurated Go view Salmonella Newport SL254 BBQ-0007412 hycD CDS
Automated Process Uncurated Go view Salmonella Newport SL317 BBR-0005647 hycD CDS
Automated Process Uncurated Go view Salmonella Paratyphi A AKU_12601 BCH-0002736 CDS
Person Approved Go view Salmonella Paratyphi A ATCC 9150 ADA-0002707 hycD CDS
Automated Process Uncurated Go view Salmonella Paratyphi B SPB7 BCC-0003559 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA23 BBN-0007576 hycD CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA29 BBM-0005648 hycD CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund CVM19633 BBO-0007074 hycD CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund SL480 BBY-0005283 hycD CDS
Person Approved Go view Salmonella Typhi CT18 ABX-0111407 hycD CDS
Person Approved Go view Salmonella Typhi Ty2 ABS-0084469 hycD CDS
Automated Process Uncurated Go view Salmonella Typhimurium 14028S AJR-0003449 hycD CDS
Person Approved Go view Salmonella Typhimurium LT2 [T] ABU-0098924 hycD CDS
Automated Process Uncurated Go view Salmonella Virchow SL491 BBS-0006448 hycD CDS
Automated Process Uncurated Go view Salmonella Weltevreden SL484 BBU-0006793 hycD CDS
Automated Process Uncurated Go view Salmonella enterica CVM23701 BBL-0008228 hycD CDS
Person Uncurated Go view Serratia proteamaculans 568 AEN-0008964 hycD CDS
Person Approved Go view Shigella boydii 227 ADV-0003076 hycD CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0008566 hycD CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0005528 hycD CDS
Person Approved Go view Shigella dysenteriae 197 ADU-0003338 hycD CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0074097 hycD CDS
Person Approved Go view Shigella flexneri 301 ABT-0088992 hycD CDS
Person Approved Go view Shigella flexneri 8401 BAG-0002972 hycD CDS
Person Approved Go view Shigella sonnei 046 ADD-0003138 hycD 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
FB20905mutantTn5 InsertionRequest the StrainABE-0008946hycDhycD::Tn5KAN-I-SceI at position 595 in Minus orientation ,- pKD465Blattner Laboratory
FB20906mutantTn5 InsertionRequest the StrainABE-0008946hycDhycD::Tn5KAN-I-SceI at position 595 in Minus 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 2841489 to 2852412
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0008928ascBCDSforward28409902842414Downstream
ABE-0285541repeat_regionforward28424232842501Downstream
ABE-0008931hycICDScomplement28425732843043Downstream
ABE-0008933hycHCDScomplement28430362843446Downstream
ABE-0008936hycGCDScomplement28434432844210Downstream
ABE-0008942hycFCDScomplement28442102844752Downstream
ABE-0008944hycECDScomplement28447622846471Downstream
ABE-0008946hycDCDScomplement28464892847412Matches
ABE-0008948hycCCDScomplement28474152849241Upstream
ABE-0008950hycBCDScomplement28492382849849Upstream
ABE-0008952hycACDScomplement28499742850435Upstream
ABE-0008958hypACDSforward28506472850997Upstream
ABE-0008960hypBCDSforward28510012851873Upstream
ABE-0008962hypCCDSforward28518642852136Upstream
ABE-0008965hypDCDSforward28521362853257Upstream
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.