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

ABE-0008942 (hycF) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0008942 showshow history
Names
hycF hevF JW2690 ECK2715 b2720
Product
formate hydrogenlyase complex iron-sulfur protein
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 2844210 2844752 543 181
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 PF12838 (PF12838 4Fe-4S dicluster domain) 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 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
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: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 hycF Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym JW2690 Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved synonym hevF Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved synonym ECK2715 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b2720 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product formate hydrogenlyase complex iron-sulfur protein Published Annotation - PubMed ID: 16397293 Jan 2006
Person Uncurated alternate product name hydrogenase 3, putative quinone oxidoreductase, Fe-S related Published Annotation - Database Name: GenProtEC Jan 2006
Person Approved alternate product name probable iron-sulfur protein of hydrogenase 3 (part of FHL complex) Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		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 PF12838 4Fe-4S dicluster domain Protein Sequence Similarity - PFAM Model Name: PF12838
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
Other
Automated Process Approved EC number 1.12.7.2 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Uncurated MultiFun 1.3.5 (metabolism; energy metabolism, carbon; fermentation) 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 6.1 (cell structure; 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:EG10479 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:947048 Published Annotation - Entrez Gene Database ID: 947048
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Person Approved db xref UniProtKB:P16432 Published Annotation - Swiss-Prot Accession Number: P16432 Jan 2005
Automated Process Approved db xref GI:1789075 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P16432 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0008942 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved function putative enzyme; Energy metabolism, carbon: Fermentation Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved note probable iron-sulfur 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; 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 AAC75762.1 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: 8.96
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Person Uncurated subsystem component of in silico model iJR904 Experimental - PubMed ID: 12952533
Reference: Escherichia coli K-12 MG1655 		Feb 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 iMC1010 Experimental - PubMed ID: 15129285
Reference: Escherichia coli K-12 MG1655 		Mar 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
Person Uncurated GO biological process GO:0006113 fermentation 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: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-0002878 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0002576 hycF CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0002449 hycF CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0004175 hycF CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0002446 hycF CDS
Ortholog
Automated Process Uncurated Go view Buttiauxella agrestis ATCC 33320 [T] APC-0004195 CDS
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0003544 nqo9 CDS
Automated Process Approved Go view Citrobacter freundii ATCC 8090 [T] AVI-0004272 nqo9 CDS
Automated Process Uncurated Go view Enterobacter cloacae subsp. cloacae ATCC 13047 [T] (AToL DRAFT) AMB-0004944 CDS
Person Uncurated Go view Enterobacter sp. 638 AEL-0003892 hycF CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0002832 hycF CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0008267 hycF CDS
Person Approved Go view Escherichia coli 536 (UPEC) AEF-0002712 hycF CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0008443 CDS
Person Approved Go view Escherichia coli APEC O1 (APEC) AEG-0002719 hycF CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0001573 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0006501 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0007423 hycF CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0007016 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0079436 hycF CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0003107 CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0003615 CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0008160 hycF CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0008824 hycF CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0003178 hycF CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0007445 hycF CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0001287 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0007310 hycF CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0005831 hycF CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0005306 hycF CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0008067 hycF CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0008807 hycF CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0007391 hycF CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0006601 hycF CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0007425 hycF CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0008243 hycF CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0008466 hycF CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0007915 hycF CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0008278 hycF CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0027698 hycF CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0006365 nqo9 CDS
Automated Process Approved Go view Escherichia coli HS ADR-0007531 hycF CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0003200 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0002549 hycF CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0002789 hycF CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0003573 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0003203 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0003140 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0003036 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0177283 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0003025 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0002843 hycF CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0133612 hycF CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0000868 CDS
Person Approved Go view Escherichia coli UTI89 (UPEC) AEA-0003092 hycF CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0003066 hycF CDS
Automated Process Uncurated Go view Leclercia adecarboxylata ATCC 23216 [T] AME-0001390 CDS
Automated Process Uncurated Go view Pantoea sp. At-9b AGM-0007658 CDS
Automated Process Uncurated Go view Salmonella Agona SL483 BBX-0007136 hycF CDS
Automated Process Uncurated Go view Salmonella Arizonae CDC 346-86 BCD-0000127 CDS
Person Approved Go view Salmonella Choleraesuis SC-B67 ADB-0003258 hycF CDS
Automated Process Uncurated Go view Salmonella Dublin CT_02021853 BCB-0007414 hycF CDS
Automated Process Uncurated Go view Salmonella Enteritidis P125109 BCF-0008793 hycF CDS
Automated Process Uncurated Go view Salmonella Gallinarum 287/91 BCG-0008341 hycF CDS
Automated Process Uncurated Go view Salmonella Hadar RI_05P066 BBT-0006554 hycF CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL476 BBV-0007395 hycF CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL486 BBW-0006353 hycF CDS
Automated Process Uncurated Go view Salmonella Javiana GA_MM04042433 BCA-0005393 hycF CDS
Automated Process Uncurated Go view Salmonella Kentucky CDC 191 BBZ-0005410 hycF CDS
Automated Process Uncurated Go view Salmonella Kentucky CVM29188 BBP-0006518 hycF CDS
Automated Process Uncurated Go view Salmonella Newport SL254 BBQ-0007410 hycF CDS
Automated Process Uncurated Go view Salmonella Newport SL317 BBR-0005649 hycF CDS
Automated Process Uncurated Go view Salmonella Paratyphi A AKU_12601 BCH-0002734 CDS
Person Approved Go view Salmonella Paratyphi A ATCC 9150 ADA-0002705 hycF CDS
Automated Process Uncurated Go view Salmonella Paratyphi B SPB7 BCC-0003557 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA23 BBN-0007574 hycF CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA29 BBM-0005650 hycF CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund CVM19633 BBO-0007072 hycF CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund SL480 BBY-0005281 hycF CDS
Person Approved Go view Salmonella Typhi CT18 ABX-0111394 hycF CDS
Person Approved Go view Salmonella Typhi Ty2 ABS-0084467 hycF CDS
Automated Process Uncurated Go view Salmonella Typhimurium 14028S AJR-0003447 hycF CDS
Person Approved Go view Salmonella Typhimurium LT2 [T] ABU-0098919 hycF CDS
Automated Process Uncurated Go view Salmonella Virchow SL491 BBS-0006450 hycF CDS
Automated Process Uncurated Go view Salmonella Weltevreden SL484 BBU-0006795 hycF CDS
Automated Process Uncurated Go view Salmonella enterica CVM23701 BBL-0008226 hycF CDS
Person Uncurated Go view Serratia proteamaculans 568 AEN-0008962 hycF CDS
Person Approved Go view Shigella boydii 227 ADV-0003078 hycF CDS
Automated Process Uncurated Go view Shigella boydii BS512 ADJ-0008568 hycF CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0005531 hycF CDS
Person Approved Go view Shigella dysenteriae 197 ADU-0003336 hycF CDS
Person Uncurated Go view Shigella flexneri 2457T ABQ-0074095 hycF pseudogene
Person Approved Go view Shigella flexneri 8401 BAG-0002974 hycF CDS
Person Approved Go view Shigella sonnei 046 ADD-0003136 hycF 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
FB20901mutantTn5 InsertionRequest the StrainABE-0008942hycFhycF::Tn5KAN-I-SceI at position 147 in Minus orientation ,- pKD465Blattner Laboratory
FB20902mutantTn5 InsertionRequest the StrainABE-0008942hycFhycF::Tn5KAN-I-SceI at position 147 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 2839210 to 2849752
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0008922ascGCDScomplement28382542839264Downstream
ABE-0008926ascFCDSforward28395242840981Downstream
ABE-0008928ascBCDSforward28409902842414Downstream
ABE-0285541repeat_regionforward28424232842501Downstream
ABE-0008931hycICDScomplement28425732843043Downstream
ABE-0008933hycHCDScomplement28430362843446Downstream
ABE-0008936hycGCDScomplement28434432844210Overlaps Downstream
ABE-0008942hycFCDScomplement28442102844752Matches
ABE-0008944hycECDScomplement28447622846471Upstream
ABE-0008946hycDCDScomplement28464892847412Upstream
ABE-0008948hycCCDScomplement28474152849241Upstream
ABE-0008950hycBCDScomplement28492382849849Upstream
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.