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

ABE-0001060 (ykgF) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0001060 showshow history
Names
ykgF JW0300 ECK0306 b0307
Product
putative amino acid dehydrogenase
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 322338 323765 1428 476
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR008948 (IPR008948 L-Aspartase-like) Apr 2008
Automated Process Approved IPR012285 (IPR012285 (DEPRECATED) Fumarate reductase, C-terminal) Apr 2008
Automated Process Approved IPR004452 (IPR004452 4Fe-4S binding protein) Apr 2008
Automated Process Approved IPR001450 (IPR001450 (DEPRECATED) 4Fe-4S binding domain) Apr 2008
Automated Process Approved IPR003741 (IPR003741 LUD domain) Apr 2008
Automated Process Approved IPR009051 (IPR009051 Alpha-helical ferredoxin) Apr 2008
Automated Process Approved IPR024569 (IPR024569 4Fe-4S binding protein, C-terminal) Jul 2018
Automated Process Approved IPR017896 (IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain) Jul 2018
Automated Process Approved IPR037171 (IPR037171 NagB/RpiA transferase-like) Jul 2018
Automated Process Approved PF02589 (PF02589 LUD domain) Jul 2018
Automated Process Approved PF11870 (PF11870 Domain of unknown function (DUF3390)) Jul 2018
Automated Process Approved PF13183 (PF13183 4Fe-4S dicluster domain) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Automated Process Uncurated GO biological process GO:0019516 lactate oxidation GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR004452
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:IPR001450
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:IPR012285
Reference: Escherichia coli K-12 MG1655 		Apr 2008
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:0009055 electron transfer activity 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:0016491 oxidoreductase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR012285
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0051536 iron-sulfur cluster binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR012285
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name ykgF Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym ECK0306 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym JW0300 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b0307 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product putative amino acid dehydrogenase Published Annotation - PubMed ID: 16397293
Reference: Escherichia coli K-12 		Oct 2021
Automated Process Approved alternate product name predicted electron transport protein with ferridoxin-like domai Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Uncurated alternate product name putative dehydrogenase Published Annotation - Database Name: GenProtEC Jan 2006
Protein Family
Automated Process Approved protein family IPR004452 4Fe-4S binding protein Protein Sequence Similarity - InterPro Domain: IPR004452
Reference: Escherichia coli K-12 MG1655 		Apr 2008
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 IPR008948 L-Aspartase-like Protein Sequence Similarity - InterPro Domain: IPR008948
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR003741 LUD domain Protein Sequence Similarity - InterPro Domain: IPR003741
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR012285 (DEPRECATED) Fumarate reductase, C-terminal Protein Sequence Similarity - InterPro Domain: IPR012285
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR009051 Alpha-helical ferredoxin Protein Sequence Similarity - InterPro Domain: IPR009051
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR024569 4Fe-4S binding protein, C-terminal Protein Sequence Similarity - InterPro Domain: IPR024569
Reference: Escherichia coli K-12 MG1655 		Jul 2018
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 PF11870 Domain of unknown function (DUF3390) Protein Sequence Similarity - PFAM Model Name: PF11870
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF13183 4Fe-4S dicluster domain Protein Sequence Similarity - PFAM Model Name: PF13183
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF02589 LUD domain Protein Sequence Similarity - PFAM Model Name: PF02589
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR037171 NagB/RpiA transferase-like Protein Sequence Similarity - InterPro Domain: IPR037171
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Person Uncurated EC number 1.-.-.- Protein Sequence Similarity - InterPro Domain: IPR012285
Reference: Escherichia coli K-12 MG1655 		Dec 2008
Person Uncurated EC number 4.-.-.- Protein Sequence Similarity - InterPro Domain: IPR008948
Reference: Escherichia coli K-12 MG1655 		Dec 2008
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 GeneID:944980 Published Annotation - Entrez Gene Database ID: 944980
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref UniProtKB/Swiss-Prot:P77536 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P77536 Published Annotation - Swiss-Prot Accession Number: P77536 Jan 2005
Automated Process Approved db xref GI:1786498 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0001060 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG13583 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC73410.1 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
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 Uncurated GO biological process GO:0019516 lactate oxidation GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR004452
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:IPR001450
Reference: Escherichia coli K-12 MG1655 		Apr 2008
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 cellular component GO:0016020 membrane GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR012285
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
Automated Process Approved GO molecular function GO:0051536 iron-sulfur cluster binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR012285
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0016491 oxidoreductase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR012285
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-0002296 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0003634 ykgF CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0003605 ykgF CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0007314 ykgF CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003215 ykgF CDS
Ortholog
Automated Process Uncurated Go view Dickeya chrysanthemi Ech1591 AFK-0007697 CDS
Person Uncurated Go view Dickeya dadantii 3937 ABF-0046582 CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0007453 CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0000379 CDS
Automated Process Uncurated Go view Escherichia coli APEC O1 (APEC) AEG-0000298 ykgG CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0004005 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0009326 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0007088 CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0005804 pseudogene
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0076499 ykgF CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0000364 CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0000451 CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0007074 CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0008097 CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0000288 ykgF CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0004772 CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0003858 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0010533 CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0008115 CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0009192 CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0007288 CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0005199 CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0008000 CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0008932 CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0007822 CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0009094 CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0007537 CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0007483 CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0008896 CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0024273 ykgF CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0008757 lutB CDS
Automated Process Approved Go view Escherichia coli HS ADR-0005042 CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0000632 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0000332 ykgF CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0000312 ykgF CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0000526 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0000600 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0000439 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0000419 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0174511 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0000333 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0000338 CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0130236 ykgF CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0004907 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0000331 ykgF CDS
Person Uncurated Go view Pectobacterium atrosepticum SCRI1043 ABL-0062179 CDS
Automated Process Uncurated Go view Pectobacterium brasiliensis 1692 AED-0003984 CDS
Automated Process Uncurated Go view Pectobacterium parmentieri WPP163 AFJ-0001070 CDS
Person Uncurated Go view Shewanella oneidensis MR-1 ACY-0265085 CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0005654 CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0071226 ykgF CDS
Person Approved Go view Shigella flexneri 301 ABT-0086620 ykgF CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0000332 ykgF CDS
Person Approved Go view Shigella sonnei 046 ADD-0000343 ykgF 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
FB20135mutantTn5 InsertionRequest the StrainABE-0001060ykgFykgF::Tn5KAN-I-SceI at position 529 in Plus orientation ,- pKD465Blattner Laboratory
FB20136mutantTn5 InsertionRequest the StrainABE-0001060ykgFykgF::Tn5KAN-I-SceI at position 529 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 317338 to 328765
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0285171ykgQpseudogeneforward317385317567Upstream
ABE-0001038rclCCDScomplement317726318319Upstream
ABE-0001043rclBCDScomplement318331318567Upstream
ABE-0001048rclACDScomplement318676320001Upstream
ABE-0001054rclRCDSforward320227321081Upstream
ABE-0001058ykgECDSforward321608322327Upstream
ABE-0001060ykgFCDSforward322338323765Matches
ABE-0001062ykgGCDSforward323758324453Overlaps Downstream
ABE-0001066ykgHCDScomplement324696325364Downstream
ABE-0001070betACDScomplement325577327247Downstream
ABE-0001072betBCDScomplement327261328733Downstream
ABE-0001076betICDScomplement328747329334Downstream
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.