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

ABE-0009418 (xdhC) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0009418 showshow history
Names
xdhC ygeU JW2836 ECK2864 b2868
Product
xanthine dehydrogenase Fe-S binding subunit
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 3003489 3003968 480 160
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR012675 (IPR012675 Beta-grasp domain superfamily) Apr 2008
Automated Process Approved IPR012241 (IPR012241 (DEPRECATED) Oxidoreductase iron-sulphur binding subunit, IorA) Apr 2008
Automated Process Approved IPR002888 (IPR002888 [2Fe-2S]-binding) Apr 2008
Automated Process Approved IPR001041 (IPR001041 2Fe-2S ferredoxin-type iron-sulfur binding domain) Apr 2008
Automated Process Approved IPR036884 (IPR036884 [2Fe-2S]-binding domain superfamily) Jul 2018
Automated Process Approved IPR036010 (IPR036010 2Fe-2S ferredoxin-like superfamily) Jul 2018
Automated Process Approved PF00111 (PF00111 2Fe-2S iron-sulfur cluster binding domain) Jul 2018
Automated Process Approved PF01799 (PF01799 [2Fe-2S] binding domain) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Automated Process Uncurated GO biological process GO:0055114 (OBSOLETE) oxidation-reduction process GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR002888
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:IPR002888
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:0051536 iron-sulfur cluster binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001041
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:IPR001041
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:IPR012241
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0051537 2 iron, 2 sulfur cluster binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR012241
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0046872 metal ion binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR002888
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name xdhC Published Annotation - Swiss-Prot Accession Number: Q46801 Aug 2002
Person Approved synonym JW2836 Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved synonym ygeU Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved synonym ECK2864 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b2868 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product xanthine dehydrogenase Fe-S binding subunit Published Annotation - PubMed ID: 16397293
Reference: Escherichia coli K-12 		Oct 2021
Person Uncurated alternate product name putative xanthine dehydrogenase, Fe-S subunit Published Annotation - Database Name: GenProtEC Jan 2006
Person Uncurated alternate product name xanthine dehydrogenase iron-sulfur binding subunit Published Annotation - Swiss-Prot Accession Number: Q46801 Jan 2006
Protein Family
Automated Process Approved protein family IPR036884 [2Fe-2S]-binding domain superfamily Protein Sequence Similarity - InterPro Domain: IPR036884
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR012675 Beta-grasp domain superfamily Protein Sequence Similarity - InterPro Domain: IPR012675
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF01799 [2Fe-2S] binding domain Protein Sequence Similarity - PFAM Model Name: PF01799
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR002888 [2Fe-2S]-binding Protein Sequence Similarity - InterPro Domain: IPR002888
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR001041 2Fe-2S ferredoxin-type iron-sulfur binding domain Protein Sequence Similarity - InterPro Domain: IPR001041
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR012241 (DEPRECATED) Oxidoreductase iron-sulphur binding subunit, IorA Protein Sequence Similarity - InterPro Domain: IPR012241
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR036010 2Fe-2S ferredoxin-like superfamily Protein Sequence Similarity - InterPro Domain: IPR036010
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF00111 2Fe-2S iron-sulfur cluster binding domain Protein Sequence Similarity - PFAM Model Name: PF00111
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Person Approved EC number 1.-.-.- Protein Sequence Similarity - InterPro Domain: IPR002888
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 EcoGene:EG13051 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0009418 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GI:1789232 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:Q46801 Published Annotation - Swiss-Prot Accession Number: Q46801 Jan 2006
Automated Process Approved db xref UniProtKB/Swiss-Prot:Q46801 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:945148 Published Annotation - Entrez Gene Database ID: 945148
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Person Approved function putative enzyme; Not classified Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved protein id AAC75906.1 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 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
Automated Process Uncurated GO biological process GO:0055114 (OBSOLETE) oxidation-reduction process GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR002888
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:IPR002888
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:0016491 oxidoreductase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR012241
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:IPR001041
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:IPR001041
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0046872 metal ion binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR002888
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0051537 2 iron, 2 sulfur cluster binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR012241
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 (205 gammaproteobacteria) APP-0003816 xdhC CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0004226 xdhC CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0007460 xdhC CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003429 xdhC CDS
Ortholog
Automated Process Uncurated Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0003750 ndhS CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0005979 xdhC CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0002892 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0008276 xdhC CDS
Person Approved Go view Escherichia coli APEC O1 (APEC) AEG-0005584 xdhC CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0001410 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0006321 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0005784 xdhC CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0006138 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0079606 xdhC CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0003290 CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0003801 CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0009152 xdhC CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0007163 xdhC CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0003322 xdhC CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0007629 xdhC CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0004239 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0007495 xdhC CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0006015 xdhC CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0005492 xdhC CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0005825 xdhC CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0008994 xdhC CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0008357 xdhC CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0006796 xdhC CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0005780 xdhC CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0006291 xdhC CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0005602 xdhC CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0007713 xdhC CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0006031 xdhC CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0027879 xdhC CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0008376 ndhS CDS
Automated Process Approved Go view Escherichia coli HS ADR-0007707 xdhC CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0002687 xdhC CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0002940 xdhC CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0003407 xdhC CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0003548 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0003275 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0003195 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0177448 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0003193 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0002999 xdhC CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0133783 xdhC CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0001036 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0003262 CDS
Person Uncurated Go view Hafnia alvei ATCC 13337 [T] AMD-0004295 CDS
Person Approved Go view Shigella boydii 227 ADV-0003413 CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0074245 CDS
Person Approved Go view Shigella flexneri 301 ABT-0089123 CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0003129 CDS
Person Approved Go view Shigella sonnei 046 ADD-0003299 xdhC CDS
Person Uncurated Go view Trabulsiella guamensis ATCC 49490 [T] APH-0004622 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 43003 APO-0001619 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 49455 [T] AMG-0000310 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
FB22493mutantTn5 InsertionRequest the StrainABE-0009418xdhCb2868::Tn5KAN-I-SceI at position 168 in Minus orientation ,+ pKD460Blattner Laboratory
FB23233mutantTn5 InsertionRequest the StrainABE-0009418xdhCb2868::Tn5KAN-I-SceI at position 168 in Minus orientation ,- pKD465Tim Durfee (durf@genome.wisc.edu)
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 2998489 to 3008968
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0285132ygeQpseudogenecomplement29976922998828Upstream
ABE-0009401ygeQ_1CDSpcomplement29980342998828Upstream
ABE-0009405glyUtRNAcomplement29989842999057Upstream
ABE-0009407actSCDScomplement29991362999891Upstream
ABE-0009413xdhACDSforward30003453002603Upstream
ABE-0009416xdhBCDSforward30026143003492Overlaps Upstream
ABE-0009418xdhCCDSforward30034893003968Matches
ABE-0009420ygeVCDScomplement30040083005786Downstream
ABE-0009425ygeWCDSforward30062623007452Downstream
ABE-0009428ygeXCDSforward30075103008706Downstream
ABE-0009434ygeYCDSforward30087643009975Downstream
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.