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

ABE-0009416 (xdhB) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0009416 showshow history
Names
xdhB JW2835 ECK2863 ygeT b2867
Product
xanthine dehydrogenase FAD-binding subunit
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 3002614 3003492 879 293
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR005107 (IPR005107 CO dehydrogenase flavoprotein, C-terminal) Apr 2008
Automated Process Approved IPR002346 (IPR002346 Molybdopterin dehydrogenase, FAD-binding) Apr 2008
Automated Process Approved IPR036683 (IPR036683 CO dehydrogenase flavoprotein, C-terminal domain superfamily) Jul 2018
Automated Process Approved IPR036318 (IPR036318 FAD-binding, type PCMH-like superfamily) Jul 2018
Automated Process Approved PF00941 (PF00941 FAD binding domain in molybdopterin dehydrogenase) Jul 2018
Automated Process Approved PF03450 (PF03450 CO dehydrogenase flavoprotein C-terminal domain) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Automated Process Approved GO biological process GO:0006118 (OBSOLETE) electron transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR002346
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO biological process GO:0055114 (OBSOLETE) oxidation-reduction process GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR002346
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Uncurated GO molecular function GO:0050660 flavin adenine dinucleotide binding GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR036318
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0016491 oxidoreductase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR002346
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name xdhB Published Annotation - Swiss-Prot Accession Number: Q46800 Aug 2002
Person Approved synonym ygeT Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym ECK2863 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym JW2835 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b2867 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product xanthine dehydrogenase FAD-binding subunit Published Annotation - PubMed ID: 16397293
Reference: Escherichia coli K-12 		Oct 2021
Person Uncurated alternate product name putative xanthine dehydrogenase subunit, FAD-binding domain Published Annotation - Database Name: GenProtEC Jan 2006
Person Uncurated alternate product name xanthine dehydrogenase, FAD binding subunit Published Annotation - Swiss-Prot Accession Number: Q46800 Jan 2006
Protein Family
Automated Process Approved protein family IPR005107 CO dehydrogenase flavoprotein, C-terminal Protein Sequence Similarity - InterPro Domain: IPR005107
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR002346 Molybdopterin dehydrogenase, FAD-binding Protein Sequence Similarity - InterPro Domain: IPR002346
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR036683 CO dehydrogenase flavoprotein, C-terminal domain superfamily Protein Sequence Similarity - InterPro Domain: IPR036683
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF03450 CO dehydrogenase flavoprotein C-terminal domain Protein Sequence Similarity - PFAM Model Name: PF03450
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR036318 FAD-binding, type PCMH-like superfamily Protein Sequence Similarity - InterPro Domain: IPR036318
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF00941 FAD binding domain in molybdopterin dehydrogenase Protein Sequence Similarity - PFAM Model Name: PF00941
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Automated Process Uncurated EC number 1.-.-.- Published Annotation - Database Name: EC2GO: GO:0016491
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Person Approved EC number 1.17.1.4 Published Annotation - Swiss-Prot Accession Number: Q46800 Feb 2006
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 GI:1789231 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:947205 Published Annotation - Entrez Gene Database ID: 947205
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Person Approved db xref UniProtKB:Q46800 Published Annotation - Swiss-Prot Accession Number: Q46800 Jan 2006
Automated Process Approved db xref EcoGene:EG13050 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0009416 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved function putative enzyme; Not classified Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved protein id AAC75905.1 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Uncurated subcellular localization Unknown Predicted by PSORTb - PSORTb Final_Score: 2.00
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: IPR002346
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:IPR002346
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO molecular function GO:0050660 flavin adenine dinucleotide binding GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR036318
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0016491 oxidoreductase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR002346
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-0003606 xdhB CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0004272 xdhB CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0003704 xdhB CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003519 xdhB CDS
Ortholog
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0003749 ndhF CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0005980 xdhB CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0002891 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0008277 xdhB CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0002869 ygeT CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0001411 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0006322 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0005785 xdhB CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0006137 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0079605 xdhB CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0003289 CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0003800 CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0009151 xdhB CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0007162 xdhB CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0003321 xdhB CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0007628 xdhB CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0004238 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0007494 xdhB CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0006014 xdhB CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0005491 xdhB CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0005826 xdhB CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0008993 xdhB CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0008356 xdhB CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0006795 xdhB CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0005779 xdhB CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0006290 xdhB CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0005601 xdhB CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0007712 xdhB CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0006030 xdhB CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0027878 xdhB CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0008375 ndhF CDS
Automated Process Approved Go view Escherichia coli HS ADR-0007706 xdhB CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0002686 xdhB CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0002939 xdhB CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0003408 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0003549 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0003276 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0003194 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0177447 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0003192 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0002998 xdhB CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0133782 xdhB CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0001035 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0003261 ygeT CDS
Person Approved Go view Shigella boydii 227 ADV-0003414 ygeT CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0074244 ygeT CDS
Person Approved Go view Shigella flexneri 301 ABT-0089122 ygeT CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0003128 ygeT CDS
Person Approved Go view Shigella sonnei 046 ADD-0003298 xdhB CDS
Person Uncurated Go view Trabulsiella guamensis ATCC 49490 [T] APH-0004623 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 43003 APO-0001622 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 49455 [T] AMG-0000309 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
FB22492mutantTn5 InsertionRequest the StrainABE-0009416xdhBygeT::Tn5KAN-I-SceI at position 245 in Minus orientation ,+ pKD460Blattner Laboratory
FB23232mutantTn5 InsertionRequest the StrainABE-0009416xdhBygeT::Tn5KAN-I-SceI at position 245 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 2997614 to 3008492
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0009393is_elementforward29963612997691Upstream
ABE-0285554mobile_elementcomplement29963612997691Upstream
ABE-0009399ygeQ_2CDSpcomplement29976892997988Upstream
ABE-0285132ygeQpseudogenecomplement29976922998828Upstream
ABE-0009401ygeQ_1CDSpcomplement29980342998828Upstream
ABE-0009405glyUtRNAcomplement29989842999057Upstream
ABE-0009407actSCDScomplement29991362999891Upstream
ABE-0009413xdhACDSforward30003453002603Upstream
ABE-0009416xdhBCDSforward30026143003492Matches
ABE-0009418xdhCCDSforward30034893003968Overlaps Downstream
ABE-0009420ygeVCDScomplement30040083005786Downstream
ABE-0009425ygeWCDSforward30062623007452Downstream
ABE-0009428ygeXCDSforward30075103008706Downstream
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.