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

ABE-0009413 (xdhA) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0009413 showshow history
Names
xdhA ygeS JW5462 ECK2862 b2866
Product
xanthine dehydrogenase molybdenum-binding subunit
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 3000345 3002603 2259 753
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR008274 (IPR008274 Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding) Apr 2008
Automated Process Approved IPR012219 (IPR012219 (DEPRECATED) Carbon monoxide dehydrogenase molybdoprotein) Apr 2008
Automated Process Approved IPR000674 (IPR000674 Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead) Apr 2008
Automated Process Approved IPR036856 (IPR036856 Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily) Jul 2018
Automated Process Approved IPR037165 (IPR037165 Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain superfamily) Jul 2018
Automated Process Approved PF01315 (PF01315 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain) Jul 2018
Automated Process Approved PF02738 (PF02738 Molybdopterin-binding domain of aldehyde dehydrogenase) 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:IPR008274
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: IPR008274, IPR037165
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0030151 molybdenum ion binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR012219
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:IPR008274
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name xdhA Experimental - PubMed ID: 10986234
Reference: Escherichia coli 		Aug 2002
Person Approved synonym ECK2862 Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved synonym ygeS Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved synonym JW5462 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b2866 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product xanthine dehydrogenase molybdenum-binding subunit Published Annotation - PubMed ID: 16397293
Reference: Escherichia coli K-12 		Oct 2021
Person Uncurated alternate product name putative xanthine dehydrogenase subunit, molybdemum cofactor-binding domain Published Annotation - Database Name: GenProtEC Jan 2006
Person Uncurated alternate product name xanthine dehydrogenase, molybdenum binding subunit Experimental - PubMed ID: 10986234
Reference: Escherichia coli 		Jan 2006
Protein Family
Automated Process Approved protein family IPR012219 (DEPRECATED) Carbon monoxide dehydrogenase molybdoprotein Protein Sequence Similarity - InterPro Domain: IPR012219
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR008274 Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding Protein Sequence Similarity - InterPro Domain: IPR008274
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR037165 Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain superfamily Protein Sequence Similarity - InterPro Domain: IPR037165
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR000674 Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead Protein Sequence Similarity - InterPro Domain: IPR000674
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF01315 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain Protein Sequence Similarity - PFAM Model Name: PF01315
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR036856 Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily Protein Sequence Similarity - InterPro Domain: IPR036856
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF02738 Molybdopterin-binding domain of aldehyde dehydrogenase Protein Sequence Similarity - PFAM Model Name: PF02738
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: Q46799 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 EcoGene:EG13049 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GI:1789230 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:947116 Published Annotation - Entrez Gene Database ID: 947116
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Person Approved db xref UniProtKB:Q46799 Published Annotation - Swiss-Prot Accession Number: Q46799 Jan 2006
Automated Process Approved db xref ASAP:ABE-0009413 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:Q46799 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC75904.1 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 Approved GO biological process GO:0006118 (OBSOLETE) electron transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR008274
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: IPR008274, IPR037165
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0030151 molybdenum ion binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR012219
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:IPR008274
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-0004173 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0003744 xdhA CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0004061 xdhA CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0003649 xdhA CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003356 xdhA CDS
Ortholog
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0003748 hcrA_1 CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0005981 xdhA CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0002890 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0008278 xdhA CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0002868 CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0001412 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0006323 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0005786 xdhA CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0006136 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0079604 xdhA CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0003288 CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0003799 CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0009150 xdhA CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0007161 xdhA CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0003320 xdhA CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0007627 xdhA CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0004237 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0007493 xdhA CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0006013 xdhA CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0005490 xdhA CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0005827 xdhA CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0008992 xdhA CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0008355 xdhA CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0006794 xdhA CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0005778 xdhA CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0006289 xdhA CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0005600 xdhA CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0007711 xdhA CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0006029 xdhA CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0027877 xdhA CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0008374 xdhA_1 CDS
Automated Process Approved Go view Escherichia coli HS ADR-0007705 xdhA CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0002685 xdhA CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0002938 xdhA CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0003409 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0003550 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0003277 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0003193 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0177446 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0003191 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0002997 xdhA CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0133781 xdhA CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0001034 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0003260 CDS
Person Uncurated Go view Hafnia alvei ATCC 13337 [T] AMD-0004293 CDS
Person Approved Go view Shigella boydii 227 ADV-0003415 CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0005502 xdhA CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0074243 CDS
Person Approved Go view Shigella flexneri 301 ABT-0089121 CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0003127 CDS
Person Approved Go view Shigella sonnei 046 ADD-0003297 xdhA CDS
Person Uncurated Go view Trabulsiella guamensis ATCC 49490 [T] APH-0004624 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 43003 APO-0001625 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 49455 [T] AMG-0000308 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
FB22491mutantTn5 InsertionRequest the StrainABE-0009413xdhAb2866::Tn5KAN-I-SceI at position 224 in Plus orientation ,+ pKD460Blattner Laboratory
FB23231mutantTn5 InsertionRequest the StrainABE-0009413xdhAb2866::Tn5KAN-I-SceI at position 224 in Plus 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 2995345 to 3007603
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0009385ygeN_2CDSpcomplement29953142995745Upstream
ABE-0285130ygeNpseudogenecomplement29953142996020Upstream
ABE-0009387ygeN_1CDSpcomplement29957482996020Upstream
ABE-0009390ygeOpseudogenecomplement29959622996360Upstream
ABE-0009393is_elementforward29963612997691Upstream
ABE-0285554mobile_elementcomplement29963612997691Upstream
ABE-0009395insD-4CDScomplement29963722997277Upstream
ABE-0009397insC-4CDScomplement29972352997600Upstream
ABE-0009399ygeQ_2CDSpcomplement29976892997988Upstream
ABE-0285132ygeQpseudogenecomplement29976922998828Upstream
ABE-0009401ygeQ_1CDSpcomplement29980342998828Upstream
ABE-0009405glyUtRNAcomplement29989842999057Upstream
ABE-0009407actSCDScomplement29991362999891Upstream
ABE-0009413xdhACDSforward30003453002603Matches
ABE-0009416xdhBCDSforward30026143003492Downstream
ABE-0009418xdhCCDSforward30034893003968Downstream
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.