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

ABE-0003410 (rutD) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0003410 showshow history
Names
rutD rarA ycdJ JW0994 ECK1000 b1009
Product
putative aminoacrylate hydrolase
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 1070965 1071765 801 267
Sequence

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View sequence with flanking regions: bases upstream and bases downstream

Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR003089 (IPR003089 (DEPRECATED) Alpha/beta hydrolase) Apr 2008
Automated Process Approved IPR000073 (IPR000073 Alpha/beta hydrolase fold-1) Apr 2008
Automated Process Approved IPR019913 (IPR019913 Pyrimidine utilisation protein RutD) Jul 2018
Automated Process Approved IPR029058 (IPR029058 Alpha/Beta hydrolase fold) Jul 2018
Automated Process Approved PF00561 (PF00561 alpha/beta hydrolase fold) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Automated Process Approved GO biological process GO:0006725 cellular aromatic compound metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR003089
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO biological process GO:0006212 uracil catabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR019913
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Uncurated GO molecular function GO:0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR019913
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0016787 hydrolase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR003089
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Uncurated name rutD Published Annotation - PubMed ID: 16540542
Reference: Escherichia coli K-12 		Aug 2007
Person Approved synonym JW0994 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ycdJ Published Annotation - Swiss-Prot Accession Number: P75895 Jan 2006
Person Approved synonym rarA Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK1000 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b1009 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product putative aminoacrylate hydrolase Published Annotation - EcoCyc Accession Number: G6520
Reference: Escherichia coli K-12 MG1655 		Jan 2021
Person Approved alternate product name predicted hydrolase Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved alternate product name putative aminoacrylate hydrolase, reactive intermediate detoxification Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Uncurated alternate product name putative hydrolase Published Annotation - Database Name: GenProtEC Jan 2006
Person Uncurated alternate product name hypothetical protein Published Annotation - Swiss-Prot Accession Number: P75895 Jan 2006
Protein Family
Automated Process Approved protein family IPR019913 Pyrimidine utilisation protein RutD Protein Sequence Similarity - InterPro Domain: IPR019913
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR003089 (DEPRECATED) Alpha/beta hydrolase Protein Sequence Similarity - InterPro Domain: IPR003089
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR029058 Alpha/Beta hydrolase fold Protein Sequence Similarity - InterPro Domain: IPR029058
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR000073 Alpha/beta hydrolase fold-1 Protein Sequence Similarity - InterPro Domain: IPR000073
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF00561 alpha/beta hydrolase fold Protein Sequence Similarity - PFAM Model Name: PF00561
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Automated Process Uncurated EC number 3.5.1.- Published Annotation - Database Name: EC2GO: GO:0016811
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Person Uncurated EC number 3.-.-.- Protein Sequence Similarity - InterPro Domain: IPR003089
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:EG13856 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GI:1787244 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:946586 Published Annotation - Entrez Gene Database ID: 946586
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Person Approved db xref UniProtKB:P75895 Published Annotation - Swiss-Prot Accession Number: P75895 Jan 2006
Automated Process Approved db xref ASAP:ABE-0003410 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P75895 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved function enzyme; Pyrimidine nitrogen catabolism Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC74094.1 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
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:0006725 cellular aromatic compound metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR003089
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO biological process GO:0006212 uracil catabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR019913
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Uncurated GO molecular function GO:0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR019913
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0016787 hydrolase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR003089
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-0003838 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0003502 rutD CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0003431 rutD CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0004123 rutD CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003193 rutD CDS
Ortholog
Automated Process Uncurated Go view Enterobacter cloacae subsp. cloacae ATCC 13047 [T] (AToL DRAFT) AMB-0002121 CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0007274 CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0001017 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0005471 CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0000935 rarA CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0003368 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0008429 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0008023 CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0007135 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0077240 rutD CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0001094 rutD CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0001338 CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0009443 CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0008305 CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0001111 rutD CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0005570 CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0005084 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0009953 CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0008993 CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0007598 CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0005555 CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0006086 CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0006355 CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0009854 CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0006287 CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0006941 CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0006401 CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0008363 CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0007819 CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0025313 CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0007477 rutD CDS
Automated Process Approved Go view Escherichia coli HS ADR-0005801 CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0001339 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0000969 rutD CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0001020 rarA CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0001310 rutD CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0001304 rutD CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0001260 rutD CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0001097 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0175232 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0001097 CDS
Automated Process Uncurated Go view Escherichia coli SMS-3-5 AFT-0002115 CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0131183 CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0000611 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0001075 ycdJ CDS
Automated Process Uncurated Go view Ewingella americana ATCC 33852 [T] AMA-0002278 CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0001039 ycdJ CDS
Automated Process Uncurated Go view Leclercia adecarboxylata ATCC 23216 [T] AME-0003996 CDS
Automated Process Uncurated Go view Pantoea agglomerans IG1 APM-0000726 CDS
Automated Process Uncurated Go view Pantoea agglomerans SL1-M5 ALY-0004419 CDS
Automated Process Uncurated Go view Pantoea sp. At-9b AGM-0009153 CDS
Automated Process Uncurated Go view Pantoea sp. aB AJV-0003141 CDS
Person Uncurated Go view Pseudomonas syringae pv. tomato DC3000 ADG-0001183 CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0004862 CDS
Person Uncurated Go view Shigella dysenteriae 197 ADU-0001106 CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0072122 CDS
Person Approved Go view Shigella flexneri 301 ABT-0087362 CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0001082 CDS
Person Approved Go view Shigella sonnei 046 ADD-0001103 CDS
Automated Process Uncurated Go view Yersinia enterocolitica 8081 BAH-0005718 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
FB22119mutantTn5 InsertionRequest the StrainABE-0003410rutDb1009::Tn5KAN-I-SceI at position 402 in Plus orientation ,+ pKD465Blattner Laboratory
FB22267mutantTn5 InsertionRequest the StrainABE-0003410rutDb1009::Tn5KAN-I-SceI at position 402 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 1065965 to 1076765
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0003388agpCDSforward10655851066826Downstream
ABE-0003390yccJCDScomplement10668641067091Downstream
ABE-0003392wrbACDScomplement10671121067708Downstream
ABE-0285039ymdFCDSforward10680811068254Downstream
ABE-0285419repeat_regionforward10683541068451Downstream
ABE-0003401rutGCDScomplement10685111069839Downstream
ABE-0003403rutFCDScomplement10698601070354Downstream
ABE-0003407rutECDScomplement10703651070955Downstream
ABE-0003410rutDCDScomplement10709651071765Matches
ABE-0003412rutCCDScomplement10717731072159Upstream
ABE-0003414rutBCDScomplement10721711072863Upstream
ABE-0003416rutACDScomplement10728631074011Upstream
ABE-0003422rutRCDSforward10742421074880Upstream
ABE-0285420repeat_regionforward10748851074912Upstream
ABE-0003424putACDScomplement10749201078882Upstream
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.