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

ABE-0004655 (paaD) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0004655 showshow history
Names
paaD ydbQ JW5217 ECK1388 b1391
Product
phenylacetate degradation protein
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 1455925 1456422 498 166
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR002744 (IPR002744 MIP18 family-like) Apr 2008
Automated Process Approved IPR011883 (IPR011883 Phenylacetate-CoA oxygenase, PaaJ subunit) Apr 2008
Automated Process Approved IPR034904 (IPR034904 Fe-S cluster assembly domain superfamily) Jul 2018
Automated Process Approved PF01883 (PF01883 Iron-sulfur cluster assembly protein) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Person Uncurated GO biological process GO:0016052 carbohydrate catabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name paaD Experimental - PubMed ID: 9748275
Reference: Escherichia coli 		Aug 2002
Automated Process Approved synonym ydbQ Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved synonym JW5217 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK1388 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b1391 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product phenylacetate degradation protein Published Annotation - EcoCyc Accession Number: G6712
Reference: Escherichia coli K-12 MG1655 		Oct 2021
Person Approved alternate product name predicted multicomponent oxygenase/reductase subunit for phenylacetic acid degradation Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved alternate product name ring 1,2-phenylacetyl-CoA epoxidase subunit Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Uncurated alternate product name putative phenylacetic acid degradation protein, possibly part of multicomponent oxygenase Published Annotation - Database Name: GenProtEC Jan 2006
Person Uncurated alternate product name phenylacetic acid degradation protein Experimental - PubMed ID: 9748275
Reference: Escherichia coli 		Jan 2006
Protein Family
Automated Process Approved protein family PF01883 Iron-sulfur cluster assembly protein Protein Sequence Similarity - PFAM Model Name: PF01883
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR034904 Fe-S cluster assembly domain superfamily Protein Sequence Similarity - InterPro Domain: IPR034904
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR002744 MIP18 family-like Protein Sequence Similarity - InterPro Domain: IPR002744
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR011883 Phenylacetate-CoA oxygenase, PaaJ subunit Protein Sequence Similarity - InterPro Domain: IPR011883
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Other
Person Uncurated MultiFun 1.1.1 (metabolism; carbon utilization; carbon compounds) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
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 UniProtKB/Swiss-Prot:P76080 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P76080 Published Annotation - Swiss-Prot Accession Number: P76080 Jan 2005
Automated Process Approved db xref GeneID:945959 Published Annotation - Entrez Gene Database ID: 945959
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref GI:226510939 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0004655 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG13738 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved function enzyme: Phenylacetic acid degradation Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved note GO_process: GO:0016052 - carbohydrate catabolic process Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC74473.4 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
Person Uncurated GO biological process GO:0016052 carbohydrate catabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Comparative to toptop
Author Approval Details Genome Feature Name Type
Member
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0005209 paaD CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0004732 paaD CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0002553 paaD CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0004216 paaD CDS
Ortholog
Automated Process Uncurated Go view Buttiauxella agrestis ATCC 33320 [T] APC-0002133 paaD CDS
Automated Process Uncurated Go view Cedecea davisae ATCC 33431 [T] ALZ-0001810 paaJ CDS
Automated Process Uncurated Go view Enterobacter cloacae subsp. cloacae ATCC 13047 [T] (AToL DRAFT) AMB-0002562 paaJ CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0009976 paaD CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0008033 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0005288 paaD CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0005166 CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0001507 paaJ CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0001826 paaJ CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0005349 paaD CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0006245 paaD CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0006016 paaJ CDS
Automated Process Approved Go view Escherichia coli HS ADR-0006156 paaJ CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0001303 paaD CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0001426 paaD CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0001385 paaJ CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0001693 paaJ CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0001582 paaJ CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0001505 CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0001476 paaD CDS
Automated Process Uncurated Go view Leclercia adecarboxylata ATCC 23216 [T] AME-0000176 paaD CDS
Automated Process Uncurated Go view Serratia marcescens subsp. marcescens ATCC 13880 [T] AMF-0002704 paaD CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0004306 paaD CDS
Person Uncurated Go view Xenorhabdus nematophila ATCC 19061 [T] ADW-0008264 paaD CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 43003 APO-0013087 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 49455 [T] AMG-0003966 paaD 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)
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 1450925 to 1461422
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0004639tynACDScomplement14490761451349Upstream
ABE-0285719matS7protein_bindforward14515311451543Upstream
ABE-0004644paaZCDScomplement14515971453642Upstream
ABE-0004649paaACDSforward14539271454856Upstream
ABE-0004651paaBCDSforward14548681455155Upstream
ABE-0004653paaCCDSforward14551641455910Upstream
ABE-0004655paaDCDSforward14559251456422Matches
ABE-0004657paaECDSforward14564301457500Downstream
ABE-0004659paaFCDSforward14574971458264Downstream
ABE-0004661paaGCDSforward14582641459052Downstream
ABE-0004663paaHCDSforward14590541460481Downstream
ABE-0285720matS8protein_bindforward14599851459997Downstream
ABE-0004666paaICDSforward14604711460893Downstream
ABE-0004668paaJCDSforward14608931462098Downstream
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.