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

ABE-0008363 (hcaD) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0008363 showshow history
Names
hcaD phdA yfhY hcaA4 JW2526 ECK2539 b2542
Product
putative 3-phenylpropionate/cinnamate dioxygenase ferredoxin reductase subunit
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 2672047 2673249 1203 401
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 IPR004099 (IPR004099 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain) Apr 2008
Automated Process Approved IPR001327 (IPR001327 (DEPRECATED) Pyridine nucleotide-disulphide oxidoreductase, NAD-binding domain) Apr 2008
Automated Process Approved IPR013027 (IPR013027 (DEPRECATED) FAD-dependent pyridine nucleotide-disulphide oxidoreductase) Apr 2008
Automated Process Approved IPR001100 (IPR001100 Pyridine nucleotide-disulphide oxidoreductase, class I) Apr 2008
Automated Process Approved IPR023753 (IPR023753 FAD/NAD(P)-binding domain) Jul 2018
Automated Process Approved IPR028202 (IPR028202 Reductase, C-terminal) Jul 2018
Automated Process Approved IPR016156 (IPR016156 FAD/NAD-linked reductase, dimerisation domain superfamily) Jul 2018
Automated Process Approved IPR036188 (IPR036188 FAD/NAD(P)-binding domain superfamily) Jul 2018
Automated Process Approved PF07992 (PF07992 Pyridine nucleotide-disulphide oxidoreductase) Jul 2018
Automated Process Approved PF14759 (PF14759 Reductase C-terminal) 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
Automated Process Approved GO biological process GO:0006118 (OBSOLETE) electron transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001100
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: IPR023753, IPR016156
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO biological process GO:0045454 cell redox homeostasis GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004099
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO cellular component GO:0005737 cytoplasm GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004099
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:0050660 flavin adenine dinucleotide binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001327
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:IPR004099
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name hcaD Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym ECK2539 Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved synonym hcaA4 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved synonym phdA Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved synonym yfhY Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved synonym JW2526 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b2542 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product putative 3-phenylpropionate/cinnamate dioxygenase ferredoxin reductase subunit Published Annotation - EcoCyc Accession Number: G7336
Reference: Escherichia coli K-12 MG1655 		Oct 2021
Person Uncurated alternate product name phenylpropionate dioxygenase, ferredoxin reductase subunit Published Annotation - Database Name: GenProtEC Jan 2006
Person Approved alternate product name ferredoxin reductase subunit of phenylpropionate dioxygenase Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Protein Family
Automated Process Approved protein family IPR013027 (DEPRECATED) FAD-dependent pyridine nucleotide-disulphide oxidoreductase Protein Sequence Similarity - InterPro Domain: IPR013027
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR004099 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain Protein Sequence Similarity - InterPro Domain: IPR004099
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR001327 (DEPRECATED) Pyridine nucleotide-disulphide oxidoreductase, NAD-binding domain Protein Sequence Similarity - InterPro Domain: IPR001327
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF14759 Reductase C-terminal Protein Sequence Similarity - PFAM Model Name: PF14759
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR016156 FAD/NAD-linked reductase, dimerisation domain superfamily Protein Sequence Similarity - InterPro Domain: IPR016156
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR028202 Reductase, C-terminal Protein Sequence Similarity - InterPro Domain: IPR028202
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR023753 FAD/NAD(P)-binding domain Protein Sequence Similarity - InterPro Domain: IPR023753
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR036188 FAD/NAD(P)-binding domain superfamily Protein Sequence Similarity - InterPro Domain: IPR036188
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF07992 Pyridine nucleotide-disulphide oxidoreductase Protein Sequence Similarity - PFAM Model Name: PF07992
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR001100 Pyridine nucleotide-disulphide oxidoreductase, class I Protein Sequence Similarity - InterPro Domain: IPR001100
Reference: Escherichia coli K-12 MG1655 		Apr 2008
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 1.18.1.3 Published Annotation - Swiss-Prot Accession Number: P77650 Feb 2006
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 GeneID:945427 Published Annotation - Entrez Gene Database ID: 945427
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref UniProtKB/Swiss-Prot:P77650 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P77650 Published Annotation - Swiss-Prot Accession Number: P77650 Jan 2005
Automated Process Approved db xref ASAP:ABE-0008363 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GI:1788892 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG13460 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved function enzyme; Degradation of small molecules: Carbon compounds Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved note ferredoxin reductase subunit of phenylpropionate dioxygenase; 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 AAC75595.1 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: 9.97
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
Person Uncurated subsystem component of in silico model iMC1010 Experimental - PubMed ID: 15129285
Reference: Escherichia coli K-12 MG1655 		Mar 2009
Person Uncurated subsystem component of in silico model iJR904 Experimental - PubMed ID: 12952533
Reference: Escherichia coli K-12 MG1655 		Feb 2009
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
Automated Process Approved GO biological process GO:0006118 (OBSOLETE) electron transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001100
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO biological process GO:0045454 cell redox homeostasis GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004099
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: IPR023753, IPR016156
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO cellular component GO:0005737 cytoplasm GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004099
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:0050660 flavin adenine dinucleotide binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001327
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:IPR004099
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-0004145 hcaD CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0004006 hcaD CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0007733 hcaD CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003593 hcaD CDS
Ortholog
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0006712 hcaD CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0008677 hcaD CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0006673 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0006857 hcaD CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0002901 CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0003383 CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0006688 hcaD CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0007757 hcaD CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0007261 hcaD CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0000888 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0007117 hcaD CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0005637 hcaD CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0005112 hcaD CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0006553 hcaD CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0008613 hcaD CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0006204 hcaD CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0006406 hcaD CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0009684 hcaD CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0008063 hcaD CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0006744 hcaD CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0006662 hcaD CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0008189 hcaD CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0027513 hcaD CDS
Automated Process Approved Go view Escherichia coli HS ADR-0007367 hcaD CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0002398 hcaD CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0002613 hcaD CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0003041 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0002989 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0002835 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0002877 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0002694 hcaD CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0133427 hcaD CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0003736 CDS
Person Uncurated Go view Photorhabdus luminescens subsp. laumondii TTO1 [T] ACD-0141880 CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0004477 hcaD CDS
Person Uncurated Go view Shigella flexneri 2457T ABQ-0073911 hcaD pseudogene
Automated Process Approved Go view Shigella flexneri 8401 BAG-0002767 hcaD CDS
Person Approved Go view Shigella sonnei 046 ADD-0002861 hcaD 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
FB22451mutantTn5 InsertionRequest the StrainABE-0008363hcaDhcaD::Tn5KAN-I-SceI at position 962 in Plus orientation ,+ pKD460Blattner Laboratory
FB23600mutantTn5 InsertionRequest the StrainABE-0008363hcaDhcaD::Tn5KAN-I-SceI at position 962 in Plus orientation ,- pKD460Blattner Laboratory
FB23726mutantTn5 InsertionRequest the StrainABE-0008363hcaDhcaD::Tn5KAN-I-SceI at position 962 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 2667047 to 2678249
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0008348hcaTCDScomplement26667072667846Upstream
ABE-0008351hcaRCDScomplement26680062668896Upstream
ABE-0285710iroKCDScomplement26680062668071Upstream
ABE-0008355hcaECDSforward26690322670393Upstream
ABE-0008357hcaFCDSforward26703902670908Upstream
ABE-0008359hcaCCDSforward26709082671228Upstream
ABE-0008361hcaBCDSforward26712252672037Upstream
ABE-0008363hcaDCDSforward26720472673249Matches
ABE-0008365yphACDSforward26733462673768Downstream
ABE-0285528repeat_regionforward26737762673809Downstream
ABE-0008368yphBCDScomplement26738162674688Downstream
ABE-0008370yphCCDScomplement26747002675761Downstream
ABE-0008373yphDCDScomplement26758272676825Downstream
ABE-0008376yphECDScomplement26768502678361Downstream
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.