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

ABE-0008361 (hcaB) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0008361 showshow history
Names
hcaB phdD yfhX JW2525 ECK2538 phd dig b2541
Product
2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 2671225 2672037 813 271
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR002198 (IPR002198 (DEPRECATED) Short-chain dehydrogenase/reductase SDR) Apr 2008
Automated Process Approved IPR002347 (IPR002347 Short-chain dehydrogenase/reductase SDR) Apr 2008
Automated Process Approved IPR036291 (IPR036291 NAD(P)-binding domain superfamily) Jul 2018
Automated Process Approved PF00106 (PF00106 short chain dehydrogenase) 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:0008152 metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR002198
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:0016491 oxidoreductase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR002198
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name hcaB Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym ECK2538 Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved synonym phdD Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved synonym yfhX Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved synonym phd Published Sequence Analysis - PubMed ID: 9729611 Aug 2003
Person Approved synonym JW2525 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym dig Published Sequence Analysis - PubMed ID: 9729611 Aug 2003
Person Approved locus tag b2541 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved alternate product name 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Protein Family
Automated Process Approved protein family IPR002198 (DEPRECATED) Short-chain dehydrogenase/reductase SDR Protein Sequence Similarity - InterPro Domain: IPR002198
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR002347 Short-chain dehydrogenase/reductase SDR Protein Sequence Similarity - InterPro Domain: IPR002347
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR036291 NAD(P)-binding domain superfamily Protein Sequence Similarity - InterPro Domain: IPR036291
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF00106 short chain dehydrogenase Protein Sequence Similarity - PFAM Model Name: PF00106
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Person Approved EC number 1.3.1.- Published Annotation - Swiss-Prot Accession Number: P77646 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 EcoGene:EG13459 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GI:1788891 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:945346 Published Annotation - Entrez Gene Database ID: 945346
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref UniProtKB/Swiss-Prot:P0CI31 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0008361 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P77646 Published Annotation - Swiss-Prot Accession Number: P77646 Jan 2005
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 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 AAC75594.1 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: 9.26
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Person Uncurated subsystem component of in silico model iJR904 Experimental - PubMed ID: 12952533
Reference: Escherichia coli K-12 MG1655 		Feb 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 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:0008152 metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR002198
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Uncurated GO biological process GO:0016052 carbohydrate catabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
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:0016491 oxidoreductase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR002198
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-0004277 hcaB CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0004846 hcaB CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0008454 hcaB CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003895 hcaB CDS
Ortholog
Automated Process Approved Go view Citrobacter freundii ATCC 8090 [T] AVI-0004071 budC CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0006713 hcaB CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0008678 hcaB CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0006675 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0006856 hcaB CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0002900 hcaB CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0003382 hcaB CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0006689 hcaB CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0007756 hcaB CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0007260 hcaB CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0000887 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0007116 hcaB CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0005636 hcaB CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0005111 hcaB CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0006554 hcaB CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0008612 hcaB CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0006205 hcaB CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0006405 hcaB CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0009685 hcaB CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0008062 hcaB CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0006743 hcaB CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0006661 hcaB CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0008188 hcaB CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0027512 hcaB CDS
Automated Process Approved Go view Escherichia coli HS ADR-0007366 hcaB CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0002397 hcaB CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0002612 hcaB CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0003042 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0002988 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0002836 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0002876 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0002693 hcaB CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0133426 hcaB CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0003735 CDS
Person Uncurated Go view Photorhabdus luminescens subsp. laumondii TTO1 [T] ACD-0141875 hcaB CDS
Person Approved Go view Shigella boydii 227 ADV-0002828 hcaB CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0004476 hcaB CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0073910 hcaB CDS
Person Approved Go view Shigella flexneri 301 ABT-0088841 hcaB CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0002766 hcaB CDS
Person Approved Go view Shigella sonnei 046 ADD-0002860 hcaB 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 2666225 to 2677037
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0008346csiECDSforward26654352666715Upstream
ABE-0008348hcaTCDScomplement26667072667846Upstream
ABE-0008351hcaRCDScomplement26680062668896Upstream
ABE-0285710iroKCDScomplement26680062668071Upstream
ABE-0008355hcaECDSforward26690322670393Upstream
ABE-0008357hcaFCDSforward26703902670908Upstream
ABE-0008359hcaCCDSforward26709082671228Overlaps Upstream
ABE-0008361hcaBCDSforward26712252672037Matches
ABE-0008363hcaDCDSforward26720472673249Downstream
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.