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

ABE-0004963 (dosP) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0004963 showshow history
Names
dosP yddU pdeO JW1484 ECK1483 dos b1489
Product
oxygen-sensing c-di-GMP phosphodiesterase
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 1563334 1565733 2400 800
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR013767 (IPR013767 PAS fold) Apr 2008
Automated Process Approved IPR013656 (IPR013656 PAS fold-4) Apr 2008
Automated Process Approved IPR000160 (IPR000160 GGDEF domain) Apr 2008
Automated Process Approved IPR001633 (IPR001633 EAL domain) Apr 2008
Automated Process Approved IPR000014 (IPR000014 PAS domain) Apr 2008
Automated Process Approved IPR001610 (IPR001610 PAC motif) Apr 2008
Automated Process Approved IPR000700 (IPR000700 PAS-associated, C-terminal) Apr 2008
Automated Process Approved IPR029787 (IPR029787 Nucleotide cyclase) Jul 2018
Automated Process Approved IPR035919 (IPR035919 EAL domain superfamily) Jul 2018
Automated Process Approved IPR035965 (IPR035965 PAS domain superfamily) Jul 2018
Automated Process Approved PF00990 (PF00990 Diguanylate cyclase, GGDEF domain) Jul 2018
Automated Process Approved PF00563 (PF00563 EAL domain) Jul 2018
Automated Process Approved PF13426 (PF13426 PAS domain) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Automated Process Approved GO biological process GO:0007165 signal transduction GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000014
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO biological process GO:0006355 regulation of transcription, DNA-templated GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR013767
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO cellular component GO:0005886 plasma membrane GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Automated Process Approved GO molecular function GO:0000155 phosphorelay sensor kinase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000700
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0004871 (OBSOLETE) signal transducer activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000014
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Uncurated name dosP Published Annotation - PubMed ID: 19764732
Reference: Escherichia coli 		Sep 2018
Person Uncurated synonym pdeO Published Annotation - PubMed ID: 26148715
Reference: Escherichia coli K-12 MG1655 		Sep 2018
Person Approved synonym ECK1483 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym JW1484 Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved synonym yddU Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved synonym dos Experimental - PubMed ID: 10704219
Reference: Escherichia coli 		Aug 2002
Person Approved locus tag b1489 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product oxygen-sensing c-di-GMP phosphodiesterase Experimental - PubMed ID: 19764732
Reference: Escherichia coli 		Sep 2018
Person Approved alternate product name cAMP phosphodiesterase, heme-regulated Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved alternate product name oxygen sensor, c-di-GMP phosphodiesterase, heme-regulated; cold- and stationary phase-induced bioflim regulator Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Uncurated alternate product name putative phosphodiesterase, oxygen-sensing protein Published Annotation - Database Name: GenProtEC Jan 2006
Protein Family
Automated Process Approved protein family IPR029787 Nucleotide cyclase Protein Sequence Similarity - InterPro Domain: IPR029787
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR035919 EAL domain superfamily Protein Sequence Similarity - InterPro Domain: IPR035919
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR000700 PAS-associated, C-terminal Protein Sequence Similarity - InterPro Domain: IPR000700
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR001610 PAC motif Protein Sequence Similarity - InterPro Domain: IPR001610
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR000014 PAS domain Protein Sequence Similarity - InterPro Domain: IPR000014
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF13426 PAS domain Protein Sequence Similarity - PFAM Model Name: PF13426
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF00563 EAL domain Protein Sequence Similarity - PFAM Model Name: PF00563
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR000160 GGDEF domain Protein Sequence Similarity - InterPro Domain: IPR000160
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF00990 Diguanylate cyclase, GGDEF domain Protein Sequence Similarity - PFAM Model Name: PF00990
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR013656 PAS fold-4 Protein Sequence Similarity - InterPro Domain: IPR013656
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR001633 EAL domain Protein Sequence Similarity - InterPro Domain: IPR001633
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR035965 PAS domain superfamily Protein Sequence Similarity - InterPro Domain: IPR035965
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR013767 PAS fold Protein Sequence Similarity - InterPro Domain: IPR013767
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Other
Person Approved EC number 3.1.4.- Published Annotation - Swiss-Prot Accession Number: P76129 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 GI:87081921 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P76129 Published Annotation - Swiss-Prot Accession Number: P76129 Jan 2005
Automated Process Approved db xref GeneID:945815 Published Annotation - Entrez Gene Database ID: 945815
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref UniProtKB/Swiss-Prot:P76129 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0004963 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG13792 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved function putative enzyme; Not classified Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved protein id AAC74562.2 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Uncurated subcellular localization Cytoplasmic Membrane Predicted by PSORTb - PSORTb Final_Score: 7.88
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:0007165 signal transduction GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000014
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO biological process GO:0006355 regulation of transcription, DNA-templated GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR013767
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO cellular component GO:0005886 plasma membrane GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Automated Process Approved GO molecular function GO:0000155 phosphorelay sensor kinase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000700
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0004871 (OBSOLETE) signal transducer activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000014
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-0005208 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0004018 dos CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0004177 dosP CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003295 dosP CDS
Ortholog
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0005497 dos CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0001497 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0010087 dos CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0001456 CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0002861 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0007919 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0005354 dos CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0005063 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0078034 dosP CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0001662 dosP CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0005246 dos CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0007983 dos CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0001730 dos CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0006117 dos CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0285343 dos pseudogene
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0007963 dosP CDS
Automated Process Approved Go view Escherichia coli HS ADR-0006250 dos CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0001398 dos CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0001530 dos CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0001750 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0001798 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0001711 CDS
Person Uncurated Go view Escherichia coli Nissle 1917 AML-0001720 pseudogene
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0175855 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0001608 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0001683 dos CDS
Person Uncurated Go view Escherichia coli Sakai (EHEC) ACA-0285278 dos pseudogene
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0001709 CDS
Automated Process Uncurated Go view Musicola paradisiaca Ech703 AGA-0009065 CDS
Person Approved Go view Shigella boydii 227 ADV-0001731 CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0007161 dos CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0004139 dos CDS
Person Uncurated Go view Shigella flexneri 2457T ABQ-0072966 dos pseudogene
Person Uncurated Go view Shigella flexneri 301 ABT-0088042 dos pseudogene
Person Uncurated Go view Shigella flexneri 8401 BAG-0001849 dos pseudogene
Person Approved Go view Shigella sonnei 046 ADD-0001779 dos 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)
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 1558334 to 1570733
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0004949ddpDCDScomplement15580311559017Downstream
ABE-0004953ddpCCDScomplement15590141559910Downstream
ABE-0004955ddpBCDScomplement15599071560929Downstream
ABE-0004958ddpACDScomplement15609311562481Downstream
ABE-0004960ddpXCDScomplement15624951563076Downstream
ABE-0285725matS13protein_bindforward15632821563294Downstream
ABE-0004963dosPCDScomplement15633341565733Matches
ABE-0004965dosCCDScomplement15657581567140Upstream
ABE-0285781yddYCDScomplement15671781567219Upstream
ABE-0004970digHCDScomplement15675041568823Upstream
ABE-0004973gadCCDScomplement15689541570489Upstream
ABE-0004976gadBCDScomplement15706451572045Upstream
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.