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

ABE-0005123 (dgcZ) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0005123 showshow history
Names
dgcZ ydeG JW1528 ECK1528 ydeH b1535
Product
diguanylate cyclase
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 1622960 1623850 891 297
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 IPR000160 (IPR000160 GGDEF domain) Apr 2008
Automated Process Approved IPR029787 (IPR029787 Nucleotide cyclase) Jul 2018
Automated Process Approved PF00990 (PF00990 Diguanylate cyclase, GGDEF domain) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
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
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name dgcZ Published Annotation - PubMed ID: 23769666
Reference: Escherichia coli K-12 		Aug 2016
Person Approved synonym JW1528 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK1528 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ydeH Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved synonym ydeG Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved locus tag b1535 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product diguanylate cyclase Experimental - PubMed ID: 23769666
Reference: Escherichia coli K-12 		Aug 2016
Automated Process Approved alternate product name diguanylate cyclase, required for pgaD induction Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Protein Family
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 IPR029787 Nucleotide cyclase Protein Sequence Similarity - InterPro Domain: IPR029787
Reference: Escherichia coli K-12 MG1655 		Jul 2018
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
Other
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:EG11643 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GI:1787816 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:946075 Published Annotation - Entrez Gene Database ID: 946075
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Person Approved db xref UniProtKB:P31129 Published Annotation - Swiss-Prot Accession Number: P31129 Jan 2005
Automated Process Approved db xref UniProtKB/Swiss-Prot:P31129 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0005123 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC74608.1 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: 8.96
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 Uncurated GO cellular component GO:0005737 cytoplasm GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Comparative to toptop
Author Approval Details Genome Feature Name Type
Member
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0003831 ydeH CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0003990 ydeH CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003380 dgcZ CDS
Ortholog
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0003935 CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0005566 CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0001533 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0010137 CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0001497 ydeH CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0002816 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0007862 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0005406 CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0005005 YdeH CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0078078 dgcZ CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0001716 ydeH CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0001982 ydeH CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0005176 CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0008044 CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0001770 ydeH CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0006182 CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0003414 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0005531 CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0009895 CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0008077 CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0006991 CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0006865 CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0011469 CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0008135 CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0008368 CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0006957 CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0007063 CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0025937 ydeH CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0009402 ydeH_1 CDS
Automated Process Approved Go view Escherichia coli HS ADR-0006300 CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0001939 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0001440 ydeH CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0001575 ydeH CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0001842 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0001845 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0001791 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0001767 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0175914 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0001660 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0001628 CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0132114 ydeH CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0000671 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0001767 ydeH CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0004217 CDS
Person Approved Go view Shigella dysenteriae 197 ADU-0001832 ydeH CDS
Person Approved Go view Shigella sonnei 046 ADD-0001727 ydeH 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
FB20356mutantTn5 InsertionRequest the StrainABE-0005123dgcZydeH::Tn5KAN-I-SceI at position 322 in Plus orientation ,- pKD465Blattner Laboratory
FB20357mutantTn5 InsertionRequest the StrainABE-0005123dgcZydeH::Tn5KAN-I-SceI at position 322 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 1617960 to 1628850
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0005103ydeACDSforward16170281618218Downstream
ABE-0005106marCCDScomplement16182431618908Downstream
ABE-0005110marRCDSforward16191201619554Downstream
ABE-0005112marACDSforward16195741619957Downstream
ABE-0285727matS15protein_bindforward16199661619978Downstream
ABE-0005114marBCDSforward16199891620207Downstream
ABE-0005116eamACDScomplement16202381621137Downstream
ABE-0005121ydeECDSforward16213321622519Downstream
ABE-0285183mgtSCDSforward16226461622741Downstream
ABE-0285749mgtTCDSforward16227411622845Downstream
ABE-0285266mgrRncRNAcomplement16228171622914Downstream
ABE-0005123dgcZCDScomplement16229601623850Matches
ABE-0005127ydeICDScomplement16241051624497Upstream
ABE-0005131ydeJCDSforward16247731625291Upstream
ABE-0005133dcpCDScomplement16253351627380Upstream
ABE-0005137ydfGCDSforward16275171628263Upstream
ABE-0005144rspRCDSforward16283521629038Upstream
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.