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

ABE-0003460 (pgaD) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0003460 showshow history
Names
pgaD JW1006 ECK1011 hmsS ycdP b1021
Product
poly-N-acetyl-D-glucosamine synthase subunit
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 1086106 1086519 414 138
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR023829 (IPR023829 Poly-beta-1,6-N-acetyl-D-glucosamine biosynthesis protein PgaD) Jul 2018
Automated Process Approved PF13994 (PF13994 PgaD-like protein) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Automated Process Uncurated GO biological process GO:0042710 biofilm formation GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR023829
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Uncurated name pgaD Published Sequence Analysis - PubMed ID: 15090514
Reference: Escherichia coli K-12 MG1655 		Jan 2007
Person Approved synonym ECK1011 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym hmsS Published Annotation - Database Name: GenProtEC Jul 2002
Person Approved synonym ycdP Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym JW1006 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b1021 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product poly-N-acetyl-D-glucosamine synthase subunit Published Annotation - EcoCyc Accession Number: G6528
Reference: Escherichia coli K-12 MG1655 		Jan 2021
Person Uncurated alternate product name predicted inner membrane protein Published Sequence Analysis - PubMed ID: 15090514
Reference: Escherichia coli K-12 MG1655 		Jan 2007
Automated Process Approved alternate product name biofilm PGA synthase PgaCD, regulatory subunit; c-di-GMP-stimulated activity and dimerization Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Protein Family
Automated Process Approved protein family IPR023829 Poly-beta-1,6-N-acetyl-D-glucosamine biosynthesis protein PgaD Protein Sequence Similarity - InterPro Domain: IPR023829
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF13994 PgaD-like protein Protein Sequence Similarity - PFAM Model Name: PF13994
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Person Approved MultiFun 6.1 (cell structure; membrane) 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 ASAP:ABE-0003460 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GI:1787258 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P69432 Published Annotation - Swiss-Prot Accession Number: P69432 Jan 2006
Automated Process Approved db xref GeneID:947503 Published Annotation - Entrez Gene Database ID: 947503
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref UniProtKB/Swiss-Prot:P69432 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG13862 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved function enzyme; Surface polysaccharides and antigens Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Uncurated function may serve to enhance PGA synthesis, an adhesin important for biofilm formation Published Annotation - PubMed ID: 15090514
Reference: Escherichia coli K-12 MG1655 		Jan 2007
Automated Process Approved note GO_component: GO:0009274 - peptidoglycan-based cell wall Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC74106.1 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
Automated Process Uncurated GO biological process GO:0042710 biofilm formation GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR023829
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Comparative to toptop
Author Approval Details Genome Feature Name Type
Homolog
Person Uncurated Go view Yersinia pestis 91001 (biovar Microtus) ACQ-0238371 hmsS CDS
Person Uncurated Go view Yersinia pestis CO92 (biovar Orientalis) ABY-0121801 hmsS CDS
Person Uncurated Go view Yersinia pestis KIM (biovar Mediaevalis) ABI-0032075 hmsS CDS
Person Uncurated Go view Yersinia pseudotuberculosis IP32953 ACZ-0002032 hmsS CDS
Member
Automated Process Uncurated Go view OrthoMCL (14 enterobacteria) AMM-0004020 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0004557 pgaD CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0005373 pgaD CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003978 pgaD CDS
Ortholog
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0007260 pgaD CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0001029 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0005458 pgaD CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0000947 ycdP CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0003355 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0008415 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0008038 pgaD CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0077254 pgaD CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0001109 pgaD CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0009429 pgaD CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0008318 pgaD CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0005584 pgaD CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0005100 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0009972 pgaD CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0009010 pgaD CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0007616 pgaD CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0005537 pgaD CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0006103 pgaD CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0006372 pgaD CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0009874 pgaD CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0006305 pgaD CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0006959 pgaD CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0006384 pgaD CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0006887 pgaD CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0007837 pgaD CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0025328 pgaD CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0007490 pgaD CDS
Automated Process Approved Go view Escherichia coli HS ADR-0005813 pgaD CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0001327 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0000981 pgaD CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0001033 pgaD CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0001325 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0001318 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0001275 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0001111 pgaD CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0175251 pgaD CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0001112 CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0131195 pgaD CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0000595 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0001087 ycdP CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0001094 ycdP 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
FB22124mutantTn5 InsertionRequest the StrainABE-0003460pgaDycdP::Tn5KAN-I-SceI at position 355 in Minus orientation ,+ pKD465Blattner Laboratory
FB22274mutantTn5 InsertionRequest the StrainABE-0003460pgaDycdP::Tn5KAN-I-SceI at position 355 in Minus 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 1081106 to 1091519
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0285421repeat_regionforward10811121081145Downstream
ABE-0003441efeU_1CDSpforward10813561081466Downstream
ABE-0285091efeUpseudogeneforward10813561082185Downstream
ABE-0003443efeU_2CDSpforward10814541082185Downstream
ABE-0003448efeOCDSforward10822431083370Downstream
ABE-0003451efeBCDSforward10833761084647Downstream
ABE-0285422repeat_regionforward10846821084767Downstream
ABE-0003458phoHCDSforward10849921086056Downstream
ABE-0003460pgaDCDScomplement10861061086519Matches
ABE-0003464pgaCCDScomplement10865211087846Upstream
ABE-0003467pgaBCDScomplement10878391089857Upstream
ABE-0003469pgaACDScomplement10898661092289Upstream
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.