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

ABE-0013442 (phnD) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0013442 showshow history
Names
phnD JW4066 ECK4098 psiD b4105
Product
periplasmic-binding component of an ABC superfamily phosphonate/organophosphate ester transporter
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 4323336 4324352 1017 339
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR005770 (IPR005770 Phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein) Apr 2008
Automated Process Approved IPR017797 (IPR017797 Phosphonate ABC transporter, substrate-binding protein) Jul 2018
Automated Process Approved PF12974 (PF12974 ABC transporter, phosphonate, periplasmic substrate-binding protein) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Person Uncurated GO biological process GO:0006793 phosphorus metabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Uncurated GO biological process GO:0055085 transmembrane transport GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR005770
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO biological process GO:0015716 organic phosphonate transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR005770
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO cellular component GO:0043190 ATP-binding cassette (ABC) transporter complex GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR005770, IPR017797
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO cellular component GO:0030288 outer membrane-bounded periplasmic space GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR005770
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Uncurated GO cellular component GO:0042597 periplasmic space Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Uncurated GO cellular component GO:0030288 outer membrane-bounded periplasmic space GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Automated Process Approved GO molecular function GO:0015604 (DEPRECATED) organic phosphonate transmembrane transporter activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR005770
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name phnD Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym JW4066 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK4098 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym psiD Published Sequence Analysis - PubMed ID: 9729611 Aug 2003
Person Approved locus tag b4105 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product periplasmic-binding component of an ABC superfamily phosphonate/organophosphate ester transporter Published Annotation - PubMed ID: 16397293
Reference: Escherichia coli K-12 		Mar 2008
Person Approved alternate product name periplasmic binding protein component of Pn transporter Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Automated Process Approved alternate product name phosphonate ABC transporter periplasmic binding protein Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Uncurated alternate product name phosphonate transport protein (ABC superfamily, peri_bind) Published Annotation - Database Name: GenProtEC Jan 2006
Protein Family
Automated Process Approved protein family IPR017797 Phosphonate ABC transporter, substrate-binding protein Protein Sequence Similarity - InterPro Domain: IPR017797
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR005770 Phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein Protein Sequence Similarity - InterPro Domain: IPR005770
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF12974 ABC transporter, phosphonate, periplasmic substrate-binding protein Protein Sequence Similarity - PFAM Model Name: PF12974
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Person Uncurated MultiFun 4.3.A.1.p (transport; Primary Active Transporters; Pyrophosphate Bond (ATP, GTP, P2) Hydrolysis-driven Active Transporters; The ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake Permeases; ABC superfamily, periplasmic binding component) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 1.8.1 (metabolism; metabolism of other compounds; phosphorous metabolism) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 7.2 (location of gene products; periplasmic space) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 4.S.8 (transport; substrate; alkylphosphonate) 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:EG10714 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P16682 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P16682 Published Annotation - Swiss-Prot Accession Number: P16682 Jan 2005
Automated Process Approved db xref GeneID:948624 Published Annotation - Entrez Gene Database ID: 948624
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref GI:1790543 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0013442 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved function transport; Transport of small molecules: Anions Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved note periplasmic binding protein component of Pn transporter; periplasmic binding component of ABC superfamily; GO_component: GO:0042597 - periplasmic space; GO_process: GO:0006793 - phosphorus metabolic process Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC77066.1 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Uncurated subcellular localization Periplasmic Predicted by PSORTb - PSORTb Final_Score: 10.00
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
Person Uncurated GO biological process GO:0006793 phosphorus metabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Uncurated GO biological process GO:0055085 transmembrane transport GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR005770
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO biological process GO:0015716 organic phosphonate transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR005770
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Uncurated GO cellular component GO:0042597 periplasmic space Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO cellular component GO:0030288 outer membrane-bounded periplasmic space GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR005770
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO cellular component GO:0030288 outer membrane-bounded periplasmic space GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Automated Process Uncurated GO cellular component GO:0043190 ATP-binding cassette (ABC) transporter complex GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR005770, IPR017797
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0015604 (DEPRECATED) organic phosphonate transmembrane transporter activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR005770
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-0003391 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0002570 phnD CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0002602 phnD CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0002211 phnD CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0002890 phnD CDS
Ortholog
Automated Process Uncurated Go view Buttiauxella agrestis ATCC 33320 [T] APC-0000392 phnD CDS
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0004119 phnD CDS
Automated Process Approved Go view Citrobacter freundii ATCC 8090 [T] AVI-0000150 phnD CDS
Automated Process Uncurated Go view Enterobacter cloacae subsp. cloacae ATCC 13047 [T] (AToL DRAFT) AMB-0000623 phnD CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0006390 phnD CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0004398 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0006863 phnD CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0004187 phnD CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0004697 phnD CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0010072 CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0009821 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0081316 phnD CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0004775 phnD CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0005371 phnD CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0006193 phnD CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0006655 phnD CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0004730 phnD CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0009095 phnD CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0003165 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0008944 phnD CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0007458 phnD CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0007103 phnD CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0006221 phnD CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0010448 phnD CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0007119 phnD CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0008263 phnD CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0007235 phnD CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0005814 phnD CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0006561 phnD CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0005970 phnD CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0005083 phnD CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0029281 phnD CDS
Automated Process Uncurated Go view Escherichia coli F11 (UPEC) ADQ-0007083 phnD CDS
Automated Process Approved Go view Escherichia coli HS ADR-0009033 phnD CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0004715 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0003797 phnD CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0004194 phnD CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0004753 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0004821 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0004564 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0004760 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0178933 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0004503 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0004562 phnD CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0135199 phnD CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0003357 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0004708 phnD CDS
Person Uncurated Go view Hafnia alvei ATCC 13337 [T] AMD-0001311 phnD CDS
Automated Process Uncurated Go view Leclercia adecarboxylata ATCC 23216 [T] AME-0002733 phnD CDS
Person Uncurated Go view Pseudomonas syringae pv. tomato DC3000 ADG-0002601 phnD CDS
Automated Process Uncurated Go view Salmonella Arizonae CDC 346-86 BCD-0003532 CDS
Person Approved Go view Shigella boydii 227 ADV-0004494 phnD CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0010025 phnD CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0004674 phnD CDS
Person Approved Go view Shigella dysenteriae 197 ADU-0004632 phnD CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0074827 phnD CDS
Person Approved Go view Shigella flexneri 301 ABT-0090333 phnD CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0004381 phnD CDS
Person Approved Go view Shigella sonnei 046 ADD-0004647 phnD CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 43003 APO-0000809 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 49455 [T] AMG-0000532 phnD 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
FB21666mutantTn5 InsertionRequest the StrainABE-0013442phnDphnD::Tn5KAN-I-SceI at position 767 in Minus orientation ,+ pKD460Blattner Laboratory
FB21667mutantTn5 InsertionRequest the StrainABE-0013442phnDphnD::Tn5KAN-I-SceI at position 767 in Minus orientation ,- pKD465Blattner 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 4318336 to 4329352
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0013424phnKCDScomplement43180064318764Downstream
ABE-0013426phnJCDScomplement43187614319606Downstream
ABE-0013428phnICDScomplement43195994320663Downstream
ABE-0013430phnHCDScomplement43206634321247Downstream
ABE-0013433phnGCDScomplement43212444321696Downstream
ABE-0013435phnFCDScomplement43216974322422Downstream
ABE-0013437phnE_2CDSpcomplement43224434322811Downstream
ABE-0285115phnEpseudogenecomplement43224434323230Downstream
ABE-0013439phnE_1CDSpcomplement43226614323230Downstream
ABE-0285677repeat_regionforward43232464323332Downstream
ABE-0013442phnDCDScomplement43233364324352Matches
ABE-0013444phnCCDScomplement43243774325165Upstream
ABE-0013447yjdNCDScomplement43252984325741Upstream
ABE-0285678repeat_regionforward43258024326384Upstream
ABE-0013451yjdMCDScomplement43263994326734Upstream
ABE-0013456rdcACDSforward43271354329363Upstream
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.