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

ABE-0009484 (idi) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0009484 showshow history
Names
idi ygfV JW2857 ECK2884 b2889
Product
isopentenyl diphosphate isomerase
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 3033065 3033613 549 183
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR011876 (IPR011876 Isopentenyl-diphosphate delta-isomerase, type 1) Apr 2008
Automated Process Approved IPR002667 (IPR002667 (DEPRECATED) Isopentenyl-diphosphate delta-isomerase) Apr 2008
Automated Process Approved IPR015797 (IPR015797 NUDIX hydrolase-like domain superfamily) Apr 2008
Automated Process Approved IPR000086 (IPR000086 NUDIX hydrolase domain) Apr 2008
Automated Process Approved PF00293 (PF00293 NUDIX domain) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Automated Process Approved GO biological process GO:0008299 isoprenoid biosynthetic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR011876
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
Person Uncurated GO cellular component GO:0005737 cytoplasm Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO molecular function GO:0016787 hydrolase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000086
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0004452 isopentenyl-diphosphate delta-isomerase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR011876
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name idi Experimental - PubMed ID: 10419945
Reference: Escherichia coli 		Aug 2002
Person Approved synonym JW2857 Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved synonym ygfV Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved synonym ECK2884 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b2889 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product isopentenyl diphosphate isomerase Published Annotation - PubMed ID: 16397293 Jan 2006
Person Uncurated alternate product name isopentenyl diphosphate isomerase Experimental - PubMed ID: 10419945
Reference: Escherichia coli 		Jan 2006
Protein Family
Automated Process Approved protein family IPR011876 Isopentenyl-diphosphate delta-isomerase, type 1 Protein Sequence Similarity - InterPro Domain: IPR011876
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF00293 NUDIX domain Protein Sequence Similarity - PFAM Model Name: PF00293
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR015797 NUDIX hydrolase-like domain superfamily Protein Sequence Similarity - InterPro Domain: IPR015797
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR000086 NUDIX hydrolase domain Protein Sequence Similarity - InterPro Domain: IPR000086
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR002667 (DEPRECATED) Isopentenyl-diphosphate delta-isomerase Protein Sequence Similarity - InterPro Domain: IPR002667
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Other
Automated Process Uncurated EC number 3.-.-.- Published Annotation - Database Name: EC2GO: GO:0016787
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Person Approved EC number 5.3.3.2 Published Annotation - Swiss-Prot Accession Number: Q46822 Feb 2006
Person Uncurated MultiFun 1.5.3.11 (metabolism; building block biosynthesis; cofactor, small molecule carrier; menaquinone, ubiquinone) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 7.1 (location of gene products; cytoplasm) 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
Person Approved db xref UniProtKB:Q46822 Published Annotation - Swiss-Prot Accession Number: Q46822 Jan 2006
Automated Process Approved db xref GeneID:949020 Published Annotation - Entrez Gene Database ID: 949020
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref GI:1789255 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0009484 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG13072 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:Q46822 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 note GO_component: GO:0005737 - cytoplasm Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC75927.1 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
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:0008299 isoprenoid biosynthetic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR011876
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Uncurated GO cellular component GO:0005737 cytoplasm 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:0004452 isopentenyl-diphosphate delta-isomerase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR011876
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0016787 hydrolase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000086
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-0002812 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0002361 idi CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0002353 idi CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0003685 idi CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0002040 idi CDS
Ortholog
Automated Process Uncurated Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0003769 idi CDS
Automated Process Uncurated Go view Enterobacter cloacae subsp. cloacae ATCC 13047 [T] (AToL DRAFT) AMB-0004797 idi CDS
Automated Process Uncurated Go view Erwinia tasmaniensis Et1/99 [T] AFI-0002308 idi CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0002669 idi CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0005957 idi CDS
Automated Process Uncurated Go view Escherichia coli 536 (UPEC) AEF-0002912 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0008255 idi CDS
Automated Process Uncurated Go view Escherichia coli APEC O1 (APEC) AEG-0002889 CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0001389 idi CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0006301 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0005762 idi CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0006159 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0079627 idi CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0009174 idi CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0007184 idi CDS
Automated Process Uncurated Go view Escherichia coli E2348/69 (EPEC) BCI-0003345 idi CDS
Automated Process Uncurated Go view Escherichia coli E24377A (ETEC) ADO-0007651 idi CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0004260 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0007516 idi CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0006036 idi CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0005513 idi CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0005804 idi CDS
Automated Process Uncurated Go view Escherichia coli EC4115 (EHEC) BAS-0009015 idi CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0008378 idi CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0006817 idi CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0005801 idi CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0006312 idi CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0005623 idi CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0007734 idi CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0006052 idi CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0027899 idi CDS
Automated Process Uncurated Go view Escherichia coli F11 (UPEC) ADQ-0008397 idi CDS
Automated Process Uncurated Go view Escherichia coli HS ADR-0007727 idi CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0002705 idi CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0002960 idi CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0003253 CDS
Automated Process Uncurated Go view Escherichia coli SE11 AFS-0003213 CDS
Automated Process Uncurated Go view Escherichia coli SMS-3-5 AFT-0003020 idi CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0133803 CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0001057 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0003283 CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0003326 idi CDS
Automated Process Uncurated Go view Leclercia adecarboxylata ATCC 23216 [T] AME-0001539 idi CDS
Automated Process Uncurated Go view Salmonella Agona SL483 BBX-0007362 idi CDS
Automated Process Uncurated Go view Salmonella Arizonae CDC 346-86 BCD-0004841 CDS
Person Uncurated Go view Salmonella Choleraesuis SC-B67 ADB-0003484 idi CDS
Automated Process Uncurated Go view Salmonella Dublin CT_02021853 BCB-0007629 idi CDS
Automated Process Uncurated Go view Salmonella Enteritidis P125109 BCF-0009400 idi CDS
Automated Process Uncurated Go view Salmonella Gallinarum 287/91 BCG-0008890 idi CDS
Automated Process Uncurated Go view Salmonella Hadar RI_05P066 BBT-0006333 idi CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL476 BBV-0007629 idi CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL486 BBW-0006590 idi CDS
Automated Process Uncurated Go view Salmonella Javiana GA_MM04042433 BCA-0005590 idi CDS
Automated Process Uncurated Go view Salmonella Kentucky CDC 191 BBZ-0005633 idi CDS
Automated Process Uncurated Go view Salmonella Newport SL254 BBQ-0007631 idi CDS
Automated Process Uncurated Go view Salmonella Newport SL317 BBR-0005434 idi CDS
Automated Process Uncurated Go view Salmonella Paratyphi A AKU_12601 BCH-0002936 CDS
Person Uncurated Go view Salmonella Paratyphi A ATCC 9150 ADA-0002906 idi CDS
Automated Process Uncurated Go view Salmonella Paratyphi B SPB7 BCC-0003801 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA23 BBN-0007791 idi CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA29 BBM-0005428 idi CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund CVM19633 BBO-0007279 idi CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund SL480 BBY-0005487 idi CDS
Person Uncurated Go view Salmonella Typhi CT18 ABX-0111831 CDS
Person Uncurated Go view Salmonella Typhi Ty2 ABS-0084675 CDS
Automated Process Uncurated Go view Salmonella Typhimurium 14028S AJR-0003677 idi CDS
Person Uncurated Go view Salmonella Typhimurium LT2 [T] ABU-0099471 idi CDS
Automated Process Uncurated Go view Salmonella Virchow SL491 BBS-0006224 idi CDS
Automated Process Uncurated Go view Salmonella Weltevreden SL484 BBU-0009199 idi CDS
Automated Process Uncurated Go view Salmonella enterica CVM23701 BBL-0008181 idi CDS
Person Approved Go view Shigella boydii 227 ADV-0003397 CDS
Automated Process Uncurated Go view Shigella boydii BS512 ADJ-0008721 idi CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0003949 idi CDS
Person Uncurated Go view Shigella dysenteriae 197 ADU-0003637 CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0074250 CDS
Person Uncurated Go view Shigella flexneri 301 ABT-0089128 CDS
Automated Process Uncurated Go view Shigella flexneri 8401 BAG-0003134 CDS
Person Approved Go view Shigella sonnei 046 ADD-0003325 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 3028065 to 3038613
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0174113ghxQCDSforward30271213028488Upstream
ABE-0009471ygfSCDScomplement30285243029012Upstream
ABE-0009473ygfTCDScomplement30290123030931Upstream
ABE-0009478uacTCDSforward30313673032815Upstream
ABE-0285227yqfGCDSforward30328173032942Upstream
ABE-0285740yqfHCDScomplement30329393033010Upstream
ABE-0009484idiCDSforward30330653033613Matches
ABE-0009486lysSCDScomplement30336573035174Downstream
ABE-0009488prfBCDScomplement30351843036206(Interval #2) Downstream
ABE-0009488prfBCDScomplement30362083036282(Interval #1) Downstream
ABE-0009492recJCDScomplement30363733038106Downstream
ABE-0009494dsbCCDScomplement30381123038822Downstream
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.