Escherichia coli K-12 MG1655
About ASAP Data Release Policy University of Wisconsin—Madison
Home    Overview    Annotations    BLAST    Downloads    Comparative Genomics    Experiments    Strains    Help (this script)    User: guest  / Log On   
Working With: Genome: Escherichia coli K-12 MG1655 Version: v3

ABE-0005651 (ydiB) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0005651 showshow history
Names
ydiB JW1682 ECK1690 b1692
Product
quinate/shikimate 5-dehydrogenase
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 1773789 1774655 867 289
Sequence

Get full DNA or protein sequence

View sequence with flanking regions: bases upstream and bases downstream

Context

Browse sequence in GaPP

You last hovered over feature (none)
Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR013708 (IPR013708 Shikimate dehydrogenase substrate binding, N-terminal) Apr 2008
Automated Process Approved IPR006151 (IPR006151 Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase) Apr 2008
Automated Process Approved IPR036291 (IPR036291 NAD(P)-binding domain superfamily) Jul 2018
Automated Process Approved PF08501 (PF08501 Shikimate dehydrogenase substrate binding domain) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Automated Process Uncurated GO biological process GO:0055114 (OBSOLETE) oxidation-reduction process GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR013708
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO cellular component GO:0005737 cytoplasm GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR006151
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0004764 shikimate 3-dehydrogenase (NADP+) activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR006151
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name ydiB Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym ECK1690 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym JW1682 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b1692 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product quinate/shikimate 5-dehydrogenase Published Annotation - PubMed ID: 16397293
Reference: Escherichia coli K-12 		Oct 2021
Person Uncurated alternate product name shikimate 5-dehydrogenase, NAD(P)-binding Published Annotation - Database Name: GenProtEC Jan 2006
Person Approved alternate product name putative oxidoreductase Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Protein Family
Automated Process Approved protein family IPR006151 Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase Protein Sequence Similarity - InterPro Domain: IPR006151
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR013708 Shikimate dehydrogenase substrate binding, N-terminal Protein Sequence Similarity - InterPro Domain: IPR013708
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF08501 Shikimate dehydrogenase substrate binding domain Protein Sequence Similarity - PFAM Model Name: PF08501
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR036291 NAD(P)-binding domain superfamily Protein Sequence Similarity - InterPro Domain: IPR036291
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Person Approved EC number 1.1.1.282 Published Annotation - Swiss-Prot Accession Number: P0A6D5 Feb 2006
Person Uncurated MultiFun 1.7.1 (metabolism; central intermediary metabolism; unassigned reversible reactions) 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 GeneID:946200 Published Annotation - Entrez Gene Database ID: 946200
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Person Approved db xref UniProtKB:P0A6D5 Published Annotation - Swiss-Prot Accession Number: P0A6D5 Jan 2006
Automated Process Approved db xref GI:1787983 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P0A6D5 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0005651 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG11234 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 putative oxidoreductase Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC74762.1 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
Person Uncurated subsystem component of in silico model iAF1260 Experimental - PubMed ID: 17593909
Reference: Escherichia coli K-12 MG1655 		Jan 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 iJR904 Experimental - PubMed ID: 12952533
Reference: Escherichia coli K-12 MG1655 		Feb 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 Uncurated GO biological process GO:0055114 (OBSOLETE) oxidation-reduction process GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR013708
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO cellular component GO:0005737 cytoplasm GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR006151
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0004764 shikimate 3-dehydrogenase (NADP+) activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR006151
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-0004960 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0003141 ydiB CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0003261 ydiB CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0004676 ydiB CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003044 ydiB CDS
Ortholog
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0002075 ydiB CDS
Automated Process Approved Go view Citrobacter freundii ATCC 8090 [T] AVI-0002675 ydiB CDS
Automated Process Uncurated Go view Dickeya parazeae Ech586 AGC-0000830 CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0004244 CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0007739 CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0001651 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0010267 CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0001608 ydiB CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0002696 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0007640 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0009242 CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0008168 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0078205 ydiB CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0001902 CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0002182 CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0007402 CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0009085 CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0001896 ydiB CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0006345 CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0006201 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0005791 CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0010095 CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0008655 CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0010008 CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0007248 CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0007650 CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0010859 CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0008632 CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0007821 CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0007837 CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0010089 CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0026481 ydiB CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0006773 ydiB CDS
Automated Process Approved Go view Escherichia coli HS ADR-0006450 CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0002094 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0001590 ydiB CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0001737 ydiB CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0002382 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0002051 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0002216 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0001895 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0176054 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0001846 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0001503 CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0132382 ydiB CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0004180 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0001891 ydiB CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0000076 aroE CDS
Automated Process Uncurated Go view Musicola paradisiaca Ech703 AGA-0005998 CDS
Automated Process Uncurated Go view Salmonella Agona SL483 BBX-0005987 CDS
Person Uncurated Go view Salmonella Choleraesuis SC-B67 ADB-0001606 ydiB CDS
Automated Process Uncurated Go view Salmonella Dublin CT_02021853 BCB-0006253 CDS
Automated Process Uncurated Go view Salmonella Enteritidis P125109 BCF-0005504 ydiB CDS
Automated Process Uncurated Go view Salmonella Gallinarum 287/91 BCG-0005322 ydiB CDS
Automated Process Uncurated Go view Salmonella Hadar RI_05P066 BBT-0008194 CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL476 BBV-0005854 CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL486 BBW-0004828 CDS
Automated Process Uncurated Go view Salmonella Javiana GA_MM04042433 BCA-0004868 CDS
Automated Process Uncurated Go view Salmonella Kentucky CDC 191 BBZ-0007842 CDS
Automated Process Uncurated Go view Salmonella Kentucky CVM29188 BBP-0004957 CDS
Automated Process Uncurated Go view Salmonella Newport SL254 BBQ-0005838 CDS
Automated Process Uncurated Go view Salmonella Newport SL317 BBR-0004951 CDS
Automated Process Uncurated Go view Salmonella Paratyphi B SPB7 BCC-0001986 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA23 BBN-0006081 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA29 BBM-0006903 CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund CVM19633 BBO-0005543 CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund SL480 BBY-0008665 CDS
Automated Process Uncurated Go view Salmonella Typhimurium 14028S AJR-0001652 aroE_1 CDS
Person Approved Go view Salmonella Typhimurium LT2 [T] ABU-0094611 ydiB CDS
Automated Process Uncurated Go view Salmonella Virchow SL491 BBS-0008009 CDS
Automated Process Uncurated Go view Salmonella Weltevreden SL484 BBU-0008389 CDS
Automated Process Uncurated Go view Salmonella enterica CVM23701 BBL-0008440 CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0007306 CDS
Person Uncurated Go view Shigella dysenteriae 197 ADU-0001697 ydiB CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0072946 ydiB CDS
Person Approved Go view Shigella flexneri 301 ABT-0088027 ydiB CDS
Automated Process Uncurated Go view Shigella flexneri 8401 BAG-0001830 ydiB CDS
Person Approved Go view Shigella sonnei 046 ADD-0001587 ydiB CDS
Automated Process Uncurated Go view Yersinia frederiksenii ATCC 33641 [T] AEI-0003809 aroE_2 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 1768789 to 1779655
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0005637ydiKCDSforward17690741770186Upstream
ABE-0047251rprAncRNAforward17703721770477Upstream
ABE-0005641ydiLCDSforward17706151770971Upstream
ABE-0005645ydiMCDSforward17710711772285Upstream
ABE-0005648ydiNCDSforward17725121773777Upstream
ABE-0005651ydiBCDSforward17737891774655Matches
ABE-0005653aroDCDSforward17746861775444Downstream
ABE-0005656ydiFCDSforward17755871777182Downstream
ABE-0005658ydiOCDSforward17771961778347Downstream
ABE-0005660ydiPCDScomplement17783901779301Downstream
ABE-0005666ydiQCDSforward17796171780381Downstream
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.