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-0006572 (shiA) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0006572 showshow history
Names
shiA yeeM JW1962 ECK1976 b1981
Product
shikimate transporter
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 2053643 2054959 1317 439
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 IPR011701 (IPR011701 Major facilitator superfamily) Apr 2008
Automated Process Approved IPR004736 (IPR004736 MFS transporter, metabolite:H symporter) Apr 2008
Automated Process Approved IPR005829 (IPR005829 Sugar transporter, conserved site) Apr 2008
Automated Process Approved IPR007114 (IPR007114 (DEPRECATED) Major facilitator superfamily) Apr 2008
Automated Process Approved IPR005828 (IPR005828 Major facilitator, sugar transporter-like) Jul 2018
Automated Process Approved IPR036259 (IPR036259 MFS transporter superfamily) Jul 2018
Automated Process Approved PF00083 (PF00083 Sugar (and other) transporter) Jul 2018
Automated Process Approved PF07690 (PF07690 Major Facilitator Superfamily) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Person Uncurated GO biological process GO:0009423 chorismate biosynthetic 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: IPR005828, IPR011701, IPR004736
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO biological process GO:0006810 transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004736
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO cellular component GO:0016020 membrane GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR005829
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO cellular component GO:0016021 integral component of membrane GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004736
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO cellular component GO:0005886 plasma membrane GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Person Uncurated GO cellular component GO:0019866 organelle inner membrane Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Uncurated GO molecular function GO:0022857 transmembrane transporter activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR005828, IPR004736
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0005215 transporter activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004736
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name shiA Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym ECK1976 Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved synonym yeeM Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved synonym JW1962 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b1981 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product shikimate transporter Published Annotation - PubMed ID: 16397293 Jan 2006
Person Uncurated alternate product name shikimate and dehydroshikimate transport protein (MFS family) Published Annotation - Database Name: GenProtEC Jan 2006
Person Uncurated alternate product name shikimate transporter Experimental - PubMed ID: 9524262
Reference: Escherichia coli 		Jan 2006
Protein Family
Automated Process Approved protein family IPR005829 Sugar transporter, conserved site Protein Sequence Similarity - InterPro Domain: IPR005829
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR007114 (DEPRECATED) Major facilitator superfamily Protein Sequence Similarity - InterPro Domain: IPR007114
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF07690 Major Facilitator Superfamily Protein Sequence Similarity - PFAM Model Name: PF07690
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF00083 Sugar (and other) transporter Protein Sequence Similarity - PFAM Model Name: PF00083
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR004736 MFS transporter, metabolite:H symporter Protein Sequence Similarity - InterPro Domain: IPR004736
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR011701 Major facilitator superfamily Protein Sequence Similarity - InterPro Domain: IPR011701
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR005828 Major facilitator, sugar transporter-like Protein Sequence Similarity - InterPro Domain: IPR005828
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR036259 MFS transporter superfamily Protein Sequence Similarity - InterPro Domain: IPR036259
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Person Uncurated MultiFun 4.2.A.1 (transport; Electrochemical potential driven transporters; Porters (Uni-, Sym- and Antiporters); The Major Facilitator Superfamily (MFS)) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 6.1 (cell structure; membrane) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 1.5.1.20 (metabolism; building block biosynthesis; amino acids; chorismate) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 7.3 (location of gene products; inner membrane) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 4.S.168 (transport; substrate; shikimate/dehydroshikimate) 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:946495 Published Annotation - Entrez Gene Database ID: 946495
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Person Approved db xref UniProtKB:P76350 Published Annotation - Swiss-Prot Accession Number: P76350 Jan 2005
Automated Process Approved db xref GI:1788292 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P76350 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0006572 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG20205 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved function putative transport; Not classified Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved note GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0009423 - chorismate biosynthetic process Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC75045.1 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Uncurated subcellular localization Cytoplasmic Membrane Predicted by PSORTb - PSORTb Final_Score: 10.00
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
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:0006810 transport GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004736
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Uncurated GO biological process GO:0009423 chorismate biosynthetic 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: IPR005828, IPR011701, IPR004736
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Person Uncurated GO cellular component GO:0019866 organelle inner membrane Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Uncurated GO cellular component GO:0005886 plasma membrane GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Automated Process Approved GO cellular component GO:0016021 integral component of membrane GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004736
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO cellular component GO:0016020 membrane GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR005829
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO molecular function GO:0022857 transmembrane transporter activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR005828, IPR004736
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0005215 transporter activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004736
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-0002076 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0002704 shiA CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0002447 shiA CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0003462 shiA CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0002389 shiA CDS
Ortholog
Automated Process Uncurated Go view Brenneria sp. EniD312 AKG-0002992 CDS
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0002826 yhjE_3 CDS
Automated Process Uncurated Go view Dickeya chrysanthemi Ech1591 AFK-0009311 CDS
Person Uncurated Go view Dickeya dadantii 3937 ABF-0018396 lfcT CDS
Automated Process Uncurated Go view Dickeya parazeae Ech586 AGC-0000061 CDS
Automated Process Uncurated Go view Enterobacter cloacae subsp. cloacae ATCC 13047 [T] (AToL DRAFT) AMB-0003471 CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0003574 shiA CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0009525 shiA CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0001970 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0009439 shiA CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0001918 CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0002402 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0007314 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0010247 shiA CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0009961 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0078569 shiA CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0002271 CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0002611 CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0009615 shiA CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0010734 shiA CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0002222 shiA CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0006700 shiA CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0005352 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0006222 shiA CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0010505 shiA CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0010585 shiA CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0010693 shiA CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0007663 shiA CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0010565 shiA CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0010886 shiA CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0009723 shiA CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0010534 shiA CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0010361 shiA CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0009669 shiA CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0026865 shiA CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0009340 yhjE_1 CDS
Automated Process Approved Go view Escherichia coli HS ADR-0006779 shiA CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0002451 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0001860 shiA CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0002033 shiA CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0001990 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0002402 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0001899 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0002290 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0176420 pseudogene
Automated Process Approved Go view Escherichia coli SE11 AFS-0002304 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0001143 shiA CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0132775 shiA CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0004692 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0002201 shiA CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0002466 shiA CDS
Automated Process Uncurated Go view Leclercia adecarboxylata ATCC 23216 [T] AME-0000795 CDS
Automated Process Uncurated Go view Musicola paradisiaca Ech703 AGA-0009048 CDS
Automated Process Uncurated Go view Pantoea sp. At-9b AGM-0006087 CDS
Person Uncurated Go view Pectobacterium atrosepticum SCRI1043 ABL-0060435 shiA CDS
Automated Process Uncurated Go view Pectobacterium brasiliensis 1692 AED-0000145 shiA CDS
Person Uncurated Go view Pectobacterium carotovorum WPP14 ADT-0000074 shiA CDS
Automated Process Uncurated Go view Pectobacterium parmentieri WPP163 AFJ-0001364 shiA CDS
Automated Process Uncurated Go view Pectobacterium sp. PC1 AFL-0004691 CDS
Automated Process Uncurated Go view Shigella boydii BS512 ADJ-0006383 CDS
Person Approved Go view Shigella dysenteriae 197 ADU-0002596 shiA CDS
Person Uncurated Go view Shigella flexneri 2457T ABQ-0073267 shiA pseudogene
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
FB22817mutantTn5 InsertionRequest the StrainABE-0006572shiAshiA::Tn5(KAN-I-SceI) at position 643 in Minus orientation ,+ pKD46 0Blattner Laboratory
FB23359mutantTn5 InsertionRequest the StrainABE-0006572shiAshiA::Tn5KAN-I-SceI at position 643 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 2048643 to 2059959
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0006563yeeJCDSforward20449382052014Upstream
ABE-0006565yeeL_2CDSpcomplement20522762052602Upstream
ABE-0285098yeeLpseudogenecomplement20522762053328Upstream
ABE-0006568yeeL_1CDSpcomplement20526242053328Upstream
ABE-0006572shiACDSforward20536432054959Matches
ABE-0006579amnCDSforward20550612056515Downstream
ABE-0006582yeeNCDSforward20568582057574Downstream
ABE-0006584asnWtRNAcomplement20580272058102Downstream
ABE-0006586yeeOCDScomplement20582032059657Downstream
ABE-0006588asnUtRNAforward20598512059926Downstream
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.