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

ABE-0013398 (alsB) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0013398 showshow history
Names
alsB JW4049 ECK4081 yjcX b4088
Product
periplasmic-binding component of an ABC superfamily D-allose transporter
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 4311107 4312042 936 312
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR001761 (IPR001761 Periplasmic binding protein/LacI sugar binding domain) Apr 2008
Automated Process Approved IPR025997 (IPR025997 Periplasmic binding protein) Jul 2018
Automated Process Approved IPR028082 (IPR028082 Periplasmic binding protein-like I) Jul 2018
Automated Process Approved PF13407 (PF13407 Periplasmic binding protein domain) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Person Uncurated GO biological process GO:0016052 carbohydrate catabolic process 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
Person Uncurated GO cellular component GO:0042597 periplasmic space Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name alsB Experimental - PubMed ID: 9401019
Reference: Escherichia coli 		Aug 2002
Person Approved synonym JW4049 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK4081 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym yjcX Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved locus tag b4088 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product periplasmic-binding component of an ABC superfamily D-allose transporter Published Annotation - PubMed ID: 16397293
Reference: Escherichia coli K-12 		Mar 2008
Person Uncurated alternate product name allose transport protein (ABC superfamily, peri_bind) Published Annotation - Database Name: GenProtEC Jan 2006
Automated Process Approved alternate product name D-allose transporter subunit Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Uncurated alternate product name D-allose-binding periplasmic protein Experimental - PubMed ID: 9401019
Reference: Escherichia coli 		Jan 2006
Protein Family
Automated Process Approved protein family IPR025997 Periplasmic binding protein Protein Sequence Similarity - InterPro Domain: IPR025997
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF13407 Periplasmic binding protein domain Protein Sequence Similarity - PFAM Model Name: PF13407
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR001761 Periplasmic binding protein/LacI sugar binding domain Protein Sequence Similarity - InterPro Domain: IPR001761
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR028082 Periplasmic binding protein-like I Protein Sequence Similarity - InterPro Domain: IPR028082
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Person Approved EC number 3.6.3.17 Published Annotation - Swiss-Prot Accession Number: P39265 Feb 2006
Person Uncurated MultiFun 1.1.1 (metabolism; carbon utilization; carbon compounds) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 4.S.10 (transport; substrate; allose/ribose) 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 4.3.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
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 UniProtKB/Swiss-Prot:P39265 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P39265 Published Annotation - Swiss-Prot Accession Number: P39265 Jan 2005
Automated Process Approved db xref GeneID:948604 Published Annotation - Entrez Gene Database ID: 948604
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref GI:1790526 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0013398 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG12458 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved function putative regulator; Not classified Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved note periplasmic-binding component of ABC superfamily; GO_component: GO:0042597 - periplasmic space; GO_process: GO:0016052 - carbohydrate catabolic process Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC77049.1 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: 9.76
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
Person Uncurated GO biological process GO:0016052 carbohydrate catabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
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
Comparative to toptop
Author Approval Details Genome Feature Name Type
Member
Automated Process Uncurated Go view OrthoMCL (14 enterobacteria) AMM-0005704 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0005305 alsB CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0005960 alsB CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0004436 alsB CDS
Ortholog
Automated Process Uncurated Go view Brenneria sp. EniD312 AKG-0001496 CDS
Automated Process Uncurated Go view Cedecea davisae ATCC 33431 [T] ALZ-0003859 CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0006374 alsB CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0004382 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0006879 alsB CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0004171 CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0004714 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0010091 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0006303 alsB CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0009202 AlsB CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0081301 alsB CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0004758 alsB CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0006639 alsB CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0004714 alsB CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0007067 alsB CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0004695 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0003781 alsB CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0004176 alsB CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0004804 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0004581 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0004744 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0178915 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0004486 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0004546 alsB CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0004692 yjcX CDS
Automated Process Uncurated Go view Yersinia intermedia ATCC 29909 [T] AEH-0001171 alsB_1 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 4306107 to 4317042
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0013377yjcSCDScomplement43046124306597Downstream
ABE-0013380alsKCDScomplement43068704307799Downstream
ABE-0013382alsECDScomplement43077834308478Downstream
ABE-0013392alsCCDScomplement43084894309469Downstream
ABE-0013394alsACDScomplement43094484310980Downstream
ABE-0285675repeat_regionforward43110144311095Downstream
ABE-0013398alsBCDScomplement43111074312042Matches
ABE-0013400alsRCDScomplement43121014312991Upstream
ABE-0013405rpiBCDSforward43133504313799Upstream
ABE-0174120yjdPCDSforward43138684314197Upstream
ABE-0013412phnPCDScomplement43143444315102Upstream
ABE-0013415phnOCDScomplement43151044315538Upstream
ABE-0013417phnNCDScomplement43155254316082Upstream
ABE-0013419phnMCDScomplement43160824317218Upstream
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.