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

ABE-0006330 (araF) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0006330 showshow history
Names
araF JW1889 ECK1899 b1901
Product
periplasmic-binding component of an ABC superfamily L-arabinose transporter
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 1985139 1986128 990 330
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 IPR028082 (IPR028082 Periplasmic binding protein-like I) Jul 2018
Automated Process Approved PF00532 (PF00532 Periplasmic binding proteins and sugar binding domain of LacI family) 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 Approved 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 GO Inferred from Direct Assay - PubMed ID: 2445995
Reference: Escherichia coli BEK180 		Jul 2006
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name araF Published Sequence Analysis - PubMed ID: 2445996
Reference: Escherichia coli K-12 		Mar 2008
Person Approved synonym ECK1899 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym JW1889 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b1901 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product periplasmic-binding component of an ABC superfamily L-arabinose transporter Published Annotation - PubMed ID: 16397293
Reference: Escherichia coli K-12 		Mar 2008
Person Approved alternate product name periplasmic-binding component of high affinity L-arabinose transport system Published Sequence Analysis - PubMed ID: 2445996
Reference: Escherichia coli K-12 		Mar 2008
Automated Process Approved alternate product name L-arabinose transporter subunit Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Protein Family
Automated Process Approved protein family PF00532 Periplasmic binding proteins and sugar binding domain of LacI family Protein Sequence Similarity - PFAM Model Name: PF00532
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 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
Person Uncurated MultiFun 4.S.100 (transport; substrate; L-arabinose) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 1.1.1 (metabolism; carbon utilization; carbon compounds) 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:946409 Published Annotation - Entrez Gene Database ID: 946409
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Person Approved db xref UniProtKB:P02924 Published Annotation - Swiss-Prot Accession Number: P02924 Jan 2005
Automated Process Approved db xref GI:1788211 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0006330 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P02924 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG10057 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved function transport; Transport of small molecules: Carbohydrates, organic acids, alcohols Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved note L-arabinose-binding periplasmic protein; 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 AAC74971.1 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved subcellular localization Periplasmic 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
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
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 GO Inferred from Direct Assay - PubMed ID: 2445995
Reference: Escherichia coli BEK180 		Jul 2006
Automated Process Approved 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-0001910 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0002477 araF CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0002386 araF CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0003624 araF CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0002620 araF CDS
Ortholog
Automated Process Uncurated Go view Brenneria salicis ATCC 15712 [T] AMK-0002775 CDS
Automated Process Uncurated Go view Brenneria sp. EniD312 AKG-0001978 CDS
Automated Process Uncurated Go view Buttiauxella agrestis ATCC 33320 [T] APC-0002576 CDS
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0002688 araF CDS
Automated Process Approved Go view Citrobacter freundii ATCC 8090 [T] AVI-0003436 araF CDS
Automated Process Uncurated Go view Dickeya chrysanthemi Ech1591 AFK-0006944 CDS
Person Approved Go view Dickeya dadantii 3937 ABF-0015566 araF CDS
Automated Process Uncurated Go view Dickeya parazeae Ech586 AGC-0001979 CDS
Automated Process Uncurated Go view Enterobacter cloacae subsp. cloacae ATCC 13047 [T] (AToL DRAFT) AMB-0003286 CDS
Automated Process Uncurated Go view Erwinia amylovora ATCC 49946 ACW-0301421 araF CDS
Automated Process Uncurated Go view Erwinia amylovora ATCC BAA-2158 APN-0001891 araF CDS
Automated Process Uncurated Go view Erwinia tasmaniensis Et1/99 [T] AFI-0001830 araF CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0004477 araF CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0008309 araF CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0001854 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0009628 araF CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0001790 araF CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0002487 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0007401 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0010359 araF CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0010246 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0078433 araF CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0002124 CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0002463 CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0008379 araF CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0002148 araF CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0006569 araF CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0002157 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0006032 araF CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0010321 araF CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0009718 araF CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0006114 araF CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0007477 araF CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0009130 araF CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0010632 araF CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0009822 araF CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0010303 araF CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0007883 araF CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0009917 araF CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0010027 araF CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0026696 araF CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0008100 araF CDS
Automated Process Approved Go view Escherichia coli HS ADR-0006675 araF CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0002338 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0001789 araF CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0001949 araF CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0002074 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0002313 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0001995 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0002169 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0176332 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0002165 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0001284 araF CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0132593 CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0003948 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0002108 araF CDS
Person Uncurated Go view Hafnia alvei ATCC 13337 [T] AMD-0002938 CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0002404 araF CDS
Automated Process Uncurated Go view Leclercia adecarboxylata ATCC 23216 [T] AME-0000653 CDS
Automated Process Uncurated Go view Musicola paradisiaca Ech703 AGA-0006643 CDS
Automated Process Uncurated Go view Pantoea agglomerans IG1 APM-0001173 CDS
Automated Process Uncurated Go view Pantoea agglomerans SL1-M5 ALY-0003927 CDS
Automated Process Uncurated Go view Pantoea ananatis AJ13355 AOV-0001187 araF CDS
Automated Process Uncurated Go view Pantoea ananatis B1-9 APL-0002928 CDS
Automated Process Uncurated Go view Pantoea ananatis LMG 20103 AKB-0001888 araF CDS
Automated Process Uncurated Go view Pantoea ananatis PA13 APK-0002338 CDS
Automated Process Uncurated Go view Pantoea sp. At-9b AGM-0009505 CDS
Automated Process Uncurated Go view Pantoea sp. aB AJV-0002586 CDS
Automated Process Uncurated Go view Pantoea stewartii DC283 ACV-0289266 araF CDS
Automated Process Uncurated Go view Pantoea vagans C9-1 ALK-0005013 araF CDS
Person Approved Go view Pectobacterium atrosepticum SCRI1043 ABL-0062537 araF CDS
Automated Process Uncurated Go view Pectobacterium brasiliensis 1692 AED-0001327 araF CDS
Person Approved Go view Pectobacterium carotovorum WPP14 ADT-0000581 araF CDS
Automated Process Uncurated Go view Pectobacterium parmentieri WPP163 AFJ-0000558 araF CDS
Automated Process Uncurated Go view Pectobacterium sp. PC1 AFL-0006907 CDS
Person Approved Go view Pseudomonas syringae pv. tomato DC3000 ADG-0002683 abP CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0006421 araF CDS
Person Approved Go view Shigella dysenteriae 197 ADU-0001268 araF CDS
Person Uncurated Go view Shigella flexneri 2457T ABQ-0073149 araF pseudogene
Person Approved Go view Shigella flexneri 301 ABT-0088232 araF pseudogene
Automated Process Approved Go view Shigella flexneri 8401 BAG-0002086 araF CDS
Person Approved Go view Shigella sonnei 046 ADD-0001312 araF CDS
Automated Process Uncurated Go view Yersinia bercovieri ATCC 43970 [T] AEK-0002791 CDS
Automated Process Uncurated Go view Yersinia enterocolitica 8081 BAH-0005887 araF CDS
Automated Process Uncurated Go view Yersinia frederiksenii ATCC 33641 [T] AEI-0003011 araF CDS
Automated Process Uncurated Go view Yersinia intermedia ATCC 29909 [T] AEH-0003345 araF CDS
Automated Process Uncurated Go view Yersinia mollaretii ATCC 43969 [T] AEJ-0000399 CDS
Person Approved Go view Yersinia pestis 91001 (biovar Microtus) ACQ-0239195 araF CDS
Automated Process Uncurated Go view Yersinia pestis Angola (biovar Pestoides) ADI-0006374 araF CDS
Automated Process Uncurated Go view Yersinia pestis Antiqua (biovar Antiqua) BAE-0001951 araF CDS
Automated Process Uncurated Go view Yersinia pestis B42003004 (biovar Antiqua) BAL-0004751 araF CDS
Automated Process Uncurated Go view Yersinia pestis CA88-4125 (biovar Orientalis) BAF-0001202 araF CDS
Person Approved Go view Yersinia pestis CO92 (biovar Orientalis) ABY-0122755 araF CDS
Automated Process Uncurated Go view Yersinia pestis E1979001 (biovar Antiqua) BAM-0007103 araF CDS
Automated Process Uncurated Go view Yersinia pestis F1991016 (biovar Orientalis) BAQ-0007668 araF CDS
Automated Process Uncurated Go view Yersinia pestis FV-1 (biovar Orientalis) BAK-0003030 CDS
Automated Process Uncurated Go view Yersinia pestis IP275 (biovar Orientalis) BAC-0007459 araF CDS
Automated Process Uncurated Go view Yersinia pestis K1973002 (biovar Mediaevalis) BAO-0005971 araF CDS
Person Approved Go view Yersinia pestis KIM (biovar Mediaevalis) ABI-0031803 araF CDS
Automated Process Uncurated Go view Yersinia pestis MG05-1020 (biovar Orientalis) BAP-0005723 araF CDS
Automated Process Uncurated Go view Yersinia pestis Nepal516 (biovar Antiqua) BAD-0002076 araF CDS
Automated Process Uncurated Go view Yersinia pestis Pestoides F (biovar Pestoides) BAI-0001048 CDS
Automated Process Uncurated Go view Yersinia pestis UG05-0454 (biovar Antiqua) BAN-0007108 araF CDS
Automated Process Uncurated Go view Yersinia pseudotuberculosis IP31758 ADS-0005856 araF CDS
Person Approved Go view Yersinia pseudotuberculosis IP32953 ACZ-0002258 araF CDS
Automated Process Uncurated Go view Yersinia pseudotuberculosis PB1/+ AFV-0002665 CDS
Automated Process Uncurated Go view Yersinia pseudotuberculosis YPIII AFW-0002363 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 43003 APO-0015409 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 49455 [T] AMG-0003348 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
FB20510mutantTn5 InsertionRequest the StrainABE-0006330araFaraF::Tn5KAN-2 at position 512 in Minus orientation ,+ pKD460Blattner Laboratory
FB20511mutantTn5 InsertionRequest the StrainABE-0006330araFaraF::Tn5KAN-2 at position 512 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 1980139 to 1991128
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0006316uspCCDSforward19797531980181Downstream
ABE-0006318otsACDScomplement19801881981612Downstream
ABE-0006320otsBCDScomplement19815871982387Downstream
ABE-0174093araHCDScomplement19825541983540Downstream
ABE-0006328araGCDScomplement19835551985069Downstream
ABE-0006330araFCDScomplement19851391986128Matches
ABE-0006333ftnBCDSforward19869251987428Upstream
ABE-0285058yecJCDScomplement19875071987758Upstream
ABE-0285207azuCCDScomplement19878731987959Upstream
ABE-0006338yecRCDSforward19882221988545Upstream
ABE-0006342ftnACDSforward19887161989213Upstream
ABE-0006344yecHCDScomplement19892511989490Upstream
ABE-0006355tyrPCDSforward19896811990892Upstream
ABE-0006357yecACDScomplement19909541991619Upstream
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.