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UniProtKB - P02924 (ARAF_ECOLI)

Entry version 167 (26 Feb 2020)
Sequence version 2 (01 Nov 1997)
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Protein

L-arabinose-binding periplasmic protein

Gene

araF

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score:

Annotation score:4 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Involved in the high-affinity L-arabinose membrane transport system. Binds with high affinity to arabinose, but can also bind D-galactose (approximately 2-fold reduction) and D-fucose (approximately 40-fold reduction).

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections ('Function', 'PTM / Processing', 'Pathology and Biotech') according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei87The binding site for the sugar molecule has not yet been established, but C-87 may be involved1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

  • ATPase-coupled monosaccharide transmembrane transporter activity Source: EcoCyc
  • carbohydrate binding Source: GO_Central
  • monosaccharide binding Source: EcoCyc
Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Biological processSugar transport, Transport

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:ARAF-MONOMER
ECOL316407:JW1889-MONOMER
MetaCyc:ARAF-MONOMER

Protein family/group databases

Transport Classification Database

More...TCDBi		3.A.1.2.2 the atp-binding cassette (abc) superfamily

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
L-arabinose-binding periplasmic protein
Short name:
ABP
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:araF
Ordered Locus Names:b1901, JW1889
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia ›
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

GO - Cellular componenti

Complete GO annotation on QuickGO ...

Keywords - Cellular componenti

Periplasm

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi277P → G: Improves binding to galactose. 1

Chemistry databases

Drug and drug target database

More...DrugBanki		DB03485 Alpha-D-Fucose
DB03142 Alpha-L-Arabinose
DB04062 Beta-D-Fucose
DB03246 Beta-L-Arabinose

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section denotes the presence of an N-terminal signal peptide.<p><a href='/help/signal' target='_top'>More...</a></p>Signal peptidei1 – 232 PublicationsAdd BLAST23
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_000003172024 – 329L-arabinose-binding periplasmic proteinAdd BLAST306

Proteomic databases

Encyclopedia of Proteome Dynamics

More...EPDi		P02924

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		P02924

PaxDb, a database of protein abundance averages across all three domains of life

More...PaxDbi		P02924

PRoteomics IDEntifications database

More...PRIDEi		P02924

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the 'Expression' section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

Induced by arabinose. Transcription is dependent on the transcription factor AraC, the cAMP receptor protein (CRP) and cAMP.1 Publication

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...BioGridi		4261850, 21 interactors

ComplexPortal: manually curated resource of macromolecular complexes

More...ComplexPortali		CPX-4314 Arabinose ABC transporter complex

Protein interaction database and analysis system

More...IntActi		P02924, 6 interactors

STRING: functional protein association networks

More...STRINGi		511145.b1901

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1329
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...SMRi		P02924

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...EvolutionaryTracei		P02924

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the bacterial solute-binding protein 2 family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		ENOG4105DMK Bacteria
COG1879 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_046821_1_0_6

KEGG Orthology (KO)

More...KOi		K10537

Database for complete collections of gene phylogenies

More...PhylomeDBi		P02924

Family and domain databases

Conserved Domains Database

More...CDDi		cd01540 PBP1_arabinose_binding, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR026266 AraF
IPR001761 Peripla_BP/Lac1_sug-bd_dom
IPR028082 Peripla_BP_I

Pfam protein domain database

More...Pfami		View protein in Pfam
PF00532 Peripla_BP_1, 1 hit

PIRSF; a whole-protein classification database

More...PIRSFi		PIRSF002816 AraF, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF53822 SSF53822, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

P02924-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MHKFTKALAA IGLAAVMSQS AMAENLKLGF LVKQPEEPWF QTEWKFADKA 
        60         70         80         90        100
GKDLGFEVIK IAVPDGEKTL NAIDSLAASG AKGFVICTPD PKLGSAIVAK 
       110        120        130        140        150
ARGYDMKVIA VDDQFVNAKG KPMDTVPLVM MAATKIGERQ GQELYKEMQK 
       160        170        180        190        200
RGWDVKESAV MAITANELDT ARRRTTGSMD ALKAAGFPEK QIYQVPTKSN 
       210        220        230        240        250
DIPGAFDAAN SMLVQHPEVK HWLIVGMNDS TVLGGVRATE GQGFKAADII 
       260        270        280        290        300
GIGINGVDAV SELSKAQATG FYGSLLPSPD VHGYKSSEML YNWVAKDVEP 
       310        320 
PKFTEVTDVV LITRDNFKEE LEKKGLGGK
Length:329
Mass (Da):35,541
Last modified:November 1, 1997 - v2
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iA79D167EA92B0C64
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Sequence' section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti194Q → E in CAA29476 (PubMed:2445996).Curated1
Sequence conflicti281V → L in CAA29476 (PubMed:2445996).Curated1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
X06091 Genomic DNA Translation: CAA29476.1
U00096 Genomic DNA Translation: AAC74971.1
AP009048 Genomic DNA Translation: BAA15721.1
K00420 Genomic DNA Translation: AAA23472.1

Protein sequence database of the Protein Information Resource

More...PIRi		E64953 JGECA

NCBI Reference Sequences

More...RefSeqi		NP_416414.1, NC_000913.3
WP_000548675.1, NZ_STEB01000026.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC74971; AAC74971; b1901
BAA15721; BAA15721; BAA15721

Database of genes from NCBI RefSeq genomes

More...GeneIDi		946409

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW1889
eco:b1901

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|1411691.4.peg.349

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X06091 Genomic DNA Translation: CAA29476.1
U00096 Genomic DNA Translation: AAC74971.1
AP009048 Genomic DNA Translation: BAA15721.1
K00420 Genomic DNA Translation: AAA23472.1
PIRiE64953 JGECA
RefSeqiNP_416414.1, NC_000913.3
WP_000548675.1, NZ_STEB01000026.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...PDBei

Protein Data Bank RCSB

More...RCSB PDBi

Protein Data Bank Japan

More...PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1ABEX-ray1.70A24-329[»]
1ABFX-ray1.90A24-329[»]
1APBX-ray1.76A24-329[»]
1BAPX-ray1.75A24-329[»]
2WRZX-ray2.20A/B24-329[»]
5ABPX-ray1.80A24-329[»]
6ABPX-ray1.67A24-329[»]
7ABPX-ray1.67A24-329[»]
8ABPX-ray1.49A24-329[»]
9ABPX-ray1.97A24-329[»]
SMRiP02924
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGridi4261850, 21 interactors
ComplexPortaliCPX-4314 Arabinose ABC transporter complex
IntActiP02924, 6 interactors
STRINGi511145.b1901

Chemistry databases

DrugBankiDB03485 Alpha-D-Fucose
DB03142 Alpha-L-Arabinose
DB04062 Beta-D-Fucose
DB03246 Beta-L-Arabinose

Protein family/group databases

TCDBi3.A.1.2.2 the atp-binding cassette (abc) superfamily

Proteomic databases

EPDiP02924
jPOSTiP02924
PaxDbiP02924
PRIDEiP02924

Genome annotation databases

EnsemblBacteriaiAAC74971; AAC74971; b1901
BAA15721; BAA15721; BAA15721
GeneIDi946409
KEGGiecj:JW1889
eco:b1901
PATRICifig|1411691.4.peg.349

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...EchoBASEi		EB0055

Phylogenomic databases

eggNOGiENOG4105DMK Bacteria
COG1879 LUCA
HOGENOMiCLU_046821_1_0_6
KOiK10537
PhylomeDBiP02924

Enzyme and pathway databases

BioCyciEcoCyc:ARAF-MONOMER
ECOL316407:JW1889-MONOMER
MetaCyc:ARAF-MONOMER

Miscellaneous databases

EvolutionaryTraceiP02924

Protein Ontology

More...PROi		PR:P02924

Family and domain databases

CDDicd01540 PBP1_arabinose_binding, 1 hit
InterProiView protein in InterPro
IPR026266 AraF
IPR001761 Peripla_BP/Lac1_sug-bd_dom
IPR028082 Peripla_BP_I
PfamiView protein in Pfam
PF00532 Peripla_BP_1, 1 hit
PIRSFiPIRSF002816 AraF, 1 hit
SUPFAMiSSF53822 SSF53822, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiARAF_ECOLI
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P02924
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: November 1, 1997
Last modified: February 26, 2020
This is version 167 of the entry and version 2 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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