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UniProtKB - P77596 (YAGF_ECOLI)

Entry version 132 (02 Dec 2020)
Sequence version 1 (01 Feb 1997)
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Protein

D-xylonate dehydratase YagF

Gene

yagF

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

Annotation score:3 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

Catalyzes the dehydration of D-xylonic acid to form 2-dehydro-3-deoxy-D-pentonate.

1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<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

Complete GO annotation on QuickGO ...

GO - Biological processi

  • aldonic acid catabolic process Source: EcoCyc
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

Molecular functionLyase

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:G6141-MONOMER
MetaCyc:G6141-MONOMER

<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:
D-xylonate dehydratase YagFCurated (EC:4.2.1.821 Publication)
<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:yagF
Ordered Locus Names:b0269, JW0262
<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

<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

<p>This subsection of the 'Pathology and Biotech' section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

Disruption mutant has reduced ability to catabolize D-xylonic acid. YjhG-yagF double mutant cannot use D-xylonate as the sole source of carbon.1 Publication

<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 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_00001035601 – 655D-xylonate dehydratase YagFAdd BLAST655

Proteomic databases

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

More...PaxDbi		P77596

PRoteomics IDEntifications database

More...PRIDEi		P77596

<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

Expression is repressed by the transcriptional regulator XynR.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		4261825, 9 interactors

STRING: functional protein association networks

More...STRINGi		511145.b0269

<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

3D structure databases

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

More...SMRi		P77596

Database of comparative protein structure models

More...ModBasei		Search...

<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 IlvD/Edd family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG0129, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_014271_5_0_6

Database for complete collections of gene phylogenies

More...PhylomeDBi		P77596

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.50.30.80, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR017798, Dehydratase_YjhG/YagF
IPR042096, Dihydro-acid_dehy_C
IPR000581, DiOHA_6PGluconate_deHydtase
IPR020558, DiOHA_6PGluconate_deHydtase_CS
IPR037237, IlvD/EDD_N

Pfam protein domain database

More...Pfami		View protein in Pfam
PF00920, ILVD_EDD, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF143975, SSF143975, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR03432, yjhG_yagF, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS00886, ILVD_EDD_1, 1 hit
PS00887, ILVD_EDD_2, 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.

P77596-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MTIEKIFTPQ DDAFYAVITH AAGPQGALPL TPQMLMESPS GNLFGMTQNA 
        60         70         80         90        100
GMGWDANKLT GKEVLIIGTQ GGIRAGDGRP IALGYHTGHW EIGMQMQAAA 
       110        120        130        140        150
KEITRNGGIP FAAFVSDPCD GRSQGTHGMF DSLPYRNDAA IVFRRLIRSL 
       160        170        180        190        200
PTRRAVIGVA TCDKGLPATM IALAAMHDLP TILVPGGATL PPTVGEDAGK 
       210        220        230        240        250
VQTIGARFAN HELSLQEAAE LGCRACASPG GGCQFLGTAG TSQVVAEALG 
       260        270        280        290        300
LALPHSALAP SGQAVWLEIA RQSARAVSEL DSRGITTRDI LSDKAIENAM 
       310        320        330        340        350
VIHAAFGGST NLLLHIPAIA HAAGCTIPDV EHWTRINRKV PRLVSVLPNG 
       360        370        380        390        400
PDYHPTVRAF LAGGVPEVML HLRDLGLLHL DAMTVTGQTV GENLEWWQAS 
       410        420        430        440        450
ERRARFRQCL REQDGVEPDD VILPPEKAKA KGLTSTVCFP TGNIAPEGSV 
       460        470        480        490        500
IKATAIDPSV VGEDGVYHHT GRVRVFVSEA QAIKAIKREE IVQGDIMVVI 
       510        520        530        540        550
GGGPSGTGME ETYQLTSALK HISWGKTVSL ITDARFSGVS TGACFGHVSP 
       560        570        580        590        600
EALAGGPIGK LRDNDIIEIA VDRLTLTGSV NFIGTADNPL TPEEGARELA 
       610        620        630        640        650
RRQTHPDLHA HDFLPDDTRL WAALQSVSGG TWKGCIYDTD KIIEVINAGK 

KALGI
Length:655
Mass (Da):69,399
Last modified:February 1, 1997 - v1
<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:i208AF2F6DB39EE8B
GO

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
U70214 Genomic DNA Translation: AAB08690.1
U00096 Genomic DNA Translation: AAC73372.1
AP009048 Genomic DNA Translation: BAE76053.1

Protein sequence database of the Protein Information Resource

More...PIRi		E64752

NCBI Reference Sequences

More...RefSeqi		NP_414803.1, NC_000913.3
WP_000151261.1, NZ_LN832404.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC73372; AAC73372; b0269
BAE76053; BAE76053; BAE76053

Database of genes from NCBI RefSeq genomes

More...GeneIDi		944928

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW0262
eco:b0269

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|511145.12.peg.273

<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
U70214 Genomic DNA Translation: AAB08690.1
U00096 Genomic DNA Translation: AAC73372.1
AP009048 Genomic DNA Translation: BAE76053.1
PIRiE64752
RefSeqiNP_414803.1, NC_000913.3
WP_000151261.1, NZ_LN832404.1

3D structure databases

SMRiP77596
ModBaseiSearch...

Protein-protein interaction databases

BioGRIDi4261825, 9 interactors
STRINGi511145.b0269

Proteomic databases

PaxDbiP77596
PRIDEiP77596

Genome annotation databases

EnsemblBacteriaiAAC73372; AAC73372; b0269
BAE76053; BAE76053; BAE76053
GeneIDi944928
KEGGiecj:JW0262
eco:b0269
PATRICifig|511145.12.peg.273

Organism-specific databases

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

More...EchoBASEi		EB3129

Phylogenomic databases

eggNOGiCOG0129, Bacteria
HOGENOMiCLU_014271_5_0_6
PhylomeDBiP77596

Enzyme and pathway databases

BioCyciEcoCyc:G6141-MONOMER
MetaCyc:G6141-MONOMER

Miscellaneous databases

Protein Ontology

More...PROi		PR:P77596

Family and domain databases

Gene3Di3.50.30.80, 1 hit
InterProiView protein in InterPro
IPR017798, Dehydratase_YjhG/YagF
IPR042096, Dihydro-acid_dehy_C
IPR000581, DiOHA_6PGluconate_deHydtase
IPR020558, DiOHA_6PGluconate_deHydtase_CS
IPR037237, IlvD/EDD_N
PfamiView protein in Pfam
PF00920, ILVD_EDD, 1 hit
SUPFAMiSSF143975, SSF143975, 1 hit
TIGRFAMsiTIGR03432, yjhG_yagF, 1 hit
PROSITEiView protein in PROSITE
PS00886, ILVD_EDD_1, 1 hit
PS00887, ILVD_EDD_2, 1 hit

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 nameiYAGF_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: P77596
Secondary accession number(s): Q2MCF3
<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: November 1, 1997
Last sequence update: February 1, 1997
Last modified: December 2, 2020
This is version 132 of the entry and version 1 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

Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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