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Entry version 59 (18 Sep 2019)
Sequence version 1 (24 Mar 2009)
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Protein

Probable 5-dehydro-4-deoxyglucarate dehydratase

Gene

Avi_5701

Organism
Agrobacterium vitis (strain S4 / ATCC BAA-846) (Rhizobium vitis (strain S4))
Status
Reviewed-Annotation score:

Annotation score:2 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>
-Protein inferred from homologyi <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

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">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>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: D-glucarate degradation

This protein is involved in step 2 of the subpathway that synthesizes 2,5-dioxopentanoate from D-glucarate.UniRule annotation
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. no protein annotated in this organism
  2. Probable 5-dehydro-4-deoxyglucarate dehydratase (Avi_5701)
This subpathway is part of the pathway D-glucarate degradation, which is itself part of Carbohydrate acid metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 2,5-dioxopentanoate from D-glucarate, the pathway D-glucarate degradation and in Carbohydrate acid metabolism.

<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

GO - Biological processi

<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
AVIT311402:GH2Y-3880-MONOMER

UniPathway: a resource for the exploration and annotation of metabolic pathways

More...
UniPathwayi
UPA00564;UER00628

<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_and_taxonomy_section">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:
Probable 5-dehydro-4-deoxyglucarate dehydrataseUniRule annotation (EC:4.2.1.41UniRule annotation)
Alternative name(s):
5-keto-4-deoxy-glucarate dehydrataseUniRule annotation
Short name:
KDGDHUniRule annotation
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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
Ordered Locus Names:Avi_5701
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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>OrganismiAgrobacterium vitis (strain S4 / ATCC BAA-846) (Rhizobium vitis (strain S4))
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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 identifieri311402 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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 lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeRhizobium/Agrobacterium groupAgrobacterium
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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
  • UP000001596 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">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 2

<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.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_10001479051 – 301Probable 5-dehydro-4-deoxyglucarate dehydrataseAdd BLAST301

Proteomic databases

PRoteomics IDEntifications database

More...
PRIDEi
B9K1N4

<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

STRING: functional protein association networks

More...
STRINGi
311402.Avi_5701

<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
B9K1N4

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 DapA family.UniRule annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105UVJ Bacteria
COG0329 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000173605

KEGG Orthology (KO)

More...
KOi
K01707

Identification of Orthologs from Complete Genome Data

More...
OMAi
MVYNRDN

Database of Orthologous Groups

More...
OrthoDBi
1438588at2

Family and domain databases

Conserved Domains Database

More...
CDDi
cd00951 KDGDH, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.20.20.70, 1 hit

HAMAP database of protein families

More...
HAMAPi
MF_00694 KDGDH, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR013785 Aldolase_TIM
IPR002220 DapA-like
IPR017655 Dehydro-deoxyglucarate_dehyd

The PANTHER Classification System

More...
PANTHERi
PTHR12128 PTHR12128, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00701 DHDPS, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF001365 DHDPS, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM01130 DHDPS, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR03249 KdgD, 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_length">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_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">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.

B9K1N4-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MEPNELKRAL GAGLLSFPVT PFDDKGEFNP DVYGAHIDWL SGYDATVLFA
60 70 80 90 100
AGGTGEMFSL SPDEIPNIVA TAKAASNGVP IVGGCGGGTR VAVEIAKGIE
110 120 130 140 150
KAGGDGILLL PQYLIDAPQA GLYAHVKAVC DAVGFGVTVY NRDNCVLQTE
160 170 180 190 200
TIQRLADDCP NLIGFKDGTG ELGLVRRITA TLGDRLTYIG GMPTAELFAE
210 220 230 240 250
AYLGAGFSTY SSAVFNFVPQ LACDFYKALR AGDRATCENI LNRFFFPFMD
260 270 280 290 300
LRSRQKGYAV AAIKAGVRLQ GFAAGSVRPP LTDLTSQEVD ILAGLIEPWK

Q
Length:301
Mass (Da):31,957
Last modified:March 24, 2009 - 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:i977A257234673D7D
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
CP000634 Genomic DNA Translation: ACM38782.1

NCBI Reference Sequences

More...
RefSeqi
WP_012654024.1, NC_011988.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
ACM38782; ACM38782; Avi_5701

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
31497700

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
avi:Avi_5701

<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
CP000634 Genomic DNA Translation: ACM38782.1
RefSeqiWP_012654024.1, NC_011988.1

3D structure databases

SMRiB9K1N4
ModBaseiSearch...

Protein-protein interaction databases

STRINGi311402.Avi_5701

Proteomic databases

PRIDEiB9K1N4

Genome annotation databases

EnsemblBacteriaiACM38782; ACM38782; Avi_5701
GeneIDi31497700
KEGGiavi:Avi_5701

Phylogenomic databases

eggNOGiENOG4105UVJ Bacteria
COG0329 LUCA
HOGENOMiHOG000173605
KOiK01707
OMAiMVYNRDN
OrthoDBi1438588at2

Enzyme and pathway databases

UniPathwayiUPA00564;UER00628
BioCyciAVIT311402:GH2Y-3880-MONOMER

Family and domain databases

CDDicd00951 KDGDH, 1 hit
Gene3Di3.20.20.70, 1 hit
HAMAPiMF_00694 KDGDH, 1 hit
InterProiView protein in InterPro
IPR013785 Aldolase_TIM
IPR002220 DapA-like
IPR017655 Dehydro-deoxyglucarate_dehyd
PANTHERiPTHR12128 PTHR12128, 1 hit
PfamiView protein in Pfam
PF00701 DHDPS, 1 hit
PIRSFiPIRSF001365 DHDPS, 1 hit
SMARTiView protein in SMART
SM01130 DHDPS, 1 hit
TIGRFAMsiTIGR03249 KdgD, 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 nameiKDGD_AGRVS
<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: B9K1N4
<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_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: March 24, 2009
Last modified: September 18, 2019
This is version 59 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

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
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